Biophysical Chemistry

Current research reports and chronological list of recent articles.


The scientific journal Biophysical Chemistry publishes original work and reviews in the areas of chemistry and physics directly impacting biological phenomena. Quantitative analysis of the properties of biological macromolecules, biologically active molecules, macromolecular assemblies and cell components in terms of kinetics, thermodynamics, spatio-temporal organization, NMR and X-ray structural biology, as well as single-molecule detection represent a major focus of the journal. Theoretical and computational treatments of biomacromolecular systems, macromolecular interactions, regulatory control and systems biology are also of interest to the journal.

The publisher is Elsevier. The copyright and publishing rights of specialized products listed below are in this publishing house. This is also responsible for the content shown.

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Additional research articles see Current Chemistry Research Articles. Magazines with similar content (biophysical chemistry):

 - Biomacromolecules.

 - Faraday Discussions.

 - Journal of Physical Chemistry B.

 - Physical Chemistry Chemical Physics PCCP.



Biophysical Chemistry - Abstracts



Quantifying the influence of 5′-RNA modifications on RNA polymerase I activity

Publication date: November 2017
Source:Biophysical Chemistry, Volume 230

Author(s): Francis D. Appling, Aaron L. Lucius, David A. Schneider

For ensemble and single-molecule analyses of transcription, the use of synthetic transcription elongation complexes has been a versatile and powerful tool. However, structural analyses demonstrate that short RNA substrates, often employed in these assays, would occupy space within the RNA polymerase. Most commercial RNA oligonucleotides do not carry a 5′-triphosphate as would be present on a natural, de novo synthesized RNA. To examine the effects of 5′-moities on transcription kinetics, we measured nucleotide addition and 3′-dinucleotide cleavage by eukaryotic RNA polymerase I using 5′-hydroxyl and 5′-triphosphate RNA substrates. We found that 5′ modifications had no discernable effect on the kinetics of nucleotide addition; however, we observed clear, but modest, effects on the rate of backtracking and/or dinucleotide cleavage. These data suggest that the 5′-end may influence RNA polymerase translocation, consistent with previous prokaryotic studies, and these findings may have implications on kinetic barriers that confront RNA polymerases during the transition from initiation to elongation.

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Datum: 18.11.2017


Full title pg and editorial board

Publication date: October 2017
Source:Biophysical Chemistry, Volume 229










Datum: 18.11.2017


“The human use of human beings”: Interdisciplinarity, transdisciplinarity and all that in biophysics and beyond

Publication date: October 2017
Source:Biophysical Chemistry, Volume 229

Author(s): Marco Elio Tabacchi, Settimo Termini

Biophysics, just by looking at its name, indicates an interdisciplinary scientific activity, although the notion of interdisciplinarity, as such, seems to be not widely or specifically discussed by biophysicists. The same seems to have happened as well in the early stages of the development of cybernetics, notably in Norbert Wiener's writings. This situation seems to contrast with what has happened in subsequent developments of cybernetics ideas, notably in general system theory and cognitive sciences. After a few general reflections on the notion of interdisciplinarity, its sophisticated variants and the path leading to the birth of cognitive science, we shall refer to Wiener's thought to extracts aspects and indications that could be useful today, also for what concerns the social responsibility of scientists, which could be seen as stemming from a very general form of interdisciplinarity. Highlights: After a few general reflections on the notion of interdisciplinarity, its sophisticated variants and the path leading to the birth of cognitive science, we shall refer to Wiener's thought to extracts aspects and indications that could be useful today, also for what concerns the social responsibility of scientists.

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Datum: 18.11.2017


Investigation of structural dynamics of Thrombocytopenia Cargeeg mutants of human apoptotic cytochrome c: A molecular dynamics simulation approach

Publication date: November 2017
Source:Biophysical Chemistry, Volume 230

Author(s): Gurusamy Muneeswaran, Subramanian Kartheeswaran, Manickam Pandiaraj, Kaliappan Muthukumar, Muniyandi Sankaralingam, Saravanavadivu Arunachalam

Naturally occurring mutations to cytochrome c (cyt-c) have been identified recently in patients with mild autosomal dominant thrombocytopenia (low platelet levels), which yield cyt-c mutants with enhanced apoptotic activity. However, the molecular mechanism underlying this low platelet production and enhanced apoptosis remain unclear. Therefore, an attempt is made herein for the first time to investigate the effects of mutations of glycine 41 by serine (G41S) and tyrosine 48 by histidine (Y48H) on the conformational and dynamic changes of apoptotic (Fe3+) cyt-c using all atom molecular dynamics (MD) simulations in explicit water solvent. Our 30ns MD simulations demonstrate considerable structural differences in G41S and Y48H compared to wild type (WT) cyt-c, such as increasing distances between the critical electron transfer residues results in open conformation at the heme active site, large fluctuations in β-turns and α-helices. Additionally, although the β-sheets remain mostly unaffected in all the three cyt-c simulations, the α-helices undergo conformational switch to β-turns in both the mutant simulations. Importantly, this conformational switch of α-helix to β-turn around heme active site should attributes to the loss of intraprotein H-bonds in the mutant simulations especially between NE2 (His26) and O (Pro44) in agreement with the experimental report. Further, essential dynamics analysis reveals that overall motions of WT cyt-c is mainly involved only in the first eigenvector, but in G41S and Y48H the overall motions are mainly in three and two eigenvectors respectively. Overall, the detailed atomistic level information provide a unifying description for the molecular mechanism of structural destabilization, disregulation of platelet formation and enhanced peroxidase activity of the mutant cyt-c's in the pathology of intrinsic apoptosis.

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Datum: 18.11.2017


Conformational dynamics and free energy of BHRF1 binding to Bim BH3

Publication date: Available online 10 November 2017
Source:Biophysical Chemistry

Author(s): Mauro Lapelosa

The interaction between the Bim BH3 peptide and the viral protein BHRF1 is pivotal to understanding the fundamental molecular details of the mechanism used by the Epstein-Barr virus to trick the mammalian immune system. Here, we study the mechanism of binding/unbinding and compute the free energy for the association of the Bim peptide to the BHRF1 protein. Key elements of the binding mechanism are the conformational rearrangement together with a main free energy barrier of 11.5 kcal/mol. The simulations show complete unbinding and rebinding of the Bim peptide to BHRF1. The peptide slowly dissociates, disrupting the hydrophobic contacts, then tilting to one side. The peptide then completely disrupts all the remaining interactions and moves into the bulk solvent. The rebinding of the peptide from the solvent to the receptor binding site occurs slowly. This is because the helix partially unfolds in the unbound state. Rebinding involves an intermediate state, in which the peptide interacts with the hydrophobic binding pocket, which mainly involves Leu 62, Arg 63, Ile 65, and Phe 69. This novel intermediate structure forms 65 contacts with the receptor before the peptide again reaches the bound state. The standard binding free energy value is close to the experimental Kd in the nanomolar range. Finally, we observe how the breathing motions of α3-α4 are coupled with the binding/unbinding of the Bim BH3 peptide. The structure of the intermediate can be used for designing novel peptide inhibitors of the BHRF1 protein.

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Datum: 18.11.2017


Biochemical and biophysical properties of positively supercoiled DNA

Publication date: November 2017
Source:Biophysical Chemistry, Volume 230

Author(s): Yingting Liu, Andrea M. Berrido, Zi-Chun Hua, Yuk-Ching Tse-Dinh, Fenfei Leng

In this paper we successfully developed a procedure to generate the (+) supercoiled (sc) plasmid DNA template pZXX6 in the milligram range. With the availability of the (+) sc DNA, we are able to characterize and compare certain biochemical and biophysical properties of (+) sc, (−) sc, and relaxed (rx) DNA molecules using different techniques, such as UV melting, circular dichroism, and fluorescence spectrometry. Our results show that (+) sc, (−) sc, and rx DNA templates can only be partially melted due to the fact that these DNA templates are closed circular DNA molecules and the two DNA strands cannot be completely separated upon denaturation at high temperatures. We also find that the fluorescence intensity of a DNA-binding dye SYTO12 upon binding to the (−) sc DNA is significantly higher than that of its binding to the (+) sc DNA. This unique property may be used to differentiate the (−) sc DNA from the (+) sc DNA. Additionally, we demonstrate that E. coli topoisomerase I cannot relax the (+) sc DNA. In contrast, E. coli DNA gyrase can efficiently convert the (+) sc DNA to the (−) sc DNA. Furthermore, our dialysis competition assays show that DNA intercalators prefer binding to the (−) sc DNA.

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Datum: 18.11.2017


A possible desensitized state conformation of the human α7 nicotinic receptor: A molecular dynamics study

Publication date: October 2017
Source:Biophysical Chemistry, Volume 229

Author(s): L. Chiodo, T.E. Malliavin, L. Maragliano, G. Cottone

The determination of the conformational states corresponding to diverse functional roles of ligand gated ion channels is subject of intense investigation with various techniques, from X-rays structure determination to electrophysiology and computational modeling. Even with a certain number of structures becoming recently available, only few major structural features distinguishing conductive open channel from the non conductive resting protein have been highlighted, while high-resolution details are still missing. The characterization of the desensitized conformation(s) is even more complex, and only few specific characteristics have been identified. Furthermore, experimental data provide conflicting information for different ion channels, adding further complexity to the topic. Desensitization is defined as the transition of the agonist-bound open channel into an ion channel configuration inactive even in the presence of agonists. In this work, we analyze a conformation corresponding to a non conductive state obtained via molecular dynamics simulations of a homology model of the human α7 nicotinic receptor complexed with agonists. We highlight some characteristics that could associate it to a desensitized state. The obtained structure is assessed against experimental data for other ligand gated ion channels that have been putatively associated to active, inactive and desensitized conditions.

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Datum: 18.11.2017


Towards understanding the E. coli PNP binding mechanism and FRET absence between E. coli PNP and formycin A.

Publication date: November 2017
Source:Biophysical Chemistry, Volume 230

Author(s): Małgorzata Prokopowicz, Bartosz Greń, Joanna Cieśla, Borys Kierdaszuk

The aim of this study is threefold: (1) augmentation of the knowledge of the E. coli PNP binding mechanism; (2) explanation of the previously observed ‘lack of FRET’ phenomenon and (3) an introduction of the correction (modified method) for FRET efficiency calculation in the PNP-FA complexes. We present fluorescence studies of the two E. coli PNP mutants (F159Y and F159A) with formycin A (FA), that indicate that the aromatic amino acid is indispensable in the nucleotide binding, additional hydroxyl group at position 159 probably enhances the strength of binding and that the amino acids pair 159–160 has a great impact on the spectroscopic properties of the enzyme. The experiments were carried out in hepes and phosphate buffers, at pH7 and 8.3. Two methods, a conventional and a modified one, that utilizes the dissociation constant, for calculations of the energy transfer efficiency (E) and the acceptor-to-donor distance (r) between FA and the Tyr (energy donor) were employed. Total difference spectra were calculated for emission spectra (λ ex 280nm, 295nm, 305nm and 313nm) for all studied systems. Time-resolved techniques allowed to conclude the existence of a specific structure formed by amino acids at positions 159 and 160. The results showed an unexpected pattern change of FRET in the mutants, when compared to the wild type enzyme and a probable presence of a structure created between 159 and 160 residue, that might influence the binding efficiency. Additionally, we confirmed the indispensable role of the modification of the FRET efficiency (E) calculation on the fraction of enzyme saturation in PNP-FA systems.

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Datum: 18.11.2017


Impact of polymer geometry on the interactions of protein-PEG conjugates

Publication date: Available online 8 November 2017
Source:Biophysical Chemistry

Author(s): Jonathan Zarzar, Whitney Shatz, Nikhil Peer, Rosalynn Taing, Brian McGarry, Yun Liu, Daniel G. Greene, Isidro E. Zarraga

The conjugation of high molecular weight polyethylene glycol (PEG) to an active pharmaceutical ingredient (API) is an attractive strategy for the modification of biophysical and biodistribution properties of the API. Indeed, several therapeutic proteins conjugated to PEG have been safely administered in the clinic. While there have been studies on the configuration of these conjugates in solution, investigations on the impact of PEG geometry on protein-PEG conjugate interactions is limited. In this study, we use dynamic light scattering (DLS), rheology, and small-angle neutron scattering (SANS) to investigate the biophysical solution and interaction behavior of a 50kDa Fab protein attached to either a linear or tetrameric (branched) 40kDa PEG molecule. The hydrodynamic radii, diffusivity, viscosity and pair distance distribution function (PDDF) were obtained for the protein-PEG conjugates in solution. An analysis revealed that interactions between unconjugated proteins were quite attractive, however linear PEG-protein conjugates exhibited net repulsive interactions, similar to that of the unconjugated polymer. Tetramer PEG-protein conjugates on the other hand, exhibited a net weak attractive interaction, indicating a more balanced distribution of repulsive and attractive interaction configurations. Further analysis of the SANS data using geometric models consistent with the PDDF elucidated the conjugates' equilibrium configuration in solution. Insights gained from measurements and analysis used here can also be useful in predicting how conjugate geometries affect viscosity and aggregation behavior, which are important in determining suitable protein-polymer drug formulations.

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Datum: 18.11.2017


Capping effects on polymorphic Aβ16–21 amyloids depend on their size: A molecular dynamics simulation study

Publication date: Available online 10 October 2017
Source:Biophysical Chemistry

Author(s): Myeongsang Lee, Hyun Joon Chang, Hyunsung Choi, Sungsoo Na

Understanding Aβ amyloid oligomers associated with neuro-degenerative diseases is needed due to their toxic characteristics and mediation of amyloid fibril growth. Depending on various physiological circumstances such as ionic strength, metal ion, and point-residue mutation, oligomeric amyloids exhibit polymorphic behavior and structural stabilities, i.e. showing different conformation and stabilities. Specifically, experimental and computational researchers have found that the capping modulates the physical and chemical properties of amyloids by preserving electrostatic energy interactions, which is one of the dominant factors for amyloid stability. Still, there is no detailed knowledge for the polymorphic amyloids with reflecting the terminal capping effects. In the present study, we investigated the role of terminal capping (i.e. N-terminal acetylation and C-terminal amidation) on polymorphic Aβ16–21 amyloid oligomer and protofibrils via molecular dynamics (MD) simulations. We found that the capping effects have differently altered the conformation of polymorphic antiparallel-homo and –hetero Aβ16–21 amyloid oligomer, but not Aβ16–21 amyloid protofibrils. However, regardless of polymorphic composition of the amyloids, the capping induces the thermodynamic instabilities of Aβ16–21 amyloid oligomers, but does not show any distinct affect on Aβ16–21 amyloid protofibrils. Specifically, among the molecular mechanic factors, electrostatic energy dominantly contributes the thermodynamic stability of the Aβ16–21 amyloids. We hope that our computation study about the role of the capping effects on the polymorphic amyloids will facilitate additional efforts to enhance degradation of amyloids and to design a selective drug in the future.

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Datum: 18.11.2017


Pathogenic Aβ A2V versus protective Aβ A2T mutation: Early stage aggregation and membrane interaction

Publication date: October 2017
Source:Biophysical Chemistry, Volume 229

Author(s): Laura Colombo, Alessio Gamba, Laura Cantù, Mario Salmona, Fabrizio Tagliavini, Valeria Rondelli, Elena Del Favero, Paola Brocca

We investigated the effects of punctual A-to-V and A-to-T mutations in the amyloid precursor protein APP, corresponding to position 2 of Aβ1–42. Those mutations had opposite effects on the onset and progression of Alzheimer disease, the former inducing early AD pathology and the latter protecting against the onset of the disease. We applied Static and Dynamic Light Scattering and Circular Dichroism, to study the different mutants in the early stages of the aggregation process, essential for the disease. Comparative results showed that the aggregation pathways differ in the kinetics and extent of the process, in the size of the aggregates and in the evolution of the secondary structure, resulting in fibrils of different morphology, as seen by AFM. Mutated peptides had comparable toxic effects on N2a cells. Moreover, as assessed by X-ray scattering, all of them displayed disordering effects on the internal structure of mixed phospholipids-gangliosides model membranes.

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Datum: 18.11.2017


Controlled single-cell cyclic compression and transcription analysis: A pilot study

Publication date: October 2017
Source:Biophysical Chemistry, Volume 229

Author(s): Paola Gavazzo, Loredana Petecchia, Paolo Facci, Massimo Vassalli, Federica Viti

An innovative platform for the study of the molecular mechanisms at the basis of mechanotransduction has been implemented, developing an experimental approach capable of providing controlled dynamic compression stimuli and retrieving the biomolecular response with single-cell sensitivity. The system provides the ability to perform compression-release cycles on single cells with controlled forces in the nN range and a user-defined repetition rate. Experimental procedures to perform qPCR from a small set of single cells were finely tuned. The experimental platform was tested in the context of bone (cell line hFOB 1.19), a physiological environment highly subjected to mechanical stimuli. Target genes were identified in the literature, based on their involvement in the osteogenesis process or in the bone response to mechanical stimuli. qPCR analysis shows an increase in expression of the chosen targets, and confirms the effectiveness of the presented approach for studying living single cells response to dynamic compression.

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Datum: 18.11.2017


Inside front cover: editorial board

Publication date: November 2017
Source:Biophysical Chemistry, Volume 230










Datum: 18.11.2017


The molten-globule residual structure is critical for reflavination of glucose oxidase

Publication date: November 2017
Source:Biophysical Chemistry, Volume 230

Author(s): Katarína Garajová, Martina Zimmermann, Martina Petrenčáková, Lenka Dzurová, Michal Nemergut, Ľudovít Škultéty, Gabriel Žoldák, Erik Sedlák

Glucose oxidase (GOX) is a homodimeric glycoprotein with tightly bound one molecule of FAD cofactor per monomer of the protein. GOX has numerous applications, but the preparation of biotechnologically interesting GOX sensors requires a removal of the native FAD cofactor. This process often leads to unwanted irreversible deflavination and, as a consequence, to the low enzyme recovery. Molecular mechanisms of reversible reflavination are poorly understood; our current knowledge is based only on empiric rules, which is clearly insufficient for further development. To develop conceptual understanding of flavin-binding competent states, we studied the effect of deflavination protocols on conformational properties of GOX. After deflavination, the apoform assembles into soluble oligomers with nearly native-like holoform secondary structure but largely destabilized tertiary structure presumambly due to the packing density defects around the vacant flavin binding site. The reflavination is cooperative but not fully efficient; after the binding the flavin cofactor, the protein directly disassembles into native homodimers while the fraction of oligomers remains irreversibly inactivated. Importantly, the effect of Hofmeister salts on the conformational properties of GOX and reflavination efficiency indicates that the native-like residual tertiary structure in the molten-globule states favorably supports the reflavination and minimizes the inactivated oligomers. We interpret our results by combining the ligand-induced changes in quaternary structure with salt-sensitive, non-equilibrated conformational selection model. In summary, our work provides the very first steps toward molecular understanding the complexity of the GOX reflavination mechanism.

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Datum: 18.11.2017


Altered ionic currents and amelioration by IGF-1 and PACAP in motoneuron-derived cells modelling SBMA

Publication date: October 2017
Source:Biophysical Chemistry, Volume 229

Author(s): Aura M. Jiménez Garduño, Leon J. Juárez-Hernández, María J. Polanco, Laura Tosatto, Daniela Michelatti, Daniele Arosio, Manuela Basso, Maria Pennuto, Carlo Musio

Spinal and bulbar muscular atrophy (SBMA), also known as Kennedy's disease, is a motor neuron disease caused by the expansion of a polymorphic CAG tandem repeat encoding a polyglutamine (polyQ) tract in the androgen receptor (AR) gene. SBMA is triggered by the binding of mutant AR to its natural ligands, testosterone and dihydrotestosterone (DHT). To investigate the neuronal alterations of motor neuron cell models of SBMA, we applied patch-clamp methods to verify how polyQ expansions in the AR alter cell ionic currents. We used mouse motoneuron-derived MN-1 cells expressing normal AR (MN24Q) and mutant AR (MN100Q treated cells with vehicle EtOH and DHT). We observed a reduction of the current flux mainly at depolarizing potentials in the DHT–treated cells, while the dissection of macroscopic currents showed single different cationic currents belonging to voltage-gated channels. Also, we treated the cells with IGF-1 and PACAP, which have previously been shown to protect MN-1 cells from the toxicity of mutant AR, and we found an amelioration of the altered currents. Our results suggest that the electrophysiological correlate of SBMA is a suitable reference point for the identification of disease symptoms and for future therapeutic targets.

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Datum: 18.11.2017


Kinetic stability and sequence/structure studies of urine-derived Bence-Jones proteins from multiple myeloma and light chain amyloidosis patients

Publication date: November 2017
Source:Biophysical Chemistry, Volume 230

Author(s): Luis M. Blancas-Mejía, Emily B. Martin, Angela Williams, Jonathan S. Wall, Marina Ramirez-Alvarado

It is now accepted that the ability of a protein to form amyloid fibrils could be associated both kinetic and thermodynamic protein folding parameters. A recent study from our laboratory using recombinant full-length (encompassing the variable and constant domain) immunoglobulin light chains found a strong kinetic control of the protein unfolding for these proteins. In this study, we are extending our analysis by using urine-derived Bence Jones proteins (BJPs) from five patients with light chain (AL) amyloidosis and four patients with multiple myeloma (MM). We observed lower stability in κ proteins compared to λ proteins (for both MM and AL proteins) in agreement with previous studies. The kinetic component of protein stability is not a universal feature of BJPs and the hysteresis observed during refolding reactions could be attributed to the inability of the protein to refold all domains. The most stable proteins exhibited 3-state unfolding transitions. While these proteins do not refold reversibly, partial refolding shows 2-state partial refolding transitions, suggesting that one of the domains (possibly the variable domain) does not refold completely. Sequences were aligned with their respective germlines and the location and nature of the mutations were analyzed. The location of the mutations were analyzed and compared with the stability and amyloidogenic properties for the proteins in this study, increasing our understanding of light chain unfolding and amyloidogenic potential.

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Datum: 18.11.2017


Full title pg and editorial board

Publication date: November 2017
Source:Biophysical Chemistry, Volume 230










Datum: 18.11.2017


Bioactive compounds from extra virgin olive oils: Correlation between phenolic content and oxidative stress cell protection

Publication date: November 2017
Source:Biophysical Chemistry, Volume 230

Author(s): G. Presti, V. Guarrasi, E. Gulotta, F. Provenzano, A. Provenzano, S. Giuliano, M. Monfreda, M.R. Mangione, R. Passantino, P.L. San Biagio, M.A. Costa, D. Giacomazza

When compared with other edible vegetable oils, the extra virgin olive oil (EVOO) exhibits excellent nutritional properties due to the presence of biophenolic compounds. Although they constitute only a very small amount of the unsaponifiable fraction of EVOO, biophenols strongly contribute to the sensorial properties of this precious food conferring it, for example, the bitter or pungent taste. Furthermore, it has been found that biophenols possess beneficial effects against many human pathologies such as oxidative stress, inflammation, cardiovascular diseases, cancer and aging-related illness. In the present work, the biophenolic content of 51 Italian and Spanish EVOOs was qualitatively and quantitatively identified and their antioxidant ability analyzed by oxygen radical absorbance capacity (ORAC) assay. Results indicated that the maximum relationship can be found if the ORAC value is correlated with the concentration of the large family composed by ligstroside and oleuropein derivatives together with their degradation products, hydroxytyrosol and tyrosol. Then, selected biophenolic extracts were tested in NIH-3T3 cell line to verify their ability in the recovery of the oxidative stress revealed by DCFH-DA assay. Results were linearly correlated with the concentration of ligstroside aglycone (aldehyde and hydroxyl form).

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Datum: 18.11.2017


Broadband diffuse optical characterization of elastin for biomedical applications

Publication date: October 2017
Source:Biophysical Chemistry, Volume 229

Author(s): Sanathana Konugolu Venkata Sekar, Joo Sin Beh, Andrea Farina, Alberto Dalla Mora, Antonio Pifferi, Paola Taroni

Elastin is a key structural protein of dynamic connective tissues widely found in the extracellular matrix of skin, arteries, lungs and ligaments. It is responsible for a range of diseases related to aging of biological tissues. The optical characterization of elastin can open new opportunities for its investigation in biomedical studies. In this work, we present the absorption spectra of elastin using a broadband (550–1350nm) diffuse optical spectrometer. Distortions caused by fluorescence and finite bandwidth of the laser source on estimated absorption were effectively accounted for in measurements and data analysis and compensated. A comprehensive summary and comparison between collagen and elastin is presented, highlighting distinct features for its accurate quantification in biological applications.

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Datum: 18.11.2017


Mechanism of aggregation of UV-irradiated glycogen phosphorylase b at a low temperature in the presence of crowders and trimethylamine N-oxide

Publication date: Available online 18 October 2017
Source:Biophysical Chemistry

Author(s): Tatiana B. Eronina, Valeriya V. Mikhaylova, Natalia A. Chebotareva, Vera A. Borzova, Igor K. Yudin, Boris I. Kurganov

To characterize the initial stages of protein aggregation, the kinetics of aggregation of UV-irradiated glycogen phosphorylase b (UV-Phb) was studied under conditions when the aggregation proceeded at a low rate (10°C, 0.03M Hepes buffer, pH6.8, containing 0.1M NaCl). Aggregation of UV-Phb was induced by polyethylene glycol and Ficoll-70, acting as crowders, or a natural osmolyte trimethylamine N-oxide (TMAO). It has been shown that the initial rate of the stage of aggregate growth is proportional to the protein concentration squared, suggesting that the order of aggregation with respect to the protein is equal to two. It has been concluded that the aggregation mechanism of UV-Phb at 10°C in the presence of crowders includes the nucleation stage and stages of protein aggregate growth (the basic aggregation pathway). The aggregation mechanism is complicated in the presence of TMAO, and the stage of aggregate-aggregate assembly induced by TMAO should be added to the basic aggregation pathway. It has been shown that the ability of TMAO at a low concentration (0.05M) to induce aggregation of UV-Phb is due to the decrease in the absolute value of zeta potential of the protein in the presence of TMAO.

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Datum: 18.11.2017


Comparison of disaggregative effect of A-type EGCG dimer and EGCG monomer on the preformed bovine insulin amyloid fibrils

Publication date: November 2017
Source:Biophysical Chemistry, Volume 230

Author(s): Rong-zu Nie, Wei Zhu, Jin-ming Peng, Zhen-zhen Ge, Chun-mei Li

In the present study, the disruptive effects of epigallocatechin-3-gallate (EGCG) and A-type dimeric epigallocatechin-3-gallate (A-type EGCG dimer) on the preformed bovine insulin amyloid fibrils were studied by several biophysical methods including thioflavin-T (ThT) fluorescence assay, 1-anilinonaphthalene-8-sulfonic (ANS) fluorescence assay, Congo red (CR) binding assay, dynamic light scattering (DLS), transmission electron microscopy (TEM), Gel electrophoresis (SDS-PAGE) and Bradford assay. Our results demonstrated that A-type EGCG dimer showed significantly more potential disaggregative effects on the bovine insulin amyloid fibrils than EGCG. A-type EGCG dimer could not only dramatically promote the disaggregation of the preformed bovine insulin amyloid fibrils, but also restructure the amyloid fibrils into amorphous aggregates. While, EGCG could only shorten and thin the fibrils, but induce no small amorphous aggregates. Our present results provided additional evidence for the more potent disaggregation effects of dimeric polyphenols than monomeric polyphenols and suggested that A-type EGCG dimer seems to have potential application as an excellent anti-amyloidogenic agent.

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Datum: 18.11.2017


Inside front cover: editorial board

Publication date: October 2017
Source:Biophysical Chemistry, Volume 229










Datum: 18.11.2017


Understanding the inhibitory mechanism of BIT225 drug against p7 viroporin using computational study

Publication date: Available online 16 November 2017
Source:Biophysical Chemistry

Author(s): Esmaeil Behmard, Parviz Abdolmaleki, Majid Taghdir

P7 is the only viral channel encoded by the Hepatitis C Virus (HCV) genome. It is a small, highly hydrophobic protein containing 63 amino acids. Structural studies have shown that p7 has two transmembrane (TM) α helices linked by a short dibasic cytoplasmic loop. P7, mostly placed in the endoplasmic reticulum (ER), is a membrane-associated protein. The results obtained from different studies revealed that p7 is a polytopic membrane protein that could oligomerize in membrane bilayer to create ion channels with cation selectivity. In addition, p7 is highly conserved and plays an important role in the assembly and release of mature viral particles. Thus, it can be considered as a potential target for anti-HCV drugs. It has been found that several compounds (amantadine, rimantadine, hexamethylene amiloride (HMA) and long-alkyl-chain iminosugar (IS) derivatives) inhibit p7 channel ability. Another new inhibitor identified as BIT225, a derivative of amiloride, also inhibits the viroporin function of HIV-1 Vpu and HCV p7. In the present study, molecular dynamics simulations were applied to get insights into molecular details of a BIT225 binding site. In addition, the g_mmpbsa approach was employed to calculate the binding free energy and free energy decomposition per residue. MD simulation results in the p7–BIT225 complex revealed that drug binding to hydrophobic pocket can allosterically inhibit ion conduction via the funnel tip by restricting significant intrinsic channel breath at the tip of the funnel. Based on the molecular dynamics simulation (MD) analysis and the energy profiles, the hydrophobic interactions were the main driving force for BIT225 binding.






Datum: 18.11.2017


SIBPA under the Tuscan sun: Introduction to the SIBPA XXIII Special Issue

Publication date: October 2017
Source:Biophysical Chemistry, Volume 229

Author(s): Daniela Giacomazza, Cristiano Viappiani, Enrico Di Cera, Carlo Musio

The Italian Society for Pure and Applied Biophysics (SIBPA) held its XXIII National Congress in the gorgeous Tuscan town of Cortona, Italy, on September 18-21, 2016. This special issue features a selection of contributions from the Congress in the areas of molecular, applied, cellular and computational biophysics. Cutting-edge developments in nanoscale biophysics were introduced for the first time in the program. SIBPA continues its successful promotion of biophysical disciplines at the national and international levels, with added strength from its partnership with Biophysical Chemistry and Elsevier.

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Datum: 18.11.2017


Thermodynamic and spectroscopic study of Al3+ interaction with glycine, l-cysteine and tranexamic acid in aqueous solution

Publication date: November 2017
Source:Biophysical Chemistry, Volume 230

Author(s): Paola Cardiano, Fausta Giacobello, Ottavia Giuffrè, Silvio Sammartano

In this paper a thermodynamic and spectroscopic study on the interaction between Al3+ and glycine (Gly), l-cysteine (Cys), tranexamic acid (Tranex) is reported. Speciation models have been obtained by processing potentiometric titration data to determine stability constants of the species formed in aqueous solution at T =298.15K, 0.15 I/molL1 1 in NaCl. Thermodynamic formation parameters have been obtained from calorimetric titration data, at T =298.15K, I =0.15molL1 using NaCl as ionic medium. Al3+-Cys system was also investigated by spectrophotometric and 1H NMR measurements. 1H NMR experiments were performed on Al3+-Tranex system as well. Different speciation models have been observed for the three systems. The results showed the formation of MLH, ML and M2L2(OH)2 species for Gly, ML, M2L and MLOH for Cys, MLH and MLOH for Tranex. The formed species are quite stable, i.e. for ML, logβ=7.18, 11.91 for Gly and Cys, respectively, at I =0.15molL1 and T =298.15K. For all the systems the dependence of formation constants on ionic strength over the range 0.1–1molL1 is reported. The sequestering ability of the ligands under study was also evaluated by pL0.5 empiric parameter. For Gly, Cys and Tranex, pL0.5 =2.51, 3.74, 3.91 respectively, at pH=5, I =0.15molL1 and T =298.15K.

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Datum: 18.11.2017


Main photophysical properties of oxyblepharismin

Publication date: October 2017
Source:Biophysical Chemistry, Volume 229

Author(s): Barbara Storti, Giovanni Checcucci, Francesco Ghetti, Riccardo Nifosi, Ranieri Bizzarri

Oxyblepharismin is the photo-oxidized form of blepharismin, the chromophore responsible for the photophobic response of heterotrich ciliate Blepharisma japonicum, and represents a nice model for the study of photo-transduction. In this work, we focused on the photophysical characterization of OxyBP, in view of highlighting the main features related to excitation and emission. By a combined experimental and computational approach we identified the main features of absorption and fluorescence emission of the molecule in solvents of different properties, identifying the nature of transitions as well as the possible heterogeneity at ground/excited state. The thorough photophysical characterization of OxyBP is meant to provide the starting point for the elucidation of the photo-transduction pathway in vivo.

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Datum: 18.11.2017


Compositional analysis of endogenous porphyrins from Helicobacter pylori

Publication date: October 2017
Source:Biophysical Chemistry, Volume 229

Author(s): A. Battisti, P. Morici, G. Signore, F. Ghetti, A. Sgarbossa

Bacteria able to accumulate porphyrins can be inactivated by visible light irradiation thanks to the photosensitizing properties of this class of aromatic pigments (photodynamic therapy, PDT). Since the bacterial resistance to antibiotic is growing, PDT is becoming a valid alternative. In this context, the pathogen Helicobacter pylori (Hp) is a suitable target for PDT since it spontaneously produces and accumulates porphyrins. It is then important to understand the spectroscopic behavior of these endogenous species to exploit them as photosensitizers, thus improving the results given by the application of PDT in the treatment of Hp infections. In this work we extracted porphyrins from both a laboratory-adapted and a virulent strain of Hp, and we performed spectroscopic and chromatographic experiments to collect information about the composition and the spectrophotometric features of the extracts. The main components of the porphyrin mixtures were identified and their relative contribution to the global red fluorescence was examined.

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Datum: 18.11.2017


Spectroscopic characterization and fluorescence imaging of Helicobacter pylori endogenous porphyrins

Publication date: October 2017
Source:Biophysical Chemistry, Volume 229

Author(s): Antonella Battisti, Paola Morici, Francesco Ghetti, Antonella Sgarbossa

Conventional antimicrobial strategies have become increasingly ineffective due to the rapid emergence of antibiotic resistance among pathogenic bacteria. In order to overcome this problem, antimicrobial PhotoDynamic Therapy (PDT) is considered a promising alternative therapy. PDT has a broad spectrum of action and low mutagenic potential. It is particularly effective when microorganisms present endogenous photosensitizing pigments. Helicobacter pylori (Hp), a pathogen notoriously responsible of severe gastric infections (chronic gastritis, peptic ulcer, MALT lymphoma and gastric adenocarcinoma), produces and accumulates the photosensitizers protoporphyrin IX and coproporphyrin, thus it might be a suitable target of antimicrobial PDT. With the aim to design and develop an ingestible LED-based robotic pill for intragastric phototherapy, so that irradiation can be performed in situ without the use of invasive endoscopic light, photophysical studies on the Hp endogenous photosensitizers were carried out. These studies represent an important prerequisite in order to select the most effective irradiation conditions for Hp eradication. The photophysical characterization of Hp porphyrins, including their spectroscopic features in terms of absorption, steady-state and time-resolved fluorescence, was performed on bacterial extracts as well as within planktonic and biofilm growing Hp cells.

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Datum: 18.11.2017


Key factors regulating protein carbonylation by α,β unsaturated carbonyls: A structural study based on a retrospective meta-analysis

Publication date: November 2017
Source:Biophysical Chemistry, Volume 230

Author(s): Giulio Vistoli, Chiara Mantovani, Silvia Gervasoni, Alessandro Pedretti, Giancarlo Aldini

Protein carbonylation represents one of the most important oxidative-based modifications involving nucleophilic amino acids and affecting protein folding and function. Protein carbonylation is induced by electrophilic carbonyl species and is an highly selective process since few nucleophilic residues are carbonylated within each protein. While considering the great interest for protein carbonylation, few studies investigated the factors which render a nucleophilic residue susceptible to carbonylation. Hence, the present study is aimed to delve into the factors which modulate the reactivity of cysteine, histidine and lysine residues towards α,β unsaturated carbonyls by a retrospective analysis of the available studies which identified the adducted residues for proteins, the structure of which was resolved. Such an analysis involved different parameters including exposure, nucleophilicity, surrounding residues and capacity to attract carbonyl species (as derived by docking simulations). The obtained results allowed a meaningful clustering of the analyzed proteins suggesting that on average carbonylation selectivity increases with protein size. The comparison between adducted and unreactive residues revealed differences in all monitored parameters which are markedly more pronounced for cysteines compared to lysines and histidines. Overall, these results suggest that cysteine's carbonylation is a finely (and reasonably purposely) modulated process, while the carbonylation of lysines and histidines seems to be a fairly random event in which limited differences influence their reactivity.

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Datum: 18.11.2017


Investigation on different chemical stability of mitochondrial Hsp60 and its precursor

Publication date: October 2017
Source:Biophysical Chemistry, Volume 229

Author(s): Caterina Ricci, Rita Carrotta, Giacoma Cinzia Rappa, Maria Rosalia Mangione, Fabio Librizzi, Pier Luigi San Biagio, Heinz Amenitsch, Maria Grazia Ortore, Silvia Vilasi

In the large class of molecules that maintain protein homeostasis, called molecular chaperones, chaperonins constitute a subclass that specifically assist the correct folding of newly synthesized proteins. Among them, Hsp60 is composed of a double heptameric ring structure with a large central cavity where the unfolded protein binds via hydrophobic interactions and is supported, in this function, by the co-chaperonin Hsp10. Hsp60 is typically located in the mitochondria, but in some pathological situations, such as cancers and chronic inflammatory diseases, Hsp60 accumulates in the cytoplasm. In these cases, cytoplasmatic Hsp60 is a mixture of mitochondrial Hsp60 secreted from mitochondria upon stress, and its precursor, called naïve Hsp60, never entered into the organella. The difference between the naïve and mitochondrial Hsp60s resides in the absence of the mitochondrial import signal (MIS) in the mitochondrial form, but information on their different structure and stability is still lacking. We present here a study on the stability against a chemical denaturant, of the different cytoplasmic Hsp60 species. By combining Circular Dichroism and Small Angle X-ray Scattering as experimental biophysical techniques to investigate Hsp60, we find that naïve and mitochondrial Hsp60 (mtHsp60) forms differ in their stability. Furthermore, specific responses from the two forms are discussed in terms of the biological environment they are working in, thus opening new questions on their biological function.

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Datum: 18.11.2017


Electron current recordings in living cells

Publication date: October 2017
Source:Biophysical Chemistry, Volume 229

Author(s): Paolo Trost, Cristiana Picco, Joachim Scholz-Starke, Margherita Festa, Laura Lagostena, Alex Costa, Francesca Sparla, Armando Carpaneto

Living cells exploit the electrical properties of matter for a multitude of fundamental physiological processes, such as accumulation of nutrients, cellular homeostasis, signal transmission. While ion channels and transporters (able to couple ions to various substrates) have been extensively studied, direct measurements of electron currents mediated by specific proteins are just at the beginning. Here, we present the various electrophysiological approaches that have allowed recordings of electron currents and highlight the future potential of such experiments.

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Datum: 18.11.2017


First moves towards photoautotrophic synthetic cells: In vitro study of photosynthetic reaction centre and cytochrome bc1 complex interactions

Publication date: October 2017
Source:Biophysical Chemistry, Volume 229

Author(s): Emiliano Altamura, Rosa Fiorentino, Francesco Milano, Massimo Trotta, Gerardo Palazzo, Pasquale Stano, Fabio Mavelli

Following a bottom-up synthetic biology approach it is shown that vesicle-based cell-like systems (shortly “synthetic cells”) can be designed and assembled to perform specific function (for biotechnological applications) and for studies in the origin-of-life field. We recently focused on the construction of synthetic cells capable to converting light into chemical energy. Here we first present our approach, which has been realized so far by the reconstitution of photosynthetic reaction centre in the membrane of giant lipid vesicles. Next, the details of our ongoing research program are presented. It involves the use of the reaction centre, the coenzyme Q–cytochrome c oxidoreductase, and the ATP synthase for creating an autonomous synthetic cell. We show experimental results on the chemistry of the first two proteins showing that they can efficiently sustain light-driven chemical oscillations. Moreover, the cyclic pattern has been reproduced in silico by a minimal kinetic model.

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Datum: 18.11.2017


Effect of protonation on the mechanism of phosphate monoester hydrolysis and comparison with the hydrolysis of nucleoside triphosphate in biomolecular motors

Publication date: November 2017
Source:Biophysical Chemistry, Volume 230

Author(s): Hammad Ali Hassan, Sadaf Rani, Tabeer Fatima, Farooq Ahmad Kiani, Stefan Fischer

Hydrolysis of phosphate groups is a crucial reaction in living cells. It involves the breaking of two strong bonds, i.e. the Oa H bond of the attacking water molecule, and the POl bond of the substrate (Oa and Ol stand for attacking and leaving oxygen atoms). Mechanism of the hydrolysis reaction can proceed either by a concurrent or a sequential mechanism. In the concurrent mechanism, the breaking of Oa H and POl bonds occurs simultaneously, whereas in the sequential mechanism, the Oa H and POl bonds break at different stages of the reaction. To understand how protonation affects the mechanism of hydrolysis of phosphate monoester, we have studied the mechanism of hydrolysis of protonated and deprotonated phosphate monoester at M06-2X/6-311+G**//M06-2X/6-31+G*+ZPE level of theory (where ZPE stands for zero point energy). Our calculations show that in both protonated and deprotonated cases, the breaking of the water Oa H bond occurs before the breaking of the POl bond. Because the two events are not separated by a stable intermediate, the mechanism can be categorized as semi-concurrent. The overall energy barrier is 41kcalmol1 in the unprotonated case. Most (5/6th) of this is due to the initial breaking of the water Oa H bond. This component is lowered from 34 to 25kcalmol1 by adding one proton to the phosphate. The rest of the overall energy barrier comes from the subsequent breaking of the POl bond and is not sensitive to protonation. This is consistent with previous findings about the effect of triphosphate protonation on the hydrolysis, where the equivalent protonation (on the γ-phosphate) was seen to lower the barrier of breaking the water Oa H bond and to have little effect on the POl bond breaking. Hydrolysis pathways of phosphate monoester with initial breaking of the POl bond could not be found here. This is because the leaving group in phosphate monoester cannot be protonated, unlike in triphosphate hydrolysis, where protonation of the β- and γ-phosphates had been shown to promote a mechanism where the POl bond breaks before the Oa H bond does. We also point out that the charge shift due to POl bond breaking during sequential ATP hydrolysis in bio-molecular motors onsets the week unbinding of hydrolysis product that finally leads to the product release during power stroke.

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Datum: 18.11.2017


Discovery of a new mexiletine-derived agonist of the hERG K+ channel

Publication date: October 2017
Source:Biophysical Chemistry, Volume 229

Author(s): Roberta Gualdani, Maria Maddalena Cavalluzzi, Francesco Tadini-Buoninsegni, Giovanni Lentini

The human Ether-a-go-go Related Gene (hERG) potassium channel plays a central role in the rapid component (IKr) of cardiac action potential repolarization phase. A large number of structurally different compounds block hERG and cause a high risk of arrhythmias. Among the drugs that block hERG channel, a few compounds have been identified as hERG channel activators. Such compounds may be useful, at least in theory, for the treatment of long term QT syndrome. Here we describe a new activator of hERG channel, named MC450. This compound is a symmetric urea, derived from (R)-mexiletine. Using patch-clamp recordings, we found that MC450 increased the activation current of hERG channel, with an EC50 of 41±4μM. Moreover MC450 caused a depolarizing shift in the voltage dependence of inactivation from −64.1±1.2mV (control), to −35.9±1.4mV, whereas it had no effect on the voltage dependence of activation. Furthermore, MC450 slowed current inactivation and the effect of MC450 was attenuated by the inactivation-impaired double mutant G628C/S631C.

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Datum: 18.11.2017


A biophysical approach to quantify skeletal stem cells trans-differentiation as a model for the study of osteoporosis

Publication date: October 2017
Source:Biophysical Chemistry, Volume 229

Author(s): L. Petecchia, F. Viti, F. Sbrana, M. Vassalli, P. Gavazzo

The stroma of human bone marrow contains a population of skeletal stem cells (hBM-MSC) which are common ancestors, among the others, of osteoblasts and adipocytes. It has been proposed that the imbalance between hBM-MSC osteogenesis and adipogenesis, which naturally accompanies bone marrow senescence, may contribute to the development of bone-associated diseases, like osteoporosis. The possibility to reproduce this mechanism in vitro has been demonstrated, providing a good model to disclose the details of the complex bone-fat generation homeostasis. Nevertheless, the lack of a simple approach to quantitatively assess the actual stage of a cellular population hindered the adoption of this in vitro model. In this work, the direct differentiation of hBM-MSCs towards a single (osteo or adipo) lineage was characterized using quantitative biophysical and biological approaches, together with the parallel process of trans-differentiation from one lineage to the other. The results confirm that the original plasticity of hBM-MSCs is maintained along the initial stages of the differentiation, showing that in vitro conversion of pre-osteoblasts into adipocytes and, vice versa, of pre-adipocytes into osteoblasts is extremely efficient, comparable with the direct differentiation. Moreover, a method based on digital holography is proposed, providing a quantitative indication of the phenotype stage along differentiation.

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Datum: 18.11.2017


Nucleocytoplasmic transport in cells with progerin-induced defective nuclear lamina

Publication date: October 2017
Source:Biophysical Chemistry, Volume 229

Author(s): Gianmarco Ferri, Barbara Storti, Ranieri Bizzarri

Recent data indicate that nuclear lamina (NL) plays a relevant role in many fundamental cellular functions. The peculiar role of NL in cells is dramatically demonstrated by the Hutchinson-Gilford progeria syndrome (HGPS), an inherited laminopathy that causes premature, rapid aging shortly after birth. In HGPS, a mutant form of Lamin A (progeria) leads to a dysmorphic NL structure, but how this perturbation is transduced into cellular changes is still largely unknown. Owing to the close structural relationship between NL and the Nuclear Pore Complex (NPC), in this work we test whether HGPS affects passive and active nucleo-cytoplasmic shuttling of cargoes by means of an established model based of fluorescence recovery after photobleaching. Our findings clearly demonstrate that dysmorphic NL is decoupled from the dynamic characteristics of passive and active transport towards and from the nucleus, as well as from the binding affinity of transport protein mediators.

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Datum: 18.11.2017


Ultracompact states of native proteins

Publication date: November 2017
Source:Biophysical Chemistry, Volume 230

Author(s): Leandro Grille Coronel, Juan P. Acierno, Mario R. Ermácora

A statistical analysis of circa 20,000 X-ray structures evidenced the effects of temperature of data collection on protein intramolecular distances and degree of compaction. Identical chains with data collected at cryogenic ultralow temperatures (≤160K) showed a radius of gyration (R g ) significantly smaller than at moderate temperatures (≥240K). Furthermore, the analysis revealed the existence of structures with a R g significantly smaller than expected for cryogenic temperatures. In these ultracompact cases, the unusually small R g could not be specifically attributed to any experimental parameter or crystal features. Ultracompaction involves most atoms and results in their displacement toward the center of the molecule. Ultracompact structures on average have significantly shorter van der Waals and hydrogen bonds than expected for ultralow temperature structures. In addition, the number of van der Waals contacts was larger in ultracompact than in ultralow temperature structures. The structure of these ultracompact states was analyzed in detail and the implication and possible causes of the phenomenon are discussed.

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Datum: 18.11.2017


Impact of molecular flexibility on the site energy shift of chlorophylls in Photosystem II

Publication date: October 2017
Source:Biophysical Chemistry, Volume 229

Author(s): Daniele Narzi, Emanuele Coccia, Marco Manzoli, Leonardo Guidoni

Light harvesting from the Sun by antenna complexes surrounding the reaction center of Photosystem II represents the first step of the natural oxygenic photosynthesis performed by plants, algae and cyanobacteria. The excitation energy derived from the sunlight is absorbed by the chlorophylls of the antenna and subsequently conveyed to the reaction center of Photosystem II through resonant energy transfer mechanisms. In the special pair of chlorophylls of the reaction center the charge separation occurs, eventually leading to the oxidation of water molecules into protons, electrons and molecular oxygen. The adsorption properties of the antenna chlorophylls are ad hoc modulated by the protein environment to guarantee fast energy transfer and minimize side and back reactions. At the same time these properties are influenced by the molecular fluctuations occurring at physiological temperature. In the present work, combining classical molecular dynamics simulations with the Charge Density Coupling method, we estimated the impact of the thermal fluctuations on the site energy shift of the chlorophylls embedded in the Photosystem II complex. Our results show how the effect of the molecular fluctuations is not homogeneous throughout the complex, although the symmetry of the homodimer is maintained. Many peripheral chromophores undergo fluctuations larger then 10kJ/mol around the average values. Possible physiological roles of such fluctuations are discussed.

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Datum: 18.11.2017


Primary cortical neurons on PMCS TiO2 films towards bio-hybrid memristive device: A morpho-functional study

Publication date: October 2017
Source:Biophysical Chemistry, Volume 229

Author(s): Alessandro Roncador, Aura Matilde Jimenez-Garduño, Laura Pasquardini, Giovanni Giusti, Nicola Cornella, Lorenzo Lunelli, Cristina Potrich, Ruben Bartali, Lucrezia Aversa, Roberto Verucchi, Mauro Dalla Serra, Silvia Caponi, Salvatore Iannotta, Paolo Macchi, Carlo Musio

We report a comprehensive study of the biocompatibility and neurocompatibility of titanium dioxide films (TiO2) prepared by Pulsed Microplasma Cluster Source (PMCS). This technique uses supersonic pulsed beams seeded by clusters of the metal oxide synthesized in a plasma discharge. The final stoichiometry of the TiO2 thin films is tuned changing the gas mixture, achieving stoichiometric or oxygen overstoichiometric films. All the films showed consistent biocompatibility and a spontaneous absorption of poly-d-lysine (PDL) that favors the adhesion and growth of murine cortical neurons. Moreover, the bioelectrical activity of the neuronal culture grown on the TiO2 film can be modulated by changing the chemistry of the surface. This work paves the way to develop a bio-hybrid neuromorphic device, where viable nerve cells are grown directly over a titanium dioxide film showing a network of memristors.

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Datum: 18.11.2017


The effect of β-sheet breaker peptides on metal associated Amyloid-β peptide aggregation process

Publication date: October 2017
Source:Biophysical Chemistry, Volume 229

Author(s): F. Stellato, Z. Fusco, R. Chiaraluce, V. Consalvi, S. Dinarelli, E. Placidi, M. Petrosino, G.C. Rossi, V. Minicozzi, S. Morante

Far-UV Circular Dichroism experiments and Atomic Force Microscopy tomography are employed to assess the impact of β-sheet breakers on the Aβ1–40 peptide aggregation process in the presence of Cu2+ or Zn2+ transition metals. In this work we focus on two specific 5-amino acids long β-sheet breakers, namely the LPFFD Soto peptide, already known in the literature, and the LPFFN peptide recently designed and studied by our team. We provide evidence that both β-sheet breakers are effective in reducing the Aβ1–40 aggregation propensity, even in the presence of metal ions.

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Datum: 18.11.2017


Two-ion theory of energy coupling in ATP synthesis rectifies a fundamental flaw in the governing equations of the chemiosmotic theory

Publication date: November 2017
Source:Biophysical Chemistry, Volume 230

Author(s): Sunil Nath

The vital coupled processes of oxidative phosphorylation and photosynthetic phosphorylation synthesize molecules of adenosine-5′-triphosphate (ATP), the universal biological energy currency, and sustain all life on our planet. The chemiosmotic theory of energy coupling in oxidative and photophosphorylation was proposed by Mitchell >50years ago. It has had a contentious history, with part of the accumulated body of experimental evidence supporting it, and part of it in conflict with the theory. Although the theory was strongly criticized by many prominent scientists, the controversy has never been resolved. Here, the mathematical steps of Mitchell's original derivation leading to the principal equation of the chemiosmotic theory are scrutinized, and a fundamental flaw in them has been identified. Surprisingly, this flaw had not been detected earlier. Discovery of such a defect negates, or at least considerably weakens, the theoretical foundations on which the chemiosmotic theory is based. Ad hoc or simplistic ways to remedy this defect are shown to be scientifically unproductive and sterile. A novel two-ion theory of biological energy coupling salvages the situation by rectifying the fundamental flaw in the chemiosmotic theory, and the governing equations of the new theory have been shown to accurately quantify and predict extensive recent experimental data on ATP synthesis by F1FO-ATP synthase without using adjustable parameters. Some major biological implications arising from the new thinking are discussed. The principles of energy transduction and coupling proposed in the new paradigm are shown to be of a very general and universal nature. It is concluded that the timely availability after a 25-year research struggle of Nath's torsional mechanism of energy transduction and ATP synthesis is a rational alternative that has the power to solve the problems arising from the past, and also meet present and future challenges in this important interdisciplinary field of research.

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Datum: 18.11.2017


High-contrast Brillouin and Raman micro-spectroscopy for simultaneous mechanical and chemical investigation of microbial biofilms

Publication date: October 2017
Source:Biophysical Chemistry, Volume 229

Author(s): S. Mattana, M. Alunni Cardinali, S. Caponi, D. Casagrande Pierantoni, L. Corte, L. Roscini, G. Cardinali, D. Fioretto

Mechanical mapping with chemical specificity of biological samples is now made possible by joint micro-Brillouin and micro-Raman measurements. In this work, thanks to the unprecedented contrast of a new tandem Fabry-Perot interferometer, we demonstrate simultaneous detection of Brillouin and Raman spectra from different Candida biofilms. Our proof-of-concept study reveals the potential of this label-free joint micro-spectroscopy technique in challenging microbiological issues. In particular, heterogeneous chemo-mechanical maps of Candida biofilms are obtained, without the need for staining or touching the sample. The correlative Raman and Brillouin investigation evidences the role of both extracellular polymeric substances and of hydration water in inducing a marked local softening of the biofilm.

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Datum: 18.11.2017


miRNA purification with an optimized PDMS microdevice: Toward the direct purification of low abundant circulating biomarkers

Publication date: October 2017
Source:Biophysical Chemistry, Volume 229

Author(s): G.C. Santini, C. Potrich, L. Lunelli, L. Vanzetti, S.L. Marasso, M. Cocuzza, F.C. Pirri, C. Pederzolli

A reliable clinical assay based on circulating microRNAs (miRNAs) as biomarkers is highly required. Microdevices offer an attractive solution as a fast and inexpensive way of concentrating these biomarkers from a low sample volume. A previously developed polydimethylsiloxane (PDMS) microdevice able to purify and detect circulating miRNAs was here optimized. The optimization of the morphological and chemical surface properties by nanopatterning and functionalization is presented. Surfaces were firstly characterized by atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS), fluorescamine assay and s-SDTB (sulphosuccinimidyl-4-o-(4,4-dimethoxytrityl) butyrate) assay and subsequently tested for their capacity to adsorb a fluorescent miRNA. From our analysis, modification of surface charge with 0.1% APTMS ((3-Aminopropyl)trimethoxysilane) and 0.9% PEG-s (2-[Methoxy-(polyethyleneoxy)propyl]trimethoxysilane) performed at 60°C for 10min was identified as the best purification condition. Our optimized microdevice integrated with real-time PCR detection, was demonstrated to selectively purify both synthetic and natural circulating miRNAs with a sensitivity of 0.01pM.






Datum: 18.11.2017


Building a biomimetic membrane for neutron reflectivity investigation: Complexity, asymmetry and contrast

Publication date: October 2017
Source:Biophysical Chemistry, Volume 229

Author(s): Valeria Rondelli, Paola Brocca, Nicola Tranquilli, Giovanna Fragneto, Elena Del Favero, Laura Cantù

The preparation and investigation of model membranes is deserving growing interest both for the physics of complex systems, and for biology. The need of simplified models should preserve mimicking the qualifying characteristics of biological membranes, and keep non-invasive and detailed description. As a main feature, biological membranes are non-homogeneous in the disposition of components, both in the lateral and in the transverse direction. We prepared asymmetric supported membranes containing GM1 ganglioside in biomimetic proportion according to different protocols. Then, we studied their internal structure by neutron reflectometry, providing few-Angstrom sensitivity in the cross direction meanwhile avoiding radiation damage. This technique can also be profitably applied to study interactions at the membrane surface. The best protocol has proven to be the Langmuir-Blodgett/Langmuir-Schaefer depositions. Notably, also the simpler and most accessible protocol of vesicle fusion was found to be suitable for straightforward and good quality deposition of compositionally asymmetric membranes.

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Datum: 18.11.2017


Sequence-selective binding of C8-conjugated pyrrolobenzodiazepines (PBDs) to DNA

Publication date: November 2017
Source:Biophysical Chemistry, Volume 230

Author(s): Mohammad A. Basher, Khondaker Miraz Rahman, Paul J.M. Jackson, David E. Thurston, Keith R. Fox

DNA footprinting and melting experiments have been used to examine the sequence-specific binding of C8-conjugates of pyrrolobenzodiazepines (PBDs) and benzofused rings including benzothiophene and benzofuran, which are attached using pyrrole- or imidazole-containing linkers. The conjugates modulate the covalent attachment points of the PBDs, so that they bind best to guanines flanked by A/T-rich sequences on either the 5′- or 3′-side. The linker affects the binding, and pyrrole produces larger changes than imidazole. Melting studies with 14-mer oligonucleotide duplexes confirm covalent attachment of the conjugates, which show a different selectivity to anthramycin and reveal that more than one ligand molecule can bind to each duplex.

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Datum: 18.11.2017


Plasma assisted surface treatments of biomaterials

Publication date: October 2017
Source:Biophysical Chemistry, Volume 229

Author(s): L. Minati, C. Migliaresi, L. Lunelli, G. Viero, M. Dalla Serra, G. Speranza

The biocompatibility of an implant depends upon the material it is composed of, in addition to the prosthetic device's morphology, mechanical and surface properties. Properties as porosity and pore size should allow, when required, cells penetration and proliferation. Stiffness and strength, that depend on the bulk characteristics of the material, should match the mechanical requirements of the prosthetic applications. Surface properties should allow integration in the surrounding tissues by activating proper communication pathways with the surrounding cells. Bulk and surface properties are not interconnected, and for instance a bone prosthesis could possess the necessary stiffness and strength for the application omitting out prerequisite surface properties essential for the osteointegration. In this case, surface treatment is mandatory and can be accomplished using various techniques such as applying coatings to the prosthesis, ion beams, chemical grafting or modification, low temperature plasma, or a combination of the aforementioned. Low temperature plasma-based techniques have gained increasing consensus for the surface modification of biomaterials for being effective and competitive compared to other ways to introduce surface functionalities. In this paper we review plasma processing techniques and describe potentialities and applications of plasma to tailor the interface of biomaterials.

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Datum: 18.11.2017


Inside front cover: editorial board

Publication date: September 2017
Source:Biophysical Chemistry, Volume 228










Datum: 18.11.2017


Interdisciplinarity in Norbert Wiener, a mathematician-philosopher of our time

Publication date: October 2017
Source:Biophysical Chemistry, Volume 229

Author(s): Leone Montagnini

The paper focuses on interdisciplinarity in Norbert Wiener looking at his scientific work from a unitary point of view. It begins with a bird's-eye view of the history of the term “interdisciplinarity”, pointing out how the word was the result of a movement of ideas that took place in US science along the whole Twentieth century. This way, the Wiener's conceptions and practices concerning interdisciplinarity are compared with their historical context, showing analogies and peculiarities. For Wiener, interdisciplinary research by very small groups whose members have a very broad interdisciplinary basis is an essential prerequisite for new fundamental ideas for invention and discoveries. On the contrary, in his opinion, mass attacks by large well financed interdisciplinary research groups with a big number of overspecialized member is useful only in a second phase in which invention and discoveries need to be implemented by designers and developers. Finally, through a conceptual matching between Wiener's ideas and the ones of José Ortega y Gasset, it appears how the Wienerian small interdisciplinary group would fit better with the Kuhnian revolutionary phase in science, while the big interdisciplinary group would fit better to the Kuhnian normal science.

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Datum: 18.11.2017


Mesoscopic modelling of Cy3 and Cy5 dyes attached to DNA duplexes

Publication date: November 2017
Source:Biophysical Chemistry, Volume 230

Author(s): Pâmella Miranda, Luciana M. Oliveira, Gerald Weber

Cy3 and Cy5 dyes linked to the 5 end of a double stranded DNA molecule are known to attach to both strands in a way that is very similar to an additional base pair and has a stabilizing effect on the oligonucleotide. Here we adapt the Peyrard-Bishop mesoscopic model to incorporate cyanine dyes and use the technique of thermal equivalence to obtain the appropriate parameters from existing melting temperatures. We have found that the stacking parameters are in the same range of ordinary AT and CG base pairs, in particular Cy3-A was found to be most rigidly stacked. While the cyanines stabilize the AT hydrogen bonds quite strongly the CG bonds are mostly unaffected.

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Datum: 18.11.2017


Full title pg and editorial board

Publication date: September 2017
Source:Biophysical Chemistry, Volume 228










Datum: 18.11.2017






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