4,867 results match your criteria Biophysical chemistry[Journal]


Gratitude and acknowledgements: "Marina Diana Mercurio" Award 2018.

Authors:
Francesco Lenci

Biophys Chem 2019 Apr 3;250:106147. Epub 2019 Apr 3.

CNR-IBF, Pisa, Italy. Electronic address:

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April 2019
1 Read

Elastic compliance as a tool to understand Hofmeister ion specific effect in DMPC liposomes.

Biophys Chem 2019 Apr 8;249:106148. Epub 2019 Apr 8.

Advanced Materials Lab., CSIR-CLRI, Adyar, Chennai 600020, India. Electronic address:

Elastic compliance of DMPC liposomes with Hofmeister electrolytes: NaCl, NaSO, NaCO, NaNO, KCl and MgCl studied using Quartz crystal microbalance with dissipation has been correlated with changes in their lamellar spacing from SAXS. The study suggests that hydration water of the different ions has an effect on the overall packing of the lipid bilayer that results as either a dehydrated liposome or where water smears the surface of the liposomes. Ratio of hydrogen bonded carbonyl and phosphate of polar region of the liposomes from ATR-FTIR spectroscopy, suggests that the polar groups are less hydrated due to the displacement of water by the electrolytes compared to pure DMPC and ordered in the sequence for cations as: K < Na,Mg and for anions as SO < CO < Cl < NO. Read More

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http://dx.doi.org/10.1016/j.bpc.2019.106148DOI Listing
April 2019
5 Reads

Ordering effect of protein surfaces on water dynamics: NMR relaxation study.

Biophys Chem 2019 Apr 8;249:106149. Epub 2019 Apr 8.

Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, Siena 53100, Italy; Centre for Colloid and Surface Science (CSGI), University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Firenze, Italy. Electronic address:

Proteins in solution affect the structural and dynamic properties of the bulk water at the protein-water interface, resulting in a contribution to the order of the hydration water. Theoretical and experimental NMR relaxation methods were developed to study the dynamic properties of water molecules in the protein hydration shell. Water non-selective and selective relaxation rates, were shown to be sensitive to contributions from ordered solvent molecules at protein surface. Read More

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http://dx.doi.org/10.1016/j.bpc.2019.106149DOI Listing
April 2019
2 Reads

Hydrodynamic volume of trehalose and its water uptake mechanism.

Biophys Chem 2019 Apr 2;249:106145. Epub 2019 Apr 2.

KN Toosi University, Tehran, Iran.

Trehalose ability to preserve water in biology has spawned research on this special disaccharide and its solutions. Trehalose unlike any other disaccharide, tend to mix with almost any amount of water. In water, Trehalose forms a hydrodynamic volume with bound waters (both coordination water and semicircular heterogeneities), capable of perturbing the very nature of normal bulk water. Read More

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http://dx.doi.org/10.1016/j.bpc.2019.03.002DOI Listing
April 2019
2 Reads

Single-molecule measurement and bioinformatics analysis suggest a preferred orientation of human coagulation factor VIII on hydrophobic interfaces.

Biophys Chem 2019 05 15;248:9-15. Epub 2019 Mar 15.

Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China; CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China. Electronic address:

Investigating the adsorption behavior of coagulation proteins on interfaces will contribute to better understating blood clotting and to the development of biocompatible materials. In this work, atomic force microscopy (AFM)-based peakforce quantitative nanomechanical mapping (PF-QNM) was combined with bioinformatics tool to study the adsorption and orientation of coagulation factor VIII (FVIII) on both hydrophilic and hydrophobic interfaces by the height and mechanical measurement of single protein molecules. We found that interfacial hydrophilicity/hydrophobicity greatly influence the heights and Young's modulus of individual proteins. Read More

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http://dx.doi.org/10.1016/j.bpc.2019.03.001DOI Listing
May 2019
1 Read
1.986 Impact Factor

Characterization of the self-assembly and size dependent structural properties of dietary mixed micelles by molecular dynamics simulations.

Biophys Chem 2019 05 5;248:16-27. Epub 2019 Feb 5.

İzmir Institute of Technology, Food Engineering Department, Gulbahce Campus,Urla, Izmir 35430, Turkey. Electronic address:

The bile salts and phospholipids are secreted by the gallbladder to form dietary mixed micelles in which the solvation of poorly absorbed lipophilic drugs and nutraceuticals take place. A comprehensive understanding of the micellization and structure of the mixed micelles are crucial to design effective delivery systems for such substances. In this study, the evolution of the dietary mixed micelle formation under physiologically relevant concentrations and the dependence of structural properties on micelle size were investigated through coarse-grained molecular dynamics simulations. Read More

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http://dx.doi.org/10.1016/j.bpc.2019.02.001DOI Listing
May 2019
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Topological effects on the designability and bactericidal potency of antimicrobial peptides.

Biophys Chem 2019 05 25;248:1-8. Epub 2019 Feb 25.

Molecular Informatics & Design Laboratory, Biosciences & Bioengineering, Indian Institute of Technology Guwahati, Assam 781039, India. Electronic address:

New ideas and methods are being developed to generate highly designable small functional protein folds beyond the confines of natural structures, from secondary to quaternary level. Highly designable folds can have multiple sequence solutions, which are thermodynamically and kinetically stable. We have previously described how short syndiotactic helices can be exceptionally stable energetically, and how they can be used as a template for designing antibacterial agents. Read More

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http://dx.doi.org/10.1016/j.bpc.2019.02.005DOI Listing
May 2019
2 Reads

Statistical thermodynamics of casein aggregation: Effects of salts and water.

Biophys Chem 2019 04 12;247:34-42. Epub 2019 Feb 12.

York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom. Electronic address:

Salts, when added to milk, profoundly influence casein aggregation. Even though this well-known phenomenon has been widely exploited, there are still many unanswered questions. How do salts affect casein aggregation? Does water contribute significantly to the aggregation change? The key to answering these questions comes from statistical thermodynamics, i. Read More

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http://dx.doi.org/10.1016/j.bpc.2019.02.004DOI Listing
April 2019
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Liposome formulations of o-carborane for the boron neutron capture therapy of cancer.

Biophys Chem 2019 04 15;247:25-33. Epub 2019 Feb 15.

School of Pharmacy and Biomedical Sciences, University of Portsmouth, St Michael's Building, White Swan Road, Portsmouth PO1 2DT, UK. Electronic address:

Based on the promise of liposomes as convenient vehicles for the transport of boronated agents for the boron neutron capture therapy (BCNT) of cancer, this paper reports a method for the formulation and characterisation of stable o-carborane-loaded liposomes (ca. 80-100 nm) of dipalmitoyl-phosphatidylcholine (DPPC) or 1,2-distearol-sn-glycerol-3-phosphocholine (DSPC). Preliminary pharmaceutical characterisation experiments have demonstrated the integrity of both DPPC and DSPC liposomal membranes in serum and in PBS and also indicate that these o-carborane-loaded liposomes are candidate carrier vehicles for further evaluation with a view to exploitation in BNCT. Read More

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http://dx.doi.org/10.1016/j.bpc.2019.01.003DOI Listing

Cooperative energetic effects elicited by the yeast Shwachman-Diamond syndrome protein (Sdo1) and guanine nucleotides modulate the complex conformational landscape of the elongation factor-like 1 (Efl1) GTPase.

Biophys Chem 2019 04 13;247:13-24. Epub 2019 Feb 13.

Universidad Nacional Autónoma de México, Instituto de Química, Ciudad Universitaria, Ciudad de México 04510, Mexico. Electronic address:

One of the final maturation steps of the large ribosomal subunit requires the joint action of the elongation factor-like 1 (human EFL1, yeast Efl1) GTPase and the Shwachman-Diamond syndrome protein (human SBDS, yeast Sdo1) to release the eukaryotic translation initiation factor 6 (human eIF6, yeast Tif6) and allow the assembly of mature ribosomes. EFL1 function is driven by conformational changes. However, the nature of such conformational changes or the mechanism by which they are prompted are still largely unknown. Read More

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http://dx.doi.org/10.1016/j.bpc.2019.02.003DOI Listing

R and R2 quaternary structures of carbonmonoxyhemoglobins: Differential effect of inositol hexakisphosphate on their affinity for Ellman's reagent.

Biophys Chem 2019 04 6;247:1-12. Epub 2019 Feb 6.

Department of Chemistry, University of Ibadan, Ibadan, Nigeria.

The reaction of 5,5'-dithiobis(2-nitrobenzoate), DTNB, with hemoglobin sulfhydryl groups is linked to three negatively contributing Bohr effect groups: His2β is present in all avian hemoglobins but absent in some mammalian hemoglobins; His77β and His143β are absent in avian but present in nearly all mammalian hemoglobins. To probe the consequences of these differences, we determined the influence of inositol hexakisphosphate (inositol-P) on the DTNB affinities of avian and mammalian carbonmonoxyhemoglobins. Inositol-Pdecreases by two orders of magnitude the DTNB affinity of guinea pig hemoglobin, which has His2β and the R2 quaternary structure. Read More

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http://dx.doi.org/10.1016/j.bpc.2019.02.002DOI Listing
April 2019
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Photophysical and thermodynamic evaluation on the in vitro and in silico binding profile of Camptothecin with DNA.

Biophys Chem 2019 03 24;246:40-49. Epub 2018 Dec 24.

School of Pure and Applied Physics, Mahatma Gandhi University, Kottayam, Kerala 686560, India.. Electronic address:

Camptothecin (CMT) is an anti-tumour alkaloid drug exhibiting selective topoisomerase-I inhibitory activity by eventually hindering dynamic functions of DNA duplex via initiating apoptosis. Unravelling the binding mechanism of CMT with bio macromolecular systems can offer fundamental information regarding the mechanism of actions which can lead to the design of rational proactive drugs. This study endeavoured the binding interactions of CMT with calf thymus DNA (ct-DNA) along with the structural alterations attained by the DNA duplex owing to CMT interactions through multi-spectroscopic, calorimetric and molecular docking studies. Read More

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http://dx.doi.org/10.1016/j.bpc.2018.12.004DOI Listing
March 2019
2 Reads

Contribution of 3'T and 3'TT overhangs to the thermodynamic stability of model siRNA duplexes.

Biophys Chem 2019 03 7;246:35-39. Epub 2019 Jan 7.

Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704 Poznań, Poland. Electronic address:

Herein, we report comprehensive thermodynamic studies on 36 RNA/DNA duplexes designed as siRNA mimics to determine the energetic contribution of 3'T and 3'TT dangling ends. The thermodynamic effect induced by the presence of 3'T overhangs on the stability of RNA duplexes ranges from -0.28 to -0. Read More

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http://dx.doi.org/10.1016/j.bpc.2018.12.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6386172PMC
March 2019
15 Reads

Chemical characterization of liposomes containing nutraceutical compounds: Tyrosol, hydroxytyrosol and oleuropein.

Biophys Chem 2019 03 14;246:25-34. Epub 2019 Jan 14.

Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, Siena 53100, Italy; Centre for Colloid and Surface Science (CSGI), University of Florence, Via della Lastruccia 3, Sesto Fiorentino, FI 50019, Italy; Operative Unit, University of Siena, CampoVerde, Calabria, Italy.

Tyrosol, hydroxytyrosol and oleuropein are among the major phenolic compounds in fruits, leaves and oils from Olea europaea L. These natural antioxidants molecules revealed several beneficial effects on human health, but a low bioavailability and accessibility to targeted site. Liposomes are drug/nutraceutical delivery carriers, used for driving bioactive molecules to desired target tissues, decreasing potential side effects and protecting the encapsulated molecule from enzymatic metabolic processes. Read More

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http://dx.doi.org/10.1016/j.bpc.2019.01.002DOI Listing
March 2019
16 Reads

Ab initio model for the chlorophyll-lutein exciton coupling in the LHCII complex.

Biophys Chem 2019 03 3;246:16-24. Epub 2019 Jan 3.

Department of Chemistry, Lomonosov Moscow State University, Leninskie gory 1-3, Moscow 119991, Russia.

2A state of lutein plays a crucial role in photoprotection of higher plants. Due to its multiconfigurational nature, accurate description of this electronic state and respective transition properties is a formidable task. In this paper, applicability of various CASSCF and RASSCF formulations for description of the 2A state is discussed. Read More

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http://dx.doi.org/10.1016/j.bpc.2019.01.001DOI Listing
March 2019
1 Read

Requirements for band-pass activation of Ca-sensitive proteins such as NFAT.

Biophys Chem 2019 02 29;245:41-52. Epub 2018 Oct 29.

Center for Modelling and Simulation in the Biosciences (BIOMS), Center for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), Heidelberg University, 69120 Heidelberg, Germany. Electronic address:

Several proteins are sensitive to frequency-modulated oscillations of calcium levels. Most of them exhibit increased activities for faster frequencies, a characteristic here referred to as high-pass activation. In contrast, the transcription factor NFAT is optimally activated at a specific frequency, a behaviour we call band-pass activation. Read More

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http://dx.doi.org/10.1016/j.bpc.2018.10.005DOI Listing
February 2019
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On empirical decomposition of volumetric data.

Biophys Chem 2019 03 23;246:8-15. Epub 2018 Dec 23.

Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada.

Volumetric characterization of proteins and their recognition events has been instrumental in providing information on the role of intra- and intermolecular interactions, including hydration, in stabilizing biomolecules. The credibility of molecular models and interpretation schemes used to rationalize experimental data are essential for the validity of microscopic insights derived from volumetric results. Current empirical schemes used to interpret volumetric data suffer from a lack of theoretical and computational substantiation. Read More

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http://dx.doi.org/10.1016/j.bpc.2018.12.005DOI Listing

Interfacial vibrational spectroscopy and Brewster angle microscopy distinguishing the interaction of terpineol in cell membrane models at the air-water interface.

Biophys Chem 2019 03 20;246:1-7. Epub 2018 Dec 20.

Institute of Envinonmental, Chemical and Pharmaceutical Sciences, Federal University of São Paulo, Diadema, SP, Brazil. Electronic address:

In this paper, γ-terpineol, a known monoterpene with biological activity, including in lipidic interfaces, was incorporated in Langmuir monolayers of selected phospholipids as a model for cellular membranes. Surface pressure-area isotherms showed that selected amounts of γ-terpineol expand DPPC and DPPE monolayers and decreased the monolayer elasticity, confirming the lipid/compound interaction. Characterization with vibrational spectroscopy and Brewster angle microscopy pointed that γ-terpineol adsorbs on the polar heads of the phospholipids, affecting the gauche conformations of the aliphatic chains, and different patterns were observed for DPPC and DPPE monolayers, indicating a characteristic molecular accommodation of γ-terpineol along the polar head of the phospholipids. Read More

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http://dx.doi.org/10.1016/j.bpc.2018.12.003DOI Listing

Molecular mechanisms for the destabilization of model membranes by islet amyloid polypeptide.

Biophys Chem 2019 02 14;245:34-40. Epub 2018 Dec 14.

Center for Incubation, Innovation, Research and Consultancy (CIIRC), Jyothy Institute of Technology, Thataguni, Off Kanakapura Road, Bangalore 560082, Karnataka, India. Electronic address:

Misfolding of human islet amyloid polypeptide (hIAPP) into insoluble aggregates is associated with Type 2 diabetes. It has been suggested that hIAPP toxicity may be due to its accumulation in pancreatic islets, causing membrane disruption and cell permeabilization, however the molecular basis underlying its lipid association are still unclear. Here, we combine solid-state NMR, fluorescence and bright field microscopy to investigate hIAPP - lipid membrane interactions. Read More

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http://dx.doi.org/10.1016/j.bpc.2018.12.002DOI Listing
February 2019
14 Reads

Detection of Mg-dependent, coaxial stacking rearrangements in a bulged three-way DNA junction by single-molecule FRET.

Biophys Chem 2019 02 5;245:25-33. Epub 2018 Dec 5.

Department of Physics, Loyola University Chicago, Chicago, IL, USA. Electronic address:

Three-way helical junctions (3WJs) arise in genetic processing, and they have architectural and functional roles in structured nucleic acids. An internal bulge at the junction core allows the helical domains to become oriented into two possible, coaxially stacked conformers. Here, the helical stacking arrangements for a series of bulged, DNA 3WJs were examined using ensemble fluorescence resonance energy transfer (FRET) and single-molecule FRET (smFRET) approaches. Read More

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http://dx.doi.org/10.1016/j.bpc.2018.12.001DOI Listing
February 2019
9 Reads

Robustness of frequency vs. amplitude coding of calcium oscillations during changing temperatures.

Biophys Chem 2019 02 26;245:17-24. Epub 2018 Nov 26.

BioQuant/COS, Heidelberg University, Heidelberg, Germany.

Intracellular calcium oscillations have been widely studied. It is assumed that information is conveyed in the frequency, amplitude and shape of these oscillations. In particular, calcium signalling in mammalian liver cells has repeatedly been reported to display frequency coding so that an increasing amount of stimulus is translated into an increasing frequency of the oscillations. Read More

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http://dx.doi.org/10.1016/j.bpc.2018.11.003DOI Listing
February 2019

DNA recognition by linear indole-biphenyl DNA minor groove ligands.

Biophys Chem 2019 02 26;245:6-16. Epub 2018 Nov 26.

Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA; Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA. Electronic address:

Linear heterocyclic cations are interesting DNA minor groove ligands due to their lack of isohelical curvature classically associated with groove-binding compounds. We determined the DNA binding properties of four related dications harboring a linear indole-biphenyl core: the diamidine DB1883, a ditetrahydropyrimidine derivative (DB1804), and their monocationic counterparts (DB1944 and DB2627). These compounds exhibit heterogeneity in binding in accordance with their structures. Read More

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http://dx.doi.org/10.1016/j.bpc.2018.11.004DOI Listing
February 2019
17 Reads

Electroactive fluorescent false neurotransmitter FFN102 partially replaces dopamine in PC12 cell vesicles.

Biophys Chem 2019 02 12;245:1-5. Epub 2018 Nov 12.

PASTEUR, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France. Electronic address:

In the last decade, following fluorescent dyes and protein tags, pH sensitive false fluorescent neurotransmitters (FFN) were introduced and were valuable for labeling secretory vesicles and monitoring exocytosis at living cells. In particular, the synthetic analog of neurotransmitters FFN102 was shown to be an electroactive probe. Here, we show that FFN102 is suitable to be used as a bioanalytic probe at the widely used PC12 cell model. Read More

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http://dx.doi.org/10.1016/j.bpc.2018.11.001DOI Listing
February 2019
1 Read

Rational cyclization-based minimization of entropy penalty upon the binding of Nrf2-derived linear peptides to Keap1: A new strategy to improve therapeutic peptide activity against sepsis.

Biophys Chem 2019 01 14;244:22-28. Epub 2018 Nov 14.

Department of Emergency, Jiangsu Provincial People's Hospital, Nanjing Medical University, Nanjing 210029, China.

Nrf2 is a critical regulator of innate immune response and survival during sepsis, which is constitutively degraded through binding to the Keap1 adapter protein of E3 ubiquitin ligase. Two linear peptides DLG and ETG derived from, respectively, the low-affinity and high-affinity motifs of Nrf2 binding site exhibit self-binding affinity to Keap1 central hole (active pocket); they can be exploited as therapeutic self-inhibitory peptides to disrupt the Nrf2-Keap1 interaction. Molecular dynamics simulation and binding energetics decomposition reveal that the two peptides possess large flexibility and intrinsic disorder in unbound free state, and thus would incur a considerable entropy penalty upon binding to Keap1. Read More

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http://dx.doi.org/10.1016/j.bpc.2018.11.002DOI Listing
January 2019
12 Reads

The maximum entropy production requirement for proton transfers enhances catalytic efficiency for β-lactamases.

Biophys Chem 2019 01 17;244:11-21. Epub 2018 Oct 17.

University of Maribor, Faculty of Natural Sciences and Mathematics, Koroška cesta 160, 2000 Maribor, Slovenia; University of Maribor, Faculty of Medicine, Taborska ulica 6b, 2000 Maribor, Slovenia.

Movement of charges during enzyme catalytic cycle may be due to conformational changes, or to fast electron or proton transfer, or to both events. In each case, entropy production can be calculated using Terrel L. Hill's method, if relevant microscopic rate constants are known. Read More

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http://dx.doi.org/10.1016/j.bpc.2018.10.004DOI Listing
January 2019

Mixing behaviour of bilayer-forming phosphatidylcholines with single-chain alkyl-branched bolalipids: effect of lateral chain length.

Biophys Chem 2019 01 24;244:1-10. Epub 2018 Oct 24.

Institute of Pharmacy, Biophysical Pharmacy, Martin Luther University (MLU) Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, Halle (Saale) 06120, Germany. Electronic address:

Liposomes are a promising class of drug delivery vehicles. However, no liposomal formulation has been approved for an oral application so far, due to stability issues of the liposomes in the gastrointestinal tract. Herein, we investigate the miscibility of three novel single-chain alkyl-branched bolalipids PC-C32(1,32Cn)-PC (n = 3, 6, 9) with either saturated or unsaturated phosphatidylcholines by means of differential scanning calorimetry (DSC), transmission electron microscopy (TEM) of stained samples, vitrified specimens, or replica of freeze-fractured samples, and dynamic light scattering (DLS). Read More

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http://dx.doi.org/10.1016/j.bpc.2018.10.003DOI Listing
January 2019

Singlet oxygen quenching- and chain-breaking antioxidant-properties of a quercetin dimer able to prevent age-related macular degeneration.

Biophys Chem 2018 12 12;243:17-23. Epub 2018 Oct 12.

Istituto di Chimica Biomolecolare del CNR, via P. Gaifami 18, I-95126 Catania, Italy.

A dimer of quercetin prepared through a Mannich reaction protects pyridinium bisretinoid A2E from photooxidation at 430 nm in aqueous medium at pH 7.4. In the presence of light and O, A2E is quickly attacked by O produced in situ (by excited A2E) to give nonaoxirane and other oxygenated compounds which can be involved in diseases of the macula. Read More

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http://dx.doi.org/10.1016/j.bpc.2018.10.001DOI Listing
December 2018
10 Reads

Hofmeister effect on catalytic properties of chymotrypsin is substrate-dependent.

Biophys Chem 2018 12 13;243:8-16. Epub 2018 Oct 13.

Department of Biochemistry, Faculty of Science, P. J. Šafárik University in Košice, Moyzesova 11, 04154 Košice, Slovakia; Centre for Interdisciplinary Biosciences, Technology and Innovation Park, P. J. Šafárik University in Košice, Jesenná 5, 04154 Košice, Slovakia. Electronic address:

Effect of Hofmeister sodium salts, sulfate, chloride, bromide and perchlorate, on catalytic properties and stability of chymotrypsin has been studied by absorbance and circular dichroism spectroscopies. To address Hofmeister effect on activity of chymotrypsin, two different substrates, N-benzoyl-L-tyrosine ethyl ester and amide N-succinyl-L-phenylalanine-p-nitroanilide, were used. Catalytic activity of chymotrypsin is dependent on salt concentration and position of anion in Hofmeister series. Read More

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http://dx.doi.org/10.1016/j.bpc.2018.10.002DOI Listing
December 2018
17 Reads

Thermal unfolding of homodimers and heterodimers of different skeletal-muscle isoforms of tropomyosin.

Biophys Chem 2018 12 20;243:1-7. Epub 2018 Sep 20.

Research Center of Biotechnology of the Russian Academy of Sciences, Bach Institute of Biochemistry, Leninsky prosp. 33, Moscow 119071, Russia; Belozersky Institute of Physico-Chemical Biology, Moscow State University, Russia. Electronic address:

We applied differential scanning calorimetry (DSC) to investigate the structural properties of three isoforms of tropomyosin (Tpm), α, β, and γ, expressed from different genes in human skeletal muscles. We compared specific features of the thermal unfolding of αα, ββ, and γγ Tpm homodimers, as well as of αβ and γβ Tpm heterodimers. The results show that the thermal stability of γγ homodimer is much higher than that of αα homodimer which, in turn, is much more thermostable than the ββ homodimer. Read More

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http://dx.doi.org/10.1016/j.bpc.2018.09.002DOI Listing
December 2018
1 Read

Bohr effect and oxygen affinity of carp, eel and human hemoglobin: Quantitative analyses provide rationale for the Root effect.

Biophys Chem 2018 11 12;242:45-59. Epub 2018 Sep 12.

Department of Chemistry, University of Ibadan, Ibadan, Nigeria. Electronic address:

The functional properties of most fish hemoglobins are more complex than those of human hemoglobin. This complexity arises in the form of the Root effect, in which the oxygen affinity of such fish hemoglobins decreases rapidly with pH relative to that of human hemoglobin. Cooperative ligand binding is also diminished below pH ≈ 6. Read More

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http://dx.doi.org/10.1016/j.bpc.2018.09.001DOI Listing
November 2018
34 Reads

A theory of reactant-stationary kinetics for a mechanism of zymogen activation.

Biophys Chem 2018 11 23;242:34-44. Epub 2018 Aug 23.

Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Computational Medicine & Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA. Electronic address:

A theoretical analysis is performed on the nonlinear ordinary differential equations that govern the dynamics of a reaction mechanism of zymogen activation. The reaction consists of a primary non-observable zymogen activation reaction that it is coupled to an indicator (observable) reaction. The product of the first reaction is the enzyme of the indicator reaction, and both reactions are governed by the Michaelis-Menten reaction mechanism. Read More

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http://dx.doi.org/10.1016/j.bpc.2018.08.003DOI Listing
November 2018
1 Read

Differential effect of multiple kinesin motors on run length, force and microtubule binding rate.

Biophys Chem 2018 11 3;242:28-33. Epub 2018 Sep 3.

Divisions of Advanced Materials, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José 2055, 78216 San Luis Potosí, Mexico.

The in vitro transport of cargo by motor proteins constitutes a model system to understand mechanisms of vesicle trafficking inside cells. Here we apply the classic bead assay with a short, stiff kinesin protein to test the effect of multiple motors on essential transport parameters: distance, force and microtubule binding rate. Measurements of unloaded run length show that the transition from single- to multiple-motor behavior can be characterized by the appearance of extended runs, in accordance with a recently proposed model that quantifies the probability of multiple-motor engagement. Read More

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http://dx.doi.org/10.1016/j.bpc.2018.08.007DOI Listing
November 2018
1 Read

An empirical analysis of enzyme function reporting for experimental reproducibility: Missing/incomplete information in published papers.

Biophys Chem 2018 11 24;242:22-27. Epub 2018 Aug 24.

Beilstein-Institut, Frankfurt am Main, Germany.

A key component of enzyme function experiments is reporting of considerable metadata, to allow other researchers to replicate, interpret properly or use fully the results. This paper evaluates the completeness of enzyme function data reporting for reproducibility. We present a detailed examination of 11 recent papers (and their supplementary material) from two leading journals. Read More

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http://dx.doi.org/10.1016/j.bpc.2018.08.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6258184PMC
November 2018

Molecular mechanistic insights into uncoupling of ion transport from ATP synthesis.

Authors:
Sunil Nath

Biophys Chem 2018 11 27;242:15-21. Epub 2018 Aug 27.

Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India. Electronic address:

A procedure is evolved to assess the maximum uncoupling activity of the classical unsubstituted phenolic uncouplers of mitochondrial oxidative phosphorylation (OX PHOS) 2,4-dinitrophenol and 2,6-dinitrophenol. The uncoupler concentrations, C, required for maximum uncoupling efficacy are found to be a strong function of the pH, and a linear relationship of pC with pH is obtained between pH 5 to pH 9. The slopes of the uncoupler concentrations in the aqueous and lipid phases as a function of pH have been estimated. Read More

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http://dx.doi.org/10.1016/j.bpc.2018.08.006DOI Listing
November 2018
14 Reads

ATP hydrolysis inactivating Walker B mutation perturbs E. coli ClpA self-assembly energetics in the absence of nucleotide.

Biophys Chem 2018 11 27;242:6-14. Epub 2018 Aug 27.

University of Alabama at Birmingham, Chemistry Department, Birmingham, AL, United States. Electronic address:

E. coli ClpA is an AAA+ (ATPase Associated with diverse cellular Activities) chaperone that catalyzes the ATP-dependent unfolding and translocation of substrate proteins for the purposes of proper proteome maintenance. Biologically active ClpA hexamers contain two nucleotide binding domains (NBD) per protomer, D1 and D2. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S03014622183008
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http://dx.doi.org/10.1016/j.bpc.2018.08.005DOI Listing
November 2018
2 Reads

X-ray observations of single bio-supramolecular photochirogenesis.

Biophys Chem 2018 11 14;242:1-5. Epub 2018 Aug 14.

Advanced Material Science, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Japan; Advanced Operando-Measurement Technology Open Innovation Laboratory (OPERANDO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Japan. Electronic address:

The binding and photochirogenic behaviour of 2-anthracenecarboxylate (AC) with human serum albumin (HSA) have hitherto been investigated and comprehended as time-averaged statistical events by spectroscopic examinations and product analyses. In this study, we employed a diffracted X-ray tracking (DXT) technique to visualize the single-molecular dynamics of free and AC-loaded HSA (AC:HSA = 0, 1, 5 and 10), as well as the AC-HSA complex under photoirradiation, all of which were tethered to gold nanocrystals and hence traceable in real time by DXT. This enabled us to draw a more dynamic picture of the bio-supramolecular photochirogenesis at a single-molecule resolution, detailing the softening and flexibility enhancement of HSA upon binding of ACs to its inter-subdomain IIA-IIB site and the dynamic extrusion of AC dimers produced upon photoirradiation. Read More

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http://dx.doi.org/10.1016/j.bpc.2018.07.003DOI Listing
November 2018

Copper(II) complexation by fragment of central part of FBP28 protein from Mus musculus.

Biophys Chem 2018 10 7;241:55-60. Epub 2018 Aug 7.

Faculty of Chemistry, University of Gdansk, ul. Wita Stwosza 63, 80-308 Gdansk, Poland.

Steady-state and time-resolved fluorescence spectroscopy, UV spectrophotometry and isothermal titration calorimetry techniques were used to study the coordinating properties of the 17aa peptide fragment (D17) derived from the central part of the mouse formin binding protein (FBP28 with the PDB code: 1E0L) towards Cu ions. All the measurements were run in the 2-(N-morpholino)ethanesulfonic acid buffer (20 mM, pH 6.0). Read More

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http://dx.doi.org/10.1016/j.bpc.2018.08.002DOI Listing
October 2018

A weighted average kinetic equation and its application in estimating mass transfer coefficients in liquid phase adsorption.

Biophys Chem 2018 10 7;241:50-54. Epub 2018 Aug 7.

College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China.

The pseudo-first-order (PFO) and pseudo-second-order (PSO) models are widely used to describe liquid phase adsorption kinetics due to their simplicity and easy application. But these models do not take into account the diffusion or mass transfer effects that exist in adsorption. In this work a new weighted average (WA) kinetic model is presented. Read More

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http://dx.doi.org/10.1016/j.bpc.2018.08.001DOI Listing
October 2018
22 Reads

Derivation and numerical profile analysis of a hierarchically formulated microscopic model of hemoglobin oxygen binding.

Biophys Chem 2018 10 4;241:38-49. Epub 2018 Aug 4.

School of Pharmacy, Division of Pharmaceutical Sciences, University of Missouri Kansas City, 2464 Charlotte Street, Kansas City, MO 64108, USA. Electronic address:

To address complex thermodynamic systems with multiple interacting events, we have developed the concept of hierarchical thermodynamic interactions. In this study, this concept is extended to protein-ligand systems with similar but not identical protein subunits, and applied to the analysis of previously published NMR and UV-vis monitored hemoglobin oxygen binding data. Non-linear regression provided estimated errors for statistically significant parameters, but not for null (zero) valued parameters. Read More

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http://dx.doi.org/10.1016/j.bpc.2018.07.008DOI Listing
October 2018
6 Reads

Conformational heterogeneity of tau: Implication on intrinsic disorder, acid stability and fibrillation in Alzheimer's disease.

Biophys Chem 2018 10 27;241:27-37. Epub 2018 Jul 27.

Clinical Proteomics Unit, Division of Molecular Medicine, St. John's Research Institute, St. John's National Academy of Health Sciences, 100 Feet Road, Koramangala, Bangalore 560034, Karnataka, India. Electronic address:

The self-assembly of intrinsically disordered protein tau into paired helical filament forms one of the hallmarks of Alzheimer's disease. However, the facets of innately disordered structure of tau and its conversion to a β-sheet-rich fibril during several tauopathies are poorly understood. Here, we provide a direct insight into the ensemble of highly heterogeneous conformational families of tau at physiological pH, by nano-electrospray mass spectrometry coupled with ion mobility. Read More

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http://dx.doi.org/10.1016/j.bpc.2018.07.005DOI Listing
October 2018
72 Reads
1.990 Impact Factor

Molecular mechanistic insights into coupling of ion transport to ATP synthesis.

Authors:
Sunil Nath

Biophys Chem 2018 10 29;241:20-26. Epub 2018 Jul 29.

Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India. Electronic address:

A wealth of molecular mechanistic insights has been provided into the coupling of ion transport to ATP synthesis based on a two-ion theory of biological energy coupling. A kinetic scheme that considers the mode of functioning of a single FF-ATP synthase molecule with H-A cotransport and unidirectional rotation of the c-rotor in the membrane-bound F-portion of the enzyme has been developed. Mathematical analysis leads to a detailed enzyme kinetic model applicable to a population of molecules which is compared with experimental data on the pH dependence of ATP synthesis. Read More

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http://dx.doi.org/10.1016/j.bpc.2018.07.006DOI Listing
October 2018
19 Reads

Mechano-molecular transduction: Putting the pieces together.

Authors:
Amit Ron

Biophys Chem 2018 10 29;241:15-19. Epub 2018 Jul 29.

Department of Mechanical Engineering, School of Engineering and Applied Science, Columbia University, New York, NY 10027, United States. Electronic address:

When subjected to extracellular mechanical loads, cells express a variety of responses ranging from differentiation to apoptosis. The transducing mechanism between the physical stimulus and the molecular response is known as mechanotransduction. In this study, a mechano-molecular model is established that facilitates the integration of cellular mechanics with molecular signaling. Read More

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http://dx.doi.org/10.1016/j.bpc.2018.07.007DOI Listing
October 2018

Carboplatin as an alternative to Cisplatin in chemotherapies: New insights at single molecule level.

Biophys Chem 2018 10 25;241:8-14. Epub 2018 Jul 25.

Laboratório de Física Biológica, Departamento de Física, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil. Electronic address:

Here we report a new study performed at single molecule level on the interaction of the antineoplastic drug Carboplatin and the DNA molecule - the main target of the drug inside cells in cancer chemotherapies. By using optical tweezers, we measure how the mechanical properties of the DNA-Carboplatin complexes changes as a function of the drug concentration in the sample, for two different ionic strengths ([Na] = 150 mM and [Na] = 1 mM). From these measurements, the binding mechanism and the physicochemical (binding) parameters of the interaction were inferred and directly compared to those obtained for the precursor drug Cisplatin under equivalent conditions. Read More

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http://dx.doi.org/10.1016/j.bpc.2018.07.004DOI Listing
October 2018

Simulating biological charge transfer: Continuum dielectric theory or molecular dynamics?

Biophys Chem 2018 10 20;241:1-7. Epub 2018 Jul 20.

Institut für Physikalische Chemie, Universität Freiburg, Albertstraße 23a, 79104 Freiburg im Breisgau, Germany. Electronic address:

We study the thermodynamic parameters of Marcus's theory of charge transfer, the driving forces and the reorganization energies, using two widely applied approaches to bioenergetic problems that seem to be radically different: continuum dielectric theory via a numerical solution of Poisson's equation, and the thermodynamic integration approach based upon classical Newtonian molecular dynamics, as perfomed by Na et al., PCCP 19, 18,938 (2017). With application to a nitrite reductase NrfHA protein heterodimer, we obtain an excellent agreement between the respective driving forces with an r. Read More

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http://dx.doi.org/10.1016/j.bpc.2018.07.001DOI Listing
October 2018
2 Reads

The hydrolysis of 6-phosphogluconolactone in the second step of pentose phosphate pathway occurs via a two-water mechanism.

Biophys Chem 2018 09 12;240:98-106. Epub 2018 Jun 12.

Research Center for Modeling and Simulation (RCMS), National University of Sciences and Technology (NUST), Sector H-12, 44000 Islamabad, Pakistan; Department of Physiology and Biophysics, Boston University School of Medicine, 700 Albany Street, 02118 Boston, MA, United States. Electronic address:

Hydrolysis reaction marks the basis of life yet the mechanism of this crucial biochemical reaction is not completely understood. We recently reported the mechanisms of hydrolysis of nucleoside triphosphate and phosphate monoester. These two reactions hydrolyze P-O-P and P-O-C linkages, respectively. Read More

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http://dx.doi.org/10.1016/j.bpc.2018.06.002DOI Listing
September 2018
108 Reads
1.990 Impact Factor

Antagonistic role of Klotho-derived peptides dynamics in the pancreatic cancer treatment through obstructing WNT-1 and Frizzled binding.

Biophys Chem 2018 09 7;240:107-117. Epub 2018 Jul 7.

National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan. Electronic address:

Klotho is an anti-aging protein that is engaged in the suppression of canonical WNT signaling. In this study, we investigated the expression pattern of human WNTs and Klotho in the pancreatic cancer. In the cancerous cells, WNT-1 exhibited much higher expression as compared to other WNTs, while no WNT expression was detected in the normal tissue. Read More

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http://dx.doi.org/10.1016/j.bpc.2018.07.002DOI Listing
September 2018
4 Reads

Effects of lyotropic anions on thermodynamic stability and dynamics of horse cytochrome c.

Biophys Chem 2018 09 19;240:88-97. Epub 2018 Jun 19.

Department of Chemical Sciences, School of Basic and Applied Sciences, Central University of Punjab, Bathinda 151001, India; School of Chemistry and Biochemistry, Thapar University, Patiala 147004, India. Electronic address:

This paper evaluates the effect of various lyotropic anions (chloride, sulfate, perchlorate, iodide, nitrate, bromide) on the thermodynamic stability and dynamics of native cytochrome c (Cyt c) at pH 7.0. The results of equilibrium and kinetic studies revealed that: (i) at low to intermediate concentrations (≤ 0. Read More

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http://dx.doi.org/10.1016/j.bpc.2018.06.003DOI Listing
September 2018
4 Reads
1.990 Impact Factor

A theoretical study on the cross-talk of stress regulatory pathways in root cells.

Biophys Chem 2018 09 19;240:82-87. Epub 2018 Jun 19.

Department of Physics, Institute of Biophysics, Huazhong Normal University, Wuhan 430070, China.

The plants developed more dedicated regulatory pathways than the animals did to response various environment stresses, since they could not run away. The cross-talk among the pathways generally introduce non-trivial regulatory behaviors, from which the plants may benefit. For better understanding the regulatory mechanism due to cross-talk, we study in this work two entangled stress regulatory pathways in root cells. Read More

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http://dx.doi.org/10.1016/j.bpc.2018.06.004DOI Listing
September 2018

Unraveling the binding interaction of a bioactive pyrazole-based probe with serum proteins: Relative concentration dependent 1:1 and 2:1 probe-protein stoichiometries.

Biophys Chem 2018 09 15;240:70-81. Epub 2018 Jun 15.

Department of Chemistry, Jadavpur University, Kolkata 700 032, India. Electronic address:

Molecular interactions and binding of probes/drugs with biomacromolecular systems are of fundamental importance in understanding the mechanism of action and hence designing of proactive drugs. In the present study, binding interactions of a biologically potent fluorophore, (E)-1,5-diphenyl-3-styryl-4,5-dihydro-1H-pyrazole (DSDP) with two serum transport proteins, human serum albumin and bovine serum albumin, have been investigated exploiting multi-spectroscopic techniques. The spectrophotometric and fluorometric studies together with fluorescence quenching, fluorescence anisotropy, urea induced denaturation studies and fluorescence lifetime measurements reveal strong binding of DSDP with both the plasma proteins. Read More

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http://dx.doi.org/10.1016/j.bpc.2018.06.001DOI Listing
September 2018
5 Reads

Development of a machine-learning model to predict Gibbs free energy of binding for protein-ligand complexes.

Biophys Chem 2018 09 7;240:63-69. Epub 2018 Jun 7.

Laboratory of Computational Systems Biology, School of Sciences, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Av. Ipiranga, 6681, Porto Alegre, RS 90619-900, Brazil; Graduate Program in Cellular and Molecular Biology, The Pontifical Catholic University of Rio Grande do Sul (PUCRS), Av. Ipiranga, 6681, Porto Alegre, RS 90619-900, Brazil. Electronic address:

The possibility of using the atomic coordinates of protein-ligand complexes to assess binding affinity has a beneficial impact in the early stages of drug development and design. From the computational view, the creation of reliable scoring functions is still an open problem in the simulation of biological systems, and the development of a new generation machine-learning model is an active research field. In this work, we propose a novel scoring function to predict Gibbs free energy of binding (ΔG) based on the crystallographic structure of complexes involving a protein and an active ligand. Read More

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http://dx.doi.org/10.1016/j.bpc.2018.05.010DOI Listing
September 2018