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Biophysical Chemistry

Sunil Nath
As the chief energy source of eukaryotic cells, it is important to determine the thermodynamic efficiency of ATP synthesis in oxidative phosphorylation (OX PHOS). Previous estimates of the thermodynamic efficiency of this vital process have ranged from Lehninger's original back-of-the-envelope calculation of 38% to the often quoted value of 55-60% in current textbooks of biochemistry, to high values of 90% from recent information theoretic considerations, and reports of realizations of close to ideal 100% efficiencies by single molecule experiments...
October 15, 2016: Biophysical Chemistry
Ximena Zottig, Mathieu Laporte Wolwertz, Makan Golizeh, Leanne Ohlund, Lekha Sleno, Steve Bourgault
Light chain amyloidosis (AL) originates from the deposition of immunoglobulin light chains (LCs) as amyloid fibrils in the extracellular space of vital organs. Although non-enzymatic post-translational modifications (PTMs) have been shown to contribute to protein misfolding diseases, little is known about their contributions to LC amyloidogenicity. In this study, we investigated the effects of three oxidative PTMs, carbonylation by hydroxynonenal (HNE), oxidation and nitration, on the structure, thermodynamic stability and self-assembly propensity of a LC variable domain from the λ6 germline, Wil...
October 11, 2016: Biophysical Chemistry
Kumar Padmapriya, Ritu Barthwal
Binding of coralyne to tetra-molecular parallel G-quadruplex DNA [d(TTGGGGT)]4 was evaluated for the first time using biophysical techniques. Absorbance titrations show hypo/hyper-chromism accompanied by 12nm red shift with binding constant Kb=0.2-4.0×10(6)M(-1). Binding induces a negative circular dichroism band of coralyne at 315nm. Quenching of fluorescence (~64%) along with 10nm blue shift in emission maxima indicates proximity of coralyne to guanine bases. Job plot indicates existence of multiple complexes...
October 1, 2016: Biophysical Chemistry
Daxu Li, Rong Chen, Shin-Ho Chung
Tertiapin (TPN), a short peptide isolated from the venom of the honey bee, is a potent and selective blocker of the inward rectifier K(+) (Kir) channel Kir3.2. Here we examine in atomic detail the binding mode of TPN to Kir3.2 using molecular dynamics, and deduce the key residue in Kir3.2 responsible for TPN selectivity. The binding of TPN to Kir3.2 is stable when the side chain of either Lys16 (TPN(K16)-Kir3.2) or Lys17 (TPN(K17)-Kir3.2) of the toxin protrudes into the channel pore. However, the binding affinity calculated from only TPN(K17)-Kir3...
September 30, 2016: Biophysical Chemistry
Jong Heon Shin, Yoon Mo Hwang, Yoon Jung Jang, Seog K Kim
trans-BMPyP induced the B-Z transition for alternated AT oligonucleotides as it was evident by inversed CD spectrum. The transition occurred simultaneously with appearance of the extensive stacking of porphyrin. Complete B-Z transition required at least 14 base-pairs long. Insertion of one or two GC base pairs prevented the B-Z transition.
September 28, 2016: Biophysical Chemistry
Vishwanath Sivalingam, Nalla Lakshmi Prasanna, Neetu Sharma, Archana Prasad, Basant K Patel
Misfolded β-sheet-rich protein aggregates termed amyloid, deposit in vivo leading to debilitating diseases such as Alzheimer's, prion and renal amyloidosis diseases etc. Strikingly, amyloid can induce conversion of their natively folded monomers into similarly aggregated conformation via 'seeding'. The specificity of seeding is well documented in vivo for prions, where prion-variants arising from conformationally altered amyloids of the same protein, faithfully seed monomers into amyloid displaying the original variant's conformation...
September 28, 2016: Biophysical Chemistry
W Jetsadawisut, B Nutho, A Meeprasert, T Rungrotmongkol, N Kungwan, P Wolschann, S Hannongbua
Hand foot and mouth disease (HFMD) epidemic has occurred in many countries. Coxsackievirus A16 (CV-A16) and Enterovirus A71 (EV-A71) are the main causes of HFMD. Up to now, there are no anti-HFMD drugs available. Rupintrivir, a broad-spectrum inhibitor, is a drug candidate for HFMD treatment, while other HFMD inhibitors designed from several studies have a relatively low efficiency. Therefore, in this work we aim to study the binding mechanisms of rupintrivir and a peptidic α,β-unsaturated ethyl ester (SG85) against both CV-A16 and EV-A71 3C proteases (3C(pro)) using all-atoms molecular dynamics simulation...
September 20, 2016: Biophysical Chemistry
Dayana Cabral da Silva, Giselle N Fontes, Luiza C S Erthal, Luís Maurício T R Lima
Amylin is a pancreatic peptide hormone co-secreted along with insulin by the β-cells. It is found in amyloid deposits in both type 2 diabetic individuals and elder non-diabetic. The triple proline amylinomimetic compound (25,28,29-Pro-human amylin) named pramlintide was designed aiming to solve the solubility and amyloid characteristics of human amylin. We have found by using ion mobility spectrometry-based mass spectrometry that pramlintide is able to assembly into multimers. Pramlintide formed amyloid fibrils in vitro in a pH-dependent kinetic process within a few hours, as followed by thioflavin T, quantification of soluble peptide and further characterized by transmission electron microscopy, atomic force microscopy and X-ray diffraction...
September 20, 2016: Biophysical Chemistry
Wylie Stroberg, Santiago Schnell
The conditions under which the Michaelis-Menten equation accurately captures the steady-state kinetics of a simple enzyme-catalyzed reaction is contrasted with the conditions under which the same equation can be used to estimate parameters, KM and V, from progress curve data. Validity of the underlying assumptions leading to the Michaelis-Menten equation are shown to be necessary, but not sufficient to guarantee accurate estimation of KM and V. Detailed error analysis and numerical "experiments" show the required experimental conditions for the independent estimation of both KM and V from progress curves...
September 16, 2016: Biophysical Chemistry
Luiza C S Erthal, Adriana F Marques, Fábio C L Almeida, Gustavo L M Melo, Camila M Carvalho, Leonardo C Palmieri, Katia M S Cabral, Giselle N Fontes, Luís Maurício T R Lima
The secretory granule of the pancreatic β-cells is a zinc-rich environment copopulated with the hormones amylin and insulin. The human amylin is shown to interact with zinc ions with major contribution from the single histidine residue, which is absent in amylin from other species such as cat, rhesus and rodents. We report here the interaction of murine amylin with zinc ions in vitro. The self-assembly of murine amylin is tightly regulated by zinc and pH. Ion mobility mass spectrometry revealed zinc interaction with monomers and oligomers...
November 2016: Biophysical Chemistry
Kubra Bilici, Steven W Morgan, Moshe C Silverstein, Yunjie Wang, Hyung Jin Sun, Yanhang Zhang, Gregory S Boutis
Elastin is a protein of the extracellular matrix that contributes significantly to the elasticity of connective tissues. In this study, we examine dynamical and structural modifications of aortic elastin exposed to cholesterol by NMR spectroscopic and relaxation methodologies. Macroscopic measurements are also presented and reveal that cholesterol treatment may cause a decrease in the stiffness of tissue. (2)H NMR relaxation techniques revealed differences between the relative populations of water that correlate with the swelling of the tissue following cholesterol exposure...
November 2016: Biophysical Chemistry
Thomas A Collier, Anthony Nash, Helen L Birch, Nora H de Leeuw
Covalently cross-linked advanced glycation end products (AGE) are among the major post-translational modifications to proteins as a result of non-enzymatic glycation. The formation of AGEs has been shown to have adverse effects on the properties of the collagenous tissue; they are even linked to a number of age related disorders. Little is known about the sites at which these AGEs form or why certain sites within the collagen are energetically more favourable than others. In this study we have used a proven fully atomistic molecular dynamics approach to identify six sites where the formation of the intra-molecular 3-deoxyglucosone-derived imidazolium cross-link (DOGDIC) is energetically favourable...
November 2016: Biophysical Chemistry
Yun Ding, Rong Tian, Zhen Yang, Jianfa Chen, Naihao Lu
The binding of protein to carboxylated single-walled carbon nanotubes (SWCNTs) was believed to play an important role in the biological effects of nanotubes. However, the effects of protein-SWCNTs interactions on the oxidative degradation of nanotubes were not stressed enough. Here, we investigated the binding of human immunoglobulin G (IgG) to SWCNTs, and found that the preferred binding site was located in the Fc region of IgG. The hydrophobic and electrostatic interactions might be the crucial factors in stabilizing the binding of SWCNTs with IgG...
November 2016: Biophysical Chemistry
Jae In Kim, Junpyo Kwon, Inchul Baek, Sungsoo Na
Cofilin is one of the most essential regulatory proteins and participates in the process of disassembling actin filaments. Cofilin induces conformational changes to actin filaments, and both the bending and torsional rigidity of the filament. In this study, we investigate the effects of cofilin on the mechanical properties of actin filaments using computational methods. Three models defined by their number of bound cofilins are constructed using coarse-grained MARTINI force field, and they are then extended with steered molecular dynamics simulation...
November 2016: Biophysical Chemistry
Sara De Bortoli, Enrico Teardo, Ildikò Szabò, Tomas Morosinotto, Alessandro Alboresi
Photosynthetic eukaryotes have a complex evolutionary history shaped by multiple endosymbiosis events that required a tight coordination between the organelles and the rest of the cell. Plant ionotropic glutamate receptors (iGLRs) form a large superfamily of proteins with a predicted or proven non-selective cation channel activity regulated by a broad range of amino acids. They are involved in different physiological processes such as C/N sensing, resistance against fungal infection, root and pollen tube growth and response to wounding and pathogens...
November 2016: Biophysical Chemistry
Alok Juneja, Lennart Nilsson, Alessandra Villa
Conformational dynamics plays a key role in mediating specific interactions between RNAs and proteins. Flexible parts, such as the loop regions, are often involved in protein binding. Characterization of the factors that influence the flexibility of loop regions will improve our understanding of RNA-protein binding. Here we use molecular dynamics simulations to study the dynamical features of the apical stem-loop of hepatitis B virus and a mutant, with two consensus-based secondary structure mutations (A-U→C-G) in the stem region...
November 2016: Biophysical Chemistry
Vitor Schuabb, Roland Winter, Claus Czeslik
Pressure is well known to affect the catalytic rate of enzymes dissolved in solution. To better understand enzyme kinetics at aqueous-solid interfaces, we have carried out a high-pressure stopped-flow activity study of α-chymotrypsin (α-CT) that is adsorbed on silica particles and, for comparison, dissolved in solution. The enzyme reaction was modulated using pressures up to 2000bar and recorded using the high-pressure stopped-flow technique. The results indicate an 8-fold enhancement of the turnover number upon α-CT adsorption and a further increase of the catalytic rate in the pressure range up to 1000bar...
November 2016: Biophysical Chemistry
S Eh Shirmovsky
A model predicting the behavior of a hole acting on the DNA strand was investigated. The hole-DNA interaction on the basis of a quantum-classical, non-linear DNA single strand model was described. The fact that a DNA molecule is formed by a furanose ring as its sugar, phosphate group and bases was taken into consideration. Based on the model, results were obtained for the probability of a hole location on the DNA base sequences, such as GTTGGG, GATGTGGG, GTTGTTGGG as well as on the sugar-phosphate groups mated with them...
October 2016: Biophysical Chemistry
Anirudha Dutta, Sudipta Bhattacharyya, Anirban Kundu, Debabrata Dutta, Amit Kumar Das
Staphylococcus aureus is a commensal and opportunistic pathogen that causes lethal infections. Biofilm forming ability of S. aureus enhances its virulence since biofilm provides the bacteria protective shield against antibiotics and host immunity. Polysaccharide independent biofilm formation by several virulent S. aureus strains have been identified recently, where protein components substitute polysaccharide intercellular adhesin (PIA) involved in bacterial cell attachment. The suhB gene has been reported to be essential in staphylococcal PIA-independent biofilm formation...
October 2016: Biophysical Chemistry
José Jardes da Gama Bitencourt, Wallance Moreira Pazin, Amando Siuiti Ito, Marina Berardi Barioni, Carolline de Paula Pinto, Maria Aparecida Dos Santos, Thales Henrique Santos Guimarães, Márcia Regina Machado Dos Santos, Claudete Justina Valduga
The toxic effects of miltefosine on the epithelial cells of the gastrointestinal tract and its hemolytic action on erythrocytes have limited its use as an antileishmanial agent. As part of our search for new strategies to overcome the side effects of miltefosine during the treatment of leishmaniasis, we have developed stable miltefosine-loaded lipid nanoparticles in an attempt to reduce the toxic effects of the drug. We have evaluated lipid nanoparticles containing varying amounts of miltefosine and cholesterol, prepared by sonication, in terms of their physicochemical properties, preliminary stability, hemolytic potential toward erythrocytes, and cytotoxicity to macrophages and to promastigote and amastigote forms of Leishmania (L...
October 2016: Biophysical Chemistry
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