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Biophysical Chemistry

Lora Stepanian, Ikbae Son, Tigran V Chalikian
We combine experimental and theoretical approaches to investigate the influence of a cosolvent on a ligand-protein association event. We apply fluorescence measurements to determining the affinity of the inhibitor tri-N-acetylglucosamine [(GlcNAc)3] for lysozyme at urea concentrations ranging from 0 to 8M. Notwithstanding that, at room temperature and neutral pH, lysozyme retains its native conformation up to the solubility limit of urea, the affinity of (GlcNAc)3 for the protein steadily decreases as the concentration of urea increases...
November 25, 2016: Biophysical Chemistry
Androulla Ioannou, Alexandra Lambrou, Vangelis Daskalakis, Eftychia Pinakoulaki
Myoglobin (Mb) is known to react slowly with nitirite to form the green pigment by NO2(-) cordination to the heme Fe in the O-binding nitrito (O1NO2) mode and to the heme 2-vinyl position. Nitrite is a powerful oxidizing agent and a biological reservoir for NO that has been implicated in a variety of aerobic biological systems. Accordingly, it is important to elucidate the nature and variety of NO2(-) reaction mechanisms with Mb. We have performed principal component analysis (PCA, or essential dynamics) on Molecular Dynamics trajectories of all MbNO2 coordination states to resolve the most important motions in the protein at 298K...
November 25, 2016: Biophysical Chemistry
M Leffak, R Gadgil, J Barthelemy, T Lewis
Microsatellites are short, tandemly repeated DNA motifs of 1-6 nucleotides, also termed simple sequence repeats (SRSs) or short tandem repeats (STRs). Collectively, these repeats comprise approximately 3% of the human genome Subramanian et al. (2003), Lander and Lander (2001) [1,2], and represent a large reservoir of loci highly prone to mutations Sun et al. (2012), Ellegren (2004) [3,4] that contribute to human evolution and disease. Microsatellites are known to stall and reverse replication forks in model systems Pelletier et al...
November 22, 2016: Biophysical Chemistry
Bhaswati Sengupta, Nilimesh Das, Pratik Sen
The local structural dynamics and denaturation profile of domain-III of HSA against guanidine hydrochloride (GnHCl) and temperature has been studied using a coumarin based solvatochromic fluorescent probe p-nitrophenyl coumarin ester (NPCE), covalently tagged to Tyr-411 residue. By the steady state, time-resolved and single molecular level fluorescence studies it has been established that the domain-III of HSA is very sensitive to GnHCl but somewhat resistant to temperature and the domain specific unfolding proceeds in an altered way as compared to the overall unfolding of HSA...
November 18, 2016: Biophysical Chemistry
Vaclav Urban, Jana Dobrovolna, Pavel Janscak
DNA replication is the most vulnerable process of DNA metabolism in proliferating cells and therefore it is tightly controlled and coordinated with processes that maintain genomic stability. Human RecQ helicases are among the most important factors involved in the maintenance of replication fork integrity, especially under conditions of replication stress. RecQ helicases promote recovery of replication forks being stalled due to different replication roadblocks of either exogenous or endogenous source. They prevent generation of aberrant replication fork structures and replication fork collapse, and are involved in proper checkpoint signaling...
November 15, 2016: Biophysical Chemistry
Patrycja Zawilska, Katarzyna Cieślik-Boczula
Long-chain alkylresorcinols (ARs) are commonly found in plant and bacteria cells, and they exhibit a wide variety of biological effects, including antifungal, antitumor, and antiphrastic activities. The cholesterol (Chol)-like effect of ARs with hydrocarbon side-chain lengths ranging from C15 to C25 on the structure of pure and Chol-doped dipalmitoylphosphocholine (DPPC) and sphingomyelin (SM) membranes was investigated by Laurdan fluorescence spectroscopy. The Laurdan emission generalized polarization parameter was analyzed as a function of the temperature and excitation wavelength in DPPC (or SM)/Chol, DPPC (or SM)/AR, and DPPC/Chol/AR systems...
November 12, 2016: Biophysical Chemistry
Caroline Schuabb, Salome Pataraia, Melanie Berghaus, Roland Winter
RNAs perform multiple vital roles within cells, including catalyzing biological reactions and expression of proteins. Small RNA hairpins (sRNAh) are the smallest functional entities of nucleic acids and are involved in various important biological functions such as ligand binding and tertiary folding initiation of proteins. We investigated the conformational and free energy landscape of the sRNAh gcUUCGgc over a wide range of temperatures and pressures using fluorescence resonance energy transfer, Fourier-transform infrared and UV/Vis spectroscopy as well as small-angle X-ray scattering on the unlabeled and/or fluorescently labeled sRNAh...
October 31, 2016: Biophysical Chemistry
Stefano Iotti, Lionel Raff, Antonio Sabatini
The thermodynamics of chemical reactions in which all species are explicitly considered with atoms and charge balanced is compared with the transformed thermodynamics generally used to treat biochemical reactions where atoms and charges are not balanced. The transformed thermodynamic quantities suggested by Alberty are obtained by execution of Legendre transformation of the usual thermodynamic potentials. The present analysis demonstrates that the transformed values for ΔrG'(0) and ΔrH'(0)can be obtained directly without performing Legendre transformations by simply writing the chemical reactions with all the pseudoisomers explicitly included and charges balanced...
October 24, 2016: Biophysical Chemistry
Mohd Afzal, Saptarshi Ghosh, Nitin Chattopadhyay
Relocation of a bioactive photosensitizer, namely phenosafranin (PSF), from the phenazinium family, has been demonstrated from non-ionic micellar carrier to the DNA. For the purpose, interaction of micelle-bound PSF with calf thymus DNA (ctDNA) has been investigated vividly exploiting various spectroscopic techniques like absorption, steady state and time resolved emission, fluorescence anisotropy, circular dichroism etc. Experimental outcomes reveal that PSF binds strongly with both the micelle as well as the DNA...
October 23, 2016: 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
Cagla Sahin, Nikolai Lorenzen, Lasse Lemminger, Gunna Christiansen, Ian Max Møller, Louise Buur Vesterager, Lars Østergaard Pedersen, Karina Fog, Pekka Kallunki, Daniel E Otzen
The 140-residue natively disordered protein α-synuclein (aSN) is a central component in the development of a family of neurodegenerative diseases termed synucleinopathies. This is attributed to its ability to form cytotoxic aggregates such as oligomers and amyloid fibrils. Consequently there have been intense efforts to avoid aggregation or reroute the aggregation pathway using pharmaceutical agents such as small molecules, chaperones and antibodies. aSN's lack of persistent structure in the monomeric state, as well as the multitude of different oligomeric and even different fibrillar states, makes it difficult to raise antibodies that would be efficacious in neutralizing all conformations of aSN...
January 2017: Biophysical Chemistry
Jian Xiong, Renee D JiJi
The hydrophobic fragment of the Alzheimer's related β-amyloid (Aβ) peptide, Aβ(25-40), aggregates and forms insoluble amyloid fibrils at a rate similar to the full-length peptide. In order to gain insight into the fibrillization of Aβ(25-40) and the ability of the flavonoid myricetin to inhibit its aggregation, the isoleucine at position 32 (I32A) and the glycine at position 37 (G37A) in the full-length peptide were replaced with alanine. Thioflavin T assays indicate that substitution of isoleucine for alanine significantly reduces the rate and extent of fibrillization compared to the Aβ(25-40) and G37A peptides...
January 2017: Biophysical Chemistry
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