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Biophysical Chemistry

Shuntaro Takahashi, Naoki Sugimoto
DNA guanine-quadruplexes (G-quadruplexes) are unique DNA structures formed by guanine-rich sequences. The loop regions of G-quadruplexes play key roles in stability and topology of G-quadruplexes. Here, we investigated volumetric changes induced by pressure in the folding of the G-quadruplex formed by the thrombin binding aptamer (TBA) with mutations within the loop regions. The change of partial molar volume in the transition from coil to G-quadruplex, ∆Vtr, of TBA with a mutation from T to A in the 5' most loop (TBA T3A) was 75...
February 6, 2017: Biophysical Chemistry
Eric A Galburt, Eric J Tomko
The linkage between macromolecular binding and conformational change that is ubiquitous in biological molecules can be understood in the context of the mechanisms of conformational selection and induced fit. Here, we explore mappings between these mechanisms of ligand binding and those underlying the translocation of molecular motors and the nucleic acid unwinding of helicases. The mechanism of biased motion exhibited by molecular motors is typically described as either a thermal ratchet or a power-stroke and nucleic acid helicases are characterized by either active or passive unwinding mechanisms...
February 3, 2017: Biophysical Chemistry
Samira Gholami, A Khalegh Bordbar, Amir Lohrasebi
Although, α2C adrenergic receptor (AR) mediates a number of physiological functions in vivo and has great therapeutic potential, the absence of its crystal structure is a major difficulty in the activation mechanism studies and drug design endeavors. Here, a homology model of α2C AR has been presented by means of multiple sequence alignment. The used templates were the latest crystal structures of the other ARs (Protein Data Bank IDs: 2R4R, 2RH1, 4GPO, 3P0G, 4BVN and 4LDO) that have 38.4% identity with the query...
February 2, 2017: Biophysical Chemistry
Paola Cardiano, Rosalia Maria Cigala, Francesco Crea, Concetta De Stefano, Ottavia Giuffrè, Silvio Sammartano, Giuseppina Vianelli
The interaction of Zn(II) with ampicillin [(2S,5R,6R)-6-([(2R)-2-amino-2-phenylacetyl]amino)-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2- carboxylic acid] and amoxicillin [(2S,5R,6R)-6-{[(2R)-2-amino-2-(4-hydroxyphenyl)-acetyl]amino}-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-24-carboxylic acid] in NaCl aqueous solution at different ionic strengths and at t=25°C was investigated by potentiometric, UV and (1)H NMR techniques. Fairly similar speciation models were obtained for the two systems...
January 31, 2017: Biophysical Chemistry
Yang Yun Li, David N Dubins, Dianna My Nhi Thi Le, Karen Leung, Robert B Macgregor
In aqueous solutions containing sodium or potassium cations, oligodeoxyribonucleotides (ODNs) rich in guanine form four-stranded DNA structures called G-quadruplexes (G4s). These structures are destabilized by elevated hydrostatic pressure. Here, we use pressure to investigate the volumetric changes arising from the formation of G4 structures. G4s display a great deal of structural heterogeneity that depends on the stabilizing cation as well as the oligonucleotide sequence. Using UV thermal unfolding at different pressures, we have investigated the volume change of the helix-coil equilibrium of a series of ODNs whose sequences are related to the G-rich ODN HTel (d[A(GGGTTA)3GGG]), which contains four repeats of the human telomeric sequence...
January 6, 2017: Biophysical Chemistry
Andrea Pica, Giuseppe Graziano
When methanol is added to water at room temperature and 1atm, poly (N-isopropylacrylamide), PNIPAM, undergoes a coil-to-globule collapse transition. This intriguing phenomenon is called cononsolvency. Spectroscopic measurements have shown that application of high hydrostatic pressure destroys PNIPAM cononsolvency in water-methanol solutions. We have developed a theoretical approach that identifies the decrease in solvent-excluded volume effect as the driving force of PNIPAM collapse on increasing the temperature...
January 5, 2017: Biophysical Chemistry
Wlodzimierz Bujalowski, Maria J Jezewska, Paul J Bujalowski
Obtaining a detailed knowledge about energetics of ligand-macromolecule interactions is a prerequisite for elucidation of the nature, behavior, and activities of the formed complexes. The most commonly used methods in characterizing molecular interactions are physico-chemical techniques based mainly on spectroscopic, calorimetric, hydrodynamic, etc., measurements. The major advantage of the physico-chemical methods is that they do not require large quantities of material and, if performed carefully, do not perturb examined reactions...
January 3, 2017: Biophysical Chemistry
Claudia Bonechi, Stefania Lamponi, Alessandro Donati, Gabriella Tamasi, Marco Consumi, Gemma Leone, Claudio Rossi, Agnese Magnani
The effect of resveratrol (RSV) in inhibiting platelet adhesion and aggregation, as well as fibrinogen (FBG) conformational changes promoted by epinephrine (EP), were studied, by using complementary experimental techniques. NMR and IR spectroscopies were used to investigate possible protective effects by RSV towards FBG, in presence of EP. The protective effect of RSV towards FBG was highlighted by spin nuclear relaxation experiments that were interpreted for determining the thermodynamic equilibrium constants of FBG-EP interaction, and by infrared measurements, that showed EP-induced conformational changes of FBG...
January 2, 2017: Biophysical Chemistry
Wlodzimierz Bujalowski, Maria J Jezewska, Paul J Bujalowski
Physico-chemical titration techniques are the most commonly used methods in characterizing molecular interactions. These methods are mainly based on spectroscopic, calorimetric, hydrodynamic, etc., measurements. However, truly quantitative physico-chemical methods are absolutely based on the determination of the relationship between the measured signal and the total average degree of binding in order to obtain meaningful interaction parameters. The relationship between the observed physico-chemical signal of whatever nature and the degree of binding must be determined and not assumed, based on some ad hoc intuitive relationship/model, leading to determination of the true binding isotherm...
December 30, 2016: Biophysical Chemistry
Yun Ding, Rong Tian, Zhen Yang, Jianfa Chen, Naihao Lu
Neutrophil myeloperoxidase (MPO) and peroxynitrite (ONOO(-)) can oxidatively biodegrade carboxylated single-walled carbon nanotubes (SWCNTs). The protein-SWCNTs interactions will play an important role in the degradation and cytotoxicity of nanotubes. Here, we investigated the binding of bovine serum albumin (BSA, a common and well-characterized model blood serum protein) to SWCNTs, and found that the hydrophobic and electrostatic interactions might be crucial factors in stabilizing the binding of SWCNTs with BSA...
December 23, 2016: Biophysical Chemistry
S Korolev
Recombination mediator proteins (RMPs) are critical for genome integrity in all organisms. They include phage UvsY, prokaryotic RecF, -O, -R (RecFOR) and eukaryotic Rad52, Breast Cancer susceptibility 2 (BRCA2) and Partner and localizer of BRCA2 (PALB2) proteins. BRCA2 and PALB2 are tumor suppressors implicated in cancer. RMPs regulate binding of RecA-like recombinases to sites of DNA damage to initiate the most efficient non-mutagenic repair of broken chromosome and other deleterious DNA lesions. Mechanistically, RMPs stimulate a single-stranded DNA (ssDNA) hand-off from ssDNA binding proteins (ssbs) such as gp32, SSB and RPA, to recombinases, activating DNA repair only at the time and site of the damage event...
December 6, 2016: Biophysical Chemistry
Alessandro Vindigni, Massimo Lopes
Replication stress is a crucial driver of genomic instability. Understanding the mechanisms of replication stress response is instrumental to improve diagnosis and treatment of human disease. Electron microscopy (EM) is currently the technique of choice to directly visualize a high number of replication intermediates and to monitor their remodeling upon stress. At the same time, DNA fiber analysis is useful to gain mechanistic insight on how genotoxic agents perturb replication fork dynamics genome-wide at single-molecule resolution...
December 3, 2016: Biophysical Chemistry
Sivaraman Padavattan, Viswanathan Thiruselvam, Toshie Shinagawa, Kazuya Hasegawa, Takashi Kumasaka, Shunsuke Ishii, Thirumananseri Kumarevel
Th2a and Th2b are the testis-specific histone variants highly expressed during spermatogenesis. Approximately 4% of the genome is retained in nucleosomes in mature human sperm, which is enriched at loci of developmental importance. Our recent studies revealed that the mouse histone variant homologs TH2a and TH2b are involved in reprogramming. In the present work, we report three nucleosome structures (NCPs) with human testis-specific histone variants hTh2a and hTh2b, [hGcH (hTh2a-hTh2b-H3-H4), hGcHV1 (hTh2a-H2b-H3-H4) and hGcHV2 (H2a-hTh2b-H3-H4)] and a 146-base pair (bp) duplex DNA fragment at ~3...
February 2017: Biophysical Chemistry
Pei-Kun Yang
The dielectric polarization (P) is the key factor in calculating the solvation free energy. P can be decomposed into the product of the electric dipole per solvent (p) and the relative solvent molecular density (g). p can be calculated from the electric field (E), and g can be calculated from the mean force (F), where the electric component of F is calculated from ∇xE. The Poisson equations were modified for E and ∇xE. Strategies to estimate the boundary conditions of E and ∇xE were proposed. The dependences of P and g on the parameters used for the numerical analysis were explored...
February 2017: 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...
February 2017: 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...
February 2017: 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...
February 2017: 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...
February 2017: 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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