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10,556 Newest Publications in journal of physical chemistry b

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Characterizing Conformational Dynamics of Proteins Using Evolutionary Couplings

16-Jan-2018 | Jiangyan Feng; Diwakar Shukla, Journal of Physical Chemistry B, 2018

Understanding of protein conformational dynamics is essential for elucidating molecular origins of protein structure–function relationship. Traditionally, reaction coordinates, i.e., some functions of protein atom positions and velocities have been used to interpret the complex dynamics of ...

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Binding Mechanisms of Electron Transport Proteins with Cyanobacterial Photosystem I: An Integrated Computational and Experimental Model

16-Jan-2018 | Karan Kapoor; Derek J. Cashman; Luke Nientimp; Barry D. Bruce; Jerome Baudry, Journal of Physical Chemistry B, 2018

The stromal domain (PsaC, D, and E) of photosystem I (PSI) in cyanobacteria accepts electrons from PsaA and PsaB of photosystem I (PSI). These electrons are then used in the reduction of transiently bound ferredoxin (Fd) or flavodoxin. Experimental X-ray and NMR structures are known for all of ...

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Glycerol Hydrogen-Bonding Network Dominates Structure and Collective Dynamics in a Deep Eutectic Solvent

16-Jan-2018 | A. Faraone; D. V. Wagle; G. A. Baker; E. C. Novak; M. Ohl; D. Reuter; P. Lunkenheimer; A. Loidl; E. Mamontov, Journal of Physical Chemistry B, 2018

The deep eutectic solvent glyceline formed by choline chloride and glycerol in 1:2 molar ratio is much less viscous compared to glycerol, which facilitates its use in many applications where high viscosity is undesirable. Despite the large difference in viscosity, we have found that the ...

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Binding Specificity Determines the Cytochrome P450 3A4 Mediated Enantioselective Metabolism of Metconazole

12-Jan-2018 | Shulin Zhuang; Leili Zhang; Tingjie Zhan; Liping Lu; Lu Zhao; Haifei Wang; Joseph A. Morrone; Weiping Liu; Ruhong Zhou, Journal of Physical Chemistry B, 2018

Cytochrome P450 3A4 (CYP3A4) is a promiscuous enzyme, mediating the biotransformations of ∼50% of clinically used drugs, many of which are chiral molecules. Probing the interactions between CYP3A4 and chiral chemicals is thus essential for the elucidation of molecular mechanisms of ...

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BOCS: Bottom-up Open-source Coarse-graining Software

12-Jan-2018 | Nicholas J. H. Dunn; Kathryn M. Lebold; Michael R. DeLyser; Joseph F. Rudzinski; W.G. Noid, Journal of Physical Chemistry B, 2018

We present the BOCS toolkit as a suite of open source software tools for parametrizing bottom-up coarse-grained (CG) models to accurately reproduce structural and thermodynamic properties of high-resolution models. The BOCS toolkit complements available software packages by providing robust ...

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RESPEC Incorporates Residue Specificity and the Ligand Effect into the Elastic Network Model

11-Jan-2018 | Burak T. Kaynak; Doga Findik; Pemra Doruker, Journal of Physical Chemistry B, 2018

RESPEC is a new framework that introduces residue specificity into elastic network modeling (ENM) to successfully render intact protein–ligand complexes as well as apo proteins. This framework establishes a broader application of coarse-graining idea via describing (i) a coarse-grained ...

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Imaging Channel Connectivity in Nafion Using Electrostatic Force Microscopy

11-Jan-2018 | Austin M. Barnes; Steven K. Buratto, Journal of Physical Chemistry B, 2018

Channel connectivity is an important material property that is considered in making higher-performance proton-exchange membranes. Our group has previously demonstrated that nearly 50% of the aqueous surface domains in Nafion films do not have a connected path to the opposite side of the membrane. ...

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Imaging Channel Connectivity in Nafion Using Electrostatic Force Microscopy

11-Jan-2018 | Austin M. Barnes; Steven K. Buratto, Journal of Physical Chemistry B, 2018

Channel connectivity is an important material property that is considered in making higher-performance proton-exchange membranes. Our group has previously demonstrated that nearly 50% of the aqueous surface domains in Nafion films do not have a connected path to the opposite side of the membrane. ...

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Unraveling the Critical Role Played by Ado762′OH in the Post-Transfer Editing by Archaeal Threonyl-tRNA Synthetase

11-Jan-2018 | Mohamed M. Aboelnga; John J. Hayward; James W. Gauld, Journal of Physical Chemistry B, 2018

Archaeal threonyl-tRNA synthetase (ThrRS) possesses an editing active site wherein tRNAThr that has been misaminoacylated with serine (i.e., Ser-tRNAThr) is hydrolytically cleaved to serine and tRNAThr. It has been suggested that the free ribose sugar hydroxyl of Ado76 of the tRNAThr (Ado762′OH) ...

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QM/MM and MM MD Simulations on the Pyrimidine-Specific Nucleoside Hydrolase: A Comprehensive Understanding of Enzymatic Hydrolysis of Uridine

11-Jan-2018 | Fangfang Fan; Nanhao Chen; Yongheng Wang; Ruibo Wu; Zexing Cao, Journal of Physical Chemistry B, 2018

The pyrimidine-specific nucleoside hydrolase Yeik (CU-NH) from Escherichia coli cleaves the N-glycosidic bond of uridine and cytidine with a 102–104-fold faster rate than that of purine nucleoside substrates, such as inosine. Such a remarkable substrate specificity and the plausible hydrolytic ...

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