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10,543 Newest Publications in journal of physical chemistry b

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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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Membrane Anchoring of α-Helical Proteins: Role of Tryptophan

11-Jan-2018 | Alan J. Situ; So-Min Kang; Benjamin B. Frey; Woojin An; Chungho Kim; Tobias S. Ulmer, Journal of Physical Chemistry B, 2018

The function of membrane proteins relies on a defined orientation of protein relative to lipid. In apparent correlation to protein anchoring, tryptophan residues are enriched in the lipid headgroup region. To characterize the thermodynamic and structural basis of this relationship in α-helical ...

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Imidazole Nitrogens of Two Histidine Residues Participating in N–H···N Hydrogen Bonds in Protein Structures: Structural Bioinformatics Approach Combined with Quantum Chemical Calculations

11-Jan-2018 | Abhishek Hariharan Iyer; R. N. V. Krishna Deepak; Ramasubbu Sankararamakrishnan, Journal of Physical Chemistry B, 2018

Protein structures are stabilized by different types of hydrogen bonds. However, unlike the DNA double helical structure, the N–H···N type of hydrogen bonds is relatively rare in proteins. N–H···N hydrogen bonds formed by imidazole groups of two histidine residues have not been investigated. We ...

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Path to the Desensitized State of Ligand-Gated Ion Channels: Why Are Inhibitory and Excitatory Receptors Different?

11-Jan-2018 | Robert S. Cantor, Journal of Physical Chemistry B, 2018

The family of pentameric ligand-gated ion channels (pLGICs) includes both inhibitory and excitatory receptors. Electrophysiological methods have explored the time-dependent ion currents induced by their neurotransmitter agonists. Kinetic modeling requires a minimum of three conformational states: ...

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