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Simulation of protein conformational freedom as a function of pH: constant‐pH molecular dynamics using implicit titration
Solution pH is a determinant parameter on protein function and stability, and its inclusion in molecular dynamics simulations is attractive for studies at the molecular level. Current molecularExpand
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Lipases and esterases: a review of their sequences, structure and evolution.
This chapter aims to provide a brief review on the enzyme family of lipases and esterases. The sequences, 3D structures and pH dependent electrostatic signatures are presented and analyzed. Since theExpand
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Thermal adaptation and clinal mitochondrial DNA variation of European anchovy
Natural populations of widely distributed organisms often exhibit genetic clinal variation over their geographical ranges. The European anchovy, Engraulis encrasicolus, illustrates this by displayingExpand
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  • Open Access
Simulation of electron-proton coupling with a Monte Carlo method: application to cytochrome c3 using continuum electrostatics.
A new method is presented for simulating the simultaneous binding equilibrium of electrons and protons on protein molecules, which makes it possible to study the full equilibrium thermodynamics ofExpand
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Comparative redox and pKa calculations on cytochrome c3 from several Desulfovibrio species using continuum electrostatic methods
Abstract A comparative study of the pH-dependent redox mechanisms of several members of the cytochrome c3 family has been carried out. In a previous work, the molecular determinants of thisExpand
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Evolution of Matrix and Bone γ-Carboxyglutamic Acid Proteins in Vertebrates*
The evolution of calcified tissues is a defining feature in vertebrate evolution. Investigating the evolution of proteins involved in tissue calcification should help elucidate how calcified tissuesExpand
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  • Open Access
Structure of beta-cinnamomin, a protein toxic to some plant species.
Phytophthora and Pythium species are among the most aggressive plant pathogens, as they invade many economically important crops and forest trees. They secrete large amounts of 10 kDa proteins calledExpand
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Genetic Diversity of the Coat Protein of Olive Mild Mosaic Virus (OMMV) and Tobacco Necrosis Virus D (TNV-D) Isolates and Its Structural Implications
The genetic variability among 13 isolates of Olive mild mosaic virus (OMMV) and of 11 isolates of Tobacco necrosis virus D (TNV-D) recovered from Olea europaea L. samples from various sites inExpand
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  • Open Access
Theoretical studies on the redox-Bohr effect in cytochrome c3 from Desulfovibrio vulgaris Hildenborough
Abstract The pH dependence of the redox potentials in the tetrahemic cytochrome c3 from Desulfovibrio vulgaris Hildenborough (redox-Bohr effect) is here investigated using continuum electrostaticsExpand
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Molecular dynamics simulation of cytochrome c3: studying the reduction processes using free energy calculations.
The tetraheme cytochrome c3 from Desulfovibrio vulgaris Hildenborough is studied using molecular dynamics simulation studies in explicit solvent. The high heme content of the protein, which has itsExpand
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