Hydration of Amino Acid Side Chains:  Nonpolar and Electrostatic Contributions Calculated from Staged Molecular Dynamics Free Energy Simulations with Explicit Water Molecules

2004 ◽  
Vol 108 (42) ◽  
pp. 16567-16576 ◽  
Author(s):  
Yuqing Deng ◽  
Benoît Roux
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Amino Acid ◽  
Water Molecules ◽  
Side Chains ◽  
Amino Acid Side Chains ◽  
Energy Simulations ◽  
Explicit Water

The Influence of Amino Acid Side Chains on the Free Energy of Helix-Coil Transitions1

1966 ◽  
Vol 70 (4) ◽  
pp. 998-1004 ◽  
Author(s):  
George Némethy ◽  
S. J. Leach ◽  
Harold A. Scheraga
Keyword(s):  
Free Energy ◽  
Amino Acid ◽  
Side Chains ◽  
Amino Acid Side Chains

scholarly journals Entropy-Enthalpy Compensations Fold Proteins in Precise Ways

2021 ◽  
Vol 22 (17) ◽  
pp. 9653
Author(s):  
Jiacheng Li ◽  
Chengyu Hou ◽  
Xiaoliang Ma ◽  
Shuai Guo ◽  
Hongchi Zhang ◽  
...  
Keyword(s):  
Free Energy ◽  
Protein Folding ◽  
Amino Acid ◽  
Gibbs Free Energy ◽  
Energy Equation ◽  
Protein Structures ◽  
Water Molecules ◽  
Side Chains ◽  
Hydrophobic Collapse ◽  
Polypeptide Chains

Exploring the protein-folding problem has been a longstanding challenge in molecular biology and biophysics. Intramolecular hydrogen (H)-bonds play an extremely important role in stabilizing protein structures. To form these intramolecular H-bonds, nascent unfolded polypeptide chains need to escape from hydrogen bonding with surrounding polar water molecules under the solution conditions that require entropy-enthalpy compensations, according to the Gibbs free energy equation and the change in enthalpy. Here, by analyzing the spatial layout of the side-chains of amino acid residues in experimentally determined protein structures, we reveal a protein-folding mechanism based on the entropy-enthalpy compensations that initially driven by laterally hydrophobic collapse among the side-chains of adjacent residues in the sequences of unfolded protein chains. This hydrophobic collapse promotes the formation of the H-bonds within the polypeptide backbone structures through the entropy-enthalpy compensation mechanism, enabling secondary structures and tertiary structures to fold reproducibly following explicit physical folding codes and forces. The temperature dependence of protein folding is thus attributed to the environment dependence of the conformational Gibbs free energy equation. The folding codes and forces in the amino acid sequence that dictate the formation of β-strands and α-helices can be deciphered with great accuracy through evaluation of the hydrophobic interactions among neighboring side-chains of an unfolded polypeptide from a β-strand-like thermodynamic metastable state. The folding of protein quaternary structures is found to be guided by the entropy-enthalpy compensations in between the docking sites of protein subunits according to the Gibbs free energy equation that is verified by bioinformatics analyses of a dozen structures of dimers. Protein folding is therefore guided by multistage entropy-enthalpy compensations of the system of polypeptide chains and water molecules under the solution conditions.

scholarly journals Application of ESMACS Binding Free Energy Protocols to Diverse Datasets: Bromodomain-Containing Protein 4

2019 ◽  
Author(s):  
David Wright ◽  
Shunzhou Wan ◽  
Christophe Meyer ◽  
Herman Van Vlijmen ◽  
Gary Tresadern ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Binding Affinity ◽  
Binding Free Energy ◽  
Water Molecules ◽  
Calculation Data ◽  
Simulation Input ◽  
Explicit Water ◽  
Entropic Contribution

<div>We investigate the robustness of our ensemble molecular dynamics binding free energy protocols, known as ESMACS, to different choices of forcefield, starting structure and analysis. ESMACS is based on MMPBSA and we examinge the influence of multiple trajectories, explicit water molecules and estimates of the entropic contribution to the binding free energy.</div><div><br></div><div>Simulation input and binding affinity calculation data:</div>https://doi.org/10.5281/zenodo.1484050

scholarly journals Application of ESMACS Binding Free Energy Protocols to Diverse Datasets: Bromodomain-Containing Protein 4

2019 ◽  
Author(s):  
David Wright ◽  
Shunzhou Wan ◽  
Christophe Meyer ◽  
Herman Van Vlijmen ◽  
Gary Tresadern ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Binding Affinity ◽  
Binding Free Energy ◽  
Water Molecules ◽  
Calculation Data ◽  
Simulation Input ◽  
Explicit Water ◽  
Entropic Contribution

<div>We investigate the robustness of our ensemble molecular dynamics binding free energy protocols, known as ESMACS, to different choices of forcefield, starting structure and analysis. ESMACS is based on MMPBSA and we examinge the influence of multiple trajectories, explicit water molecules and estimates of the entropic contribution to the binding free energy.</div><div><br></div><div>Simulation input and binding affinity calculation data:</div>https://doi.org/10.5281/zenodo.1484050

scholarly journals Structural dynamics in the water and proton channels of photosystem II during the S2 to S3 transition

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Rana Hussein ◽  
Mohamed Ibrahim ◽  
Asmit Bhowmick ◽  
Philipp S. Simon ◽  
Ruchira Chatterjee ◽  
...  
Keyword(s):  
Amino Acid ◽  
Photosystem Ii ◽  
Water Oxidation ◽  
Water Molecules ◽  
Back Reaction ◽  
Side Chains ◽  
Oxygen Evolving Complex ◽  
Proton Release ◽  
Ps Ii ◽  
Amino Acid Side Chains

AbstractLight-driven oxidation of water to molecular oxygen is catalyzed by the oxygen-evolving complex (OEC) in Photosystem II (PS II). This multi-electron, multi-proton catalysis requires the transport of two water molecules to and four protons from the OEC. A high-resolution 1.89 Å structure obtained by averaging all the S states and refining the data of various time points during the S2 to S3 transition has provided better visualization of the potential pathways for substrate water insertion and proton release. Our results indicate that the O1 channel is the likely water intake pathway, and the Cl1 channel is the likely proton release pathway based on the structural rearrangements of water molecules and amino acid side chains along these channels. In particular in the Cl1 channel, we suggest that residue D1-E65 serves as a gate for proton transport by minimizing the back reaction. The results show that the water oxidation reaction at the OEC is well coordinated with the amino acid side chains and the H-bonding network over the entire length of the channels, which is essential in shuttling substrate waters and protons.

scholarly journals Application of ESMACS Binding Free Energy Protocols to Diverse Datasets: Bromodomain-Containing Protein 4

2018 ◽  
Author(s):  
David Wright ◽  
Shunzhou Wan ◽  
Christophe Meyer ◽  
Herman Van Vlijmen ◽  
Gary Tresadern ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Binding Affinity ◽  
Binding Free Energy ◽  
Water Molecules ◽  
Calculation Data ◽  
Simulation Input ◽  
Explicit Water ◽  
Entropic Contribution

<div>We investigate the robustness of our ensemble molecular dynamics binding free energy protocols, known as ESMACS, to different choices of forcefield, starting structure and analysis. ESMACS is based on MMPBSA and we examinge the influence of multiple trajectories, explicit water molecules and estimates of the entropic contribution to the binding free energy.</div><div><br></div><div>Simulation input and binding affinity calculation data:</div>https://doi.org/10.5281/zenodo.1484050

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