Entropy of Proteins Using Multiscale Cell Correlation
| Autor: | Arghya Chakravorty, Jonathan Higham, Richard H. Henchman |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2020 |
| Předmět: |
Length scale
Protein Conformation Entropy General Chemical Engineering Molecular Conformation Thermodynamics Polar amino acids Molecular Dynamics Simulation Library and Information Sciences 01 natural sciences Correlation chemistry.chemical_compound Molecular dynamics 0103 physical sciences Molecule Physics Quantitative Biology::Biomolecules 010304 chemical physics Proteins General Chemistry Conformational entropy 0104 chemical sciences Computer Science Applications 010404 medicinal & biomolecular chemistry chemistry Solvents Solvent exposure Vibrational entropy |
| Zdroj: | Chakravorty, A, Higham, J & Henchman, R H 2020, ' Entropy of Proteins Using Multiscale Cell Correlation ', Journal of Chemical Information and Modeling . https://doi.org/10.1021/acs.jcim.0c00611 |
| DOI: | 10.1021/acs.jcim.0c00611 |
| Popis: | A new multiscale method is presented to calculate the entropy of proteins from molecular dynamics simulations. Termed Multiscale Cell Correlation (MCC), the method decomposes the protein into sets of rigid-body units based on their covalent-bond connectivity at three levels of hierarchy: molecule, residue, and united atom. It evaluates the vibrational and topographical entropy from forces, torques, and dihedrals at each level, taking into account correlations between sets of constituent units that together make up a larger unit at the coarser length scale. MCC gives entropies in close agreement with normal-mode analysis and smaller than those using quasiharmonic analysis as well as providing much faster convergence. Moreover, MCC provides an insightful decomposition of entropy at each length scale and for each type of amino acid according to their solvent exposure and whether they are terminal residues. While the residue entropy depends weakly on solvent exposure, there is greater variation in entropy components for larger, more polar amino acids, which have increased conformational entropy but reduced vibrational entropy with greater solvent exposure. |
| Databáze: | OpenAIRE |
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