Subsystem Analysis for the Fragment Molecular Orbital Method and Its Application to Protein–Ligand Binding in Solution
| Autor: | Dmitri G. Fedorov, Kazuo Kitaura |
|---|---|
| Rok vydání: | 2016 |
| Předmět: |
Alanine
Binding Sites 010304 chemical physics Stereochemistry Chemistry Binding energy Protein Data Bank (RCSB PDB) Proteins Ligands 010402 general chemistry 01 natural sciences 0104 chemical sciences Solutions Fragment (logic) 0103 physical sciences Quantum Theory Physical and Theoretical Chemistry Binding site Fragment molecular orbital Protein ligand |
| Zdroj: | The Journal of Physical Chemistry A. 120:2218-2231 |
| ISSN: | 1520-5215 1089-5639 |
| DOI: | 10.1021/acs.jpca.6b00163 |
| Popis: | A subsystem analysis is derived incorporating interfragment interactions into the fragment properties, such as energies or charges. The relative stabilities of three alanine isomers, the α-helix, the β-turn, and the extended form are studied and the differences in fragment properties are elucidated. The analysis is further elaborated for studies of binding energies. The binding of the Trp-cage protein (PDB: 1L2Y ) to two ligands is studied in detail. Binding energies defined for each fragment can be used as a convenient descriptor for analyzing contributions to binding in solution. |
| Databáze: | OpenAIRE |
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