ArticleScientific reports2017
Influences of lone-pair electrons on directionality of hydrogen bonds formed by hydrophilic amino acid side chains in molecular dynamics simulation.
Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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8 citing papers in PubMed, 26 citations in OpenAlex.
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- CryoEM and crystal structure analyses reveal the indirect role played by Trp89 in glutamate dehydrogenase enzymatic reactions.The FEBS journal · 2025Article
- Improvement in positional accuracy of neural-network predicted hydration sites of proteins by incorporating atomic details of water-protein interactions and site-searching algorithm.Biophysics and physicobiology · 2025Article
- First isolation and characterization of a bovine parainfluenza virus type 3 genotype C strain from an aborted Holstein fetus.Frontiers in veterinary science · 2025Article
- The Fabrication of Polyimide-Based Tunable Charge Traps Ternary Memristors Doped with Ni-Co Coated Carbon Composite Nanofibers.Polymers · 2024Article
- CryoEM-sampling of metastable conformations appearing in cofactor-ligand association and catalysis of glutamate dehydrogenase.Scientific reports · 2024Article
- Prediction of hydrophilic and hydrophobic hydration structure of protein by neural network optimized using experimental data.Scientific reports · 2023Article
- Molecular dynamics simulation of protein-mediated biomineralization of amorphous calcium carbonate.RSC advances · 2019Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The influence of lone-pair electrons on the directionality of hydrogen bonds that are formed by oxygen and nitrogen atoms in the side chains of nine hydrophilic was investigated using molecular dynamics simulations. The simulations were conducted using two types of force fields; one incorporated lone-pair electrons placed at off-atom sites and the other did not. The density distributions of the hydration water molecules around the oxygen and nitrogen atoms were calculated from the simulation trajectories, and were compared with the empirical hydration distribution functions, which were constructed from a large number of hydration water molecules found in the crystal structures of proteins. Only simulations using the force field explicitly incorporating lone-pair electrons reproduced the directionality of hydrogen bonds that is observed in the empirical distribution functions for the deprotonated oxygen and nitrogen atoms in the sp
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