How well do force fields capture the strength of salt bridges in proteins?
نویسندگان
چکیده
منابع مشابه
Evaluating the Strength of Salt Bridges: A Comparison of Current Biomolecular Force Fields
Recent advances in computer hardware and software have made rigorous evaluation of current biomolecular force fields using microsecond-scale simulations possible. Force fields differ in their treatment of electrostatic interactions, including the formation of salt bridges in proteins. Here we conducted an extensive evaluation of salt bridge interactions in the latest AMBER, CHARMM, and OPLS for...
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Stability of "salt bridges" in membrane proteins.
We estimate the free energies of transfer of ionized amino acid side chains in water to both their ion-paired and neutral hydrogen-bonded states in low-dielectric media. The difference between the two free energies corresponds to the proton transfer free energy in a "salt bridge" formed between acidic and basic groups (i.e., lysine and glutamic acid residues). Our approach is to use gas phase p...
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ژورنال
عنوان ژورنال: PeerJ
سال: 2018
ISSN: 2167-8359
DOI: 10.7717/peerj.4967