The molecular flexibility of an inhibitor in ligand-binding process has been investigated by the mass-weighted molecular-dynamics simulation, a computational method adopted from the standard molecular-dynamics simulation and one by which the conformational space of a biomolecular system over potential energy barriers can be sampled effectively. The bimolecular complex of the aspartyl proteinase from Rhizopus chinensis, rhizopuspepsin, and an octapeptide inhibitor was previously studied in a mass-weighted molecular-dynamics simulation; the study has been extended for investigating the molecular flexibility in ligand binding. A series of mass-weighted molecular-dynamics simulations was carried out in which libration of the inhibitor dihedral angles was parametrically controlled, and threshold values of dihedral angle libration amplitudes were observed from monitoring the sampling of the enzyme binding pocket by the inhibitor in the simulations. The computational results are consistent with the general notion of molecular-flexibility requirement for ligand binding; the freedom of dihedral rotations of side-chain groups was found to be particularly important for ligand binding. Thus the critical degree of molecular flexibility which would contribute to effective enzyme inhibition can be obtained precisely from the modified molecular-dynamics simulations; the procedure described herein represents a first step toward providing quantitative measures of such a molecular-flexibility index for inhibitor molecules that have been otherwise targeted for optimal protein-ligand interactions.
Skip Nav Destination
Follow us on Twitter @Biochem_Journal
Article navigation
November 1992
-
Cover Image
Cover Image
- PDF Icon PDF LinkFront Matter
- PDF Icon PDF LinkTable of Contents
- PDF Icon PDF LinkAdvertising
Research Article|
November 15 1992
Molecular-dynamics investigation of molecular flexibility in ligand binding
B Mao
B Mao
1Upjohn Research Laboratories, Kalamazoo, MI 49001, U.S.A.
Search for other works by this author on:
Publisher: Portland Press Ltd
Online ISSN: 1470-8728
Print ISSN: 0264-6021
© 1992 The Biochemical Society, London
1992
Biochem J (1992) 288 (1): 109–116.
Citation
B Mao; Molecular-dynamics investigation of molecular flexibility in ligand binding. Biochem J 15 November 1992; 288 (1): 109–116. doi: https://doi.org/10.1042/bj2880109
Download citation file:
Sign in
Don't already have an account? Register
Sign in to your personal account
You could not be signed in. Please check your email address / username and password and try again.
Could not validate captcha. Please try again.
Biochemical Society Member Sign in
Sign InSign in via your Institution
Sign in via your InstitutionGet Access To This Article
Cited By
Follow us on Twitter @Biochem_Journal
Open Access for all
We offer compliant routes for all authors from 2025. With library support, there will be no author nor reader charges in 5 journals. Check here |
![]() View past webinars > |