Science exchange logo white
  • Solutions
      Buyers

      We are making R&D services readily available to every organization that seeks to make scientific impact. Learn More

      Providers

      We are changing the way providers access and engage customers to streamline the sale and delivery of R&D services. Learn More

      Industries Agriscience Animal Health Basic Research Biopharmaceutical Chemicals Consumer Health Food Science Medical Devices
      Reproducibility

      We believe that good experiments can and should be independently replicated and validated. Learn More

  • Resources
    Innovation Blog
    Customer Stories
    Events
    Industry Trends
    News
    Product Updates
    Help Center
  • About
    About
    Our Story
    Leadership
    Partners
    Join the Team
  • Contact
  • Log In Sign Up
  • Get a Demo
  • Side-chain rotamer changes upon ligand binding: common, crucial, correlate with entropy and rearrange hydrogen bonding.

    Bioinformatics. 28(18):i423-i430. doi: 10.1093/bioinformatics/bts395. September 15, 2012. View on PubMed.
  • Authors

    Gaudreault F, Chartier M, and Najmanovich R
  • Abstract

    MOTIVATIONProtein movements form a continuum from large domain rearrangements (including folding and restructuring) to side-chain rotamer changes and small rearrangements. Understanding side-chain flexibility upon binding is important to understand molecular recognition events and predict ligand binding.METHODSIn the present work, we developed a well-curated non-redundant dataset of 188 proteins in pairs of structures in the Apo (unbound) and Holo (bound) forms to study the extent and the factors that guide side-chain rotamer changes upon binding.RESULTSOur analysis shows that side-chain rotamer changes are widespread with only 10% of binding sites displaying no conformational changes. Overall, at most five rotamer changes account for the observed movements in 90% of the cases. Furthermore, rotamer changes are essential in 32% of flexible binding sites. The different amino acids have a 11-fold difference in their probability to undergo changes. Side-chain flexibility represents an intrinsic property of amino acids as it correlates well with configurational entropy differences. Furthermore, on average b-factors and solvent accessible surface areas can discriminate flexible side-chains in the Apo form. Finally, there is a rearrangement of the hydrogen-bonding network upon binding primarily with a loss of H-bonds with water molecules and a gain of H-bonds with protein residues for flexible residues. Interestingly, only 25% of side chains capable of forming H-bonds do so with the ligand upon binding. In terms of drug design, this last result shows that there is a large number of potential interactions that may be exploited to modulate the specificity and sensitivity of inhibitors.CONTACT[email protected]

Science exchange logo white

  • Facebook
  • Twitter
  • LinkedIn

Solutions

  • Buyers
  • Providers
  • Reproducibility

Industries

  • Agriscience
  • Animal Health
  • Basic Research
  • Biopharmaceutical
  • Chemicals
  • Consumer Health
  • Food Science
  • Medical Devices

Resources

  • Innovation Blog
  • Customer Stories
  • Events
  • Industry Trends
  • News
  • Product Updates

About

  • Our Story
  • Leadership
  • Partners
  • Join the Team

Support

  • Contact Us
  • Help Center
  • Trust
  • Terms of Use
  • Privacy Policy

Copyright © 2021 Science Exchange, Inc. All rights reserved.