Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

FF12MC: A revised AMBER forcefield and new protein simulation protocol

Yuan-Ping Pang
doi: https://doi.org/10.1101/061184
Yuan-Ping Pang
Computer-Aided Molecular Design Laboratory, Mayo Clinic, Rochester, MN 55905, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Preview PDF
Loading

ABSTRACT

Specialized to simulate proteins in molecular dynamics (MD) simulations with explicit solvation, FF12MC is a combination of a new protein simulation protocol employing uniformly reduced atomic masses by tenfold and a revised AMBER forcefield FF99 with (i) shortened CH bonds, (ii) removal of torsions involving a nonperipheral sp3 atom, and (iii) reduced 1-4 interaction scaling factors of torsions ϕ and ψ This article reports that in multiple, distinct, independent, unrestricted, unbiased, isobaric-isothermal, and classical MD simulations FF12MC can (i) simulate the experimentally observed flipping between left-and right-handed configurations for C14-C38 of BPTI in solution, (ii) autonomously fold chignolin, CLN025, and Trp-cage with folding times that agree with the experimental values, (iii) simulate subsequent unfolding and refolding of these miniproteins, and (iv) achieve a robust Z score of 1.33 for refining protein models TMR01, TMR04, and TMR07. By comparison, the latest general-purpose AMBER forcefield FF14SB locks the C14-C38 bond to the right-handed configuration in solution under the same protein simulation conditions. Statistical survival analysis shows that FF12MC folds chignolin and CLN025 in isobaric-isothermal MD simulations 2-4 times faster than FF14SB under the same protein simulation conditions. These results suggest that FF12MC may be used for protein simulations to study kinetics and thermodynamics of miniprotein folding as well as protein structure and dynamics.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
Back to top
PreviousNext
Posted July 11, 2016.
Download PDF

Supplementary Material

Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
FF12MC: A revised AMBER forcefield and new protein simulation protocol
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
FF12MC: A revised AMBER forcefield and new protein simulation protocol
Yuan-Ping Pang
bioRxiv 061184; doi: https://doi.org/10.1101/061184
Reddit logo Twitter logo Facebook logo LinkedIn logo Mendeley logo
Citation Tools
FF12MC: A revised AMBER forcefield and new protein simulation protocol
Yuan-Ping Pang
bioRxiv 061184; doi: https://doi.org/10.1101/061184

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Biophysics
Subject Areas
All Articles
  • Animal Behavior and Cognition (4369)
  • Biochemistry (9543)
  • Bioengineering (7068)
  • Bioinformatics (24766)
  • Biophysics (12559)
  • Cancer Biology (9923)
  • Cell Biology (14297)
  • Clinical Trials (138)
  • Developmental Biology (7929)
  • Ecology (12073)
  • Epidemiology (2067)
  • Evolutionary Biology (15954)
  • Genetics (10901)
  • Genomics (14704)
  • Immunology (9842)
  • Microbiology (23582)
  • Molecular Biology (9453)
  • Neuroscience (50691)
  • Paleontology (369)
  • Pathology (1535)
  • Pharmacology and Toxicology (2674)
  • Physiology (3996)
  • Plant Biology (8638)
  • Scientific Communication and Education (1505)
  • Synthetic Biology (2388)
  • Systems Biology (6413)
  • Zoology (1344)