Next Article in Journal
Tsallis Relative Entropy and Anomalous Diffusion
Next Article in Special Issue
Substrate Effect on Catalytic Loop and Global Dynamics of Triosephosphate Isomerase
Previous Article in Journal
Experimental Test of the “Special State” Theory of Quantum Measurement
Previous Article in Special Issue
Application of Solution NMR Spectroscopy to Study Protein Dynamics
Article Menu

Export Article

Open AccessArticle
Entropy 2012, 14(4), 687-700; doi:10.3390/e14040687

Protein Loop Dynamics Are Complex and Depend on the Motions of the Whole Protein

L. H. Baker Center for Bioinformatics and Biologic Statistics, Iowa State University, Ames, IA 50011, USA
Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011, USA
Author to whom correspondence should be addressed.
Received: 16 February 2012 / Revised: 27 March 2012 / Accepted: 29 March 2012 / Published: 10 April 2012
(This article belongs to the Special Issue Loop Entropy)
View Full-Text   |   Download PDF [493 KB, uploaded 24 February 2015]   |  


We investigate the relationship between the motions of the same peptide loop segment incorporated within a protein structure and motions of free or end-constrained peptides. As a reference point we also compare against alanine chains having the same length as the loop. Both the analysis of atomic molecular dynamics trajectories and structure-based elastic network models, reveal no general dependence on loop length or on the number of solvent exposed residues. Rather, the whole structure affects the motions in complex ways that depend strongly and specifically on the tertiary structure of the whole protein. Both the Elastic Network Models and Molecular Dynamics confirm the differences in loop dynamics between the free and structured contexts; there is strong agreement between the behaviors observed from molecular dynamics and the elastic network models. There is no apparent simple relationship between loop mobility and its size, exposure, or position within a loop. Free peptides do not behave the same as the loops in the proteins. Surface loops do not behave as if they were random coils, and the tertiary structure has a critical influence upon the apparent motions. This strongly implies that entropy evaluation of protein loops requires knowledge of the motions of the entire protein structure. View Full-Text
Keywords: protein dynamics; protein loops; molecular dynamics; elastic network models; correlated motions protein dynamics; protein loops; molecular dynamics; elastic network models; correlated motions

This is an open access article distributed under the Creative Commons Attribution License (CC BY 3.0).

Supplementary material

Scifeed alert for new publications

Never miss any articles matching your research from any publisher
  • Get alerts for new papers matching your research
  • Find out the new papers from selected authors
  • Updated daily for 49'000+ journals and 6000+ publishers
  • Define your Scifeed now

SciFeed Share & Cite This Article

MDPI and ACS Style

Zimmermann, M.T.; Jernigan, R.L. Protein Loop Dynamics Are Complex and Depend on the Motions of the Whole Protein. Entropy 2012, 14, 687-700.

Show more citation formats Show less citations formats

Related Articles

Article Metrics

Article Access Statistics



[Return to top]
Entropy EISSN 1099-4300 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
Back to Top