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

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

Received: 16 February 2012; in revised form: 27 March 2012 / Accepted: 29 March 2012 / Published: 10 April 2012
(This article belongs to the Special Issue Loop Entropy)
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Abstract: 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.
Keywords: protein dynamics; protein loops; molecular dynamics; elastic network models; correlated motions
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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.

AMA Style

Zimmermann MT, Jernigan RL. Protein Loop Dynamics Are Complex and Depend on the Motions of the Whole Protein. Entropy. 2012; 14(4):687-700.

Chicago/Turabian Style

Zimmermann, Michael T.; Jernigan, Robert L. 2012. "Protein Loop Dynamics Are Complex and Depend on the Motions of the Whole Protein." Entropy 14, no. 4: 687-700.

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