Header

UZH-Logo

Maintenance Infos

Improved atomistic Monte Carlo simulations demonstrate that poly-L-proline adopts heterogeneous ensembles of conformations of semi-rigid segments interrupted by kinks


Radhakrishnan, Aditya; Vitalis, Andreas; Mao, Albert H; Steffen, Adam T; Pappu, Rohit V (2012). Improved atomistic Monte Carlo simulations demonstrate that poly-L-proline adopts heterogeneous ensembles of conformations of semi-rigid segments interrupted by kinks. Journal of Physical Chemistry B, 116(23):6862-6871.

Abstract

Poly-L-proline (PLP) polymers are useful mimics of biologically relevant proline-rich sequences. Biophysical and computational studies of PLP polymers in aqueous solutions are challenging because of the diversity of length scales and the slow time scales for conformational conversions. We describe an atomistic simulation approach that combines an improved ABSINTH implicit solvation model, with conformational sampling based on standard and novel Metropolis Monte Carlo moves. Refinements to forcefield parameters were guided by published experimental data for proline-rich systems. We assessed the validity of our simulation results through quantitative comparisons to experimental data that were not used in refining the forcefield parameters. Our analysis shows that PLP polymers form heterogeneous ensembles of conformations characterized by semirigid, rod-like segments interrupted by kinks, which result from a combination of internal cis peptide bonds, flexible backbone ψ angles, and the coupling between ring puckering and backbone degrees of freedom.

Abstract

Poly-L-proline (PLP) polymers are useful mimics of biologically relevant proline-rich sequences. Biophysical and computational studies of PLP polymers in aqueous solutions are challenging because of the diversity of length scales and the slow time scales for conformational conversions. We describe an atomistic simulation approach that combines an improved ABSINTH implicit solvation model, with conformational sampling based on standard and novel Metropolis Monte Carlo moves. Refinements to forcefield parameters were guided by published experimental data for proline-rich systems. We assessed the validity of our simulation results through quantitative comparisons to experimental data that were not used in refining the forcefield parameters. Our analysis shows that PLP polymers form heterogeneous ensembles of conformations characterized by semirigid, rod-like segments interrupted by kinks, which result from a combination of internal cis peptide bonds, flexible backbone ψ angles, and the coupling between ring puckering and backbone degrees of freedom.

Statistics

Citations

12 citations in Web of Science®
11 citations in Scopus®
Google Scholar™

Altmetrics

Downloads

0 downloads since deposited on 09 Oct 2012
0 downloads since 12 months

Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:04 Faculty of Medicine > Department of Biochemistry
07 Faculty of Science > Department of Biochemistry
Dewey Decimal Classification:570 Life sciences; biology
Language:English
Date:2012
Deposited On:09 Oct 2012 15:10
Last Modified:05 Apr 2016 15:59
Publisher:American Chemical Society
ISSN:1520-6106
Publisher DOI:https://doi.org/10.1021/jp212637r
PubMed ID:22329658

Download

Preview Icon on Download
Filetype: PDF - Registered users only
Size: 1MB
View at publisher

TrendTerms

TrendTerms displays relevant terms of the abstract of this publication and related documents on a map. The terms and their relations were extracted from ZORA using word statistics. Their timelines are taken from ZORA as well. The bubble size of a term is proportional to the number of documents where the term occurs. Red, orange, yellow and green colors are used for terms that occur in the current document; red indicates high interlinkedness of a term with other terms, orange, yellow and green decreasing interlinkedness. Blue is used for terms that have a relation with the terms in this document, but occur in other documents.
You can navigate and zoom the map. Mouse-hovering a term displays its timeline, clicking it yields the associated documents.

Author Collaborations