NDLI: A MULTISCALE APPROACH TO SAMPLING NASCENT PEPTIDE CHAINS IN THE RIBOSOMAL EXIT TUNNEL

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A MULTISCALE APPROACH TO SAMPLING NASCENT PEPTIDE CHAINS IN THE RIBOSOMAL EXIT TUNNEL

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A MULTISCALE APPROACH TO SAMPLING NASCENT PEPTIDE CHAINS IN THE RIBOSOMAL EXIT TUNNEL

Content Provider	PubMed Central
Author	Voelz, V. A. Petrone, P. Pande, V. S.
Abstract	We present a new multiscale method that combines all-atom molecular dynamics with coarse-grained sampling, towards the aim of bridging two levels of physiology: the atomic scale of protein side chains and small molecules, and the huge scale of macromolecular complexes like the ribosome. Our approach uses all-atom simulations of peptide (or other ligand) fragments to calculate local 3D spatial potentials of mean force (PMF). The individual fragment PMFs are then used as a potential for a coarse-grained chain representation of the entire molecule. Conformational space and sequence space are sampled efficiently using generalized ensemble Monte Carlo. Here, we apply this method to the study of nascent polypeptides inside the cavity of the ribosome exit tunnel. We show how the method can be used to explore the accessible conformational and sequence space of nascent polypeptide chains near the ribosome peptidyl transfer center (PTC), with the eventual aim of understanding the basis of specificity for co-translational regulation. The method has many potential applications to predicting binding specificity and design, and is sufficiently general to allow even greater separation of scales in future work.
Starting Page	340
File Format	PDF
ISSN	23356936
Journal	Pacific Symposium on Biocomputing
Language	English
Publisher Date	2009-01-01
Access Restriction	Open
Subject Keyword	Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Medicine Computational Theory and Mathematics Biomedical Engineering

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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A MULTISCALE APPROACH TO SAMPLING NASCENT PEPTIDE CHAINS IN THE RIBOSOMAL EXIT TUNNEL

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