Investigating Nonnative Contacts in Protein Folding

Investigating Nonnative Contacts in Protein Folding

Bibliographic Details
Main Author: Chen, Chong
Language:English
Published: University of Akron / OhioLINK 2009
Subjects:
Polymers
PROTEIN
NONNATIVE CONTACTS
residues
conformations
interacting model
FOLDING
Online Access:http://rave.ohiolink.edu/etdc/view?acc_num=akron1238087880
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spelling ndltd-OhioLink-oai-etd.ohiolink.edu-akron12380878802021-08-03T05:25:56Z Investigating Nonnative Contacts in Protein Folding Chen, Chong Polymers PROTEIN NONNATIVE CONTACTS residues conformations interacting model FOLDING Proteins are organic compounds, consisting of amino acids (residues) bound by peptide bonds into polypeptide chains, and can fold into their unique functional structures (native state) without any chaperones. There is more than one simple model of proteins, among which Go model, HP model and “perturbed homopolymer model” are widely used. Amino acids in these models are considered as beads lying on the sites of a lattice. By extracting information from the system with different kind of computer algorithms, one hopes to predict the folding process.How and why do protein fold in this particular way is still not clear although it has been extensively investigated for more than half a century. Experimental techniques (NMR, X-ray crystallography, etc) as well as computer aided theoretical works (energy landscape, homology, etc) have been used to understand how a protein starts from its amino acids sequence into a functional structure.Nonnative contacts are defined as contacts (nearest-neighbor) not found in the native state, and can be used to study the process of folding. According to the recent literature, nonnative contacts affect protein folding rates, and make contributions to the unfolding pathways. Folding intermediates are also found rich in nonnative contacts. We have investigated nonnative contacts for proteins in a modified HP model by generating all possible conformations (enumeration) which enable us to carry out exact calculation for the nonnative contact density nc(e) as a function of the energy e as well as thermodynamically average nonnative contacts as a function of temperature of T. We have investigated different sequences to understand the sequence dependence of nc(e) and nc(T) . These results provide us with new understandings of the role for nonnative contacts play in the protein folding process, as are listed below:1) The density nc(e)is always monotonically increasing in the standard model. In weakly interacting and strongly interacting model, the density nc(e)is spread out, but generally increasing.2) The nc(T) for all models is generally monotonically increasing. A few violations can be seen.3) The protein property is sequence dependent. 2009-06-09 English text University of Akron / OhioLINK http://rave.ohiolink.edu/etdc/view?acc_num=akron1238087880 http://rave.ohiolink.edu/etdc/view?acc_num=akron1238087880 unrestricted This thesis or dissertation is protected by copyright: all rights reserved. It may not be copied or redistributed beyond the terms of applicable copyright laws.
collection NDLTD
language English
sources NDLTD
topic Polymers
PROTEIN
NONNATIVE CONTACTS
residues
conformations
interacting model
FOLDING
spellingShingle Polymers
PROTEIN
NONNATIVE CONTACTS
residues
conformations
interacting model
FOLDING
Chen, Chong
Investigating Nonnative Contacts in Protein Folding
author Chen, Chong
author_facet Chen, Chong
author_sort Chen, Chong
title Investigating Nonnative Contacts in Protein Folding
title_short Investigating Nonnative Contacts in Protein Folding
title_full Investigating Nonnative Contacts in Protein Folding
title_fullStr Investigating Nonnative Contacts in Protein Folding
title_full_unstemmed Investigating Nonnative Contacts in Protein Folding
title_sort investigating nonnative contacts in protein folding
publisher University of Akron / OhioLINK
publishDate 2009
url http://rave.ohiolink.edu/etdc/view?acc_num=akron1238087880
work_keys_str_mv AT chenchong investigatingnonnativecontactsinproteinfolding
_version_ 1719419991579688960

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