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Investigating Nonnative Contacts in Protein Folding

Chen, Chong
http://rave.ohiolink.edu/etdc/view?acc_num=akron1238087880

Abstract Details

2009, Master of Science, University of Akron, Polymer Science.
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.
Purushottam Gujrati, PhD (Advisor)
67 p.
Polymers
PROTEIN; NONNATIVE CONTACTS; residues; conformations; interacting model; FOLDING

Recommended Citations

Citations

  • Chen, C. (2009). Investigating Nonnative Contacts in Protein Folding [Master's thesis, University of Akron]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=akron1238087880

    APA Style (7th edition)

  • Chen, Chong. Investigating Nonnative Contacts in Protein Folding. 2009. University of Akron, Master's thesis. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=akron1238087880.

    MLA Style (8th edition)

  • Chen, Chong. "Investigating Nonnative Contacts in Protein Folding." Master's thesis, University of Akron, 2009. http://rave.ohiolink.edu/etdc/view?acc_num=akron1238087880

    Chicago Manual of Style (17th edition)

akron1238087880
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© 2009, all rights reserved.
This open access ETD is published by University of Akron and OhioLINK.