The goal of this proposal is a molecular level description of protein unfolding, and by extension folding, using realistic molecular dynamics (MD) simulations in solution. Both the general and sequence-specific rules of unfolding will be pursued. The general rules will be investigated by making use of a large database of protein unfolding trajectories that already exist in the lab. In addition, new trajectories will be added. So far, this database contains nearly 11,000 simulations of more than 2200 protein and peptide systems. This repository represents the largest collection of protein simulations and protein structures in the world. The simulations were designed so that representatives of all proteins folds will eventually be investigated, working from the most to least populated folds. The current set represents over 80% of all known protein structures. We have already developed a novel relational/multidimensional database to house these data.
Specific Aim 1 of this proposal seeks to determine the general rules of protein unfolding by mining this database. In addition, multiple representatives of highly populated folds are being investigated to determine sequence-specific effects in Specific Aim 2. Our hypothesis is that all-atom molecular dynamics simulations of isolated proteins in solution can provide continuous and realistic protein unfolding pathways and that the general rules for unfolding and folding can be determined once a large number of protein folds have been simulated. While most relatives within a fold family fold by the same mechanism based on experimental studies, there are some exceptions. Consequently, sequence-specific effects will be determined by investigating multiple members of four common fold families with different architectures.
Specific Aim 3 focuses on the unfolding of structural motifs in isolation and in different structural contexts, i.e., within different structures. Finally, Specific Aim 4 focuses on characterizing the unfolding behavior and sequence determinants of unfolding for a pair of designed proteins with high sequence identity but they adopt different folds with different functions.

Public Health Relevance

Protein folding remains one of the most important unsolved problems in molecular biology, and it represents an important missing link necessary for full utilization of the information becoming available from the mapping of genomic sequences. Characterization of the unfolding process is equally important, both from the perspective of fully understanding a fundamental biochemical phenomenon and for the light shed on the folding process. An understanding of protein folding/unfolding also has important implications for all biological processes, including protein degradation, protein translocation, aging, and many human diseases, including amyloid diseases and single-nucleotide polymorphism associated disorders.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM050789-18
Application #
8494633
Study Section
Macromolecular Structure and Function B Study Section (MSFB)
Program Officer
Wehrle, Janna P
Project Start
1995-08-01
Project End
2015-06-30
Budget Start
2013-07-01
Budget End
2014-06-30
Support Year
18
Fiscal Year
2013
Total Cost
$278,968
Indirect Cost
$94,598
Name
University of Washington
Department
Biomedical Engineering
Type
Schools of Engineering
DUNS #
605799469
City
Seattle
State
WA
Country
United States
Zip Code
98195
Towse, Clare-Louise; Rysavy, Steven J; Vulovic, Ivan M et al. (2016) New Dynamic Rotamer Libraries: Data-Driven Analysis of Side-Chain Conformational Propensities. Structure 24:187-99
Childers, Matthew Carter; Towse, Clare-Louise; Daggett, Valerie (2016) The effect of chirality and steric hindrance on intrinsic backbone conformational propensities: tools for protein design. Protein Eng Des Sel 29:271-80
Towse, Clare-Louise; Vymetal, Jiri; Vondrasek, Jiri et al. (2016) Insights into Unfolded Proteins from the Intrinsic ϕ/ψ Propensities of the AAXAA Host-Guest Series. Biophys J 110:348-61
Towse, Clare-Louise; Hopping, Gene; Vulovic, Ivan et al. (2014) Nature versus design: the conformational propensities of D-amino acids and the importance of side chain chirality. Protein Eng Des Sel 27:447-55
Bromley, Dennis; Rysavy, Steven J; Su, Robert et al. (2014) DIVE: a data intensive visualization engine. Bioinformatics 30:593-5
Rysavy, Steven J; Beck, David A C; Daggett, Valerie (2014) Dynameomics: data-driven methods and models for utilizing large-scale protein structure repositories for improving fragment-based loop prediction. Protein Sci 23:1584-95
Rysavy, Steven J; Bromley, Dennis; Daggett, Valerie (2014) DIVE: a graph-based visual-analytics framework for big data. IEEE Comput Graph Appl 34:26-37
Merkley, Eric D; Rysavy, Steven; Kahraman, Abdullah et al. (2014) Distance restraints from crosslinking mass spectrometry: mining a molecular dynamics simulation database to evaluate lysine-lysine distances. Protein Sci 23:747-59
Bromley, Dennis; Anderson, Peter C; Daggett, Valerie (2013) Structural consequences of mutations to the *-tocopherol transfer protein associated with the neurodegenerative disease ataxia with vitamin E deficiency. Biochemistry 52:4264-73
Wang, Dan; McCully, Michelle E; Luo, Zhaoxiong et al. (2013) Structural and functional consequences of cardiac troponin C L57Q and I61Q Ca(2+)-desensitizing variants. Arch Biochem Biophys 535:68-75

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