The primary objective of this research is the development of links between the nature of the protein folding free energy landscape and the underlying mechanism and rate at which proteins fold. Key questions to be addressed by Dr. Brooks include: 1) How are the topology of the final folded state of the protein, and the features of the free energy landscape that determine the general mechanism of folding; e.g., local secondary structure formation followed by collapse, collapse and concomitant secondary structure formation, collapse and search through compact states for native interactions, etc., linked?; 2) What is the balance between local and longer range (in sequence) interactions in stabilizing protein structure throughout the folding process?; 3) What is the nature of fluctuations between different conformations within the same region of configuration space; i.e., at the same point on the folding coordinate? Dr. Brooks will use molecular dynamics simulations, with specialized sampling techniques, in explicit solvent to study detailed models of proteins; i.e., Langevin dynamics to study the kinetics and thermodynamics of folding in minimalist off-lattice models for proteins of differing topology. Theoretical models will be employed to express the general features of thermodynamics and kinetics on correlated landscapes. The focus will be on small single domain proteins of differing topology. The folding of fragment B of Staphyococcal protein A and segment B1 of Streptococcal protein G will be studied as representatives of structurally distinct classes of protein architecture. The analyses will be extended to include all beta proteins from the Cold Shock protein family, CspA, and CspB. Comparisons will be made between key interactions anticipated during folding (based on calculations) and observations from experimental folding studies on these and similar proteins. Finally, simplified (off-lattice minimalist) models will be used to examine different folding scenarios. The simulation studies of Dr. Brooks will be used to: 1) Build on approaches developed to cluster self-similar structures along folding/unfolding trajectories, 2) Compute free energy surfaces using specialized sampling and analysis methods, and 3)project the free energy onto interesting folding coordinates; e.g., the radius of gyration, the fraction of native contacts, the total number of contacts, and measures of native secondary structure. These studies aim to provide a link between physically based theories of protein folding; (e.g., based on lattice models or folding landscape ideas), and detailed experimental studies.
Showing the most recent 10 out of 47 publications
