Chicken Lysozyme Dynamics
This movie clip is hosted by Wonpil Im at the University of Kansas as part of the CHARMM-GUI resource pages. The images were produced by Carol during her post-doctoral work in the group of Martin Karplus at Harvard.
Structure Determination
The application of spin magnetic resonance to the determination of macromolecular structures is a field that is currently under a considerable amount of development. The ability to determine protein structures aids in advancing our understanding of biological processes at the molecular level, and serves as a valuable tool in the process of rational drug design. The group is actively working to determine the structures of viral capsid proteins and kinase proteins involved in B-cell signaling. We are also developing expanded computational protocols that should improve the efficiency and accuracy of structure determination.
As a part of the Purdue Cancer Center we are determining the structures of key domains of the kinases involved in B-cell activation. In collaboration with Bob Gaehlen and Marietta Harrison, we are working to understand the binding and specificity of the Src Homolgy 2 (SH2) domains of these proteins. SH2 domains recognize phosphorylated tyrosine residues in a sequence dependent manner to aid in proper recruiting and activation of signaling proteins. Detailed knowledge of these interactions will aid in our understanding of the mechanisms behind the regulation of these pathways, which are important to cancer research.
Work done in collaboration with Chris Bailey-Kellogg is aimed at improving the structure determination process. Computer protocols are under development that incorporate structural information obtained with comparative modeling techniques of related proteins with known structure to help increase the accuracy of calculated protein structures. Methods to improve the accuracy of analyzing and predicting NMR data are also being examined in these efforts.
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Activation/Inactivation Mechanisms
Members of our group are applying computational techniques to understand the conformational changes involved in protein activation. These studies are probing the enzymatic activation of Src Kinases as well as the changes involved in the final stages of virus maturation. Biased molecular dynamics simulations are employed to model the transition from an active conformation to an inactive conformation and vice versa. Analysis of these pathways will potentially uncover key transitional events that remain unobserved and cannot be deduced from the static crystal structures of each end state alone. Deeper understanding of the events of an activation or inactivation process could aid in rational drug design efforts to target and inhibit key protein functions.
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Drug Design
Molecular dynamics and docking simulations are also being employed to understand drug binding in atomic detail. Docking simulations serve to predict the affinity of a drug for a predicted binding pocket. This allows an initial screening of large libraries of potential drug candidates, in an effort to increase the speed and efficiency of the design process. Screening is currently being conducted for the development of antiviral agents. Molecular dynamics simulations and free energy calculations are also being conducted and compared to experimental thermodynamic data in an effort to better understand the structural basis of drug binding.
Biased molecular dynamics simulations are being employed to study drug dissociation events in an effort to refine currently developed drug candidates.
These simulations predict likely key interactions that occur as a drug binds and dissociates from the target protein.
As with the activation and inactivation of activity, the dynamics simulations have the potential to uncover transient interactions that are not likely to be deduced from static structures of the bound and unbound states.
Knowledge of these dynamic interactions may indicate sites on the drug candidate for potential improvement that would not have been predicted otherwise.
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Protein Stability
Molecular dynamics simulations are also providing insight into the forces controlling protein stability. This insight is derived from comparison of simulations of mesophilic proteins with their thermophilic counterparts, undertaken to investigate the structural elements that are mutated or conserved to shift the folding free energy minimum to different temperatures. Recent results (Dadarlat V and Post CB: PNAS 2003) indicate that the charge distribution between the protein surface and core correlates to the protein compressibility across a series of mesophile/thermophile comparisons. Further detailed analysis of simulation trajectories is being conducted to further understand the interactions resulting in this correlation.
We are also interested in a deeper understanding of ligand binding thermodynamics. The size and complexity of protein systems has long frustrated attempts at fully decomposing free energy, enthalpy, and entropy measurements from calorimetric binding studies into contributions from specific interactions that are observed in static structures. New work in the group is attempting to compare free energies, entropy contributions, and dynamic order parameters calculated from molecular dynamics simulations to experimental data obtained from calorimetry and NMR, to more completely characterize important interactions and fluctuations in the complex structure that contribute to each thermodynamic property. Improved understanding of these contributions has the potential to help improve binding affinity through rational drug design.
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Search Keywords
biomolecular nmr, protein nmr, protein structure determination, protein dynamics, molecular dynamics, simulations, structural biology, computational biology, purdue university research lab, kinase activation, viral protein, antiviral drug design