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Center for Nonlinear Studies |
Ligand binding is a complex event mediated by both enthalpic and entropic effects. In their unbound state, both ligand and receptor have access to a multitude of conformational substates. Upon binding, protein environments remodel their small molecule partners, and, simultaneously, the small molecules remodel the protein environment. Advances in experimental techniques such as X-ray crystallography, cryoEM, and NMR spectroscopy, combined with sensitive computer modeling of multiple conformational substates now enable us to visualize minor populations of these structural ensembles. These approaches can lead to important new insights.
In structure-based drug design, access to this conformational ensemble is critical to understandthe balance between entropy and enthalpy in lead optimization. We examined a large set of protein receptors with drug-like ligands from the protein data bank, and found wide-spread evidence of unmodeled, averaged, relatively isoenergetic conformations in ligand-receptor interactions. We found that in many retrospective cases, these alternate conformations were adventitiously exploited to guide compound design, resulting in improved potency or selectivity.
In another example, we examined how covalent modification of the active site cysteine residue in isocyanide hydratase (ICH) alters the protein conformational ensemble. ICH is a 230-residuehomodimeric enzyme that hydrates diverse isocyanides to yield N-formamide. Conventional andserial time-resolved mix-and-inject X-ray crystallography, computer simulations, and enzymekinetics together revealed a cascade of conformational changes that propagate across the entire ICH dimer in an asymmetric manner related to the formation of a catalytic intermediate. Wepropose that the shifting ensemble maps to transient intermediate states populated duringenzyme turnover. Examining how these changes propagate can connect molecular mechanismsand motion to function for the large class of enzymes that employ a cysteine nucleophile, whichare central to many cellular processes.
Host: Michael Wall