Conformational Ensembles from Experimental Data and Computer Simulations

Conformational Ensembles from Experimental Data and Computer Simulations

Monday Speaker Abstracts

Resolving Catalytic Motions and Dynamics of Isocyanide Hydratase from X-ray Crystallography Henry Van den Bedem . Stanford University, Menlo Park, CA, USA. Biomolecules rely on accessing transient, excited states to interact with their partners or perform their biochemical functions. Advances in experimental techniques such as X-ray crystallography and NMR spectroscopy have resulted in unprecedented access to structural snapshots of the conformational landscapes of proteins, RNA, and their binding partners. However, these snapshots often present themselves as spatiotemporally averaged data. Resolving averaged, sparse, and heterogeneous data into constituent, structural contributions remains a formidable challenge. We have developed computational procedures to resolve biomolecular ensembles, collective motions and allostery directly from X-ray crystallography, measured at ambient temperature, as well as NMR spectroscopy data. We present results for several proteins, their ligands, and RNA. We applied our procedures to probe the catalytic motions of isocyanide hydratase (ICH), a 230- residue homodimeric enzyme that hydrates diverse isocyanides to yield N-formamide. Oxidation of the catalytic nucleophile by irradiation forms a sulfenic acid that resembles the proposed thioimidate intermediate of ICH catalysis. The altered electrostatic environment weakens a critical hydrogen bond, which results in large conformational rearrangements of the active site. To examine how formation of a catalytic intermediate alters the structure and fast dynamics in ICH, we designed a radiation-dose perturbation series for X-ray diffraction, from minimal radiation exposure at the LCLS, to maximum radiation-induced oxidation at a synchrotron at ambient temperature. These data sets reveal a striking shift of the conformational ensemble around the active site, including a 2 Հ displacement of an α-helix, as the catalytic intermediate forms. Analysis of X-ray crystallography-derived order parameters reveal widespread changes in dynamics throughout the protein.

Diffuse X-ray Scattering to Model the Protein Conformational Ensemble

Michael Wall Los Alamos National Laboratory, Los Alamos, NM, USA

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