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

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

No Abstract