Analytical trapping: extraction of time-independent structures from time-dependent crystallographic data.

Journal Article

All chemical and biological reactions involve atomic motion, embodied in dynamic structural changes. Identifying these changes is the goal of time-resolved crystallography. The "raw" output of a time-resolved macromolecular crystallography experiment is the time-dependent set of difference electron density maps that span the desired time range and display the time-dependent changes in density (and underlying structure) as the reaction progresses. The goal is to interpret such data in terms of a small number of crystallographically refinable, time-independent structures, each associated with a reaction intermediate; to establish the pathways and rate coefficients by which the intermediates interconvert; and thus to establish a chemical kinetic mechanism. We review briefly the various strategies that may be used to achieve this goal and concentrate on two promising advances: singular value decomposition and cluster analysis. The strategies are illustrated by using data on the photocycle of the bacterial blue light photoreceptor, photoactive yellow protein.

Full Text

Duke Authors

Cited Authors

  • Rajagopal, S; Kostov, KS; Moffat, K

Published Date

  • September 2004

Published In

Volume / Issue

  • 147 / 3

Start / End Page

  • 211 - 222

PubMed ID

  • 15450291

Electronic International Standard Serial Number (EISSN)

  • 1095-8657

International Standard Serial Number (ISSN)

  • 1047-8477

Digital Object Identifier (DOI)

  • 10.1016/j.jsb.2004.04.007

Language

  • eng