Journal
JOURNAL OF STRUCTURAL BIOLOGY
Volume 147, Issue 3, Pages 211-222Publisher
ACADEMIC PRESS INC ELSEVIER SCIENCE
DOI: 10.1016/j.jsb.2004.04.007
Keywords
time-resolved crystallography; analytical trapping; Laue diffraction; singular value decomposition; cluster analysis; chemical kinetic mechanism; photoactive yellow protein
Funding
- NIGMS NIH HHS [GM 36452] Funding Source: Medline
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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. (C) 2004 Elsevier Inc. All rights reserved.
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