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J Mol Graph Model. 2013 Mar;40:48-53. doi: 10.1016/j.jmgm.2012.12.012. Epub 2013 Jan 5.

ViewMotions Rainbow: a new method to illustrate molecular motions in proteins.

Author information

1
Boston College, Department of Chemistry, Merkert Chemistry Center, Chestnut Hill, MA 02467, USA.

Abstract

The biological functions of many enzymes are often coupled with significant conformational changes. The end states of these conformational changes can often be determined by X-ray crystallography. These X-ray structures are snapshots of the two extreme conformations in which the macromolecule exists, but the dynamic movements between the states are not easily visualized in a two-dimensional illustration. Here we have developed a new method to visualize macromolecular motions called a ViewMotions Rainbow diagram. These diagrams show the initial and final states overlaid along with approximately 30 intermediate structures calculated by linear interpolation of the backbone coordinates of the initial and final states. This group of structures is then spectrally colored from the initial structure in blue to the final structure in red. ViewMotions Rainbow diagrams provide the reader with a much easier way to understand the macromolecular motions using a single two-dimensional illustration. Since producing these diagrams requires a number of different software packages, we have setup the ViewMotions Web Server (http://viewmotions.bc.edu) to automatically generate these diagrams from two Protein Data Bank files or from the Database of Macromolecular Movements (http://molmovdb.org).

PMID:
23353585
PMCID:
PMC3670142
DOI:
10.1016/j.jmgm.2012.12.012
[Indexed for MEDLINE]
Free PMC Article

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