REDCRAFT

A tool for simultaneous characterization of protein backbone structure and motion from RDC data

Michael Bryson, Fang Tian, James H. Prestegard, Homayoun Valafar

Research output: Contribution to journalArticle

27 Citations (Scopus)

Abstract

REDCRAFT, a new open source software tool that accommodates the analysis of RDC data for simultaneous structure and dynamics characterization of proteins is presented in this article. Simultaneous consideration of structure and motion is believed to be necessary for accurate representation of the solution-state of a protein. REDCRAFT is designed to primarily utilize RDC data from multiple alignment media in two stages. During Stage-I, a list of possible torsion angles joining any two neighboring peptide planes is ranked based on their fitness to experimental constraints; in Stage-II, a dipeptide fragment is extended by addition of one peptide plane at a time. The algorithm adopted by REDCRAFT is very efficient and can produce a structure for an 80 residue protein within two hours on a typical desktop computer. REDCRAFT exhibits robustness with respect to noise and missing data. REDCRAFT describes the overall alignment of the molecule in the form of an order tensor matrix and is capable of identifying peptide fragments with internal dynamics. Identification of the location of internal motion will permit a more accurate structural representation. Experimental data from two proteins as well as simulated data are presented to illustrate the capabilities of REDCRAFT in both structure determination and identification of the dynamical regions.

Original languageEnglish (US)
Pages (from-to)322-334
Number of pages13
JournalJournal of Magnetic Resonance
Volume191
Issue number2
DOIs
StatePublished - Apr 1 2008

Fingerprint

peptides
proteins
Proteins
alignment
fragments
Peptides
Peptide Fragments
fitness
software development tools
Dipeptides
Joining
Personal computers
Torsional stress
lists
torsion
Tensors
Noise
Software
tensors
Molecules

All Science Journal Classification (ASJC) codes

  • Biophysics
  • Biochemistry
  • Nuclear and High Energy Physics
  • Condensed Matter Physics

Cite this

Bryson, Michael ; Tian, Fang ; Prestegard, James H. ; Valafar, Homayoun. / REDCRAFT : A tool for simultaneous characterization of protein backbone structure and motion from RDC data. In: Journal of Magnetic Resonance. 2008 ; Vol. 191, No. 2. pp. 322-334.
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REDCRAFT : A tool for simultaneous characterization of protein backbone structure and motion from RDC data. / Bryson, Michael; Tian, Fang; Prestegard, James H.; Valafar, Homayoun.

In: Journal of Magnetic Resonance, Vol. 191, No. 2, 01.04.2008, p. 322-334.

Research output: Contribution to journalArticle

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