AssignFit: a program for simultaneous assignment and structure refinement from solid-state NMR spectra. J Magn Reson 2012 Jan;214(1):42-50
Date
11/01/2011Pubmed ID
22036904Pubmed Central ID
PMC3257385DOI
10.1016/j.jmr.2011.10.002Scopus ID
2-s2.0-84855687118 (requires institutional sign-in at Scopus site) 17 CitationsAbstract
AssignFit is a computer program developed within the XPLOR-NIH package for the assignment of dipolar coupling (DC) and chemical shift anisotropy (CSA) restraints derived from the solid-state NMR spectra of protein samples with uniaxial order. The method is based on minimizing the difference between experimentally observed solid-state NMR spectra and the frequencies back calculated from a structural model. Starting with a structural model and a set of DC and CSA restraints grouped only by amino acid type, as would be obtained by selective isotopic labeling, AssignFit generates all of the possible assignment permutations and calculates the corresponding atomic coordinates oriented in the alignment frame, together with the associated set of NMR frequencies, which are then compared with the experimental data for best fit. Incorporation of AssignFit in a simulated annealing refinement cycle provides an approach for simultaneous assignment and structure refinement (SASR) of proteins from solid-state NMR orientation restraints. The methods are demonstrated with data from two integral membrane proteins, one α-helical and one β-barrel, embedded in phospholipid bilayer membranes.
Author List
Tian Y, Schwieters CD, Opella SJ, Marassi FMAuthor
Francesca M. Marassi PhD Chair, Professor in the Biophysics department at Medical College of WisconsinMESH terms used to index this publication - Major topics in bold
AlgorithmsAmino Acid Sequence
Computer Simulation
Magnetic Resonance Spectroscopy
Models, Chemical
Models, Molecular
Molecular Sequence Data
Protein Conformation
Proteins
Software
