Protein structure elucidation from minimal NMR data: the CLOUDS approach.

Printer-friendly versionPrinter-friendly versionPDF versionPDF version
TitleProtein structure elucidation from minimal NMR data: the CLOUDS approach.
Publication TypeJournal Article
Year of Publication2005
AuthorsGrishaev, A, Llinás, M
JournalMethods Enzymol
Volume394
Pagination261-95
Date Published2005
ISSN0076-6879
KeywordsBayes Theorem, Computer Simulation, Data Interpretation, Statistical, Magnetic Resonance Spectroscopy, Monte Carlo Method, Protein Structure, Tertiary, Proteins, Software
Abstract

In this chapter we review automated methods of protein NMR data analysis and expand on the assignment-independent CLOUDS approach. As presented, given a set of reliable NOEs it is feasible to derive a spatial H-atom distribution that provides a low-resolution image of the protein structure. In order to generate such a list of unambiguous NOEs, a probabilistic assessment of the NOE identities (in terms of frequency-labeled H-atom sources) was developed on the basis of Bayesian inference. The methodology, encompassing programs SPI and BACUS, provides a list of "clean" NOEs that does not hinge on prior knowledge of sequence-specific resonance assignments or a preliminary structural model. As such, the combined SPI/BACUS approach, intrinsically adaptable to include 13C- and/or 15N-edited experiments, affords a useful tool for the analysis of NMR data irrespective of whether the adopted structure calculation protocol is assignment-dependent.

DOI10.1016/S0076-6879(05)94010-X
Alternate JournalMeth. Enzymol.
PubMed ID15808224
Grant ListGM67964 / GM / NIGMS NIH HHS / United States
HL29409 / HL / NHLBI NIH HHS / United States