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Pseudocontact shifts as constraints for energy minimization and molecular dynamics calculations on solution structures of paramagnetic metalloproteins
Author(s) -
Banci Lucia,
Bertini Ivano,
Savellini Giovanni Gori,
Romagnoli Andrea,
Turano Paola,
Cremonini Mauro A.,
Luchinat Claudio,
Gray Harry B.
Publication year - 1997
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/(sici)1097-0134(199709)29:1<68::aid-prot5>3.0.co;2-b
Subject(s) - paramagnetism , metalloprotein , energy minimization , molecular dynamics , dynamics (music) , chemistry , minification , computational chemistry , biological system , chemical physics , statistical physics , physics , condensed matter physics , mathematical optimization , biochemistry , biology , mathematics , enzyme , acoustics
The pseudocontact shifts of NMR signals, which arise from the magnetic susceptibility anisotropy of paramagnetic molecules, have been used as structural constraints under the form of a pseudopotential in the SANDER module of the AMBER 4.1 molecular dynamics software package. With this procedure, restrained energy minimization (REM) and restrained molecular dynamics (RMD) calculations can be performed on structural models by using pseudocontact shifts. The structure of the cyanide adduct of the Met80Ala mutant of the yeast iso‐1‐cytochrome c has been used for successfully testing the calculations. For this protein, a family of structures is available, which was obtained by using NOE and pseudocontact shifts as constraints in a distance geometry program. The structures obtained by REM and RMD calculations with the inclusion of pseudocontact shifts are analyzed. Proteins 29:68–76, 1997. © 1997 Wiley‐Liss, Inc.