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The conformations of hirudin in solution: a study using nuclear magnetic resonance, distance geometry and restrained molecular dynamics
Author(s) -
Clore G. Marius,
Sukumaran Dinesh K.,
Nilges Michael,
Zarbock Jutta,
Gronenborn Angela M.
Publication year - 1987
Publication title -
the embo journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 7.484
H-Index - 392
eISSN - 1460-2075
pISSN - 0261-4189
DOI - 10.1002/j.1460-2075.1987.tb04785.x
Subject(s) - biology , nuclear magnetic resonance , dynamics (music) , nuclear magnetic resonance spectroscopy , magnetic resonance imaging , molecular conformation , molecular dynamics , geometry , biophysics , physics , molecule , mathematics , quantum mechanics , medicine , acoustics , radiology
The solution conformations of the protein hirudin have been investigated by the combined use of distance geometry and restrained molecular dynamics calculations. The basis for the structure determination comprised 359 approximate interproton distance restraints and 10 φ backbone torsion angle restraints derived from n.m.r. measurements. It is shown that hirudin is composed of three domains: a central core made up of residues 3‐30, 37‐46 and 56‐57; a protruding ‘finger’ (residues 31‐36) consisting of the tip of an antiparallel β sheet, and an exposed loop (residues 47‐55). The structure of each individual domain is relatively well defined with average backbone atomic r.m.s. differences of <2 Å between the final seven converged restrained dynamic structures and the mean structure obtained by averaging their coordinates. The orientation of the two minor domains relative to the central core, however, could not be determined as no long‐range (ǀi‐jǀ>5) interdomain proton–proton contacts could be observed in the two‐dimensional nuclear Overhauser enhancement spectra. From the restrained molecular dynamics calculations it appears that the two minor domains exhibit large rigid‐body motions relative to the central core.