A method for incorporating dipolar couplings into structure calculations in cases of (near) axial symmetry of alignment.
A method for incorporating dipolar coupling restraints into structure calculations is described which follows closely on methodology that has been recently presented for orienting peptide planes using dipolar couplings [Mueller et al. (2000) J. Mol. Biol., 300, 197-212] and is specifically developed for use in cases of an axially symmetric alignment tensor. Modeling studies on an all alpha-helical protein, farnesyl diphosphate synthase, establish the utility of the approach. A global fold of the 370-residue maltose binding protein in complex with beta-cyclodextrin is obtained from experimentally derived restraints. The average pairwise rmsd values between the N- and C-terminal domains in this NMR structure and the corresponding regions in the X-ray structure of the protein are 2.8 and 3.1 A, respectively.
Mueller
G A
GA
Protein Engineering Network Centers of Excellence and the Department of Medical Genetics, The University of Toronto, ON, Canada.
Choy
W Y
WY
Skrynnikov
N R
NR
Kay
L E
LE
D019883:Alkyl and Aryl Transferases / Q000737:chemistry / Q000378:metabolism; D003505:Cyclodextrins / Q000737:chemistry / Q000378:metabolism; D051228:Geranyltranstransferase; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D011485:Protein Binding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D013816:Thermodynamics
D003505:Cyclodextrins; D019883:Alkyl and Aryl Transferases; D051228:Geranyltranstransferase