Direct structure refinement of high molecular weight proteins against residual dipolar couplings and carbonyl chemical shift changes upon alignment: an application to maltose binding protein.
The global fold of maltose binding protein in complex with beta-cyclodextrin has been determined using a CNS-based torsion angle molecular dynamics protocol involving direct refinement against dipolar couplings and carbonyl chemical shift changes that occur upon alignment. The shift changes have been included as structural restraints using a new module, CANI, that has been incorporated into CNS. Force constants and timesteps have been determined that are particularly effective in structure refinement applications involving high molecular weight proteins with small to moderate numbers of NOE restraints. Solution structures of the N- and C-domains of MBP calculated with this new protocol are within approximately 2 A of the X-ray conformation.
Choy
W Y
WY
Protein Engineering Network Center of Excellence and Department of Medical Genetics and Microbiology, University of Toronto, Ontario, Canada.
Tollinger
M
M
Mueller
G A
GA
Kay
L E
LE
D002352:Carrier Proteins / Q000737:chemistry* / Q000378:metabolism; D018360:Crystallography, X-Ray; D003505:Cyclodextrins / Q000737:chemistry / Q000378:metabolism; D006860:Hydrogen Bonding; D058619:Maltose-Binding Proteins; D008958:Models, Molecular; D008970:Molecular Weight; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D013696:Temperature; D013816:Thermodynamics; D047392:beta-Cyclodextrins
D002352:Carrier Proteins; D003505:Cyclodextrins; D058619:Maltose-Binding Proteins; D047392:beta-Cyclodextrins; C031215:betadex