Effect of cofactor binding and loop conformation on side chain methyl dynamics in dihydrofolate reductase.
Dihydrofolate reductase (DHFR) has several flexible active site loops that facilitate ligand binding and catalysis. Previous studies of backbone dynamics in several complexes of DHFR indicate that the time scale and amplitude of motion depend on the conformation of the active site loops. In this study, information on dynamics is extended to methyl-containing side chains. To understand the role of side chain dynamics in ligand binding and loop conformation, methyl deuterium relaxation rates of Escherichia coli DHFR in binary folate and ternary folate:NADP+ complexes have been measured, together with chi(1) rotamer populations for threonine, isoleucine, and valine residues, determined from measurements of 3J(CgammaCO) and 3J(CgammaN) coupling constants. The results indicate that, in addition to backbone motional restriction in the adenosine-binding site, side chain flexibility in the active site and the surrounding active site loops is diminished upon binding NADP+. Resonances for several methyls in the active site and the surrounding active site loops were severely broadened in the folate:NADP+ ternary complex, suggesting the presence of motion on the chemical shift time scale. The side chains of Ile14 and Ile94, which pack against the nicotinamide and pterin rings of the cofactor and substrate, respectively, exhibit rotamer disorder in the ternary folate:NADP+ complex. Conformational fluctuations of these side chains may play a role in transition state stabilization; the observed line broadening for Ile14 suggests motions on a microsecond/millisecond time scale.
Schnell
Jason R
JR
Department of Molecular Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.
Dyson
H Jane
HJ
Wright
Peter E
PE
D001665:Binding Sites; D003903:Deuterium / Q000737:chemistry; D029968:Escherichia coli Proteins / Q000737:chemistry*; D005492:Folic Acid / Q000737:chemistry; D007532:Isoleucine / Q000737:chemistry; D009249:NADP / Q000737:chemistry; D036103:Nanotechnology; D019906:Nuclear Magnetic Resonance, Biomolecular; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D013053:Spectrophotometry; D013379:Substrate Specificity; D013762:Tetrahydrofolate Dehydrogenase / Q000737:chemistry*; D013816:Thermodynamics; D013912:Threonine / Q000737:chemistry; D014633:Valine / Q000737:chemistry
D029968:Escherichia coli Proteins; D007532:Isoleucine; D013912:Threonine; D009249:NADP; D005492:Folic Acid; D003903:Deuterium; D013762:Tetrahydrofolate Dehydrogenase; D014633:Valine