Structural determinants of protein dynamics: analysis of 15N NMR relaxation measurements for main-chain and side-chain nuclei of hen egg white lysozyme.
15N-labeled hen lysozyme has been studied by 2D and 3D NMR in order to characterize its dynamic behavior. The resonances of all main-chain amide nitrogen atoms were assigned, as were resonances of nitrogen atoms in 28 side chains. Relaxation measurements for the main-chain and arginine and tryptophan side-chain 15N nuclei used standard methods, and those for the 15N nuclei of asparagine and glutamine side chains used pulse sequences designed to remove unwanted relaxation pathways in the NH2 groups. The calculated order parameters (S2) show that the majority of main-chain amides undergo only small amplitude librational motions on a fast time scale (S2 > or = 0.8). Increased main-chain motion (0.5 < S2 < 0.8) is observed for a total of 19 residues located at the C-terminus, in loop and turn regions, and in the first strand of the main beta-sheet. Order parameters derived for the side chains range from 0.05 to 0.9; five of the six tryptophan residues have high order parameters (S2 > or = 0.8), consistent with their location in the closely packed core of the protein, whereas the order parameters between 0.05 and 0.3 for arginine residues confirm increased side-chain mobility at the protein surface. Order parameters for the side chains of asparagine and glutamine residues range from 0.2 to 0.8; high values are found for side chains that have low solvent accessible surfaces and well-defined chi 1 values, as measured by 3J alpha beta coupling constants. Many of the main-chain and side-chain groups with low order parameters have higher than average temperature factors in X-ray crystal structures and increased positional uncertainty in NMR solution structures. They also tend to lack persistent hydrogen bond interactions and protection against amide hydrogen exchange. The most significant correlations are found between residues with low order parameters and high surface accessibility in both crystal and solution structures. The results suggest that a lack of van der Waals contacts is a major determinant of side-chain and main-chain mobility in proteins.
Buck
M
M
Oxford Centre for Molecular Sciences, University of Oxford, England.
Boyd
J
J
Redfield
C
C
MacKenzie
D A
DA
Jeenes
D J
DJ
Archer
D B
DB
Dobson
C M
CM
D000595:Amino Acid Sequence; D000818:Animals; D001216:Asparagine; D002645:Chickens; D018360:Crystallography, X-Ray; D005260:Female; D005973:Glutamine; D009682:Magnetic Resonance Spectroscopy / Q000379:methods; D008958:Models, Molecular; D009113:Muramidase / Q000096:biosynthesis / Q000737:chemistry*; D009587:Nitrogen Isotopes; D017433:Protein Structure, Secondary; D011993:Recombinant Fusion Proteins / Q000096:biosynthesis; D011994:Recombinant Proteins / Q000737:chemistry; D013816:Thermodynamics
D009587:Nitrogen Isotopes; D011993:Recombinant Fusion Proteins; D011994:Recombinant Proteins; D005973:Glutamine; D001216:Asparagine; D009113:Muramidase