Amplitudes and directions of internal protein motions from a JAM analysis of15N relaxation data

Abstract

A method has been developed for characterizing dynamic structures of proteins in solution by using nuclear magnetic resonance (NMR) restraints and 15N relaxation data. This method is based on the concept of the jumping-among-minima (JAM) model. In this model we assume that protein dynamics can be described on the basis of conformational substates, and involves intra- and inter-substate motion. A set of substates is created by picking energy-minimized conformations from the conformational space consistent with the geometric NMR restraints. Intra-substate motions, which occur on the timescale of approximately 10 ps, are simulated with molecular dynamics (MD) calculations with force-field energy terms. Statistical weights of the conformational substates are determined to reproduce the NMR relaxation parameters. The refinement procedure consists of four stages: (i) determination of the ensemble of structures that satisfy NMR restraints, (ii) determination of intra-substate fluctuation, (iii) determination of statistical weights of conformational substates to reproduce model-free relaxation parameters, and (iv) analysis of the resulting dynamic structure to determine amplitudes and directions of internal protein motions. This method was employed to investigate structure and dynamics of the adhesion domain of human CD2 (hCD2) in solution. Two major collective modes, whose contributions to atomic mean-square fluctuations are 77.1% in total, are identified by the refinement. The first mode is interpreted as a rigid-body motion of a protein segment consisting of a part of the B--C loop, a part of the F strand, and the F--G loop. Another type of smaller-amplitude mode is indicated for the C'--C'' loop. The motions affect primarily the curvature of the slightly concave counterreceptor-binding site and represent transitions between a concave (closed) and flat (open) binding face. By comparing the ensemble of structures in solution to the complex structure with counterreceptor CD58, we found that these two types of motions resemble the change upon counterreceptor binding.

An Improved Picture of Methyl Dynamics in Proteins from Slowly Relaxing Local Structure Analysis of 2H Spin Relaxation

“…In the case of zero potential, , the solution of the diffusion operator associated to the time evolution operator features three distinct eigenvalues for the probe motion: (7) where R L ∥ = 1/(6τ ∥ ) and R L ⊥ = 1/(6τ ⊥ ) = 1/(6τ 0 ). Only the diagonal terms, j K (ω) (the functions j KK' denote the real part of j 2 M,KK' -see ref.…”

Methyl Dynamics of a Ca2+−Calmodulin−Peptide Complex from NMR/SRLS

“…15 N spin relaxation of the N–H bond is typically used to study backbone dynamics,1–5,7–10 and 2 H spin relaxation of the 13 CDH 2 methyl group,5,6,11–13 to study side-chain dynamics. We developed in recent years the slowly relaxing local structure (SRLS) approach14–16 for analyzing NMR spin relaxation in proteins17–19.…”

“…NMR spin relaxation is a powerful method for elucidating protein dynamics. − 15 N spin relaxation of the N−H bond is typically used to study backbone dynamics, − ,− and 2 H spin relaxation of the 13 CDH 2 methyl group ,,− to study side-chain dynamics. We developed in recent years the slowly relaxing local structure (SRLS) approach − for analyzing NMR spin relaxation in proteins. − So far, SRLS has been implemented in the overdamped diffusion limit within the scope of a two-body coupled-rotator formalism.…”

Backbone Dynamics of Deoxy and Carbonmonoxy Hemoglobin by NMR/SRLS

“…The 15 N nucleus of the amide 15 N– 1 H bond is typically used to study backbone dynamics,1–5,7–10 and the 2 H nucleus of the 13 CDH 2 methyl group,5,6,11–13 to study side-chain dynamics. We developed in recent years the slowly relaxing local structure (SRLS) approach14–16 for analyzing NMR spin relaxation in proteins17–19.…”