New methods of structure refinement for macromolecular structure determination by NMR

Abstract

Recent advances in multidimensional NMR methodology have permitted solution structures of proteins in excess of 250 residues to be solved. In this paper, we discuss several methods of structure refinement that promise to increase the accuracy of macromolecular structures determined by NMR. These methods include the use of a conformational database potential and direct refinement against three-bond coupling constants, secondary 13 C shifts, 1 H shifts, T 1 ͞T 2 ratios, and residual dipolar couplings. The latter two measurements provide long range restraints that are not accessible by other solution NMR parameters.The two major techniques for determining the threedimensional structures of macromolecules at atomic resolution are x-ray crystallography in the solid state (single crystals) and NMR spectroscopy in solution. Unlike crystallography, NMR measurements are not hampered by the ability or inability of a protein to crystallize. The size of macromolecular structures that can be solved by NMR has been increased dramatically over the last few years (1). The development of a wide range of two-dimensional (2D) NMR experiments in the early 1980s culminated in the determination of the structures of a number of small proteins (2, 3). Under exceptional circumstances, 2D NMR techniques can be applied successfully to determine structures of proteins up to Ϸ100 residues (4, 5). Beyond Ϸ100 residues, however, 2D NMR methods fail, principally because of spectral complexity that cannot be resolved in two dimensions. In the late 1980s and early 1990s, a series of major advances took place in which the spectral resolution was increased by extending the dimensionality to three and four dimensions (1). In addition, by combining such multidimensional experiments with heteronuclear NMR, problems associated with large linewidths can be circumvented by making use of heteronuclear couplings that are large relative to the linewidths. The first successful application of these methods to a protein greater than Ϸ12 kDa was achieved in 1991 with the determination of the solution structure of interleukin 1␤, a protein of 18 kDa and 153 residues (6). Concomitant with spectroscopic advances, significant improvements have taken place in the accuracy with which macromolecular structures can be determined. Thus, it is now potentially feasible to determine the structures of proteins in the 15-to 35-kDa range at a resolution comparable to Ϸ2.5-Å resolution crystal structures (7). The upper limit of applicability is probably 60-70 kDa, and the largest single-chain proteins solved to date are Ϸ30 kDa, comprising Ϸ260 residues (8, 9). In this paper, we discuss a number of new refinement strategies aimed at both facilitating NMR structure determination and increasing the accuracy of the resulting structures. These include direct refinement against three-bond coupling constants (10) and 13 C and 1 H shifts (11-13), as well as the use of conformational database potentials (14, 15). More recently, methods have been developed to obtain structural...

A Physical Picture of Atomic Motions within the Dickerson DNA Dodecamer in Solution Derived from Joint Ensemble Refinement against NMR and Large-Angle X-ray Scattering Data

“…Average structures were calculated by restrained regularization of the ensemble average structures for each value of N e in the presence of experimental restraints (13,48,49,51). A comparison of the restrained regularized average structures for cases where N e ) 1 and N e ) 4 is shown in Figure 2.…”

“…Force constants for the various potential terms were either scaled geometrically during refinement or held constant, while the atomic radius used in the nonbonded interaction term was scaled down such that the initial energy surface is smoothed (9,(48)(49)(50). Additionally, the globic scattering correction c glob was computed at each temperature, before dynamics.…”

Probing the Dynamic Distribution of Bound States for Methylcytosine-binding Domains on DNA

“…Structure Calculations-The structure of the MBD3 MBD was calculated by simulated annealing as implemented in the Xplor-NIH software package (21) and based on NOE-derived distance constraints, torsion angle restraints, and residual dipolar couplings, as well as a torsion angle database potential of mean force (22) and a quartic van der Waals repulsion term for nonbonded contacts (23). Backbone torsional angle restraints were derived from chemical shifts using the TALOSϩ software (24), and hydrogen bond distance and angle restraints were introduced based on backbone torsional angles and characteristic NOE patterns.…”

Nuclear Magnetic Resonance-Based Modeling and Refinement of Protein Three-Dimensional Structures and Their Complexes

“…Although several software packages exist that allow prediction of chemical shifts, such as ShiftX [14], SHIFTS [15], SHIFTCALC [16], and PROSHIFT [17], both computational and accuracy limits have prevented their common use as restraints in structure calculations, although direct refinement against chemical shifts has been described [18]. Their deviations from random coil values provide, however, valuable information regarding secondary structure preferences; they can be used to restrict the local conformation of a residue to a given region of the Ramachandran plot, either through torsion angle restraints [19] or by special database potential functions [20].…”