Comparison of the solution and X-ray structures of barley serine proteinase inhibitor 2

Clore, G. Marius; Gronenborn, Angela M.; James, Michael N.G.; Kjær, Mogens; McPhalen, Catherine A.; Poulsen, F M

doi:10.1093/protein/1.4.313

Cited by 70 publications

(26 citation statements)

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“…lower coordinate standard errors). The latter is important as calculations with model data on crambin (this paper and [8,33]), as well as with experimental data on potato carboxypeptidase inhibitor [22] and barley serine proteinase inhibitor 2 [34], indicate that the atomic RMS difference between the average structure and the X-ray structure becomes smaller as the number of calculated structures as well as their quality is increased.…”

Section: Discussionmentioning

confidence: 98%

Determination of three‐dimensional structures of proteins from interproton distance data by hybrid distance geometry‐dynamical simulated annealing calculations

1988

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A new hybrid distance space-real space method for determining three-dimensional structures of proteins on the basis of interproton distance restraints is presented. It involves the following steps: (i) the approximate polypeptide fold is obtained by generating a set of substructures comprising only a small subset of atoms by projection from multi-dimensional distance space into three-dimensional Cartesian coordinate space using a procedure known as 'embedding'; (ii) all remaining atoms are then added by best fitting extended amino acids one residue at a time to the substructures; (iii) the resulting structures are used as the starting point for real space dynamical simulated annealing calculations. The latter involve heating the system to a high temperature followed by slow cooling in order to overcome potential barriers along the pathway towards the global minimum region. This is carried out by solving Newton's equations of motion. Unlike conventional restrained molecular dynamics, however, the non-bonded interactions are represented by a simple van der Waals repulsion term. The method is illustrated by calculations on crambin (46 residues) and the globular domain of histone H5 (79 residues). It is shown that the hybrid method is more efficient computationally and samples a larger region of conformational space consistent with the experimental data than full metric matrix distance geometry calculations alone, particularly for large systems.

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Section: Discussionmentioning

confidence: 98%

Determination of three‐dimensional structures of proteins from interproton distance data by hybrid distance geometry‐dynamical simulated annealing calculations

1988

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“…The straight line represents a linear fit to the data with a slope of 0.70, an intercept of 0.45 Å, and a correlation coefficient of 0.9. The structures are as follows: p53(mon), p53(dim), and p53(tet) are the monomer, dimer, and tetramer, respectively, of the p53 oligomerization domain (51); IL-8, interleukin-8 monomer (52); Hir (new), highly refined structure of hirudin (53) (63). The values given exclude conformationally disordered regions as described in the papers cited.…”

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confidence: 99%

New methods of structure refinement for macromolecular structure determination by NMR

Clore

Gronenborn²

1998

Proc. Natl. Acad. Sci. U.S.A.

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231

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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...

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“…The structure of the first 19 residues is not resolved by either x-ray crystallography (10) or two-dimensional NMR studies (11)(12)(13)(14)(15). The structure of a pseudo-wild-type form of C12 in which these residues have been omitted has recently been solved to 1.7-A resolution ( Fig.…”

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Characterization of the transition state of protein unfolding by use of molecular dynamics: chymotrypsin inhibitor 2.

Daggett

1994

Proc. Natl. Acad. Sci. U.S.A.

238

212

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Temperature-induced unfolding of chymotrypsin inhibitor 2 in water was investigated by molecular dynamics smulations. (6,9). These studies suggest that the edges of the core are significantly weakened in the transition state, while the center of the core remains partially intact. One particular residue, Val-38, is special in that it is more buried in the transition state than it is in the native state.

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Comparison of the solution and X-ray structures of barley serine proteinase inhibitor 2

Cited by 70 publications

References 1 publication

Determination of three‐dimensional structures of proteins from interproton distance data by hybrid distance geometry‐dynamical simulated annealing calculations

Determination of three‐dimensional structures of proteins from interproton distance data by hybrid distance geometry‐dynamical simulated annealing calculations

New methods of structure refinement for macromolecular structure determination by NMR

Characterization of the transition state of protein unfolding by use of molecular dynamics: chymotrypsin inhibitor 2.

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