Normal mode refinement: crystallographic refinement of protein dynamic structure. II. Application to human lysozyme.

The dynamic structure of a protein, human lysozyme, is determined by the normal mode refinement of X-ray crystal structure. This method uses the normal modes of both internal and external motions to distinguish the real internal dynamics from the external terms such as lattice disorder, and gives an anisotropic and concerted picture of atomic fluctuations. The refinement is carried out with diffraction data of 5.0 to 1.8 A resolution, which are collected on an imaging plate. The results of the refinement show: (1) Debye-Waller factor consists of two parts, highly anisotropic internal fluctuations and almost isotropic external terms. The former is smaller than the latter by a factor of 0.72 in the scale of B-factor. Therefore, the internal dynamics cannot be recognized directly from the apparent electron density distribution. (2) The internal fluctuations show basically similar features as those predicted by the normal mode analysis, with almost the same amplitude and a similar level of anisotropy. (3) Correlations of fluctuations are detected between two lobes forming the active site cleft, which move simultaneously in opposite directions. This corresponds to the hinge-bending motion of lysozyme.

[1]  H. Scheraga,et al.  Energy parameters in polypeptides. 9. Updating of geometrical parameters, nonbonded interactions, and hydrogen bond interactions for the naturally occurring amino acids , 1983 .

[2]  C. K. Johnson,et al.  OR TEP-II: a FORTRAN Thermal-Ellipsoid Plot Program for crystal structure illustrations , 1976 .

[3]  K. N. Trueblood,et al.  On the rigid-body motion of molecules in crystals , 1968 .

[4]  N. Yasuoka,et al.  Evaluation of x-ray diffraction data from protein crystals by use of an imaging plate. , 1991, Acta crystallographica. Section B, Structural science.

[5]  R. Huber,et al.  A group refinement procedure in protein crystallography using Fourier transforms , 1985 .

[6]  Hiroshi Wako,et al.  Algorithm for rapid calculation of Hessian of conformational energy function of proteins by supercomputer , 1987 .

[7]  A. R. Srinivasan,et al.  Quasi‐harmonic method for studying very low frequency modes in proteins , 1984, Biopolymers.

[8]  R Diamond,et al.  On the use of normal modes in thermal parameter refinement: theory and application to the bovine pancreatic trypsin inhibitor. , 1990, Acta crystallographica. Section A, Foundations of crystallography.

[9]  B. Matthews,et al.  A mutant T4 lysozyme displays five different crystal conformations , 1990, Nature.

[10]  M. Karplus,et al.  Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor. , 1983, Proceedings of the National Academy of Sciences of the United States of America.

[11]  Jones Ta,et al.  Diffraction methods for biological macromolecules. Interactive computer graphics: FRODO. , 1985, Methods in enzymology.

[12]  N Go,et al.  Normal mode analysis of human lysozyme: Study of the relative motion of the two domains and characterization of the harmonic motion , 1991, Proteins.

[13]  N Go,et al.  Refinement of protein dynamic structure: normal mode refinement. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[14]  W. Hendrickson,et al.  Description of Overall Anisotropy in Diffraction from Macromolecular Crystals , 1987 .

[15]  M. Karplus,et al.  The hinge-bending mode in lysozyme , 1976, Nature.

[16]  Thermal motion in protein crystals estimated using laser‐generated ultrasound and Young's modulus measurements , 1990 .

[17]  Yoshiyuki Amemiya,et al.  A new type of X-ray area detector utilizing laser stimulated luminescence , 1986 .

[18]  N Go,et al.  Calculation of protein conformations by proton-proton distance constraints. A new efficient algorithm. , 1985, Journal of molecular biology.

[19]  P J Artymiuk,et al.  Refinement of human lysozyme at 1.5 A resolution analysis of non-bonded and hydrogen-bond interactions. , 1981, Journal of molecular biology.

[20]  Peter A. Kollman,et al.  AMBER: Assisted model building with energy refinement. A general program for modeling molecules and their interactions , 1981 .

[21]  Wayne A. Hendrickson,et al.  A restrained-parameter thermal-factor refinement procedure , 1980 .

[22]  Y. Satow,et al.  Design and performance of an imaging plate system for X-ray diffraction study , 1988 .

[23]  Haruki Nakamura,et al.  Presto(protein Engineering Simulator): A Vectorized Molecular Mechanics Program for Biopolymers , 1992, Comput. Chem..

[24]  Hans Frauenfelder,et al.  Temperature-dependent X-ray diffraction as a probe of protein structural dynamics , 1979, Nature.

[25]  N Go,et al.  Normal mode refinement: crystallographic refinement of protein dynamic structure. I. Theory and test by simulated diffraction data. , 1992, Journal of molecular biology.

[26]  W. Hendrickson.  Stereochemically restrained refinement of macromolecular structures. , 1985, Methods in enzymology.

[27]  N Go,et al.  Deoxymyoglobin studied by the conformational normal mode analysis. I. Dynamics of globin and the heme-globin interaction. , 1990, Journal of molecular biology.

[28]  I. Tanaka,et al.  An automatic diffraction data collection system with an imaging plate , 1990 .

[29]  M Karplus,et al.  Effect of anisotropy and anharmonicity on protein crystallographic refinement. An evaluation by molecular dynamics. , 1986, Journal of molecular biology.

[30]  N Go,et al.  Projection of monte carlo and molecular dynamics trajectories onto the normal mode axes: Human lysozyme , 1991, Proteins.