Models of protein crystal growth.

The growth of large and well ordered protein crystals remains the major obstacle in protein structure determination by means of X-ray crystallography. One of the reasons is that the physico-chemical aspect of protein crystallization process is not understood. This article reviews efforts towards formulation of models that could become theoretical frameworks for the interpretation of voluminous experimental data collected on protein crystal growth. Special attention is devoted to microscopic models that recognize the role of the shape of protein molecules in crystal formation.

[1]  A. Kierzek,et al.  Microscopic model of protein crystal growth. , 2000, Biophysical chemistry.

[2]  L. Degrève,et al.  Structure of concentrated aqueous NaCl solution: A Monte Carlo study , 1999 .

[3]  W. Hol,et al.  Atomic structure of the cubic core of the pyruvate dehydrogenase multienzyme complex. , 1993, Science.

[4]  G. Torrie,et al.  Monte Carlo free energy estimates using non-Boltzmann sampling: Application to the sub-critical Lennard-Jones fluid , 1974 .

[5]  A. Tamura,et al.  The entropy cost of protein association. , 1997, Journal of molecular biology.

[6]  N. I. Wakayama,et al.  Quantitative study of crystallization kinetics of hen egg-white lysozyme using magnetic orientation , 1998 .

[7]  G. Gilmer,et al.  Computer Models of Crystal Growth , 1980, Science.

[8]  L M Amzel,et al.  Loss of translational entropy in binding, folding, and catalysis , 1997, Proteins.

[9]  Dusanka Janezic,et al.  Harmonic analysis of large systems. I. Methodology , 1995, J. Comput. Chem..

[10]  J Deisenhofer,et al.  Structure of the complex formed by bovine trypsin and bovine pancreatic trypsin inhibitor. II. Crystallographic refinement at 1.9 A resolution. , 1974, Journal of molecular biology.

[11]  W. Saenger,et al.  Molecular interactions in crystallizing lysozyme solutions studied by photon correlation spectroscopy , 1994 .

[12]  L. R. Scott,et al.  Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian dynamics program , 1995 .

[13]  R C Wade,et al.  Simulation of the diffusional association of barnase and barstar. , 1997, Biophysical journal.

[14]  G. H. Gilmer,et al.  Simulation of Crystal Growth with Surface Diffusion , 1972 .

[15]  D. Gallagher,et al.  Role of competitive interactions in growth rate trends of subtilisin s88 crystals , 2000 .

[16]  J. Banavar,et al.  Computer Simulation of Liquids , 1988 .

[17]  L. Degrève,et al.  LARGE IONIC CLUSTERS IN CONCENTRATED AQUEOUS NACL SOLUTION , 1999 .

[18]  A. Cooper,et al.  Thermodynamic analysis of biomolecular interactions. , 1999, Current opinion in chemical biology.

[19]  J. Frank,et al.  Protein crystallization screening through scattering techniques , 1995 .

[20]  G. Feher,et al.  Nucleation and growth of protein crystals: general principles and assays. , 1985, Methods in enzymology.

[21]  A Nadarajah,et al.  Growth of (101) faces of tetragonal lysozyme crystals: measured growth-rate trends. , 1999, Acta crystallographica. Section D, Biological crystallography.

[22]  G. Rose,et al.  Side-chain entropy opposes alpha-helix formation but rationalizes experimentally determined helix-forming propensities. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[23]  A. Lenhoff,et al.  Molecular origins of osmotic second virial coefficients of proteins. , 1998, Biophysical journal.

[24]  W. Kauzmann.  Some factors in the interpretation of protein denaturation. , 1959, Advances in protein chemistry.

[25]  H. Erickson,et al.  Kinetics of protein-protein association explained by Brownian dynamics computer simulation. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[26]  Paul Smith,et al.  Computer Simulation of Cosolvent Effects on Hydrophobic Hydration , 1999 .

[27]  Rosenberger,et al.  Morphological evolution of growing crystals: A Monte Carlo simulation. , 1988, Physical review. A, General physics.

[28]  L. Degrève,et al.  Detailed microscopic study of 1 M aqueous NaCl solution by computer simulations , 2000 .

[29]  J. Janin.  The kinetics of protein‐protein recognition , 1997, Proteins.

[30]  A. D. McLachlan,et al.  Solvation energy in protein folding and binding , 1986, Nature.

[31]  D. Frenkel,et al.  Enhancement of protein crystal nucleation by critical density fluctuations. , 1997, Science.

[32]  M. Smoluchowski.  Versuch einer mathematischen Theorie der Koagulationskinetik kolloider Lösungen , 1918 .

[33]  A. Kierzek,et al.  Cluster Formation in Aqueous Electrolyte Solutions Observed by Dynamic Light Scattering , 2000 .

[34]  M Karplus,et al.  Comment on: 'The entropy cost of protein association'. , 1999, Protein engineering.

[35]  Y. Minezaki,et al.  Aggregation in supersaturated lysozyme solution studied by time-resolved small angle neutron scattering , 1995 .

[36]  T. Richmond,et al.  Crystal structure of the nucleosome core particle at 2.8 Å resolution , 1997, Nature.

[37]  J Novotny,et al.  Empirical free energy calculations: a blind test and further improvements to the method. , 1997, Journal of molecular biology.

[38]  Daan Frenkel,et al.  Determination of phase diagrams for the hard-core attractive Yukawa system , 1994 .

[39]  R Giegé,et al.  Crystallogenesis of biological macromolecules: facts and perspectives. , 1994, Acta crystallographica. Section D, Biological crystallography.

[40]  G. Feher,et al.  Studies of crystal growth mechanisms of proteins by electron microscopy. , 1990, Journal of molecular biology.

[41]  A. Chernov.  Protein versus conventional crystals: creation of defects , 1997 .

[42]  M. Pusey,et al.  Modeling the growth rates of tetragonal lysozyme crystals , 1995 .

[43]  W. Saenger,et al.  Precrystallization structures in supersaturated lysozyme solutions studied by dynamic light scattering and scanning force microscopy , 1997 .

[44]  A. Miele,et al.  Free energy of burying hydrophobic residues in the interface between protein subunits. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[45]  A George,et al.  Predicting protein crystallization from a dilute solution property. , 1994, Acta crystallographica. Section D, Biological crystallography.

[46]  J. Janin,et al.  Quantifying biological specificity: the statistical mechanics of molecular recognition. , 1996, Proteins.

[47]  Arnaud Ducruix,et al.  Crystallization of nucleic acids and proteins , 1992 .

[48]  M J Sternberg,et al.  Protein side-chain conformational entropy derived from fusion data--comparison with other empirical scales. , 1994, Protein engineering.

[49]  C. Carter.  [5] Response surface methods for optimizing and improving reproducibility of crystal growth. , 1997, Methods in enzymology.

[50]  Kim A. Sharp,et al.  Electrostatic interactions in macromolecules , 1994 .

[51]  A. McPherson,et al.  Protein and virus crystal growth on international microgravity laboratory-2. , 1995, Biophysical journal.

[52]  K. B. Ward,et al.  Observation of growth steps, spiral dislocations and molecular packing on the surface of lysozyme crystals with the atomic force microscope. , 1994, Acta crystallographica. Section D, Biological crystallography.

[53]  O. Velev,et al.  Why is the osmotic second virial coefficient related to protein crystallization , 1999 .

[54]  MICROCALORIMETRIC AND SMALL-ANGLE LIGHT SCATTERING STUDIES ON NUCLEATING LYSOZYME SOLUTIONS , 1997 .

[55]  M S Chapman,et al.  Crystal structure of human rhinovirus serotype 1A (HRV1A). , 1989, Journal of molecular biology.

[56]  I. Lifshitz,et al.  The kinetics of precipitation from supersaturated solid solutions , 1961 .

[57]  W. Saenger,et al.  Dynamics and Microstructure Formation during Nucleation of Lysozyme Solutions , 1998 .

[58]  K. Sharp,et al.  Entropy in protein folding and in protein-protein interactions. , 1997, Current opinion in structural biology.

[59]  T. Richmond,et al.  Solvent accessible surface area and excluded volume in proteins. Analytical equations for overlapping spheres and implications for the hydrophobic effect. , 1984, Journal of molecular biology.

[60]  C. Chothia,et al.  Principles of protein–protein recognition , 1975, Nature.

[61]  A. McPherson,et al.  Light-scattering investigations of nucleation processes and kinetics of crystallization in macromolecular systems. , 1994, Acta crystallographica. Section D, Biological crystallography.

[62]  A. Fersht,et al.  Rapid, electrostatically assisted association of proteins , 1996, Nature Structural Biology.

[63]  Piotr Zielenkiewicz,et al.  Electrostatic Potential and Free Energy of Proteins: A Comparison of the Poisson−Boltzmann and the Bogolyubov−Born−Green−Yvon Equations , 1997 .

[64]  T. Przybycien,et al.  Simulations of reversible protein aggregate and crystal structure. , 1996, Biophysical journal.

[65]  Ivan Rayment,et al.  [12] Reductive alkylation of lysine residues to alter crystallization properties of proteins. , 1997, Methods in enzymology.

[66]  A. E. Nielsen.  Kinetics of precipitation , 1964 .

[67]  O. Velev,et al.  Protein interactions in solution characterized by light and neutron scattering: comparison of lysozyme and chymotrypsinogen. , 1998, Biophysical journal.

[68]  D. Soumpasis,et al.  Potential of mean force treatment of salt-mediated protein crystallization. , 1997, Biophysical journal.

[69]  Rosenberger,et al.  Growth morphologies of crystal surfaces. , 1991, Physical review. A, Atomic, molecular, and optical physics.

[70]  K. P. Murphy,et al.  Structural energetics of peptide recognition: Angiotensin II/antibody binding , 1993, Proteins.

[71]  G. Feher,et al.  Simulation of lysozyme crystal growth by the Monte Carlo method , 1991 .

[72]  A. McPherson.  Crystallization of Biological Macromolecules , 1999 .

[73]  A. McPherson,et al.  Mechanisms of growth for protein and virus crystals , 1995, Nature Structural Biology.

[74]  M. L. Connolly.  Solvent-accessible surfaces of proteins and nucleic acids. , 1983, Science.

[75]  M. Lewis,et al.  Calculation of the free energy of association for protein complexes , 1992, Protein science : a publication of the Protein Society.

[76]  M. Pusey,et al.  Growth mechanism of the (110) face of tetragonal lysozyme crystals. , 1997, Acta crystallographica. Section D, Biological crystallography.

[77]  A. Minton,et al.  Macromolecular crowding: biochemical, biophysical, and physiological consequences. , 1993, Annual review of biophysics and biomolecular structure.

[78]  M. Ataka,et al.  Analysis of the crystallization kinetics of lysozyme using a model with polynuclear growth mechanism. , 1994, Biophysical journal.

[79]  A. Kierzek,et al.  Lattice simulations of protein crystal formation. , 1999, Biophysical chemistry.

[80]  W. Saenger,et al.  TIME-RESOLVED SMALL-ANGLE STATIC LIGHT SCATTERING ON LYSOZYME DURING NUCLEATION AND GROWTH , 1998 .

[81]  Arnaud Ducruix,et al.  Crystallization of Nucleic Acids and Proteins: A practical Approach , 1998 .

[82]  A. Kierzek,et al.  Simulations of nucleation and early growth stages of protein crystals. , 1997, Biophysical journal.