Simulations of nucleation and early growth stages of protein crystals
Identifieur interne : 003D23 ( Main/Exploration ); précédent : 003D22; suivant : 003D24Simulations of nucleation and early growth stages of protein crystals
Auteurs : A. M. Kierzek [Pologne] ; W. M. Wolf [Pologne] ; P. Zielenkiewicz [Pologne]Source :
- Biophysical Journal [ 0006-3495 ] ; 1997.
English descriptors
- Teeft :
- Accessible surface areas, Acta crystallogr, Additional nucleation, Aggregation, Atomic force microscopy observations, Atomic solvation parameters, Average number, Biophysical journal volume, Ccp4 suite, Central molecule, Classical nucleation theory, Cluster aggregation, Complex formation, Computer simulations, Constant speed, Crystal environment, Crystal face, Crystal growth, Crystal lattice, Crystal structure, Crystallization, Crystallization batch, Crystallization conditions, Crystallization process, Dimer, Dislocation, Early growth stages, Early stages, Electron microscopy, Entropic, Entropic cost, Entropic penalties, Entropic penalty, Entropic penalty value, Entropy loss, Experimental data, Experimental techniques, Flat surface, Flat surfaces, Form interactions, Free energies, Free energy, Georgalis, Good site, Good sites, Hydrodynamic radius, Interaction energies, Interaction energy, Interface, Intermolecular distance, Iteration, Janin, Larger complexes, Lattice, Lattice coordinates, Letter codes, Lower layer, Lysozyme, Lysozyme crystallization, Lysozyme solutions, Molecule, Monomer, Negative energies, Node, Nucleation, Orientational, Orientational probabilities, Orientational probability, Orientational states, Particular molecule, Piotr zielenkiewicz, Program iterations, Protein aggregation, Protein complexes, Protein crystallization, Protein crystallization kierzek, Protein data bank, Protein molecule, Protein molecules, Protein solutions, Qualitative behavior, Same orientational state, Schematic diagram, Several simulations, Simulation, Simulation steps, Single molecules, Solid phase, Specific interactions, Stable complexes, Stable nuclei, Stable tetramer, Step movement, Surface area, Surface areas, Symmetry operator, Symmetry operators, Tetragonal, Tetragonal lysozyme crystal, Tetramer, Time scale, Time scales, Time step, True number, Unit cell, Unit cells, Volume fraction.
Abstract
Analysis of known protein crystal structures reveals that interaction energies between monomer pairs alone are not sufficient to overcome entropy loss related to fixing monomers in the crystal lattice. Interactions with several neighbors in the crystal are required for stabilization of monomers in the lattice. A microscopic model of nucleation and early growth stages of protein crystals, based on the above observations, is presented. Anisotropy of protein molecules is taken into account by assigning free energies of association (proportional to the buried surface area) to individual monomer-monomer contacts in the lattice. Lattice simulations of the tetragonal lysozyme crystal based on the model correctly reproduce structural features of the movement of dislocation on the (110) crystal face. The dislocation shifts with the speed equal to the one determined experimentally if the geometric probability of correct orientation is set to 10(-5), in agreement with previously published estimates. At this value of orientational probability, the first nuclei, the critical size of which for lysozyme is four monomers, appear in 1 ml of supersaturated solution on a time scale of microseconds. Formation of the ordered phase proceeds through the growth of nuclei (rather then their association) and requires nucleations on the surface at certain stages.
Url:
DOI: 10.1016/S0006-3495(97)78094-9
Affiliations:
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<profileDesc><textClass><keywords scheme="Teeft" xml:lang="en"><term>Accessible surface areas</term>
<term>Acta crystallogr</term>
<term>Additional nucleation</term>
<term>Aggregation</term>
<term>Atomic force microscopy observations</term>
<term>Atomic solvation parameters</term>
<term>Average number</term>
<term>Biophysical journal volume</term>
<term>Ccp4 suite</term>
<term>Central molecule</term>
<term>Classical nucleation theory</term>
<term>Cluster aggregation</term>
<term>Complex formation</term>
<term>Computer simulations</term>
<term>Constant speed</term>
<term>Crystal environment</term>
<term>Crystal face</term>
<term>Crystal growth</term>
<term>Crystal lattice</term>
<term>Crystal structure</term>
<term>Crystallization</term>
<term>Crystallization batch</term>
<term>Crystallization conditions</term>
<term>Crystallization process</term>
<term>Dimer</term>
<term>Dislocation</term>
<term>Early growth stages</term>
<term>Early stages</term>
<term>Electron microscopy</term>
<term>Entropic</term>
<term>Entropic cost</term>
<term>Entropic penalties</term>
<term>Entropic penalty</term>
<term>Entropic penalty value</term>
<term>Entropy loss</term>
<term>Experimental data</term>
<term>Experimental techniques</term>
<term>Flat surface</term>
<term>Flat surfaces</term>
<term>Form interactions</term>
<term>Free energies</term>
<term>Free energy</term>
<term>Georgalis</term>
<term>Good site</term>
<term>Good sites</term>
<term>Hydrodynamic radius</term>
<term>Interaction energies</term>
<term>Interaction energy</term>
<term>Interface</term>
<term>Intermolecular distance</term>
<term>Iteration</term>
<term>Janin</term>
<term>Larger complexes</term>
<term>Lattice</term>
<term>Lattice coordinates</term>
<term>Letter codes</term>
<term>Lower layer</term>
<term>Lysozyme</term>
<term>Lysozyme crystallization</term>
<term>Lysozyme solutions</term>
<term>Molecule</term>
<term>Monomer</term>
<term>Negative energies</term>
<term>Node</term>
<term>Nucleation</term>
<term>Orientational</term>
<term>Orientational probabilities</term>
<term>Orientational probability</term>
<term>Orientational states</term>
<term>Particular molecule</term>
<term>Piotr zielenkiewicz</term>
<term>Program iterations</term>
<term>Protein aggregation</term>
<term>Protein complexes</term>
<term>Protein crystallization</term>
<term>Protein crystallization kierzek</term>
<term>Protein data bank</term>
<term>Protein molecule</term>
<term>Protein molecules</term>
<term>Protein solutions</term>
<term>Qualitative behavior</term>
<term>Same orientational state</term>
<term>Schematic diagram</term>
<term>Several simulations</term>
<term>Simulation</term>
<term>Simulation steps</term>
<term>Single molecules</term>
<term>Solid phase</term>
<term>Specific interactions</term>
<term>Stable complexes</term>
<term>Stable nuclei</term>
<term>Stable tetramer</term>
<term>Step movement</term>
<term>Surface area</term>
<term>Surface areas</term>
<term>Symmetry operator</term>
<term>Symmetry operators</term>
<term>Tetragonal</term>
<term>Tetragonal lysozyme crystal</term>
<term>Tetramer</term>
<term>Time scale</term>
<term>Time scales</term>
<term>Time step</term>
<term>True number</term>
<term>Unit cell</term>
<term>Unit cells</term>
<term>Volume fraction</term>
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<front><div type="abstract">Analysis of known protein crystal structures reveals that interaction energies between monomer pairs alone are not sufficient to overcome entropy loss related to fixing monomers in the crystal lattice. Interactions with several neighbors in the crystal are required for stabilization of monomers in the lattice. A microscopic model of nucleation and early growth stages of protein crystals, based on the above observations, is presented. Anisotropy of protein molecules is taken into account by assigning free energies of association (proportional to the buried surface area) to individual monomer-monomer contacts in the lattice. Lattice simulations of the tetragonal lysozyme crystal based on the model correctly reproduce structural features of the movement of dislocation on the (110) crystal face. The dislocation shifts with the speed equal to the one determined experimentally if the geometric probability of correct orientation is set to 10(-5), in agreement with previously published estimates. At this value of orientational probability, the first nuclei, the critical size of which for lysozyme is four monomers, appear in 1 ml of supersaturated solution on a time scale of microseconds. Formation of the ordered phase proceeds through the growth of nuclei (rather then their association) and requires nucleations on the surface at certain stages.</div>
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