The "Sticky Patch" Model of Crystallization and Modification of Proteins for Enhanced Crystallizability

Methods Mol Biol. 2017;1607:77-115. doi: 10.1007/978-1-4939-7000-1_4.

Abstract

Crystallization of macromolecules has long been perceived as a stochastic process, which cannot be predicted or controlled. This is consistent with another popular notion that the interactions of molecules within the crystal, i.e., crystal contacts, are essentially random and devoid of specific physicochemical features. In contrast, functionally relevant surfaces, such as oligomerization interfaces and specific protein-protein interaction sites, are under evolutionary pressures so their amino acid composition, structure, and topology are distinct. However, current theoretical and experimental studies are significantly changing our understanding of the nature of crystallization. The increasingly popular "sticky patch" model, derived from soft matter physics, describes crystallization as a process driven by interactions between select, specific surface patches, with properties thermodynamically favorable for cohesive interactions. Independent support for this model comes from various sources including structural studies and bioinformatics. Proteins that are recalcitrant to crystallization can be modified for enhanced crystallizability through chemical or mutational modification of their surface to effectively engineer "sticky patches" which would drive crystallization. Here, we discuss the current state of knowledge of the relationship between the microscopic properties of the target macromolecule and its crystallizability, focusing on the "sticky patch" model. We discuss state-of-the-art in silico methods that evaluate the propensity of a given target protein to form crystals based on these relationships, with the objective to design variants with modified molecular surface properties and enhanced crystallization propensity. We illustrate this discussion with specific cases where these approaches allowed to generate crystals suitable for structural analysis.

Keywords: Lysine methylation; Protein crystallization; Sticky patch model; Surface entropy reduction.

Publication types

  • Review
  • Research Support, N.I.H., Extramural

MeSH terms

  • Amino Acids / chemistry*
  • Computational Biology / methods*
  • Crystallization / methods*
  • Crystallography, X-Ray / methods*
  • Gene Expression
  • Models, Molecular
  • Mutation
  • Protein Conformation, alpha-Helical
  • Protein Conformation, beta-Strand
  • Protein Engineering
  • Proteins / chemistry
  • Proteins / genetics
  • Proteins / ultrastructure*
  • Solubility
  • Surface Properties
  • Thermodynamics

Substances

  • Amino Acids
  • Proteins