Characterizing protein crystal contacts and their role in crystallization: rubredoxin as a case study

Abstract

The fields of structural biology and soft matter have independently sought out fundamental principles to rationalize protein crystallization. Yet the conceptual differences and the limited overlap between the two disciplines have thus far prevented a comprehensive understanding of the phenomenon to emerge. We conduct a computational study of proteins from the rubredoxin family that bridges the two fields. Using atomistic simulations, we characterize their crystal contacts, and accordingly parameterize patchy particle models. Comparing the phase diagrams of these schematic models with experimental results enables us to critically examine the assumptions behind the two approaches. The study also reveals features of protein-protein interactions that can be leveraged to crystallize proteins more generally.

13 pages, 10 figures, accepted in Soft Matter

References in corpus (5)

• On the possibility of extending the Nore-Frenkel generalized law of correspondent states to non-isotropic patchy interactions
• Inhibition of protein crystallization by evolutionary negative design
• The crystallization of asymmetric patchy models for globular proteins in solution
• Design rules for the self-assembly of a protein crystal
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Cited by in corpus (11)

• The Statistical Mechanics of Dynamic Pathways to Self-assembly
• Equilibrium gels of limited valence colloids
• Soft Matter Perspective on Protein Crystal Assembly
• Soft Metamaterials: Adaptation and Intelligence
• Minimal positive design for self-assembly of the Archimedean tilings
• Statistical analysis of crystallization database links protein physico-chemical features with crystallization mechanisms
• Computational Crystallization
• Temperature-dependent non-covalent protein-protein interactions explain normal and inverted solubility in a mutant of human gamma D-crystallin
• Competition between monomeric and dimeric crystals in schematic models for globular proteins
• Protein-Polymer Mixtures in the Colloid Limit: Aggregation, Sedimentation and Crystallization
• Using schematic models to understand the microscopic basis for inverted solubility in $\gamma$D-crystallin