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.

Soft matter perspective on protein crystal assembly

“…This last point is interesting because experimental phase diagrams of proteins, such as lysozyme and γ-crystallin, have a binodal whose width and critical packing fraction are much smaller than those of isotropic models [53,58,104]. Although patchiness requires the specification of more model parameters and results in a certain loss of universality [107,119], it also weakens high-order correlations in the fluid structure, which enables the use of relatively simple liquid-state descriptions, such as Wertheim's theory, for their analysis [59,[120][121][122][123][124][125]. B FIG.…”

Collective translational and rotational Monte Carlo moves for attractive particles

“…This can make it resemble Brownian or Stokesian dynamics, if the parameters within the method are chosen with regard to physical quantities, such as size-dependent diffusion coefficients. Although VMMC has begun to be used in the simulation of various aggregation or self-assembly processes [10][11][12][13][14][15][16][17], we believe that there is a need to present the algorithm in a completely clear form, especially in its symmetrized version. For clarity, and for reasons described below, the Brownian or Stokesian dynamical aspects are not considered here.…”

The self assembly of proteins; probing patchy protein interactions

“…The formation of new crystal contacts is considered a driving force in promoting protein crystallization. 38 For some proteins this is likely to be true, but for the four individual mutant proteins described here, only the R36S mutant forms a new crystal contact. It is possible that new crystal contacts are formed in the double mutants that do not exist in the single mutants.…”