2D Monte Carlo Simulation of Patchy Particles Association and Protein Crystal Polymorph Selection

Abstract

Typically, protein crystals inherit the polymorphic form selected by nuclei arising in the solution. However, a transition of a polymorphic form may also occur at a later crystal growth stage. Unfortunately, due to the molecular-scale processes involved, the earliest stages of protein crystal nucleation and polymorph selection remain poorly understood. This paper attempts to elucidate the polymorph selection and crystal growth process in proteins (and colloidal crystals) using 2D Monte Carlo simulations and a computational model with short-range attraction for ‘protein-like’ patchy particles (PPs) of a specific patch geometry, bond width and strength. A relatively narrow temperature range is established whereby parts of the PPs monomers arrange initially in a rapidly growing unstable rhombohedral lattice (Rh). Stable trimers form simultaneously from the monomers remaining in the solution and monomers released from the Rh lattice. These trimers serve as building blocks of a more stable Kagome trihexagonal lattice (TriHex), which appears after a prolonged simulation time. The step-by-step scenario of this polymorphic transition and the specific role of PPs’ geometric and interaction anisotropies are discussed in detail.

Patchy Nanoparticle Synthesis and Self-Assembly

“…The same group also suggests through rational design of patch shape and symmetry that triblock patchy particles can selectively crystallize into tetrastack lattice with unique photonic properties, and even a colloidal clathrate-like structure [149]. Other structures including icosahedra, tetrahedra, square pyramids [8], helical structures [150], quasicrystals of dodecagonal symmetry [35,151], and open lattices [152,143] (Figure 9a and b) with high structural selectivity over other polymorphs are studied (Figure 9c) [153]. Together with recent studies in mechanical and functional properties of the exotic structures formed as bottom-up [154,155], these theoretical studies have been paving ways to experimentally achieve novel functional nanostructures.…”

“…For the past two decades, simulation of patchy particles has been extensively developed using simplified models to understand complicated assembly systems [142], including protein folding [143], viral capsid formation [144,145], and even phase transition of atoms and molecules [146]. In the field of synthetic patchy nanoparticles, simulation aids understanding of experimental observations.…”

Inverse design of two-dimensional structure by self-assembly of patchy particles

“…Intuitively, the design based on narrow sticky patch consists of four small patches located the same plane at alternating interval of 60 • and 120 • so that they fit the four contact points [35][36][37][38]. However, self-assembly of those particles shows that a rhombus lattice is more favourable and formed instead of kagome one [35][36][37][38]. The kagome lattice structure is formed only when constraint on patch selectivity is added [37,38].…”

Self-Assembly of Nanostructures and Patchy Nanoparticles

“…The same group also suggests through rational design of patch shape and symmetry that triblock patchy particles can selectively crystallize into tetrastack lattice with unique photonic properties, and even a colloidal clathrate-like structure [149]. Other structures including icosahedra, tetrahedra, square pyramids [8], helical structures [150], quasicrystals of dodecagonal symmetry [35,151], and open lattices [152,143] (Figure 9a and b) with high structural selectivity over other polymorphs are studied (Figure 9c) [153]. Together with recent studies in mechanical and functional properties of the exotic structures formed as bottom-up [154,155], these theoretical studies have been paving ways to experimentally achieve novel functional nanostructures.…”