Evolutionary drivers of protein shape

Abstract

Diffusional motion within the crowded environment of the cell is known to be crucial to cellular function as it drives the interactions of proteins. However, the relationships between protein diffusion, shape and interaction, and the evolutionary selection mechanisms that arise as a consequence, have not been investigated. Here, we study the dynamics of triaxial ellipsoids of equivalent steric volume to proteins at different aspect ratios and volume fractions using a combination of Brownian molecular dynamics and geometric packing. In general, proteins are found to have a shape, approximately Golden in aspect ratio, that give rise to the highest critical volume fraction resisting gelation, corresponding to the fastest long-time self-diffusion in the cell. The ellipsoidal shape also directs random collisions between proteins away from sites that would promote aggregation and loss of function to more rapidly evolving nonsticky regions on the surface, and further provides a greater tolerance to mutation.

Novel Bifunctional Acylase from Actinoplanes utahensis: A Versatile Enzyme to Synthesize Antimicrobial Compounds and Use in Quorum Quenching Processes

“…This value is compatible with the behavior of a globular protein with a molecular weight of 66.2 kDa, being a smaller size than the molecular weight determined by MALDI-TOF analysis for Au AHLA. This result revealed that this protein probably shows a spheroid oblate-shape with different hydrodynamic properties [ 35 ], as previously observed for Sl PVA and Au AAC (unpublished data).…”

Predicting the Shapes of Protein Complexes Through Collision Cross Section Measurements and Database Searches

“…This is not an unreasonable assumption, as previous studies have established that the majority of soluble, ordered proteins adopt a roughly elliptical shape that might facilitate optimal diffusion in the intracellular environment. 11,12 Multiple studies have revealed that native-like ions of small, single-domain proteins such as ubiquitin have a relatively constant density of approximately 0.8 -1.1 g/cm 3 in the gas phase, 25 similar to the values determined for proteins in solution. 26 For uniformly shaped protein complexes, at this constant density, CCS should be tightly connected to molecular weight.…”

Protein Dielectrophoresis: A Tale of Two Clausius-Mossottis—Or Something Else?

“…Displacement currents tend to dominate above ~50 kHz, so that the relative permittivity values, ε p and ε m, are used directly in Equation (7), to be replaced with conductivity parameters σ p and σ m below ~1 kHz. Equation ( 7) describes a spherical particle, but ~75% of globular proteins take the form of prolate spheroids, with ~25% being oblate [29]. The following general result for M int aligned along an axis parallel to the direction of E m can be applied [15]:…”

“…Based on common aspect ratios for prolate and oblate proteins [29], the depolarization factor of relevance has limits 0.2 < A < 0.8. Provided that the protein sample is large enough for it to be characterized using macroscopic electrostatics then, from Equation (10), the corresponding DEP susceptibilities related to their induced moments are:…”

“…Equation (29) indicates that the Lorentz cavity field, unlike the Maxwell cavity field of Equation (5), is always larger than the applied macroscopic field E m . This arises because the Lorentz cavity, being virtual and without a physical boundary between it and the surrounding dielectric, does not experience the field-shielding effect of induced interfacial charges as produced for the Maxwell cavity.…”