Search arXivSearch

arXiv · physics/0602020

Buckling transition in icosahedral shells subjected to volume conservation constraint and pressure: relations to virus maturation

Abstract

Minimal energy shapes of closed, elastic shells with twelve pentagonal disclinations introduced in otherwise hexagonally coordinated crystalline lattice are studied. The geometry and the total energy of shells are studied as a function of the elastic properties of the material they are made of. Particular emphasis is put on the buckling transition of the shells, that is a strong preference of the shell shapes to 'buckle out' in spatial regions close to the pentagonal disclinations for certain range of the elastic parameters of the problem. The transition effectively increases the mean square aspherity of shapes, making them look more like an icosahedron, rather than a sphere which is a preferred shape prior to the onset of the transition. The properties of the buckling transition are studied in cases when (i) the total volume enclosed by the elastic shell has to be fixed and when (ii) there is an internal pressure acting on the shell. This may be related to maturation process in non-enveloped dsDNA viruses, where the insertion of the genetic material in a pre-formed protein shell (viral coating) may effectively impose the fixed volume and/or pressure constraint. Several scenarios that may explain the experimentally observed feature of mature viruses being more aspherical (facetted) from their immature precursors are discussed and new predictions for the elastic properties of viral coatings are obtained on the basis of the presented studies.

Explore related subjects

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Antonio Siber. 2006-06-23. Buckling transition in icosahedral shells subjected to volume conservation constraint and pressure: relations to virus maturation. https://doi.org/10.1103/physreve.73.061915

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related papers

Signature of mechanically induced cell extrusions in cell size distribution

How a growing tissue organizes its own homeostatic state is a central question in the physics of living matter. We show that when a growing epithelial sheet counteracts increasing cell density by mechanically squeezing cells out of its plane, a homeostatic in-plane pressure emerges as a generalization of a yield stress. We find that in the quasistatic growth limit the homeostatic state is marginally stable, with a pseudogap in the distribution of local distances to the extrusion threshold pressure. Because such mechanically induced extrusions arise from an instability of individual cells, the pseudogap is imprinted in the distribution of cell areas. This provides an image-based way to test for presence of mechanically induced extrusions and we identify this signature in the developing wing epithelium of \textit{D.~melanogaster}. We expect the same principles to apply to confined three-dimensional tissues.

physics.bio-ph

Towards Accurate Prediction of Mutation-Induced Changes in Protein Structure

Proteins can possess numerous mutations relative to their wild-type amino acid sequences with minimal impact to their structure and function. However, in other cases, even a single amino acid mutation relative to the wild-type sequence can lead to a large change in structure or even a disease phenotype. While the accuracy of wild-type protein structure prediction has improved significantly in recent years, it remains difficult to accurately predict the structure of mutant proteins. Here, we characterize the local mutation-induced structural changes in proteins for a dataset of wildtype and the corresponding single-amino acid mutant x-ray crystal structures from the Protein Data Bank (PDB). We find that mutation-induced structural changes in these proteins are localized at the site of the mutation, decaying rapidly with increasing spatial distance from the mutation site. In addition, we evaluate how well AlphaFold3 can recapitulate the observed mutation-induced structural deformations in the x-ray crystal structures. We find that the accuracy of the AlphaFold3 predictions decreases strongly with increasing mutation-induced deformation. In contrast to the results for AlphaFold3, the Pearson correlation between a single physical feature, i.e. the change in solvent accessibility, and the mutation-induced deformation does not depend on the magnitude of the deformation. Our results and analyses provide a framework for further studies aimed at predicting the structural changes in proteins caused by single amino acid mutations.

physics.bio-ph

Biology and Physics

This article frames the relation between biology and physics by characterizing the former as a subdiscipline rather than a special case of the latter. To do this, we posit biological physics as the science of living matter in contrast to classic biophysics, the study of organismal properties by physical techniques. At the scale of the individual cell, living matter is nonunitary, i.e., not composed of aggregated subunits, and has features (e.g., intracellular organizational arrangements and biomolecular condensates) that are unlike any materials of the nonliving world. In transiently or constitutively multicellular forms (social microorganisms, animals, plants), living matter sustains physical processes that are generic (shared with nonliving matter, e.g., subunit communication by molecular diffusion in cellular slime molds), biogeneric (analogous to nonliving matter but realized through cellular activities, e.g., subunit demixing in animal embryos) or nongeneric (pertaining to sui generis materials, e.g., budding of active solids in plants). This "forms of matter" perspective is philosophically situated in the dialectical materialism of Engels and Hessen and the multilevel physicalism of Neurath and the logical empiricists. We counterpose this view to informationism and to genetic and other hierarchically reductionist physical theories of biological systems and highlight open questions regarding incompletely characterized and enigmatic forms of living matter.

physics.bio-ph