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Shape and evolution of thermostable protein structure.

ABSTRACT: Organisms evolved at high temperatures must maintain their proteins' structures in the face of increased thermal disorder. This challenge results in differences in residue utilization and overall structure. Focusing on thermostable/mesostable pairs of homologous structures, we have examined these differences using novel geometric measures: specifically burial depth (distance from the molecular surface to each atom) and travel depth (distance from the convex hull to the molecular surface that avoids the protein interior). These along with common metrics like packing and Wadell Sphericity are used to gain insight into the constraints experienced by thermophiles. Mean travel depth of hyperthermostable proteins is significantly less than that of their mesostable counterparts, indicating smaller, less numerous and less deep pockets. The mean burial depth of hyperthermostable proteins is significantly higher than that of mesostable proteins indicating that they bury more atoms further from the surface. The burial depth can also be tracked on the individual residue level, adding a finer level of detail to the standard exposed surface area analysis. Hyperthermostable proteins for the first time are shown to be more spherical than their mesostable homologues, regardless of when and how they adapted to extreme temperature. Additionally, residue specific burial depth examinations reveal that charged residues stay unburied, most other residues are slightly more buried and Alanine is more significantly buried in hyperthermostable proteins.

SUBMITTER: Coleman RG

PROVIDER: S-EPMC3383796 | biostudies-literature | 2010 Feb

REPOSITORIES: biostudies-literature

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Shape and evolution of thermostable protein structure.

Coleman Ryan G RG Sharp Kim A KA

Proteins 20100201 2

Organisms evolved at high temperatures must maintain their proteins' structures in the face of increased thermal disorder. This challenge results in differences in residue utilization and overall structure. Focusing on thermostable/mesostable pairs of homologous structures, we have examined these differences using novel geometric measures: specifically burial depth (distance from the molecular surface to each atom) and travel depth (distance from the convex hull to the molecular surface that avo ...[more]

PMID: 19731381

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Project description:The distribution and genetic structure of most plant species in Britain and Ireland bear the imprint of the last ice age. These patterns were largely shaped by random processes during recolonization but, in angiosperms, whole-genome duplication may also have been important. We investigate the distribution of cytotypes of Campanula rotundifolia, considering DNA variation, postglacial colonization, environmental partitioning and reproductive barriers. Cytotypes and genome size variation from across the species' range were determined by flow cytometry and genetic variation was assessed using cpDNA markers. A common garden study examined growth and flowering phenology of tetraploid, pentaploid and hexaploid cytotypes and simulated a contact zone for investigation of reproductive barriers. Irish populations were entirely hexaploid. In Britain, hexaploids occurred mostly in western coastal populations which were allopatric with tetraploids, and in occasional sympatric inland populations. Chloroplast markers resolved distinct genetic groups, related to cytotype and geographically segregated; allopatric hexaploids were distinct from tetraploids, whereas sympatric hexaploids were not. Genome downsizing occurred between cytotypes. Progeny of open-pollinated clones from the contact zone showed that maternal tetraploids rarely produced progeny of other cytotypes, whereas the progeny of maternal hexaploids varied, with frequent pentaploids and aneuploids. The presence of distinctive hexaploid chloroplast types in Ireland, Scottish islands and western mainland Britain indicates that its establishment preceded separation of these land masses by sea-level rise c. 16 000 years BP. This group did not originate from British tetraploids and probably diverged before postglacial invasion from mainland Europe. The combination of cytotype, molecular, contact zone and common garden data shows an overall pattern reflecting postglacial colonization events, now maintained by geographic separation, together with more recent occasional local in situ polyploidisation. Reproductive barriers favour the persistence of the tetraploid to the detriment of the hexaploid.

Dataset Information

Shape and evolution of thermostable protein structure.

Publications

Shape and evolution of thermostable protein structure.

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