Arrangements in the modular evolution of proteins

Moore, Andrew D.; Björklund, Åsa K.; Ekman, Diana; Bornberg‐Bauer, Erich; Elofsson, Arne

doi:10.1016/j.tibs.2008.05.008

Cited by 196 publications

(162 citation statements)

References 74 publications

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“…The present review focuses primarily on the effect of point mutations (change of a single nucleotide) and will consider only proteins but not RNA, although many general principles of evolution are applicable to both classes of biomolecules. We refer to other authors for the evolution of protein structures via sequence re-arrangements such as domain-wise evolution [2][3][4], the fusion of small peptide fragments [5] or the 'chimeric' recombination of fragments that is also exploited in protein engineering [6][7][8][9].…”

Section: Introductionmentioning

confidence: 99%

Biophysics of protein evolution and evolutionary protein biophysics

Sikosek

Chan

2014

J. R. Soc. Interface.

219

207

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The study of molecular evolution at the level of protein-coding genes often entails comparing large datasets of sequences to infer their evolutionary relationships. Despite the importance of a protein's structure and conformational dynamics to its function and thus its fitness, common phylogenetic methods embody minimal biophysical knowledge of proteins. To underscore the biophysical constraints on natural selection, we survey effects of protein mutations, highlighting the physical basis for marginal stability of natural globular proteins and how requirement for kinetic stability and avoidance of misfolding and misinteractions might have affected protein evolution. The biophysical underpinnings of these effects have been addressed by models with an explicit coarse-grained spatial representation of the polypeptide chain. Sequence-structure mappings based on such models are powerful conceptual tools that rationalize mutational robustness, evolvability, epistasis, promiscuous function performed by 'hidden' conformational states, resolution of adaptive conflicts and conformational switches in the evolution from one protein fold to another. Recently, protein biophysics has been applied to derive more accurate evolutionary accounts of sequence data. Methods have also been developed to exploit sequence-based evolutionary information to predict biophysical behaviours of proteins. The success of these approaches demonstrates a deep synergy between the fields of protein biophysics and protein evolution.

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Section: Introductionmentioning

confidence: 99%

Biophysics of protein evolution and evolutionary protein biophysics

Sikosek

Chan

2014

J. R. Soc. Interface.

219

207

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“…Criteria A and B have a similar percentage of homologs not detected in Ensembl, while criterion C, follows a different trend. This last criterion is the only one that allows for insertion of external domains after duplication, which is an event that has been observed and can be expected from our knowledge of the evolutionary dynamics of proteins [31,32,33].…”

Section: Discussionmentioning

confidence: 94%

“…Three different homology criteria were used to compare the domain architecture of proteins [17,32]. Criterion A considers exactly matching architectures.…”

Section: Methodsmentioning

confidence: 99%

Identity and divergence of protein domain architectures after the yeast whole-genome duplication event

et al. 2010

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Analyzing the properties of duplicate genes during evolution is useful to understand the development of new cell functions. The yeast S. cerevisiae is a useful testing ground for this problem, because its duplicated genes with different evolutionary birth and destiny are well distinguishable. In particular, there is a clear detection for the occurrence of a Whole Genome Duplication (WGD) event in S. cerevisiae, and the genes derived from this event ("WGD paralogs") are known. We studied WGD and non-WGD duplicates by two parallel analysis based on structural protein domains and on Gene Ontology annotation scheme respectively. The results show that while a large number of "duplicable" structural domains is shared in local and global duplications, WGD and non-WGD paralogs tend to have different functions. The reason for this is the existence of WGD and non-WGD specific domains with largely different functions. In agreement with the recent findings of Wapinski and collaborators (Nature 449, 2007), WGD paralogs often perform "core" cell functions, such as translation and DNA replication, while local duplications associate with "peripheral" functions such as response to stress. Our results also support the fact that domain architectures are a reliable tool to detect homology, as the domains of duplicates are largely invariant with date and nature of the duplication, while their sequences and also their functions might migrate.

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“…5 Furthermore, in addition to the generation of whole protein homologs, partial gene duplications resulting in domain duplication and elongation are also common features of protein evolution. 6 In many cases such enlargements have resulted from the addition of sub-domains, variability in loop length and/or changes to the structural core, such as β-sheet extensions. Examples of such protein duplication events include cutinase and bovine bile-salt activated cholesterol esterase (Fig.…”

Section: What Is Shaping Protein Structure?mentioning

confidence: 99%

Proteins

Sleator

2012

Bioengineered

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Arrangements in the modular evolution of proteins

Cited by 196 publications

References 74 publications

Biophysics of protein evolution and evolutionary protein biophysics

Biophysics of protein evolution and evolutionary protein biophysics

Identity and divergence of protein domain architectures after the yeast whole-genome duplication event

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