ADH evolution and the phylogenetic footprint

Dorit, Robert L.; Ayala, Francisco J.

doi:10.1007/bf00160514

Cited by 10 publications

(7 citation statements)

References 33 publications

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“…Tree-determinant positions correspond to residues that are conserved within a subfamily of proteins, but differ between subfamilies. Several algorithms have been developed to search for the best tree-determinants involved in the function of a Computational study of GPCR oligomerization protein family [52,53,[70][71][72][73][74][75][76][77][78][79]. It is clear that each of the different implementations of this bioinformatics approach presents special advantages as well as specific drawbacks.…”

Section: Methods That Detect Tree-determinant Positionsmentioning

confidence: 99%

The study of G‐protein coupled receptor oligomerization with computational modeling and bioinformatics

2005

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To achieve a structural context for the analysis of G‐protein coupled receptor (GPCR) oligomers, molecular modeling must be used to predict the corresponding interaction interfaces. The task is complicated by the paucity of detailed structural data at atomic resolution, and the large number of possible modes in which the bundles of seven transmembrane (TM) segments of the interacting GPCR monomers can be packed together into dimers and/or higher‐order oligomers. Approaches and tools offered by bioinformatics can be used to reduce the complexity of this task and, combined with computational modeling, can serve to yield testable predictions for the structural properties of oligomers. Most of the bioinformatics methods take advantage of the evolutionary relation that exists among GPCRs, as expressed in their sequences and measurable in the common elements of their structural and functional features. These common elements are responsible for the presence of detectable patterns of motifs and correlated mutations evident from the alignment of the sequences of these complex biological systems. The decoding of these patterns in terms of structural and functional determinants can provide indications about the most likely interfaces of dimerization/oligomerization of GPCRs. We review here the main approaches from bioinformatics, enhanced by computational molecular modeling, that have been used to predict likely interfaces of dimerization/oligomerization of GPCRs, and compare results from their application to rhodopsin‐like GPCRs. A compilation of the most frequently predicted GPCR oligomerization interfaces points to specific regions of TMs 4–6.

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Section: Methods That Detect Tree-determinant Positionsmentioning

confidence: 99%

The study of G‐protein coupled receptor oligomerization with computational modeling and bioinformatics

2005

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“…This amount of data contrasts with the scarcity of studies on the evolution and divergence of the Drosophila ADH protein Dorit and Ayala 1995), which could give more clues about a possible linkage between ADH features and biological fitness. One reason for this is the lack of the three-dimensional structure of Drosophila ADH, which precludes any detailed study of the structure/function relationship and, thus, any possibility of direct correlation between protein variability and adaptive trends of the molecule.…”

Section: Drosophila Alcohol Dehydrogenasementioning

confidence: 75%

Shaping of Drosophila Alcohol Dehydrogenase Through Evolution: Relationship with Enzyme Functionality

et al. 1998

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Drosophilidae is a large, widely distributed family of Diptera including 61 genera, of which Drosophila is the most representative. Drosophila feeding is part of the saprophytic trophic chain, because of its dependence upon decomposing organic matter. Many species have adapted to fermenting fruit feeding or to artificial (man-made) fermentation habitats, such as cellars and breweries. Actually, the efficient exploitation of niches with alcohols is considered one of the reasons for the worldwide success of this genus. Drosophila alcohol dehydrogenase (ADH), a member of the short-chain dehydrogenase/reductase family (SDR), is responsible for the oxidation of alcohols, but its direct involvement in fitness, including alcohol tolerance and utilization, gives rise to much controversy. Thus, it remains unclear whether ADH differentiation through evolution is somehow associated with natural adaptation to new feeding niches, and thus maybe to Drosophila speciation, or if it is a simple reflection of neutral divergence correlated with time separation between species. To build a hypothesis which could shed light on this dilemma, we analyzed the amino acid variability found in the 57 protein ADH sequences reported up to now, identified the taxon-specific residues, and localized them in a three-dimensional ADH model. Our results define three regions whose shaping has been crucial for ADH differentiation and would be compatible with a contribution of ADH to Drosophila speciation.

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“…It is related to other recently proposed methods for analyzing regional heterogeneity in DNA and protein sequences (e.g., Dorit and Ayala 1995;Goss and Lewontin 1996;Tang and Lewontin 1999 and references therein). Our procedure involves several steps.…”

Section: Methodsmentioning

confidence: 89%

“…quences (see Dorit and Ayala 1995;McDonald 1996;Goss and Lewontin 1996;Tang and Lewontin 1999). Here, we have developed a new procedure, which we have called constraint analysis, to establish whether runs of amino acids show significant departures from randomness when two pairs of paralogous proteins are compared.…”

Section: Detecting Regional Heterogeneity In Paralogous Proteinsmentioning

confidence: 99%

Detecting Changes in the Functional Constraints of Paralogous Genes

et al. 2001

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Abstract. We describe a new procedure to determine whether regional alterations in the evolutionary constraints imposed on paralogous proteins have occurred. We used as models the A and B (alternatively called ␣ and ␤) subunits of V/F/A-ATPases, originated by a gene duplication more than 3 billion years ago. Changes associated to three major splits (eubacteria versus Archaeaeukaryotes; Archaea versus eukaryotes; and among freeliving bacteria and symbiotic mitochondria) were studied. Only in the first case, when we compared eubacterial or mitochondrial F-ATPases versus eukaryotic vacuolar V-ATPases or archaeal A-ATPases, constraint changes were observed. Modifications in the degree of regional constraining were not detected for the other two types of comparisons (V-ATPases versus A-ATPases and within F-ATPases, respectively). When the rates of evolution of the two subunits were compared, it was found that F-ATPases regulatory subunits evolved faster than catalytic subunits, but the opposite was true for Aand V-ATPases. Our results suggest that, even for universal and essential proteins, selective constraints may be occasionally altered. On the other hand, in some cases no changes were detected after periods of more than 2.2 billion years.

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ADH evolution and the phylogenetic footprint

Cited by 10 publications

References 33 publications

The study of G‐protein coupled receptor oligomerization with computational modeling and bioinformatics

The study of G‐protein coupled receptor oligomerization with computational modeling and bioinformatics

Shaping of Drosophila Alcohol Dehydrogenase Through Evolution: Relationship with Enzyme Functionality

Detecting Changes in the Functional Constraints of Paralogous Genes

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