And evolutionary relationships

Weitzman, S. H. (1974). Osteology and evolutionary relationships of the Sternoptychidae, with a new classification of stomiatoid fishes. Bull. Am. Mus. Nat. Hist. 153 329-478. 

Haller, J. R. 1966. Systematic and evolutionary relationships of Pinus torreyana. Amer. 1. Bot. 53 635 (abstract). 

P. Baumann, L. Baumann, C.-Y. Lai, and D. Rouhbakhsh, Genetics, physiology and evolutionary relationships of the genus Buchnera intracellular symbionts of aphids, Annii. Rev. Microbiol. 49 55 (1995). 

Baumann, P., Baumann, L., Lai, C.Y., Rouhbakhsh, D., Moran, N.A. and Clark, M.A. (1995) Genetics, physiology, and evolutionary relationships of the genus Buchnercv. intracellular symbionts of aphids. Annual Review of Microbiology 49, 55-94. 

Tam, R. and Saier, M. H., Jr. (1993). Structural, functional, and evolutionary relationships among extracellular solute-binding receptors of bacteria. Microbiol. Rev. 57, 320-46. 

II. Detecting Nontrivial Structural and Evolutionary Relationships Between... 

This overview presents some cases in which sequence profile-based methods have been able to predict nontrivial structural and evolutionary relationships between proteins and then discusses the current state of structural genomics as assesed using these methods. This discussion is not a comprehensive review of profile-based methods for sequence analysis and their application in structural genomics rather observations made with PSI-BLAST-constructed PSSMs are emphasized, and results produced by other methods are cited only as needed for discussion. 

McCord, J. M. Iron- and manganese containing superoxide dismutases Structure, distribution, and evolutionary relationships. In Iron and Copper Proteins (Yasunobu, K. T., Mower, H. F., Hayaishi, O., eds.), New York-London, Plenum Press, 1976, pp. 540-550... 

Furukawa, K. (1994). Molecular genetics and evolutionary relationship of PCB-degrading bacteria. Biodegradation, 5, 289-300. 

Hermans, J. Westhoff, P. (1990). Analysis of expression and evolutionary relationships of PEPCase genes in Flaveria trinervia (C4) and F. pringlei (Q). Molecular and General Genetics 224, 459-68. 

ME Hahn Woods Hole Oceanographic Institution, Woods Hole, MA Characterize the structure, function, regulation, and evolutionary relationships of the Ah receptor in non-mammalian species, particularly fish ... 

The amino acid sequence of a protein not only reveals the primary structure of the protein but also information on possible protein families or groups and evolutionary relationships, potential gene duplication(s) and possible post-translational modifications. In addition, a knowledge of the amino acid sequence can be used to generate specific antibodies and DNA probes. 

When we compare the sequences of proteins, we analyze the similarities and differences at the level of individual amino acids with the aim of inferring structural, functional, and evolutionary relationships among the sequences under study. The most common comparative method is sequence alignment, which provides an explicit mapping between the residues of two or more sequences. 

Mills, E.N., Jenkins, J.A., Alcocer, MJ. et al. 2004. Structural, biological, and evolutionary relationships of plant food allergens sensitizing via the gastrointestinal tract. Crit Rev Food Sci Nutr 44 379-407. 

Jespersen, H. M., MacGregor, A., Henrissat, B., Sierks, M. R., and Svensson, B. 1993. Starch-and glycogen-debranching and branching enzymes prediction of structural features of the catalytic (/S/a)g-barrel domain and evolutionary relationship to other amylolytic enzymes. J. Protein Chem. 12,781-805. 

There is an ongoing effort to reveal the correlation patterns of protein functions and sequences [27-29]. Although we are still far away from a deep and consistent understanding, and analysis is hampered by the small number of available X-ray structures of proteins with bound small-molecule ligands, some interesting observations relevant to the topic of the theme discussed in this chapter have been made about the diversity and evolutionary relationships of ligand binding sites in proteins [30-32]. 

R. A. and Matthews, B.W., Type II restriction endonucleases structural, functional, and evolutionary relationships, Curr. Opin. Chem. Biol. 3, 578-583, 1999 Akar, A., Orkunoglu, F.E., Ozata, M., Sengul, A., and Gur, A.R., Lack of association between vitamin D receptor Fokl polymorphism and alopecia areata, Eur. J. Dermatol. 14, 156-158, 2004 Guy, M., Lowe, L.C., Bretherton-Watt, D. et al., Vitamin D receptor gene polymorphisms and breast cancer risk, Clin. Cancer Res. 10, 5472-5481, 2004 Claassen, M., Nouwen, J., Fang, Y. et al., Staphylococcus aureus nasal carriage is not associated with known polymorphism in the Vitamin D receptor gene, FEMS Immunol. Med. Microbiol. 43,173-176, 2005 Bolu,... 

M. Bergdoll, L.D. Eltis, A.D. Cameron, P. Dumas, and J.T. Bolin. 1998. All in the family Structural and evolutionary relationships among three modular proteins with diverse functions and variable assembly Protein Sci. 1 1661-1670. (PubMed)... 

An adage of biochemistry is, Never waste pure thoughts on an impure protein. Starting from pure proteins, we can determine amino acid sequences and evolutionary relationships between proteins in diverse organisms and we can investigate a protein s biochemical function. Moreover, crystals of the protein may be grown from pure protein, and from such crystals we can obtain x-ray data that will provide us with a picture of the protein s tertiary structure—the actual functional unit. 

The jS-eSer-a motif is likely to be present in other enzymes with esterase or thioesterase activity, although their structure may be different from that of the a/jS hydrolases. Some of these proteins have already been crystallized for X-ray studies [e.g.. Vibrio harveyi acyltransferase (Swenson et al., 1992)], and their cryst structures should throw some more light on the structural and evolutionary relationships within the lipase/esterase superfamily. 

Barrett, M. (2006). Identification, sequencing, expression and evolutionary relationships of the 11s seed storage protein gene in Chenopodium quinoa Willd. Thesis of Master of Science Department of Plant and Animal Sciences Brigham Young University. 

Blobel, C.P. and White, J.M. (1992). Structure, function, and evolutionary relationship of proteins containing a disintegrin domain. Curr. Opin. Cell Biol. 4 760-765. 

Andersen JN, Mortensen OH, Peters GH et al (2001) Structural and evolutionary relationships among protein tyrosine phosphatase domains. Mol CeU Biol 21 7117-7136... 

Harayama, S., M. Kok, and E.L. Neidle. 1992. Functional and evolutionary relationships among diverse oxygenases. Annu. Rev. Microbiol. 46 565-601. 

Mannhaupt, G. Pohlenz, H.D. Seefluth, A.K. Pilz, U. Feldmann, H. Yeast homoserine kinase. Characteristics of the corresponding gene, THRl, and the purified enzyme, and evolutionary relationships with other enzymes of threonine metabolism. Eur. J. Biochem., 191, 115-122 (1990)... 

The first step in cofnparative modelling is the identification of the known 3D structure(s) which can act as the basis stmcture(s) for the target sequence this can be done from stmctural knowledge, similarity of function, gene grouping, sequence similarity and evolutionary relationship. 

Krcjci, H., Duval, N., Chatonnet, A., Vincens, P, and Mas-soulie. J. (1991). Cholinesteiasc-Likc domains in enzymes and structural proteins Functional and evolutionary relationships and identification of a catalyiically essential aspartic acid. Proc. Natl. Acad. Sci USA 88,6647-6651. 

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