Computer-aided analyses of transport protein sequences: gleaning evidence concerning function, structure, biogenesis, and evolution
- PMID: 8177172
- PMCID: PMC372954
- DOI: 10.1128/mr.58.1.71-93.1994
Computer-aided analyses of transport protein sequences: gleaning evidence concerning function, structure, biogenesis, and evolution
Abstract
Three-dimensional structures have been elucidated for very few integral membrane proteins. Computer methods can be used as guides for estimation of solute transport protein structure, function, biogenesis, and evolution. In this paper the application of currently available computer programs to over a dozen distinct families of transport proteins is reviewed. The reliability of sequence-based topological and localization analyses and the importance of sequence and residue conservation to structure and function are evaluated. Evidence concerning the nature and frequency of occurrence of domain shuffling, splicing, fusion, deletion, and duplication during evolution of specific transport protein families is also evaluated. Channel proteins are proposed to be functionally related to carriers. It is argued that energy coupling to transport was a late occurrence, superimposed on preexisting mechanisms of solute facilitation. It is shown that several transport protein families have evolved independently of each other, employing different routes, at different times in evolutionary history, to give topologically similar transmembrane protein complexes. The possible significance of this apparent topological convergence is discussed.
Similar articles
-
Phylogenetic approaches to the identification and characterization of protein families and superfamilies.Microb Comp Genomics. 1996;1(3):129-50. doi: 10.1089/mcg.1996.1.129. Microb Comp Genomics. 1996. PMID: 9689209 Review.
-
The MIP family of integral membrane channel proteins: sequence comparisons, evolutionary relationships, reconstructed pathway of evolution, and proposed functional differentiation of the two repeated halves of the proteins.Crit Rev Biochem Mol Biol. 1993;28(3):235-57. doi: 10.3109/10409239309086796. Crit Rev Biochem Mol Biol. 1993. PMID: 8325040 Review.
-
The amino acid/auxin:proton symport permease family.Biochim Biophys Acta. 1999 Jan 8;1415(2):306-22. doi: 10.1016/s0005-2736(98)00196-5. Biochim Biophys Acta. 1999. PMID: 9889387
-
The mitochondrial carrier family of transport proteins: structural, functional, and evolutionary relationships.Crit Rev Biochem Mol Biol. 1993;28(3):209-33. doi: 10.3109/10409239309086795. Crit Rev Biochem Mol Biol. 1993. PMID: 8325039 Review.
-
TRAP transporters: an ancient family of extracytoplasmic solute-receptor-dependent secondary active transporters.Microbiology (Reading). 1999 Dec;145 ( Pt 12):3431-3445. doi: 10.1099/00221287-145-12-3431. Microbiology (Reading). 1999. PMID: 10627041
Cited by
-
Characterization of the Erwinia chrysanthemi osmoprotectant transporter gene ousA.J Bacteriol. 1996 Jan;178(2):447-55. doi: 10.1128/jb.178.2.447-455.1996. J Bacteriol. 1996. PMID: 8550465 Free PMC article.
-
Major facilitator superfamily.Microbiol Mol Biol Rev. 1998 Mar;62(1):1-34. doi: 10.1128/MMBR.62.1.1-34.1998. Microbiol Mol Biol Rev. 1998. PMID: 9529885 Free PMC article. Review.
-
Molecular and evolutionary characterization of the cp32/18 family of supercoiled plasmids in Borrelia burgdorferi 297.Infect Immun. 2000 Mar;68(3):1574-86. doi: 10.1128/IAI.68.3.1574-1586.2000. Infect Immun. 2000. PMID: 10678977 Free PMC article.
-
Transport protein evolution deduced from analysis of sequence, topology and structure.Curr Opin Struct Biol. 2016 Jun;38:9-17. doi: 10.1016/j.sbi.2016.05.001. Epub 2016 Jun 4. Curr Opin Struct Biol. 2016. PMID: 27270239 Free PMC article. Review.
-
The Alcaligenes eutrophus protein HoxN mediates nickel transport in Escherichia coli.J Bacteriol. 1995 Apr;177(7):1840-3. doi: 10.1128/jb.177.7.1840-1843.1995. J Bacteriol. 1995. PMID: 7896709 Free PMC article.
References
Publication types
MeSH terms
Substances
Grants and funding
LinkOut - more resources
Full Text Sources