Selective and Structural Constraints

Austin L Hughes, University of South Carolina, South Carolina, USA

Published online: July 2006

DOI: 10.1038/npg.els.0005124

The neutral theory of molecular evolution predicts that the rate of evolution will be low in portions of genes and of proteins that are functionally important. This insight is the basis for bioinformatics strategies that use sequence information to make functional predictions.

Keywords: amino acid sequence evolution; neutral theory; purifying selection; protein function; synonymous and nonsynonymous substitution

Figure 1. Alignment (Thompson et al., 1994) of the mature polypeptide sequences of four vertebrate aspartic proteinases. The conserved active site residues are boxed.
close
 References
    Duret L and Mouchiroud D (2000) Determinants of substitution rates in mammalian genes: expression pattern affects selection intensity but not mutation rate. Molecular Biology and Evolution 17: 68–74.
    book Hughes AL (1999) Adaptive Evolution of Genes and Genomes. New York, NY: Oxford University Press.
    Hughes AL, Friedman R and Murray M (2002) Genome-wide pattern of synonymous nucleotide substitution in two complete genomes of Mycobacterium tuberculosis. Emerging Infectious Diseases 8: 1342–1346.
    Hughes AL and Nei M (1988) Pattern of nucleotide substitution at MHC class I loci reveals overdominant selection. Nature 335: 167–170.
    Jordan IK, Rogozin IB, Wolf YI and Koonin EV (2002) Microevolutionary genomics of bacteria. Theoretical Population Genetics 61: 435–444.
    Kimura M (1977) Preponderance of synonymous changes as evidence for the neutral theory of molecular evolution. Nature 267: 275–276.
    book Kimura M (1983) The Neutral Theory of Molecular Evolution. Cambridge, UK: Cambridge University Press.
    Li W-H, Wu C-I and Luo C-C (1985) A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes. Molecular Biology and Evolution 2: 150–174.
    Sielecki AR, Fedorov AA, Boodhoo A, Andreeva NS and James NG (1990) Molecular and crystal structures of monoclinic porcine pepsin refined at 1.8 Å resolution. Journal of Molecular Biology 214: 143–170.
    Thompson JD, Higgins DG and Gibson TJ (1994) CLUSTALW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research 22: 4673–4680.
 Further Reading
    Kimura M (1986) DNA and the neutral theory. Philosophical Transactions of the Royal Society of London B312: 343–354.
    book Li W-H (1997) Molecular Evolution. Sunderland MA: Sinauer.
    book Mount DW (2001) Bioinformatics: Sequence and Genome Analysis. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.

Related Sub-Topics:

Molecular Evolution | Variation by Mutation and Recombination | Evolution Rates | Evolution of Coding and Functional Modules
Contact Editor close
Submit a note to the editor about this article by filling in the form below.

* Required Field

Article Title: Selective and Structural Constraints
 
How to Cite close
Hughes, Austin L(Jul 2006) Selective and Structural Constraints. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1038/npg.els.0005124]