Pair-preferences: a quantitative measure of regularities in protein sequences.
We present here the results obtained by applying several different methods to quantitatively measure regularities in protein sequences based on pair-preferences. We have studied the distribution of amino acid residues, singly as well as in pairs in a large data base and have attempted this task. We confirmed the existence of well-defined pair-preferences in proteins which were shown to be remarkably absent in simulated random sequences of similar amino acid distribution. The analysis of the sequences from the SWISS-PROT data base using simple statistical tests. Fourier analysis, fractal analysis and statistical thermodynamical tests were used to derive parameters to define a natural sequence. As a consequence of the existence of pair-preferences, parameters like fractal dimension (D), spectral exponent (beta), scaling parameter (H) and entropy (statistical) were found to be characteristic for natural sequences. For a reference state we chose a randomised state devoid of any pair-preference. The pair-preferences qualified well to be used as quantitative measures of regularities in protein sequences.
Rani
M
M
Department of Biochemistry, School of Life Sciences, University of Hyderabad, India.
Mitra
C K
CK
D000465:Algorithms; D000595:Amino Acid Sequence; D016208:Databases, Factual; D015195:Drug Design; D004735:Energy Transfer; D005583:Fourier Analysis; D008958:Models, Molecular; D008962:Models, Theoretical; D011336:Probability; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*
D011506:Proteins