CLASSIFICATION OF AMINO ACIDS BY MULTIVARIATE DATA ANALYSIS, BASED ON THERMODYNAMIC AND STRUCTURAL CHARACTERISTICS
DOI:
https://doi.org/10.24193/subbchem.2017.2.02Keywords:
principal component analysis, cluster analysis, amino acids, thermodynamic characteristics, structural characteristicsAbstract
Principal component analysis (PCA) and cluster analysis (CA) were applied to classify 20 natural amino acids. We selected 18 characteristics, properties available from literature, as a basis for the classification. The correlations between these characteristics and their classification were investigated, as well as the classification of the amino acids. The results are presented as score plots of the first 3 principal components and as dendrograms obtained by clustering analysis. The resulting classification is consistent with the chemical behavior of amino acids and their mutual substitution possibilities in peptides and proteins.
References
C.D. Neniţescu, “Chimie organică”, Vol. II, 6th Edition, EDP Bucureşti, 1968.
***, „Molecular Biology Web Book”, Chap. 2, „Protein Structure and Function”, http://www.web-books.com/MoBio/Free/Chap2.htm (accessed September 2016).
U.C. Davis, „Biological Sciences: Amino Acid Structure/Function”, https://www.mcb.ucdavis.edu/courses/bis102/AAProp.html, (accessed September 2016).
W.R. Taylor, Journal of Theoretical Biology, 1986, 119, 205.
M.J. Betts, R.B. Russell. „Amino acid properties and consequences of substitutions“. In „Bioinformatics for Geneticists“, M.R. Barnes, I.C. Gray eds., Wiley, Chichester, 2003.
O. Horovitz, A. Mocanu, Gh. Tomoaia, M. Crisan, L.-D. Bobos, Cs. Racz, M. Tomoaia-Cotisel, Studia UBB Chemia, 2007, 52, 53.
D. Bordo, P. Argos, Journal of Molecular Biology, 1991, 217, 721.
T.P.E. auf der Heyde, Journal of Chemical Education, 1990, 67, 461.
H. Pop, C. Sârbu, O. Horovitz, D. Dumitrescu, Journal of Chemical Information and Computer Sciences, 1996, 36, 465.
C. Sârbu, O. Horovitz, H.Pop, Journal of Chemical Information and Computer Sciences, 1996, 36, 1098.
O. Horovitz, C.Sarbu, H.F.Pop, „Clasificarea ratională a elementelor chimice”, Ed. Dacia, Cluj-Napoca, 2000.
O.Horovitz, C.Sârbu, H.F.Pop, Revista de Chimie (Bucharest), 2000, 51, 17.
O. Horovitz, C. Sârbu, Journal of Chemical Education, 2005, 82, 473.
O. Horovitz, C. Sârbu, Revista de Chimie (Bucharest), 2006, 57, 413.
J. Reichert, A. Jabs, P. Slickers, J. Sühnela, Nucleic Acids Research, 2000, 28, 246.
D.R. Lide, “Handbook of Chemistry and Physics”, 12nd Ed., CRC Press, Boca Raton, 1991.
P.Y. Chou, G.D. Fasman, Biochemistry, 1974, 13, 211.
P. Prevelige, Jr., G.D. Fasman, Chou-Fasman, Prediction of Secondary Structure, in Prediction of Protein Structure and the Principles of Protein Conformation, ed. G. B. Fasman, Plenum Press, New York, 1989.
***, Chemistry WebBook, NIST Standard Reference Database Number 69 - June, http://webbook.nist.gov/chemistry/ (accessed September 2016).
J. J. P. Stewart, Journal of Computational Chemistry, 1989, 10, 209.
***, HyperChem7.5 Molecular Modeling System, Hypercube Inc., Gainesville, 2002.
C. Chotia, J. Mol. Biol., 1975, 105, 1.
***, CRC Handbook of Chem.& Phys., 58 Ed., Cleveland, Ohio, 1977.
D. Eisner, R.M. Weiss, T.C. Terwilliger, William Wilcox, Faraday Symp. Chem. Soc., 1982, 17, 109.
J.L. Cornette, K.B. Cease, H. Margalit, J.L. Spouge, J.A. Berzofsky, C. DeLisi, J. Mol. Biol., 1987, 195, 659.
A. Neumaier, W. Huyer, E. Bornberg-Bauer, „Hydrophobicity Analysis of Amino Acids”, http://www.mat.univie.ac.at/~neum/software/protein/aminoacids.html, (accessed September 2016).
J. Kyte, R.F. Doolittle, Journal of Molecular Biology, 1982, 157, 105.
R.C Beavis, D. Fenyo, “Amino Acid Properties of Interest in Protein Chemistry”, http://prowl.rockefeller.edu/aainfo/contents.htm (accessed September 2016).
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