Journal of Lipid Research, Vol 33, 287-296, Copyright © 1992 by Lipid Research, Inc.

ARTICLES

Computer programs to identify and classify amphipathic alpha helical domains

MK Jones, GM Anantharamaiah and JP Segrest
Department of Medicine, UAB Medical Center, Birmingham 35294.

The amphipathic alpha helix is an often-encountered secondary structural motif in biologically active peptides and proteins. An amphipathic helix is defined as an alpha helix with opposing polar and nonpolar faces oriented along the long axis of the helix. In a recent review article we grouped amphipathic helixes into seven distinct classes (A, H, L, G, K, C, and M) based upon a detailed analysis of their physical-chemical and structural properties (Segrest, J. P., et al. Amphipathic helix motif: classes and properties. Proteins. 1990. 8: 103-117). We have developed five computer programs that automate analysis and classification of potential amphipathic helical domains from primary amino acid sequence data. Here we describe these five programs and illustrate their usefulness by comparing two data sets of sequences representing different amphipathic alpha helical motifs from the exchangeable apolipoproteins. In a companion review article (Segrest, J. P., et al. The amphipathic helix in the exchangeable apolipoproteins: a review of secondary structure and function. J. Lipid Res. 1992. 33: 000-000) these five programs are used to localize and characterize the putative amphipathic helixes in the exchangeable apolipoproteins.
CiteULike    Complore    Connotea    Del.icio.us    Digg    Reddit    Technorati    What's this?

This article has been cited by other articles:

				S. A. Carlson, V. K. Sharma, Z. P. McCuddin, M. A. Rasmussen, and S. K. Franklin Involvement of a Salmonella Genomic Island 1 Gene in the Rumen Protozoan-Mediated Enhancement of Invasion for Multiple-Antibiotic-Resistant Salmonella enterica Serovar Typhimurium Infect. Immun., February 1, 2007; 75(2): 792 - 800. [Abstract] [Full Text] [PDF]

				R. Bussell Jr., T. F. Ramlall, and D. Eliezer Helix periodicity, topology, and dynamics of membrane-associated {alpha}-Synuclein Protein Sci., April 1, 2005; 14(4): 862 - 872. [Abstract] [Full Text] [PDF]

				R. J. Sharp, M. A. Perugini, S. M. Marcovina, and S. P. A. McCormick Structural features of apolipoprotein B synthetic peptides that inhibit lipoprotein(a) assembly J. Lipid Res., December 1, 2004; 45(12): 2227 - 2234. [Abstract] [Full Text] [PDF]

				C. Y. Y. Liu, R. Broadhurst, S. M. Marcovina, and S. P. A. McCormick Mutation of lysine residues in apolipoprotein B-100 causes defective lipoprotein[a] formation J. Lipid Res., January 1, 2004; 45(1): 63 - 70. [Abstract] [Full Text] [PDF]

				R. J. Sharp, M. A. Perugini, S. M. Marcovina, and S. P.A. McCormick A Synthetic Peptide That Inhibits Lipoprotein(a) Assembly Arterioscler. Thromb. Vasc. Biol., March 1, 2003; 23(3): 502 - 507. [Abstract] [Full Text] [PDF]

				J. P. Segrest, M. K. Jones, A. E. Klon, C. J. Sheldahl, M. Hellinger, H. De Loof, and S. C. Harvey A Detailed Molecular Belt Model for Apolipoprotein A-I in Discoidal High Density Lipoprotein J. Biol. Chem., November 5, 1999; 274(45): 31755 - 31758. [Abstract] [Full Text] [PDF]

				G Wang and M. Mulligan Comparative sequence analysis and predictions for the envelope glycoproteins of foamy viruses J. Gen. Virol., January 1, 1999; 80(1): 245 - 254. [Abstract]

				S. A. Carlson, T. K. Chatterjee, K. P. Murphy, and R. A. Fisher Mutation of a Putative Amphipathic alpha -Helix in the Third Intracellular Domain of the Platelet-Activating Factor Receptor Disrupts Receptor/G Protein Coupling and Signaling Mol. Pharmacol., March 1, 1998; 53(3): 451 - 458. [Abstract] [Full Text]

				J. P. Segrest, M. K. Jones, V. K. Mishra, V. Pierotti, S. H. Young, J. Borén, T. L. Innerarity, and N. Dashti Apolipoprotein B-100: conservation of lipid-associating amphipathic secondary structural motifs in nine species of vertebrates J. Lipid Res., January 1, 1998; 39(1): 85 - 102. [Abstract] [Full Text]

				J. K. Okamuro, B. Caster, R. Villarroel, M. Van Montagu, and K. D. Jofuku The AP2 domain of APETALA2 defines a large new family of DNA binding proteins in Arabidopsis PNAS, June 24, 1997; 94(13): 7076 - 7081. [Abstract] [Full Text] [PDF]