dd@beta.UUCP (Dan Davison) (10/05/87)
In a recent discussion of protein structure, I mentioned in a posting that I would provide references if asked. Well, I was asked, so here goes: Hydrophobicity of amino acid residues in globular proteins, Rose et al, Science 229:834-838 (30 Aug 1985 *The detection and classification of membrane-spanning proteins. Klein, Kanehisa, and DeLisi, BBA 815:468-476 1985 Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. Garnier, Osguthorpe and Robson, JMB 97-20 1978 *Protein secondary structure: Studies on the limits of prediction accuracy. Palau, Argos, and Puigdomenech. Intl. J. Peptide and Protein Research. 19:394-401 1982 Amino acid distribution in protein secondary structures. Argos and Palau. Int. J. Peptide and Protein Research 19: 380-393 1982 *Logical Analysis of the mechanism of protein folding. Predictions of helices, loops and beta structures from primary structure. Nagano, JMB 75:401-420 1973 On the computation of the tertiary structure of globular proteins--IV. Use of secondary structure information. Cariani and Goel. Bull. Math. Biol. 47(3):367-407 1985 Secondary structure prediction of human salivary proline-rich proteins. Cid et al, FEBS Letters 198(1):140-144 March 1986 *Automatic identification of secondary structure in globular proteins. Levitt and Greer, JMB 114:181-293. 1977 *Evaluation of methods for the prediction of membrane protein secondary structures. Wallace, Cascio, and Mielke. PNAS 83:9423-9427 December 1986. *Identifying non-polar transmembrane helices in amino acid sequences of membrane proteins. Engelman, Steitz, and Goldman. Ann Rev. Biophys. and Biophys. Chem. 15:321-353 1986 *Algorithms for prediction of alpha helical and beta-structural regions in globular proteins. Lim. JMB 88:873-894 1974. Prediction of beta-turns. Chou and Fasman. Biophys. J. 26:367-384 June 1979 *Prediction of the secondary structure of proteins from their amino acid sequence. Chou and Fasman Adv. Enz 47:45-147 1979 *Turn Prediction in proteins using a pattern-matching approach. Cohen, Abarbanel, Kuntz, and Fletterick. Biochemistry 25:266-275 1986 *also see Cohen et al. Biochemistry 22:4894-4904 1983. Prediction of protein secondary structure and active sites using alignment of homologous sequences. JMB (1987) 957-961. Vol number is cut off in the photocopy, sorry. It's between May and August of 1987, I think. *T-cell antigenic sites tend to be amphipathic structures. DeLisi and Berzofsky PNAS 82:7048-7052 1985 (October) *and Strong Conformational propensities enhance t-cell antigenicity Spouge et al. J. Immunology, 138(1):204-212 1987 ---------------------------------------------------------------------- The references with asterisks are either historically important or ones that I consider worthy of a great deal of attention. Notice that attention gradually turned to specific classes of proteins and specific parts of secondary structure (beta sheets *or* beta turns *or* alpha helices) from the 1970s to the 1980s. This generally reflects appreciation of the fact that all proteins are not generically alike, and represents a very healthy trend in approaching the problem of calculating and predicting protein properties. I've left off classics like Kyte and Doolittle hydropathicity values because most of the 1980s papers reference them; see especially the J. of Immunology paper as a good source of references. dan davison/theoretical biology/t-10 ms k710/los alamos national laboratory/ dd@lanl.gov / dd@lanl.uucp or ...cmcl2!lanl!dd/ 505-665-1355 (FTS 885-1355) /