Geometrical criteria for left-handed twists within protein beta-strands


Using a statistical analysis on beta-sheet structures from the Protein Data Bank, characteristic angles within beta-strands were correlated to the nature of the side chains. The twists were computed from the atomic coordinates of five consecutive amino acids’ alpha carbons from single beta-strand sequences. Conditions on the angles for twists to be mainly left-handed are given together with the frequency of occurrence for these non-standard geometrical properties within protein beta-strands. Applications in protein structure prediction and CASP challenges in particular are envisioned by making use of the probabilities of occurrence in protein structures of angle value ranges for given amino acids.

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Caudron, B. and Jestin, J. (2014) Geometrical criteria for left-handed twists within protein beta-strands. Journal of Biophysical Chemistry, 5, 5-12. doi: 10.4236/jbpc.2014.51002.

Conflicts of Interest

The authors declare no conflicts of interest.


[1] Iliopoulos, I., Tsoka, S., Andrade, M.A., et al.(2003) Evaluation of annotation strategies using an entire genome sequence. Bioinformatics, 19, 717-726.
[2] Juncker, A.S., Jensen, L.J., Pierleoni, A., et al. (2009) Sequence-based feature prediction and annotation of proteins. Genome Biology, 10, 206.
[3] Blicher, T., Gupta, R., Wesolowska, A., et al. (2010) Protein annotation in the era of personal genomics. Current Opinion in Structural Biology,20,335-341.
[4] Moult, J., Hubbard, T., Bryant, S.H., et al. (1997) Critical assessment of methods of protein structure prediction (CASP): Round II. Proteins, 29, 2-6.<2::AID-PROT2>3.0.CO;2-T
[5] Kryshtafovych, A., Fidelis, K. and Moult, J. (2011) CASP9 results compared to those of previous CASP experiments. Proteins, 79, 196-207.
[6] Seno, F., Trovato, A., Banavar, J.R. and Maritan, A. (2008) Maximum entropy approach for deducing amino acid interactions in proteins. Physical Review Letters, 100, Article ID: 078102.
[7] Vassura, M., Margara, L., Di Lena, P., et al. (2008) Reconstruction of 3D structures from protein contact maps. IEEE-ACM Transactions on Computational Biology and Bioinformatics, 5, 357-367.
[8] Sulkowska, J.I., Morcos, F., Weigt, M., et al. (2012) Genomics-aided structure prediction. Proceedings of the National Academy of Sciences of USA, 109,10340-10345.
[9] Taylor, W.R., Jones, D.T. and Sadowski, M.I. (2012) Protein topology from predicted residue contacts. Protein Science, 21, 299-305.
[10] Hopf, T.A., Colwell, L.J., Sheridan, R., et al. (2012) Three-dimensional structures of membrane proteins from genomic sequencing. Cell, 149, 1607-1621.
[11] Abola, E.E., Sussman, J.L., Prilusky, J. and Manning, N.O. (1997) Protein Data Bank archives of three-dimensional macromolecular structures. Methods in Enzymology, 277, 556-571.
[12] Sussman, J.L., Lin, D., Jiang, J., et al. (1998) Protein Data Bank (PDB): Database of three-dimensional structural information of biological macromolecules. Acta Crystallographica Section D, 54, 1078-1084.
[13] Brenner, S.E., Koehl, P. and Levitt, M. (2000) The ASTRAL compendium for protein structure and sequence analysis. Nucleic Acids Research, 28, 254-256.
[14] Bateman, A., Birney, E., Cerruti, L., et al. (2002) The Pfam protein families database. Nucleic Acids Research, 30, 276-280.
[15] Banavar, J.R., Maritan, A., Micheletti, C. and Trovato, A. (2002) Geometry and physics of proteins. Proteins, 47, 315-322.
[16] Pal, L., Dasgupta, B. and Chakrabarti, P. (2005) 3(10)-Helix adjoining alpha-helix and beta-strand: Sequence and structural features and their conservation. Biopolymers, 78, 147-162.
[17] Greene, L.H., Lewis, T.E., Addou, S., et al. (2007) The CATH domain structure database: New protocols and classification levels give a more comprehensive resource for exploring evolution. Nucleic Acids Research, 35, D291-D297.
[18] Andreeva, A., Howorth, D., Chandonia, J.M., et al. (2008) Data growth and its impact on the SCOP database: New developments. Nucleic Acids Research, 36, D419-D425.
[19] Rost, B. and Sander, C. (1993) Prediction of protein secondary structure at better than 70% accuracy. Journal of Molecular Biology, 232, 584-599.
[20] Martin, J., Letellier, G., Marin, A., et al. (2005) Protein secondary structure assignment revisited: A detailed analysis of different assignment methods. BMC Structural Biology, 5, 17.
[21] Pauling, L. and Corey, R.B. (1951) Configurations of polypeptide chains with favored orientations around single bonds: two new pleated sheets. Proceedings of the National Academy of Sciences of USA, 37, 729-740.
[22] Sternberg, M.J. and Thornton, J.M. (1977) On the conformation of proteins: An analysis of beta-pleated sheets. Journal of Molecular Biology, 110, 285-296.
[23] Salemme, F.R. (1983) Structural properties of protein beta-sheets. Progress in Biophysics and Molecular Biology, 42, 95-133.
[24] Koh, E., Kim, T. and Cho, H.S. (2006) Mean curvature as a major determinant of beta-sheet propensity. Bioinformatics, 22, 297-302.
[25] Jestin, J. and Caudron, B. (2013) Characterizing the topology of protein beta-sheets by an axis. 162-1466-1-SP, HAL-Pasteur 00907789.
[26] Guilloux, A., Caudron, B. and Jestin, J.L. (2014) A method to predict amino acids at proximity of beta-sheet axes from protein sequences. Applied Mathematics, 5, 79-89.
[27] Chan, A.W., Hutchinson, E.G., Harris, D. and Thornton, J.M. (1993) Identification, classification, and analysis of beta-bulges in proteins. Protein Science, 2, 1574-1590.
[28] Chothia, C. (1973) Conformation of twisted beta-pleated sheets in proteins. Journal of Molecular Biology, 75, 295-302.
[29] Chou, K.C., Pottle, M., Nemethy, G., et al. (1982) Structure of beta-sheets-origin of the right handed twist and of the increased stability of anti-parallel over parallel sheets. Journal of Molecular Biology, 162, 89-112.
[30] Lasters, I. (1990) Estimating the twist of beta-strands embedded within a regular parallel beta-barrel structure. Protein Engineering, 4, 133-135.
[31] Shamovsky, I.L., Ross, G.M. and Riopelle, R.J. (2000) Theoretical studies on the origin of beta-sheet twisting. The Journal of Physical Chemistry B, 104, 11296-11307.
[32] Lifson, S. and Sander, C. (1979) Antiparallel and parallel beta-strands differ in amino acid residue preferences. Nature, 282, 109-111.
[33] Farzadfard, F., Gharaei, N., Pezeshk, H. and Marashi, S.A. (2008) Beta-sheet capping: Signals that initiate and terminate beta-sheet formation. Journal of Structural Biology, 161, 101-110.
[34] Bhattacharjee, N. and Biswas, P. (2009) Structural patterns in alpha helices and beta sheets in globular proteins. Protein and Peptide Letters, 16, 953-960.
[35] Caudron, B. and Jestin, J.L. (2012) Sequence criteria for the anti-parallel character of protein beta-strands. Journal of Theoretical Biology, 315, 146-149.
[36] Sternberg, M.J. and Thornton, J.M. (1977) On the conformation of proteins: Towards the prediction of strand arrangements in β-pleated sheets. Journal of Molecular Biology, 113, 401-418.
[37] Sternberg, M.J. and Thornton, J.M. (1977) On the conformation of proteins: Hydrophobic ordering of strands in β-pleated sheets. Journal of Molecular Biology, 115, 1-17.
[38] Wang, W. and Hecht, M.H. (2002) Rationally designed mutations convert de novo amyloid-like fibrils into monomerric β-sheet proteins. Proceedings of the National Academy of Sciences of the United States of America, 99, 2760-2765.
[39] Richardson, J.S. and Richardson, D.C. (2002) Natural β-sheet proteins use negative design to avoid edge-to-edge aggregation. Proceedings of the National Academy of Sciences of the United States of America, 99, 2754-2759.
[40] Koga, N., Tatsumi-Koga, R., Liu, G., Xiao, R., Acton, T.B., Montelione, G.T. and Baker, D. (2012) Principles for designing ideal protein structures. Nature, 491, 222-227.
[41] Guilloux, A., Caudron, B. and Jestin, J.L. (2013) A method to predict edge strands in beta-sheets from protein sequences. Computational and Structural Biotechnology Journal, 7, 1-7.
[42] Chothia, C., Levitt, M. and Richardson, D. (1977) Structure of proteins: Packing of alpha-helices and pleated sheets. Proceedings of the National Academy of Sciences of the United States of America, 74, 4130-4134.
[43] Cheng, J. and Baldi, P. (2005) Three-stage prediction of protein β-sheets by neural networks, alignments and graph algorithms. Bioinformatics, 21, i75-i84.
[44] Zafer, A., Yucel, A. and Hakan, E. (2011) Bayesian models and algorithms for protein β-sheet prediction. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 8, 395-409.
[45] Subramani, A. and Floudas, C.A. (2012) β-sheet topology prediction with high precision and recall for β and mixed α/β proteins. PLoS ONE, 7, Article ID: e32461.
[46] Peng, K., Obradovic, Z. and Vucetic, S. (2004) Exploring the bias in the PDB using contrast classifiers. In: Altman R.B., Dunker, K., et al., Eds., Pacific Symposium Biocomputing, World Scientific, Singapore.
[47] Hobohm, U., Scharf, M., Schneider, R. and Sander, C. (1992) Selection of representative protein data sets. Protein Science, 1, 409-417.
[48] Kabsch, W. and Sander, C. (1983) Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22, 2577-2637.
[49] Efimov, A.V. (1986) Standard conformations of a polypeptide chain in irregular protein regions. Molekuliarnaia Biologiia, 20, 250-260.
[50] Richards, F.M. and Kundrot, C.E. (1988) Identification of structural motifs from protein coordinate data: Secondary structure and first-level supersecondary structure. Proteins, 3, 71-84.
[51] Taylor, W.R. and Orengo, C.A. (1989) A holistic approach to protein structure alignment. Protein Engineering Design & Selection, 2, 505-519.
[52] Rose, G.D. and Seltzer, J.P. (1977) A new algorithm for finding the peptide chain turns in a globular protein. Journal of Molecular Biology, 113, 153-164.
[53] MacArthur, M.W. and Thornton, J.M. (1991) Influence of proline residues on protein conformation. Journal of Molecular Biology, 218, 397-412.
[54] Ho, B.K. and Brasseur, R. (2005) The Ramachandran plots of glycine and pre-proline. BMC Structural Biology, 5, 14.
[55] Skolnick, J., Kolinski, A. and Ortiz, A.R. (1997) Monsster: A method for folding globular proteins with a small number of distance restraints. Journal of Molecular Biology, 265, 217-241.
[56] Costantini, S., Facchiano, A.M. and Colonna, G. (2007) Evaluation of the structural quality of modeled proteins by using globularity criteria. BMC Structural Biology, 7, 9.
[57] DeRonne, K.W. and Karypis, G. (2009) Improved estimation of structure predictor quality. BMC Structural Biology, 9, 41.
[58] Benkert, P., Biasini, M. and Schwede, T. (2011) Toward the estimation of the absolute quality of individual protein structure models. Bioinformatics, 27,343-350.
[59] Moult, J., Fidelis, K., Kryshtafovych, A., Rost, B. and Tramontano, A. (2009) Critical assessment of methods of protein structure prediction—Round VIII. Proteins, 77, 1-4.
[60] Moult, J., Fidelis, K., Kryshtafovych, A. and Tramontano, A. (2011) Critical assessment of methods of protein structure prediction (CASP)—Round IX. Proteins, 79, 1-5.
[61] Ito, N., Phillips, S.E., Stevens, C., Ogel, Z.B., Mcpherson, M.J., Keen, J.N., Yadav, K.D.S. and Knowles, P.F. (1991) Novel thioether bond revealed by a 1.7 A crystal structure of galactose oxidase. Nature, 350, 87-90.

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