Modularity in protein structures: study on all-alpha proteins

References

• Alcántara, R., Axelsen, K. B., Morgat, A., Belda, E., Coudert, E., Bridge, A., … Steinbeck, C. (2012). Rhea–a manually curated resource of biochemical reactions. Nucleic Acids Research, 40, D754–D760.
   PubMedGoogle Scholar
• Banerji, A., & Ghosh, I. (2011). Fractal symmetry of protein interior: What have we learned? Cellular and Molecular Life Sciences, 68, 2711–2737.10.1007/s00018-011-0722-6
   PubMed Web of Science ®Google Scholar
• Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, N. T., Weissig, H., … Bourne, E. P. (2000). The Protein Data Bank. Nucleic Acids Research, 28, 235–242.10.1093/nar/28.1.235
   PubMed Web of Science ®Google Scholar
• Broom, A., Doxey, A. C., Lobsanov, Y. D., Berthin, G. L., Rose, R. D., Howell, L. P., ... Meiering, M. E. (2012). Modular evolution and the origins of symmetry: Reconstruction of a three-fold symmetric globular protein. Structure, 20, 161–171.10.1016/j.str.2011.10.021
   PubMed Web of Science ®Google Scholar
• Chothia, C. (1981). Helix to helix packing in proteins. Journal of Molecular Biology, 145, 215–250.10.1016/0022-2836(81)90341-7
   PubMed Web of Science ®Google Scholar
• Chothia, C., & Gough, J. (2009). Genomic and structural aspects of protein evolution. Biochemical Journal, 419, 15–28.10.1042/BJ20090122
   PubMed Web of Science ®Google Scholar
• Chothia, C., & Lesk, A. (1985). Helix movements in proteins. Trends in Biochemical Sciences, 10, 116–118.10.1016/0968-0004(85)90270-1
   Web of Science ®Google Scholar
• Cossio, P., Trovato, A., Pietrucci, F., Seno, F., Maritan, A., & Laio, A. (2010). Exploring the universe of protein structures beyond the protein data bank. PLoS Computational Biology, 6, e1000957.10.1371/journal.pcbi.1000957
   PubMed Web of Science ®Google Scholar
• Cuff, A., Redfern, O. C., Greene, L., Sillitoe, I., Lewis, T., Dibley, M., ... Orengo, C. (2009). The CATH hierarchy revisited-structural divergence in domain superfamilies and the continuity of fold space. Structure, 17, 1051–1062.10.1016/j.str.2009.06.015
   PubMed Web of Science ®Google Scholar
• Day, R., Lennox, K. P., Dahl, D. B., Vannucci, A., & Tsai, W. J. (2010). Characterizing the regularity of tetrahedral packing motifs in protein tertiary structure. Bioinformatics, 26, 3059–3066.10.1093/bioinformatics/btq573
   PubMed Web of Science ®Google Scholar
• de Lima Morais, D. A., Fang, H., Rackham, O. J. L., Wilson, D., Pethica, R., Chothia, C., & Gough, J. 2011. SUPERFAMILY 1.75 including a domain-centric gene ontology method. Nucleic Acids Research 39, D427–D434.10.1093/nar/gkq1130
   PubMedGoogle Scholar
• Dellus-Gur, E., Toth-Petroczy, A., Elias, M., & Tawfik, S. D. (2013). What makes a protein fold amenable to functional innovation? Fold polarity and stability trade-offs. Journal of Molecular Biology, 425, 2609–2621.10.1016/j.jmb.2013.03.033
   PubMed Web of Science ®Google Scholar
• Dokholyan, N. V., Li, L., Ding, F., & Shakhnovich, I. E. (2002). Topological determinants of protein folding. Proceedings of the National academy of Sciences of the United States of America, 99, 8637–8641.10.1073/pnas.122076099
   PubMed Web of Science ®Google Scholar
• Efimov, A. V. (1997). A structural tree for proteins containing 3beta-corners. FEBS Letters, 407, 37–41.10.1016/S0014-5793(97)00296-2
   PubMed Web of Science ®Google Scholar
• Efimov, A. V. (1998). A structural tree for proteins containing S-like beta-sheets. FEBS Letters, 437, 246–250.10.1016/S0014-5793(98)01244-7
   PubMed Web of Science ®Google Scholar
• Efimov, A. V., & Kondratova, M. S. (2003). A comparative analysis of interhelical polar interactions of various alpha-helix packings in proteins. Molecular Biology, 37, 515–521.
   Web of Science ®Google Scholar
• Eisenbeis, S., Proffitt, W., Coles, M., Truffault, V., Shanmugaratnam, S., Meiler, J., & Hocker, B. (2012). Potential of fragment recombination for rational design of proteins. Journal of the American Chemical Society, 134, 4019–4022.10.1021/ja211657k
   PubMed Web of Science ®Google Scholar
• Emmert-Streib, F., & Mushegian, A. (2007). A topological algorithm for identification of structural domains of proteins. BMC Bioinformatics, 8, 237–247.10.1186/1471-2105-8-237
   PubMed Web of Science ®Google Scholar
• Engelhardt, B. E., Jordan, M. I., Srouji, J. R., et al. (2011). Genome-scale phylogenetic function annotation of large and diverse protein families. Genome Research, 1969–1980.10.1101/gr.104687.109
   PubMed Web of Science ®Google Scholar
• Furnham, N., Holliday, G. L., de Beer, T. A. P., Jacobsen, J. O. B., Pearson, W. R., & Thornton, M. J. (2014). The Catalytic Site Atlas 2.0: Cataloging catalytic sites and residues identified in enzymes. Nucleic Acids Research, 42, D485–D489.
   PubMedGoogle Scholar
• Gianni, S., Brunori, M., Jemth, P., Mikael, O., & Mingjie, Z. (2009). Distinguishing between smooth and rough free energy barriers in protein folding. Biochemistry, 48, 11825–11830.10.1021/bi901585q
   PubMed Web of Science ®Google Scholar
• Gordeev, A. B., & Efimov, A. V. (2013). Modeling of folds and folding pathways for some protein families of (α+β)- and (α/β)-classes. Journal of Biomolecular Structure and Dynamics, 31, 4–16.
   PubMed Web of Science ®Google Scholar
• Grainger, B., Sadowski, M. I., & Taylor, W. R. (2010). Re-evaluating the “rules” of protein topology. Journal of Computational Biology, 17, 1371–1384.10.1089/cmb.2009.0265
   PubMed Web of Science ®Google Scholar
• Hattori, M., Okuno, Y., Goto, S., & Minoru, K. (2003). Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathways. Journal of the American Chemical Society, 125, 11853–11865.10.1021/ja036030u
   PubMed Web of Science ®Google Scholar
• Hegyi, H., & Gerstein, M. (1999). The relationship between protein structure and function: A comprehensive survey with application to the yeast genome. Journal of Molecular Biology, 288, 147–164.10.1006/jmbi.1999.2661
   PubMed Web of Science ®Google Scholar
• Hleap, J. S., Susko, E., & Blouin, C. (2013). Defining structural and evolutionary modules in proteins: A community detection approach to explore sub-domain architecture. BMC Structural Biology, 13, 20.10.1186/1472-6807-13-20
   PubMed Web of Science ®Google Scholar
• Höcker, B. (2014). Design of proteins from smaller fragments-learning from evolution. Current Opinion in Structural Biology, 27, 56–62.10.1016/j.sbi.2014.04.007
   PubMed Web of Science ®Google Scholar
• Holliday, G. L., Rahman, S. A., Furnham, N., & Thornton, M. J. (2014). Exploring the biological and chemical complexity of the ligases. Journal of Molecular Biology, 426, 2098–2111.
   PubMed Web of Science ®Google Scholar
• Ivankov, D. N., Bogatyreva, N. S., Lobanov, M. Y., & Galzitskaya, V. O. (2009). Coupling between properties of the protein shape and the rate of protein folding. PLoS ONE, 4, e6476.10.1371/journal.pone.0006476
   PubMed Web of Science ®Google Scholar
• Kabsch, W., & Sander, C. (1983). Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22, 2577–2637.10.1002/(ISSN)1097-0282
   PubMed Web of Science ®Google Scholar
• Kamat, A. P. and Lesk, A. M. 2007. Contact patterns between helices and strands of sheet define protein folding patterns. Proteins: Structure, Function, and Bioinformatics, 66, 869–876.10.1002/prot.21241
   PubMed Web of Science ®Google Scholar
• Khersonsky, O., & Tawfik, D. S. (2010). Enzyme promiscuity: A mechanistic and evolutionary perspective. Annual Review of Biochemistry, 79, 471–505.
   PubMed Web of Science ®Google Scholar
• Kitano, H. (2004). Biological robustness. Nature Reviews Genetics, 5, 826–837.10.1038/nrg1471
   PubMed Web of Science ®Google Scholar
• Kloczkowski, A., Jernigan, R. L., Wu, Z., Song, G., Lei, Y., Kolinski, A., & Pokarowski, P. (2009). Distance matrix-based approach to protein structure prediction. Journal of Structural and Functional Genomics, 10, 67–81.10.1007/s10969-009-9062-2
   PubMedGoogle Scholar
• Kolodny, R., Pereyaslavets, L., Samson, A. O., & Levitt, M. (2013). On the universe of protein folds. Annual Review of Biophysics, 42, 559–582.10.1146/annurev-biophys-083012-130432
   PubMed Web of Science ®Google Scholar
• Konagurthu, A. S., Lesk, A. M., & Allison, L. (2012). Minimum message length inference of secondary structure from protein coordinate data. Bioinformatics, 28, i97–i105.10.1093/bioinformatics/bts223
   PubMedGoogle Scholar
• Konagurthu, A. S., Stuckey, P. J., & Lesk, A. M. (2008). Structural search and retrieval using a tableau representation of protein folding patterns. Bioinformatics, 24, 645–651.10.1093/bioinformatics/btm641
   PubMed Web of Science ®Google Scholar
• Kun, Á., & Scheuring, I. (2009). Evolution of cooperation on dynamical graphs. BioSystems, 96, 65–68.10.1016/j.biosystems.2008.11.009
   PubMed Web of Science ®Google Scholar
• Lammert, H., Schug, A., & Onuchic, J. N. (2009). Robustness and generalization of structure-based models for protein folding and function. Proteins, 77, 881–891.10.1002/prot.v77:4
   PubMed Web of Science ®Google Scholar
• Leopold, P. E., Montal, M., and Onuchic, J. N. 1992. Protein folding funnels: A kinetic approach to the sequence-structure relationship. Proceedings of the National academy of Sciences of the United States of America, 89, 8721–8725.10.1073/pnas.89.18.8721
   PubMed Web of Science ®Google Scholar
• Li, W., & Godzik, A. (2006). Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics, 22, 1658–1659.10.1093/bioinformatics/btl158
   PubMed Web of Science ®Google Scholar
• Lorenz, D. M., Jeng, A., & Deem, M. W. (2011). The emergence of modularity in biological systems. Physics of Life Reviews, 8, 129–160.
   PubMed Web of Science ®Google Scholar
• Mann, P. 1999. Introduction to statistics. New Jersey, NJ: John Wiley & Sons.
   Google Scholar
• Martinez Cuesta, S., Furnham, N., Rahman, S. A., Sillitoe, I., & Thornton, M. J. (2014). The evolution of enzyme function in the isomerases. Current Opinion in Structural Biology, 26, 121–130.10.1016/j.sbi.2014.06.002
   PubMed Web of Science ®Google Scholar
• Murzin, A. G., Brenner, S. E., Hubbard, T., & Chothia, C. (1995). SCOP: A structural classification of proteins database for the investigation of sequences and structures. Journal of Molecular Biology, 247, 536–540.
   PubMed Web of Science ®Google Scholar
• Myers-Turnbull, D., Bliven, S. E., Rose, P. W., Aziz, K. Z., Youkharibache, P., Bourne, E. P., & Prlic, A. (2014). Systematic detection of internal symmetry in proteins using CE-Symm. Journal of Molecular Biology, 426, 2255–2268.10.1016/j.jmb.2014.03.010
   PubMed Web of Science ®Google Scholar
• Onuchic, J. N., & Wolynes, P. G. (2004). Theory of protein folding. Current Opinion in Structural Biology, 14, 70–75.10.1016/j.sbi.2004.01.009
   PubMed Web of Science ®Google Scholar
• Orengo, C., Michie, A., Jones, S., Jones, D. T., Swindells, M. B., & Thornton, M. J. (1997). CATH-a hierarchic classification of protein domain structures. Structure, 5, 1093–1109.10.1016/S0969-2126(97)00260-8
   PubMed Web of Science ®Google Scholar
• Panchenko, A. R., Luthey-Schulten, Z., & Wolynes, P. G. (1996). Foldons, protein structural modules, and exons. Proceedings of the National academy of Sciences of the United States of America, 93, 2008–2013.10.1073/pnas.93.5.2008
   PubMed Web of Science ®Google Scholar
• Paola, L. D., Paci, P., Santoni, D., Ruvo, M. D., & Giuliani, A. (2012). Proteins as sponges: A statistical journey along protein structure organization principles. Journal of Chemical Information and Modeling, 52, 474–482.10.1021/ci2005127
   PubMed Web of Science ®Google Scholar
• Pereira-Leal, J. B., Levy, E. D., and Teichmann, S. A. 2006. The origins and evolution of functional modules: Lessons from protein complexes. Philosophical Transactions of the Royal Society B: Biological Sciences, 361, 507–517.10.1098/rstb.2005.1807
   PubMed Web of Science ®Google Scholar
• Plaxco, K. W., Simons, K. T., & Baker, D. (1998). Contact order, transition state placement and the refolding rates of single domain proteins. Journal of Molecular Biology, 277, 985–994.10.1006/jmbi.1998.1645
   PubMed Web of Science ®Google Scholar
• Plaxco, K. W., Simons, K. T., Ruczinski, I., Baker, D., & February, V. R. (2000). Topology, stability, sequence, and length: Defining the determinants of two-state protein folding kinetics. Biochemistry, 39 11177–11183.10.1021/bi000200n
   PubMed Web of Science ®Google Scholar
• Przytycka, T., Srinivasan, R., & Rose, G. D. (2002). Recursive domains in proteins. Protein Science, 11, 409–417.
   PubMed Web of Science ®Google Scholar
• Rahman, S. A., Cuesta, S. M., Furnham, N., Holliday, G. L., & Thornton, M. J. (2014). EC-BLAST: A tool to automatically search and compare enzyme reactions. Nature Methods, 1–7.
   PubMedGoogle Scholar
• Rorick, M. M. (2012). Quantifying protein modularity and evolvability: A comparison of different techniques. Biosystems, 110, 22–33.10.1016/j.biosystems.2012.06.006
   PubMed Web of Science ®Google Scholar
• Skolnick, J., Arakaki, A. K., Lee, S. Y., & Brylinkski, M. (2009). The continuity of protein structure space is an intrinsic property of proteins. Proceedings of the National academy of Sciences of the United States of America, 106, 15690–15695.10.1073/pnas.0907683106
   PubMed Web of Science ®Google Scholar
• Skolnick, J., & Gao, M. (2013). Interplay of physics and evolution in the likely origin of protein biochemical function. Proceedings of the National academy of Sciences of the United States of America, 110, 9344–9349.10.1073/pnas.1300011110
   PubMed Web of Science ®Google Scholar
• Srinivasan, R., & Rose, G. D. (1995). LINUS: A hierarchic procedure to predict the fold of a protein. Proteins: Structure, Function, and Genetics, 99, 81–99.
   Web of Science ®Google Scholar
• Takada, S. (2012). Coarse-grained molecular simulations of large biomolecules. Current Opinion in Structural Biology, 22, 130–137.10.1016/j.sbi.2012.01.010
   PubMed Web of Science ®Google Scholar
• Tasdighian, S., Paola, L. D., Ruvo, M. D., Paci, P., Santoni, D., Palquale, P., … Guillani, A. (2013). Modules identification in protein structures: The topological and geometrical solutions. Journal of Chemical Information and Modeling, 54, 159–168.
   PubMed Web of Science ®Google Scholar
• Taylor, W. R. (2002). A “periodic table” for protein structures. Nature, 416, 657–660.10.1038/416657a
   PubMed Web of Science ®Google Scholar
• Taylor, W. R., Chelliah, V., Hollup, S. M., MacDonald, T. J., & Jonassen, I. (2009). Probing the “dark matter” of protein fold space. Structure, 17, 1244–1252.10.1016/j.str.2009.07.012
   PubMed Web of Science ®Google Scholar
• Thiruv, B., Quon, G., Saldanha, S. A., & Steipe, B. (2005). Nh3D: A reference dataset of non-homologous protein structures. BMC Structural Biology, 5, 12.10.1186/1472-6807-5-12
   PubMed Web of Science ®Google Scholar
• Todd, A. E., Orengo, C. A., & Thornton, J. M. (2001). Evolution of function in protein superfamilies, from a structural perspective. Journal of Molecular Biology, 307, 1113–1143.10.1006/jmbi.2001.4513
   PubMed Web of Science ®Google Scholar
• Tomatis, P. E., Fabiane, S. M., Simona, F., Carloni, P., Sutton, B. J., & Vila, A. J. (2008). Adaptive protein evolution grants organismal fitness by improving catalysis and flexibility. Proceedings of the National academy of Sciences of the United States of America, 105, 20605–20610.10.1073/pnas.0807989106
   PubMed Web of Science ®Google Scholar
• Wagner, G. P., Pavlicev, M., & Cheverud, J. M. (2007). The road to modularity. Nature Reviews Genetics, 8, 921–931.10.1038/nrg2267
   PubMed Web of Science ®Google Scholar
• Wang, G., & Dunbrack, R. L. 2005. PISCES: Recent improvements to a PDB sequence culling server. Nucleic Acids Research, 33, W94–W98.10.1093/nar/gki402
   PubMedGoogle Scholar
• Wang, J., Oliveira, R. J., Chu, X., Whitford, C. P., Chahine, J., Han, W., ... Leite, V. (2012). Topography of funneled landscapes determines the thermodynamics and kinetics of protein folding. Proceedings of the National academy of Sciences of the United States of America, 109, 15763–15768.10.1073/pnas.1212842109
   PubMed Web of Science ®Google Scholar
• Wathen, B., & Jia, Z. (2013). A hierarchical order within protein structures underlies large separations between strands in β -sheets. Proteins: Structure, Function, and Bioinformatics, 81, 163–175.10.1002/prot.24173
   PubMed Web of Science ®Google Scholar
• Yuan, C., Chen, H., & Kihara, D. (2012). Effective inter-residue contact definitions for accurate protein fold recognition. BMC Bioinformatics, 13, 292–305.10.1186/1471-2105-13-292
   PubMed Web of Science ®Google Scholar
• Zuo, G., Wang, J., & Wang, W. (2006). Folding with downhill behavior and low cooperativity of proteins. Proteins, 63, 165–173.10.1002/prot.20857
   PubMed Web of Science ®Google Scholar