Share This Article:

Hierarchy of Protein Loop-Lock Structures: A New Server for the Decomposition of a Protein Structure into a Set of Closed Loops

DOI: 10.4236/cmb.2013.31001    2,764 Downloads   6,617 Views   Citations

ABSTRACT

HoPLLS (Hierarchy of protein loop-lock structures) (http://leah.haifa.ac.il/~skogan/Apache/mydata1/main.html) is a web server that identifies closed loops-a structural basis for protein domain hierarchy. The server is based on the loop-and-lock theory for structural organisation of natural proteins. We describe this web server, the algorithms for the decomposition of a 3D protein into loops and the results of scientific investigations into a structural “alphabet” of loops and locks.

Conflicts of Interest

The authors declare no conflicts of interest.

Cite this paper

S. Kogan, Z. Frenkel, O. Kupervasser and Z. Volkovich, "Hierarchy of Protein Loop-Lock Structures: A New Server for the Decomposition of a Protein Structure into a Set of Closed Loops," Computational Molecular Bioscience, Vol. 3 No. 1, 2013, pp. 1-8. doi: 10.4236/cmb.2013.31001.

References

[1] I. N. Berezovsky, A. Y. Grosberg and E. N. Trifonov, “Closed Loops of Nearly Standard Size: Common Basic Element of Protein Structure,” FEBS Letters, Vol. 466, No. 2, 2000, pp. 283-286. Hdoi:10.1016/S0014-5793(00)01091-7
[2] I. N. Berezovsky and E. N. Trifonov, “Protein Structure and Folding: A New Start,” Journal of Biomolecular Structure & Dynamics, Vol. 19, No. 3, 2001, pp. 397-403. Hdoi:10.1080/07391102.2001.10506749
[3] I. N. Berezovsky and E. N. Trifonov, “Loop Fold Structure of Proteins: Resolution of Levinthal’s Paradox,” Journal of Biomolecular Structure & Dynamics, Vol. 20, No. 1, 2002, pp. 5-6. Hdoi:10.1080/07391102.2002.10506817
[4] I. N. Berezovsky, V. M. Kirzhner, A. Kirzhner and E. N. Trifonov, “Protein Folding: Looping from Hydrophobic Nuclei,” Proteins-Structure Function and Genetics, Vol. 45, No. 4, 2001, pp. 346-350. Hdoi:10.1002/prot.1155
[5] E. N. Trifonov, A. Kirzhner, V. M. Kirzhner and I. N. Berezovsky, “Distinct Stages of Protein Evolution as Suggested by Protein Sequence Analysis,” Journal of Molecular Evolution, Vol. 53, No. 4-5, 2001, pp. 394-401. Hdoi:10.1007/s002390010229
[6] E. N. Trifonov and I. N. Berezovsky, “Evolutionary Aspects of Protein Structure and Folding,” Current Opinion in Structural Biology, Vol. 13, No. 1, 2003, pp. 110-114. Hdoi:10.1016/S0959-440X(03)00005-8
[7] I. N. Berezovsky, A. Kirzhner, V. M. Kirzhner, V. R. Rosenfeld and E. N. Trifonov, “Protein Sequences Yield a Proteomic Code,” Journal of Biomolecular Structure & Dynamics, Vol. 21, No. 3, 2003, pp. 317-325. Hdoi:10.1080/07391102.2003.10506928
[8] I. N. Berezovsky, A. Kirzhner, V. M. Kirzhner and E. N. Trifonov, “Spelling Protein Structure,” Journal of Biomolecular Structure & Dynamics, Vol. 21, No. 3, 2003, pp. 327-339. Hdoi:10.1080/07391102.2003.10506929
[9] G. Koczyk and I. N. Berezovsky, “Domain Hierarchy and Closed Loops (DHcL): A Server for Exploring Hierarchy of Protein Domain Structure,” Nucleic Acids Research, Vol. 36 Suppl 2, 2008, pp. W239-W245. Hdoi:10.1093/nar/gkn326
[10] I. N. Berezovsky and E. N. Trifonov, “Van Der Waals Locks: Loop-N-Lock Structure of Globular Proteins,” Journal of Molecular Biology, Vol. 307, No. 5, 2001, pp. 1419-1426. Hdoi:10.1006/jmbi.2001.4554
[11] E. Aharonovsky and E. N. Trifonov, “Sequence Structure of Van Der Waals Locks in Proteins,” Journal of Biomolecular Structure & Dynamics, Vol. 22, No. 5, 2005, pp. 545-553. Hdoi:10.1080/07391102.2005.10507024
[12] J. Y. Hsiao, C. Y. Tang and R. S. Chang, “An Efficient Algorithm for Finding a Maximum Weight 2-Independent Set on Interval-Graphs,” Information Processing Letters, Vol. 43, No. 5, 1992, pp. 229-235. Hdoi:10.1016/0020-0190(92)90216-I
[13] I. N. Berezovsky and E. N. Trifonov, “Flowering Buds of Globular Proteins: Transpiring Simplicity of Protein Organization,” Comparative and Functional Genomics, Vol. 3, No. 6, 2002, pp. 525-534. Hdoi:10.1002/cfg.223
[14] Z. M. Frenkel and E. N. Trifonov, “Closed Loops of TIM Barrel Protein Fold,” Journal of Biomolecular Structure & Dynamics, Vol. 22, No. 6, 2005, pp. 643-655. Hdoi:10.1080/07391102.2005.10507032
[15] R. Durbin, S. Eddy, A. Krogh and G. Mitchison, “Biological Sequence Analysis,” Cambridge University Press, Cambridge, 1998. Hdoi:10.1017/CBO9780511790492
[16] E. N. Trifonov, “The Triplet Code from First Principles,” Journal of Biomolecular Structure & Dynamics, Vol. 22, No. 1, 2004, pp. 1-11. Hdoi:10.1080/07391102.2004.10506975
[17] E. N. Trifonov, “Theory of Early Molecular Evolution: Predictions and Confirmations,” Discovering Biomolecular Mechanisms with Computational Biology, 2006, pp. 107-116. Hdoi:10.1007/0-387-36747-0_9
[18] G. Ausiello, P. F. Gherardini, P. Marcatili, A. Tramontano, A. Via and M. Helmer-Citterich, “FunClust: A Web Server for the Identification of Structural Motifs in a Set of Non-Homologous Protein Structures,” BMC Bioinformatics, Vol. 9 Suppl 2, 2008, Article No: S2. Hdoi:10.1186/1471-2105-9-S2-S2
[19] R. Helling, H. Li, R. Melin, J. Miller, N. Wingreen, C. Zeng and C. Tang, “The Designability of Protein Structures,” Journal of Molecular Graphics & Modelling, Vol. 19, No. 1, 2001, pp. 157-167. Hdoi:10.1016/S1093-3263(00)00137-6
[20] Z. M. Frenkel and E. N. Trifonov, “Walking through Protein Sequence Space,” Journal of Theoretical Biology, Vol. 244, No. 1, 2007, pp. 77-80. Hdoi:10.1016/j.jtbi.2006.07.027
[21] Z. M. Frenkel and E. N. Trifonov, “Walking through the Protein Sequence Space: Towards New Generation of the Homology Modeling,” Proteins-Structure Function and Bioinformatics, Vol. 67, No. 2, 2007, pp. 271-284. Hdoi:10.1002/prot.21325
[22] Z. M. Frenkel, “Does Protein Relatedness Require Sequence Matching? Alignment via Networks in Sequence Space,” Journal of Biomolecular Structure & Dynamics, Vol. 26, No. 2, 2008, pp. 215-222. Hdoi:10.1080/07391102.2008.10507237
[23] S. F. Altschul, T. L. Madden, A. A. Schaffer, J. H. Zhang, Z. Zhang, W. Miller and D. J. Lipman, “Gapped BLAST and PSI-BLAST: A New Generation of Protein Database Search Programs,” Nucleic Acids Research, Vol. 25, No. 17, 1997, pp. 3389-3402. Hdoi:10.1093/nar/25.17.3389
[24] S. F. Altschul, J. C. Wootton, E. M. Gertz, R. Agarwala, A. Morgulis, A. A. Schaffer and Y. K. Yu, “Protein Database Searches Using Compositionally Adjusted Substitution Matrices,” FEBS Journal, Vol. 272, No. 20, 2005, pp. 5101-5109. Hdoi:10.1111/j.1742-4658.2005.04945.x

  
comments powered by Disqus

Copyright © 2018 by authors and Scientific Research Publishing Inc.

Creative Commons License

This work and the related PDF file are licensed under a Creative Commons Attribution 4.0 International License.