302
Views
7
CrossRef citations to date
0
Altmetric
Research Article

Comparing protein structures and inferring functions with a novel three-dimensional Yau–Hausdorff method

, , &
Pages 4151-4160 | Received 31 Jul 2018, Accepted 22 Oct 2018, Published online: 05 Dec 2018

References

  • Bilder, P. W., Ding, H., & Newcomer, M. E. (2004). Crystal structure of the ancient, Fe − S scaffold IscA reveals a novel protein fold. Biochemistry, 43(1), 133–139. DOI: 10.1021/bi035440s.
  • Chew, L., Goodrich, M., Huttenlocher, D., Kedem, K., Kleinberg, J., & Kravets, D. (1997). Geometric pattern matching under Euclidean motion. Computational Geometry, 7(1–2), 113–124.
  • Deng, M., Yu, C., Liang, Q., He, R., & Yau, S. S.-T. (2011). A novel method of characterizing genetic sequences: Genome space with biological distance and applications. PLoS One, 6, 1–9. DOI: 10.1371/journal.pone.0017293.
  • DePristo, M. A., Weinreich, D. M., & Hartl, D. L. (2005). Missense meanderings in sequence space: A biophysical view of protein evolution. Nature Reviews Genetics, 6(9), 678–687. DOI: 10.1038/nrg1672.
  • Gao, F., Shen, X. Z., Jiang, F., Wu, Y., & Han, C. (2016). DNA-guided genome editing using the Natronobacterium gregoryi Argonaute. Nature Biotechnology, 34(7), 768–773. DOI: 10.1038/nbt.3547.
  • Hebert, P. D. N., Ratnasingham, S., & de Waard, J. R. (2003). Barcoding animal life: Cytochrome c oxidase subunit 1 divergences among closely related species. Proceedings of the Royal Society of London B: Biological Sciences, 270(Suppl_1), S96–S99. DOI: 10.1098/rsbl.2003.0025.
  • Henikoff, S., & Henikoff, J. G. (1992). Amino acid substitution matrices from protein blocks. Proceedings of the National Academy of Sciences, 89, 10915–10919.
  • Holm, L., & Sander, C. (1996). Mapping the protein universe. Science, 273, 595–603.
  • Huang, H. H., Yu, C., Zheng, H., Hernandez, T., Yau, S. C., He, R., … Yau, S. S.-T. (2014). Global comparison of multiple-segmented viruses in 12-dimensional genome space. Molecular Phylogenetics and Evolution, 81, 29–36. DOI: 10.1016/j.ympev.2014.08.003.
  • Kabsch, W. (1978). A discussion of the solution for the best rotation to relate two sets of vectors. Acta Crystallographica Section A, 34(5), 827–828. DOI: 10.1107/S0567739478001680.
  • Li, B., Shen, Y., & Li, B. (2008). A new algorithm for computing the minimum Hausdorff distance between two point sets on a line under translation. Information Processing Letters, 106(2), 52–58. DOI: 10.1016/j.ipl.2007.10.003.
  • Mali, P., Yang, L., Esvelt, K. M., Aach, J., Guell, M., DiCarlo, J. E., … Church, G. M. (2013). RNA-guided human genome engineering via Cas9. Science, 339(6121), 823–826. DOI: 10.1126/science.1232033.
  • Mishra, A., Rana, P. S., Mittal, A., & Jayaram, B. (2014). D2N: Distance to the native. Biochimica et Biophysica Acta, 1844(10), 1798–1807. DOI: 10.1016/j.bbapap.2014.07.010.
  • Mishra, A., Rao, S., Mittal, A., & Jayaram, B. (2013). Capturing native/native like structures with a physico-chemical metric (pcSM) in protein folding. Biochimica et Biophysica Acta, 1834(8), 1520–1531. DOI: 10.1016/j.bbapap.2013.04.023.
  • Mittal, A., & Acharya, C. (2012). Extracting signatures of spatial organization for biomolecular nanostructures. Journal of Nanoscience and Nanotechnology, 12(11), 8249–8257. DOI: 10.1166/jnn.2012.6732.
  • Mittal, A., & Jayaram, B. (2011). Backbones of folded proteins reveal novel invariant amino acid neighborhoods. Journal of Biomolecular Structure and Dynamics, 28(4), 443–454. DOI: 10.1080/073911011010524954.
  • Mittal, A., Jayaram, B., Shenoy, S., & Bawa, T. S. (2010). A stoichiometry driven universal spatial organization of backbones of folded proteins: Are there Chargaffs rules for protein folding?. Journal of Biomolecular Structure and Dynamics, 28(2), 133–142. DOI: 10.1080/07391102.2010.10507349.
  • Noel, M. D., & Natasa, P. (2014). GR-Align: Fast and flexible alignment of protein 3D structures using Graphlet degree similarity. Bioinformatics, 30, 1259–1265. DOI: 10.1093/bioinformatics/btu020.
  • Ollagnier-de-Choudens, S., Sanakis, Y., & Fontecave, M. (2004). SufA/IscA: Reactivity studies of a class of scaffold proteins involved in [Fe-S] cluster assembly. JBIC Journal of Biological Inorganic Chemistry, 9(7), 828–838. DOI: 10.1007/s00775-004-0581-9.
  • Prlic, A., Bliven, S., Rose, P. W., Bluhm, W. F., Bizon, C., Godzik, A., & Bourne, P. E. (2010). Pre-calculated protein structure alignments at the RCSB PDB website. Bioinformatics, 26(23), 2983–2985. DOI: 10.1093/bioinformatics/btq572.
  • Saio, T., Kumeta, H., Ogura, K., Yokochi, M., Asayama, M., Katoh, S., … Inagaki, F. (2007). The cooperative role of OsCnfU-1A Domain I and Domain II in the iron–sulphur cluster transfer process as revealed by NMR. Journal of Biochemistry, 142(1), 113–121. DOI: 10.1093/jb/mvm120.
  • Smith, J. M. (1970). Natural selection and the concept of a protein space. Nature, 225, 563–564. DOI: 10.1038/225563a0.
  • Tian, K., Yang, X., Kong, Q., Yin, C., He, R., & Yau, S. S.-T. (2015). Two dimensional Yau–Hausdorff distance with applications on comparison of DNA and protein sequences. PloS One, 10, 1–19. DOI: 10.1371/journal.pone.0136577.
  • Tian, K., Zhao, X., & Yau, S. S.-T. (2018). Convex hull analysis of evolutionary and phylogenetic relationships between biological groups. Journal of Theoretical Biology, 456, 34–40. DOI: 10.1016/j.jtbi.2018.07.035.
  • Wilson, A. C., & Sarich, V. W. (1969). A molecular time scale for human evolution. Proceedings of the National Academy of Sciences, 63, 1088–1093.
  • Yu, C., Deng, M., Cheng, S. Y., Yau, S. C., He, R., & Yau, S. S.-T. (2013). Protein space: A natural method for realizing the nature of protein universe. Journal of Theoretical Biology, 318, 197–204. DOI: 10.1016/j.jtbi.2012.11.005.
  • Yu, C., Hernandez, T., Zheng, H., Yau, S. C., Huang, H. H., He, R., … Yau, S. S.-T. (2013b). Real time classification of viruses in 12 dimensions. PLoS One, 8, 1–10. DOI: 10.1371/journal.pone.0064328.
  • Zhang, Y., & Skolnick, J. (2004). Scoring function for automated assessment of protein structure template quality. Proteins: Structure, Function, and Bioinformatics, 57(4), 702–710. DOI: 10.1002/prot.20264.
  • Zhao, X., Tian, K., He, R., & Yau, S. S.-T. (2017). Establishing the phylogeny of Prochlorococcus with a new alignment-free method. Ecology and Evolution, 7(24), 11057–11065. DOI: 10.1002/ece3.3535.
  • Zhao, X., Wan, X., He, R., & Yau, S. S.-T. (2016). A new method for studying the evolutionary origin of the SAR11 clade marine bacteria. Molecular Phylogenetics and Evolution, 98, 271–279. DOI: 10.1016/j.ympev.2016.02.015.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.