PMID: 24229215Nov 16, 2013Paper

Topology and structural self-organization in folded proteins

Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics
Martin LundgrenAntti J Niemi

Abstract

Topological methods are indispensable in theoretical studies of particle physics, condensed matter physics, and gravity. These powerful techniques have also been applied to biological physics. For example, knowledge of DNA topology is pivotal to the understanding as to how living cells function. Here, the biophysical repertoire of topological methods is extended, with the aim to understand and characterize the global structure of a folded protein. For this, the elementary concept of winding number of a vector field on a plane is utilized to introduce a topological quantity called the folding index of a crystallographic protein. It is observed that in the case of high resolution protein crystals, the folding index, when evaluated over the entire length of the crystallized protein backbone, has a very clear and strong propensity towards integer values. The observation proposes that the way how a protein folds into its biologically active conformation is a structural self-organization process with a topological facet that relates to the concept of solitons. It is proposed that the folding index has a potential to become a useful tool for the global, topological characterization of the folding pathways.

References

May 21, 1977·Journal of Theoretical Biology·A S Davydov
Dec 1, 1992·Protein Science : a Publication of the Protein Society·L HolmG Vriend
Nov 5, 1983·Journal of Molecular Biology·M Levitt
Jun 25, 1983·Journal of Molecular Biology·Janet M Thornton, B L Sibanda
Jul 15, 1982·Nature·Janet M Thornton, B L Chakauya
Mar 22, 1996·Journal of Molecular Biology·J A Christopher, T O Baldwin
Aug 2, 1996·Science·L Holm, C Sander
Feb 12, 1998·Proceedings of the National Academy of Sciences of the United States of America·D G DonneH J Dyson
Oct 31, 1998·Protein Engineering·I N Shindyalov, P E Bourne
Dec 11, 1999·Nucleic Acids Research·H M BermanP E Bourne
Sep 28, 2002·Acta Crystallographica. Section D, Biological Crystallography·Rajasri BhattacharyyaPinak Chakrabarti
Dec 31, 2002·Proceedings of the National Academy of Sciences of the United States of America·Peter Rogen, Boris Fain
Jan 4, 2003·Nature·William R Taylor, Kuang Lin
Feb 20, 2003·Mathematical Biosciences·Peter Røgen, Henrik Bohr
Jun 26, 2003·Nucleic Acids Research·Adam Zemla
Jul 1, 1963·Journal of Molecular Biology·G N RAMACHANDRANV SASISEKHARAN
Jan 20, 2005·Proceedings of the National Academy of Sciences of the United States of America·Mallela M G Krishna, S Walter Englander
Apr 26, 2005·Nucleic Acids Research·Yang Zhang, Jeffrey Skolnick
Nov 11, 2005·Proteins·Alessandro Laio, Cristian Micheletti
May 20, 2006·PLoS Computational Biology·Rhonald C Lua, Alexander Y Grosberg
Sep 19, 2006·PLoS Computational Biology·Peter VirnauMehran Kardar
Jul 29, 2010·ChemMedChem·Herbert NarOlivier Potterat
Sep 28, 2010·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Maxim ChernodubAntti J Niemi
Jul 30, 2011·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Shuangwei HuAntti J Niemi
May 17, 2012·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Andrei KrokhotinXubiao Peng
Jul 27, 2012·The Journal of Chemical Physics·Andrey KrokhotinHarold A Scheraga
Sep 26, 2012·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Martin LundgrenFan Sha
Sep 26, 2012·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Martin Lundgren, Antti J Niemi
Nov 7, 2012·Journal of Biomolecular NMR·Shujing WangDaiwen Yang
Oct 5, 2013·The Journal of Chemical Physics·Konrad HinsenAntti J Niemi

Citations

Jan 21, 2014·The Journal of Chemical Physics·Andrey KrokhotinHarold A Scheraga
Oct 30, 2015·BMC Structural Biology·Xubiao PengAntti J Niemi
Jan 24, 2015·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Adam SieradzanXubiao Peng
Jan 1, 2020·Proceedings of the National Academy of Sciences of the United States of America·Dana KrepelJosé N Onuchic
Oct 12, 2019·Scientific Reports·Dmitry MelnikovAra Sedrakyan

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