Towards Symmetry-Based Explanation of (Approximate) Shapes of Alpha-Helices and Beta-Sheets (and Beta-Barrels) in Protein Structure 英文参考文献.docVIP

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Towards Symmetry-Based Explanation of (Approximate) Shapes of Alpha-Helices and Beta-Sheets (and Beta-Barrels) in Protein Structure 英文参考文献.doc

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Towards Symmetry-Based Explanation of (Approximate) Shapes of Alpha-Helices and Beta-Sheets (and Beta-Barrels) in Protein Structure 英文参考文献

Symmetry2012,4,15-25;doi:10.3390/sym4010015 OPENACCESS symmetry ISSN2073-8994 /journal/symmetry Article TowardsSymmetry-BasedExplanationof(Approximate)Shapes ofAlpha-HelicesandBeta-Sheets(andBeta-Barrels)in ProteinStructure JaimeNavaandVladikKreinovich* DepartmentofComputerScience,UniversityofTexasatElPaso,500WestUniversityAvenue,ElPaso, TX79968,USA;E-Mail:jenava@ *Authortowhomcorrespondenceshouldbeaddressed;E-Mail:vladik@; Tel.:+1-915-747-6951;Fax:+1-915-747-5030. Received:22December2011;inrevisedform:6January2012/Accepted:12January2012/ Published:19January2012 Abstract: Protein structure is invariably connected to protein function. There are two important secondary structure elements: alpha-helices and beta-sheets (which sometimes comeinashapeofbeta-barrels). Theactualshapesofthesestructurescanbecomplicated, butinthe?rstapproximation,theyareusuallyapproximatedby,correspondingly,cylindrical spirals and planes (and cylinders, for beta-barrels). In this paper, following the ideas pioneered by a renowned mathematician M. Gromov, we use natural symmetries to show that, under reasonable assumptions, these geometric shapes are indeed the best approximatingfamiliesforsecondarystructures. Keywords:symmetries;secondaryproteinstructures;alpha-helices;beta-sheets;beta-barrels 1.Introduction Alpha-helicesandbeta-sheets:briefreminder.Proteinsarebiologicalpolymersthatperformmostof life’sfunction.Asinglechainpolymer(protein)isfoldedinsuchawaythatitformslocalsubstructures called secondary structure elements. In order to study the structure and function of proteins it is extremelyimportanttohaveagoodgeometricaldescriptionoftheproteinsstructure. Therearetwo importantsecondarystructureelements: alpha-helicesandbeta-sheets. Apartoftheproteinstructure wheredifferentfragmentsofthepolypeptidealignnexttoeachotherinextendedconformationforming Symmetry2012,4 16 aline-likefeaturede?nesasecondarystructurecalledanalpha-helix. Apartoftheproteinstructure wheredifferentfragme