title: Detection of secondary and supersecondary structures of proteins from cryo-electron microscopy.
abstract: Recent advances in three-dimensional electron microscopy (3D EM) have enabled the quantitative visualization of the structural building blocks of proteins at improved resolutions. We provide algorithms to detect the secondary structures (α-helices and β-sheets) from proteins for which the volumetric maps are reconstructed at 6-10Å resolution. Additionally, we show that when the resolution is coarser than 10Å, some of the supersecondary structures can be detected from 3D EM maps. For both these algorithms, we employ tools from computational geometry and differential topology, specifically the computation of stable/unstable manifolds of certain critical points of the distance function induced by the molecular surface. Our results connect mathematically well-defined constructions with bio-chemically induced structures observed in proteins.
authors.affiliation: Center for Computational Visualization, The Institute for Computational Engineering and Sciences, Department of Computer Science, The University of Texas at Austin, University Station C0200, Austin, TX 78712, USA. bajaj@cs.utexas.edu
authors.forename: Chandrajit
authors.initials: C
authors.lastname: Bajaj
authors.forename: Samrat
authors.initials: S
authors.lastname: Goswami
authors.forename: Qin
authors.initials: Q
authors.lastname: Zhang
mesh_terms: D000465:Algorithms; D020816:Amino Acid Motifs; D000818:Animals; D036022:Capsid Proteins / Q000737:chemistry; D018834:Chaperonin 60 / Q000737:chemistry; D020285:Cryoelectron Microscopy / Q000379:methods*; D003850:Deoxyribonuclease I / Q000737:chemistry; D056385:Group II Chaperonins / Q000737:chemistry; D006801:Humans; D047908:Intracellular Signaling Peptides and Proteins; D008958:Models, Molecular; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry; D011972:Receptor, Insulin / Q000737:chemistry; D013499:Surface Properties; D013552:Swine
chemical_list: D036022:Capsid Proteins; D018834:Chaperonin 60; D047908:Intracellular Signaling Peptides and Proteins; D011506:Proteins; C066953:ribonuclease inhibitor, porcine; D011972:Receptor, Insulin; D003850:Deoxyribonuclease I; D056385:Group II Chaperonins