Topology in Molecular Biology

Contents IX

6.5 Conclusion .................................................
References...................................................... 125

7 Combinatories and Topology of theβ-Sandwich
andβ-Barrel Proteins
A.E. Kister, M.V. Kleyzit, T.I. Gelfand, I.M. Gelfand................ 127
7.1 Introduction................................................ 127
7.2 Overview of the Structures...................................
7.3 Common Features in Structures and Sequences of Sandwich-
Like Proteins...............................................
7.3.1 General Features of the Sandwich-Like Proteins.......... 130
7.3.2 Supersecondary Patterns in the Sandwich-Like Proteins... 130
7.3.3 Structurally Based Sequence Alignment................. 132
7.3.4 Sequence Characteristics of thei, i+1,k,andk+
Strands .............................................
7.3.5 Structural Features of the Sequence Determinants........ 132
7.3.6 Method of the Sequence Determinants for Identification
of Proteins ..........................................
7.4 Common Structural and Sequence Features of Barrel-Like Proteins 135
7.4.1 Search for Sequence and Structural Invariants in Barrel
Proteins: An Outline of the Approach................... 135
7.4.2 Overview of theβ-Barrel Structures.....................
7.4.3 Defining of theβ-Strands and Loops ....................
7.4.4 Arrangement of the Strands in theβ-Sheet.............. 136
7.4.5 Two Subsheets in the Barrel Structures................. 139
7.4.6 Four Types of Connection Between the Strands
in Two Subsheets..................................... 139
7.4.7 Classification of Barrel Based on the Strands Arrangement 140
7.4.8 Characterizing the Place of Distortion of Barrel Structures 141
7.4.9 The Rule of the Arrangement of the “Edge Strands”
in the Barrel Structures ...............................
7.4.10 Arrangement of the Barrel and Sandwich Structures
is Different ..........................................
7.4.11 Invariant Substructure at the Place of Distortion:
A Hydrophobic Tetrahedral............................ 142
7.4.12 The Two Hydrophobic Tetrahedrals Present the
Structural Invariant of Barrel Proteins ..................
7.5 Conclusion .................................................
References...................................................... 144

8 The Structure of Collagen
N. Rivier, J.-F. Sadoc............................................ 147
8.1 Collagen: Chain, Molecule, Fibril............................. 147
8.2 The Boerdijk–Coxeter Helix and its Approximants.............. 149
8.3 The Collagen Molecule...................................... 151