Taylor / Aszodi Protein Geometry, Classification, Topology and Symmetry

A Computational Analysis of Structure
Erscheinungsjahr 2010
ISBN: 978-1-4200-3363-2
Verlag: Taylor & Francis
Format: PDF
Kopierschutz: Adobe DRM (»Systemvoraussetzungen)

E-Book, Englisch, 348 Seiten

Reihe: Series in Biophysics

Using a geometric perspective, Protein Geometry, Classification, Topology, and Symmetry reviews and analyzes the structural principals of proteins with the goal of revealing the underlying regularities in their construction. It also reviews computer methods for structure analysis and the automatic comparison and classification of these structures with an analysis of the statistical significance of comparing different shapes. Following an analysis of the current state of protein classification, the authors explore more abstract geometric and topological representations, including the occurrence of knotted topologies. The book concludes with a consideration of the origin of higher-level symmetries in protein structure.

The authors focus on simple geometric methods that are deterministic rather than probabilistic and on the more abstract simplifications of protein structure that allow a better understanding of the overall fold of the structure. Most of the methods described in this book have corresponding computer programs. These can be found (as C source code) at the ftp site of the Division of Mathematical Biology at the National Institute for Medical Research. This collection of ideas contains pedagogical material that make it ideal for post-graduate courses as well as new ideas and results essential for researchers investigating protein structures.

Zielgruppe

Graduate students and researchers in biophyics, molecular biology, computational biology and chemistry, and biochemistry

Autoren/Hrsg.

Taylor, William R.

Aszodi, Andras

Fachgebiete

• Naturwissenschaften Biowissenschaften Proteinforschung

Inhaltsverzeichnis

INTRODUCTION

Prologue

Basic Principles of Protein Structure

GEOMETRY

Ellipsoids and Embedding

Geometric Representations of Structure

Distance Geometry

Sticks to Strings

Secondary Structure Geometries

Simplified Architectures

Sheets and Barrels

Beta-Sheet Geometry

Beta-Barrels

CLASSIFICATION

Networks and Domains

Hydrogen-Bond Networks

Protein Domain Definitions

Protein Structure Comparison

Overview of Comparison Methods

Assessment of Significance

Classification and Fold Spaces

Protein Structure Classification

Protein Fold Spaces

A "Periodic Table" for Protein Structures

Evolutionary' steps in fold-space

TOPOLOGY

Folds, Tangles and Knots

Topology and Knots

Random Walks in Fold-Space

Protein Fold Complexity

Structure Prediction and Modelling

Random Folds from Distance Geometry

Modelling with Distance Geometry

Protein Tertiary Structure Prediction

SYMMETRY

Structural Symmetry

Symmetry

A Fourier Analysis of Symmetry

Evolution and Origins

Evolution of Structure and Function

The Origins of Proteins

The Secret of Life

References

Index