Structural Approaches to Sequence Evolution: Molecules, Networks, Populations

by Ugo Bastolla (Editor), Markus Porto (Editor), Eduardo Roman (Editor), Michele Vendruscolo (Editor)

Overview

Structural requirements constrain the evolution of biological entities at all levels, from macromolecules to their networks, right up to populations of biological organisms. Classical models of molecular evolution, however, are focused at the level of the symbols - the biological sequence - rather than that of their resulting structure. Now recent advances in understanding the thermodynamics of macromolecules, the topological properties of gene networks, the organization and mutation capabilities of genomes, and the structure of populations make it possible to incorporate these key elements into a broader and deeply interdisciplinary view of molecular evolution. This book gives an account of such a new approach, through clear tutorial contributions by leading scientists specializing in the different fields involved.

Product Details

ISBN-13:	9783540353058
Publisher:	Springer Berlin Heidelberg
Publication date:	08/17/2007
Series:	Biological and Medical Physics, Biomedical Engineering
Edition description:	2007
Pages:	367
Product dimensions:	6.10(w) x 9.25(h) x 0.03(d)

About the Author

Ugo Bastolla is researcher in the laboratory of bioinformatics of the

Centro de Astrobiologia in Madrid (Spain), on leave to the Centro de

Biologia Molecular of the Spanish CSIC. Since his degree in physics

with Luca Peliti he has always been interested in biological topics,

above all evolution. He got is PhD in Rome with Giorgio Parisi working

on disordered dynamical systems inspired to biology and was postdoc in

Julich (Germany) with Peter Grassberger, studying statistical mechanical

models of polymers, in Berlin (Germany) with E.W. Knapp studying simple

protein models, in Golm (Germany) with Michael Laessig, studying

ecological models, and finally in Madrid (Spain) in the bioinformatics

group of Alfonso Valencia. His main research interest consists in combining

simple models of protein thermodynamics and evolution.

Markus Porto is professor of Theoretical Solid State Physics at the

Institut fur Festkorperphysik at the Technische Universitat Darmstadt

(Germany). He received his PhD at the Universitat Giessen (Germany). His

research interests cover many aspects of solid state and statistical

physics, including transport and relaxation in disordered systems and

biophysics, as well as applying methods of statistical physics to model

molecular evolution.

H. Eduardo Roman is Research Fellow at the Department of Physics of the

University of Milan-Bicocca. He earned his Ph.D at the International School

for Advanced Studies, Trieste (Italy), and has been Privat Dozent at the

Universities of Hamburg and Giessen (Germany). His research interests cover

many aspects of Statistical Physics, from fractals to shastic phenomena,

biophysics, proteins and evolution, and ab-initio electronic calculations in

molecules.

Michele Vendruscolo is a Royal Society University Research Fellow at the

Department of Chemistry, University of Cambridge. He received his PhD in

Condensed Matter Physics in 1996 at the International School for Advanced

Studies, Trieste (Italy). His research is mainly focussed on understanding

the biophysical principles regulating the behaviour and the evolution of

proteins.

Table of Contents

Molecules: Proteins and RNA.- Modeling Conformational Flexibility and Evolution of Structure: RNA as an Example.- Gene3D and Understanding Proteome Evolution.- The Evolution of the Globins: We Thought We Understood It.- The Structurally Constrained Neutral Model of Protein Evolution.- Towards Unifying Protein Evolution Theory.- Molecules: Genomes.- A Twenty-First Century View of Evolution: Genome System Architecture, Repetitive DNA, and Natural Genetic Engineering.- Genomic Changes in Bacteria: From Free-Living to Endosymbiotic Life.- Phylogenetic Analysis.- Molecular Phylogenetics: Mathematical Framework and Unsolved Problems.- Phylogenetics and Computational Biology of Multigene Families.- SeqinR 1.0-2: A Contributed Package to the R Project for Statistical Computing Devoted to Biological Sequences Retrieval and Analysis.- Networks.- Evolutionary Genomics of Gene Expression.- From Biophysics to Evolutionary Genetics: Statistical Aspects of Gene Regulation.- Populations.- Drift and Selection in Evolving Interacting Systems.- Adaptation in Simple and Complex Fitness Landscapes.- Genetic Variability in RNA Viruses: Consequences in Epidemiology and in the Development of New Stratgies for the Extinction of Infectivity.