Structural Approaches to Sequence Evolution: Molecules, Networks, Populations 2007 ed. [Kietas viršelis]

Part I Molecules: Proteins and RNA
Modeling Conformational Flexibility and Evolution of Structure: RNA as an Example		3	(34)
P. Schuster
P.F. Stadler
Definition and Computation of RNA Structures		3	(16)
RNA Secondary Structures		4	(4)
Compatibility of Sequences and Structures		8	(3)
Sequence Space, Shape Space, and Conformation Space		11	(3)
Computation of RNA Secondary Structures		14	(1)
Mapping Sequences into Structures		15	(3)
Suboptimal Structures and Partition Functions		18	(1)
Design of RNA Structures		19	(4)
Inverse Folding		19	(1)
Multiconformational RNAs		20	(2)
Riboswitches		22	(1)
Processes in Conformation, Sequence, and Shape Space		23	(14)
Kinetic Folding		23	(2)
Evolutionary Optimization		25	(5)
Evolution of Noncoding RNAs		30	(2)
References		32	(5)
Gene3D and Understanding Proteome Evolution		37	(20)
J.G. Ranea
C. Yeats
R. Marsden
C. Orengo
Protein Family Clustering		42	(1)
Systers		42	(1)
ProtoNet		42	(1)
ADDA		42	(1)
ProDom		43	(1)
The PFscape Method		43	(1)
The NewFams		44	(1)
Describing the Proteome		45	(1)
Superfamily Evolution and Genome Complexity		46	(2)
Superfamily Evolution and Functional Relationships		48	(2)
Limits to Genome Complexity in Prokaryotes		50	(2)
The Bacterial Factory		52	(1)
Conclusions		53	(4)
References		54	(3)
The Evolution of the Globins: We Thought We Understood It		57	(18)
A.M. Lesk
Introduction		58	(1)
Coordinates and Calculations		59	(1)
Results		59	(3)
Description of Secondary and Tertiary Structure of Full-Length (~150--Residue) Globins		59	(1)
Description of Secondary and Tertiary Structure of Truncated Globins		60	(1)
Alignment		60	(2)
Helix Contacts		62	(6)
Geometry of Inter-Helix Contacts		62	(1)
Pairs of Helices Making Contacts		63	(2)
Structures of Helix Interfaces in Truncated Globins, Compared to Those in Sperm Whale Myoglobin		65	(1)
The B/G Interface		65	(1)
The A/H Interface		66	(1)
The B/E Interface		67	(1)
Patterns of Residue--Residue Contacts at Helix Interfaces		68	(4)
The G/H Interface		69	(3)
Haem Contacts		72	(1)
The Tunnel		72	(1)
Conclusions		72	(3)
References		73	(2)
The Structurally Constrained Neutral Model of Protein Evolution		75	(38)
U. Bastolla
M. Porto
H.E. Roman
M. Vendruscolo
Aspects of Population Genetics		76	(7)
Population Size and Mutation Rate		76	(1)
Natural Selection		77	(1)
Mutant Spectrum		78	(2)
Neutral Substitutions		80	(1)
Beyond the Small M μ Regime: Neutral Networks		81	(2)
Structural Aspects of Molecular Evolution		83	(4)
Neutral Theory and Protein Folding Thermodynamics		83	(1)
Structural Conservation and Functional Changes in Protein Evolution		84	(1)
Models of Molecular Evolution with Structural Conservation		85	(2)
The SCN Model of Evolution		87	(10)
Representation of Protein Structures		88	(1)
Stability Against Unfolding		88	(1)
Stability Against Misfolding		89	(1)
Calculation of α(A)		89	(2)
Sampling the Neutral Networks		91	(1)
Fluctuations and Correlations in the Evolutionary Process		91	(2)
Substitution Process		93	(4)
Site-Specific Amino Acid Distributions		97	(12)
Vectorial Representation of Protein Sequences		98	(1)
Vectorial Representation of Protein Folds		99	(1)
Relation Between Sequence and Structure		99	(1)
The PE as a Structural Determinant of Evolutionary Conservation		100	(1)
Site-Dependent Amino Acid Distributions		101	(3)
Sequence Conservation and Structure Designability		104	(1)
Site-Specific Amino Acid Distributions in the PDB		105	(2)
Mean-Field Model of Mutation plus Selection		107	(2)
Conclusions		109	(4)
References		109	(4)
Towards Unifying Protein Evolution Theory		113	(16)
N. V. Dokholyan
E.I. Shakhnovich
Two Views on Protein Evolution		113	(1)
Challenges in Functionally Annotating Structures		113	(2)
The Importance of the Tree of Life		115	(1)
Building the PDUG		116	(1)
Properties of the PDUG: Power Laws on Very Different Evolutionary Scales		117	(1)
Functional Flexibility Score: Calculating Entropy in Function Space		118	(1)
Lattice Proteins and Its Random Subspaces: Structure Graphs		119	(1)
Divergence and Convergence Explored: What Power Laws Tell Us about Evolution		120	(2)
Context Is Important		122	(1)
Not All Functions Are Created Equal and Neither Are Structures		122	(2)
Concluding Remarks		124	(5)
References		124	(5)
Part II Molecules: Genomes
A Twenty-First Century View of Evolution: Genome System Architecture, Repetitive DNA, and Natural Genetic Engineering		129	(20)
J.A. Shapiro
Introduction: Cellular Computation and DNA as an Interactive Data Storage Medium		129	(1)
Genome System Architecture and Repetitive DNA		130	(2)
Genomes and Cellular Computation: E. coli lac Operon		132	(3)
New Principles of Evolution: The Lessons of Sequenced Genomes		135	(1)
Natural Genetic Engineering		136	(5)
Conclusions: A Twenty-First Century View of Evolution		141	(2)
Twenty-First Century Directions in Evolution Research		143	(6)
References		144	(5)
Genomic Changes in Bacteria: From Free-Living to Endosymbiotic Life		149	(20)
F.J. Silva
A. Latorre
L. Gomez-Valero
A. Moya
Introduction		149	(4)
Genetic and Genomic Features of Endosymbiotic Bacteria		153	(9)
Sequence Evolution in Endosymbionts		153	(5)
Reductive Evolution: DNA Loss and Genome Reduction in Obligate Bacterial Mutualists		158	(2)
Chromosomal Rearrangements Throughout Endosymbiont Evolution		160	(2)
Conclusions and Prospects		162	(7)
References		163	(6)
Part III Phylogenetic Analysis
Molecular Phylogenetics: Mathematical Framework and Unsolved Problems		169	(22)
X. Xia
Introduction		169	(1)
Substitution Models		170	(8)
Nucleotide-Based Substitution Models and Genetic Distances		171	(5)
Amino Acid-Based and Codon-Based Substitution Models		176	(2)
Tree-Building Methods		178	(9)
Distance-Based Methods		178	(3)
Maximum Parsimony Methods		181	(1)
Maximum Likelihood Methods		182	(3)
Bayesian Inference		185	(2)
Final Words		187	(4)
References		187	(4)
Phylogenetics and Computational Biology of Multigene Families		191	(16)
P. Lio
M. Brilli
R. Fani
Introduction		191	(2)
How Do Large Gene Families Arise?		193	(1)
The Classical Model of Gene Duplication		193	(1)
Subfunctionalization Model		194	(1)
Subneofunctionalization		195	(1)
Tests for Subfunctionalization		196	(1)
Tests for Functional Divergence After Duplication		196	(11)
Case Study 1: Chemokine Receptors Expansion in Vertebrates		197	(2)
Case Study 2: The Evolution of TIM Barrel Coding Genes		199	(5)
References		204	(3)
SeqinR 1.0-2: A Contributed Package to the R Project for Statistical Computing Devoted to Biological Sequences Retrieval and Analysis		207	(28)
D. Charif
J.R. Lobry
Introduction		207	(6)
About R and CRAN		207	(1)
About this Document		208	(1)
About Sequin and seqinR		208	(1)
About Getting Started		208	(1)
About Running R in Batch Mode		208	(1)
About the Learning Curve		209	(4)
How to Get Sequence Data		213	(7)
Importing Raw Sequence Data from Fasta Files		213	(1)
Importing Aligned Sequence Data		214	(4)
Complex Queries in ACNUC Databases		218	(2)
How to Deal with Sequence		220	(5)
Sequence Classes		220	(1)
Generic Methods for Sequences		220	(1)
Internal Representation of Sequences		221	(4)
Multivariate Analyses		225	(10)
Correspondence Analysis		225	(5)
Synonymous and Nonsynonymous Analyses		230	(2)
References		232	(3)
Part IV Networks
Evolutionary Genomics of Gene Expression		235	(18)
I.K. Jordan
L. Marino-Ramirez
Sequence Divergence		236	(4)
Ortholog Identification		236	(1)
Sequence Alignment		237	(1)
Sequence Distance Calculation		237	(3)
Gene Expression Divergence		240	(6)
Database Sources		241	(1)
Probe-to-Gene Mapping		241	(1)
Structure of the Data		242	(1)
Transformation and Normalization		242	(1)
Measuring Divergence		243	(2)
Clustering and Visualization		245	(1)
Integrated Analysis		246	(7)
Sequence vs. Expression Divergence		246	(1)
Neutral Changes in Gene Expression		247	(3)
Evolutionary Conservation of Gene Expression		250	(1)
References		251	(2)
From Biophysics to Evolutionary Genetics: Statistical Aspects of Gene Regulation		253	(32)
M. Lassig
Introduction		253	(1)
Biophysics of Transcriptional Regulation		254	(7)
Factor-DNA Binding Energies		255	(2)
Energy Distribution in the Genome		257	(1)
Search Kinetics		258	(1)
Thermodynamics of Factor Binding		258	(2)
Sensitivity and Genomic Design of Regulation		260	(1)
Programmability and Evolvability of Regulatory Networks		260	(1)
Bioinformatics of Regulatory DNA		261	(5)
Markov Model for Background Sequence		261	(1)
Probabilistic Model for Functional Sites		262	(1)
Bayesian Model for Genomic Loci		263	(1)
Dynamic Programming and Sequence Analysis		264	(2)
Evolution of Regulatory DNA		266	(12)
Deterministic Population Dynamics and Fitness		267	(1)
Stochastic Dynamics and Genetic Drift		268	(2)
Mutation Processes and Evolutionary Equilibria		270	(1)
Substitution Dynamics		271	(2)
Neutral Dynamics in Sequence Space, Sequence Entropy		273	(1)
Dynamics Under Selection, the Score-Fitness Relation		274	(1)
Measuring Selection for Binding Sites		275	(1)
Nucleotide Frequency Correlations		276	(1)
Stationary Evolution of Binding Sites		276	(2)
Adaptive Evolution of Binding Sites		278	(1)
Toward a Dynamical Picture of the Genome		278	(7)
Evolutionary Interactions Between Sites		279	(1)
Site--Shadow Interactions		280	(1)
Gene Interactions		280	(1)
Evolutionary Innovations		281	(1)
References		281	(4)
Part V Populations
Drift and Selection in Evolving Interacting Systems		285	(14)
T. Ohta
Hierarchy of Networks		286	(1)
Drift and Selection, a Historical Perspective		287	(1)
Molecular Clock and Near-Neutrality		288	(3)
Mutants' Effects on Fitness		291	(3)
Evolution of Form and Shape: Cooption		294	(5)
References		296	(3)
Adaptation in Simple and Complex Fitness Landscapes		299	(42)
K. Jain
J. Krug
Basic Concepts and Models		300	(7)
Fitness, Mutations, and Sequence Space		300	(4)
Mutation--Selection Models		304	(3)
Simple Fitness Landscapes		307	(14)
The Error Threshold: Preliminary Considerations		307	(1)
Error Threshold in the Sharp Peak Landscape		308	(3)
Exact Solution of a Sharp Peak Model		311	(1)
Modifying the Shape of the Fitness Peak		312	(5)
Beyond the Standard Model		317	(4)
Complex Fitness Landscapes		321	(6)
An Explicit Genotype--Phenotype Map for RNA Sequences		322	(1)
Uncorrelated Random Landscapes		322	(1)
Correlated Landscapes		323	(3)
Neutrality		326	(1)
Dynamics of Adaptation		327	(6)
Peak Shifts and Punctuated Evolution		328	(1)
Evolutionary Trajectories for the Quasispecies Model		328	(4)
Dynamics in Smooth Fitness Landscapes		332	(1)
Evolution in the Laboratory		333	(2)
RNA Evolution In Vitro		333	(1)
Quasispecies Formation in RNA Viruses		334	(1)
Dynamics of Microbial Evolution		334	(1)
Conclusions		335	(6)
References		336	(5)
Genetic Variability in RNA Viruses: Consequences in Epidemiology and in the Development of New Strategies for the Extinction of Infectivity		341	(22)
E. Lazaro
Introduction		341	(2)
Replication of RNA Viruses and Generation of Genetic Variability		343	(1)
Structure of Viral Populations		344	(1)
Viral Quasi-Species and Adaptation		345	(3)
Population Dynamics of Host--Pathogen Interactions		348	(2)
The Limit of the Error Rate		350	(9)
Increases in the Error Rate of Replication. Lethal Mutagenesis As a New Antiviral Strategy		352	(3)
Evolution of Viral Populations Through Successive Bottlenecks		355	(4)
Conclusions		359	(4)
References		360	(3)
Index		363

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 stochastic 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.