This book provides an up-to-date summary of the principles of protein evolution and discusses both the methods available to analyze the evolutionary history of proteins as well as those for predicting their structure-function relationships. Includes a significantly expanded chapter on genome evolution to cover genomes of model organisms sequenced since the completion of the first edition, and organelle genome evolution Retains its reader-friendly, accessible style and organization Contains an updated glossary and new references, including a list of online reference sites

This volume presents a diverse collection of methodologies used to study various problems at the protein sequence and structure level. The chapters in this book look at issues ranging from broad concepts like protein space to specifics like antibody modeling. Topics include point mutations, gene duplication, de novo emergence of new genes, pairwise correlated mutations, ancestral protein reconstruction, homology modelling, protein stability and dynamics, and protein-protein interactions. The book also covers a wide range of computational approaches, including sequence and structure alignments, phylogenies, physics-based and mathematical approaches, machine learning, and more. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and prerequisites, step-by-step, readily reproducible computational protocols (using command line or graphical user interfaces, sometimes including computer code), and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and authoritative, Computational Methods in Protein Evolution is a valuable resource that offers useful workflows and techniques that will help both novice and expert researchers working with proteins computationally.

The “omics” era has given a new perspective to the findings on the origin and evolution of the process of translation. This book provides insight into the evolution of the translation process and machinery from a modern perspective. Written by leading experts in molecular biology, this text looks into the origins and evolution of the protein synthetic machinery.

In Gene Sharing and Evolution Piatigorsky explores the generality and implications of gene sharing throughout evolution and argues that most if not all proteins perform a variety of functions in the same and in different species, and that this is a fundamental necessity for evolution.

"Our way of understanding evolution has changed completely with the era of genomics, particularly since the emergence of comparative genomics, a discipline allowing the analysis of complete genomes and biological processes over vast periods of time. In this volume, internationally recognized experts present and discuss an update of the evolutionary processes at the onset of organismal diversification and complexity, and review the mechanisms leading to the acquisition of new traits and functions. Different levels of evolution are considered, from internal modules in genes and proteins to interactomes and biological networks, with integration of the influence of both the genomic environment and the ecological context. Particular emphasis will be given to the origin of novel genes and gene functions as well as to the evolutionary impact of the duplication of genetic information, with several chapters devoted to transposable elements. Providing an excellent update on gene and protein evolution, this book will be appreciated by researchers in biology and medicine, biology teachers and anyone interested in evolution and genomics."--Publisher's description.

A one-stop reference that reviews protein design strategies to applications in industrial and medical biotechnology Protein Engineering: Tools and Applications is a comprehensive resource that offers a systematic and comprehensive review of the most recent advances in the field, and contains detailed information on the methodologies and strategies behind these approaches. The authors—noted experts on the topic—explore the distinctive advantages and disadvantages of the presented methodologies and strategies in a targeted and focused manner that allows for the adaptation and implementation of the strategies for new applications. The book contains information on the directed evolution, rational design, and semi-rational design of proteins and offers a review of the most recent applications in industrial and medical biotechnology. This important book: Covers technologies and methodologies used in protein engineering Includes the strategies behind the approaches, designed to help with the adaptation and implementation of these strategies for new applications Offers a comprehensive and thorough treatment of protein engineering from primary strategies to applications in industrial and medical biotechnology Presents cutting edge advances in the continuously evolving field of protein engineering Written for students and professionals of bioengineering, biotechnology, biochemistry, Protein Engineering: Tools and Applications offers an essential resource to the design strategies in protein engineering and reviews recent applications.

Provides a synthesis of our current understanding of hemoglobin (Hb) function and evolution, and illustrates how research on this protein has provided more general insights into mechanisms of protein evolution and biochemical adaptation.

Sequence - Evolution - Function is an introduction to the computational approaches that play a critical role in the emerging new branch of biology known as functional genomics. The book provides the reader with an understanding of the principles and approaches of functional genomics and of the potential and limitations of computational and experimental approaches to genome analysis. Sequence - Evolution - Function should help bridge the "digital divide" between biologists and computer scientists, allowing biologists to better grasp the peculiarities of the emerging field of Genome Biology and to learn how to benefit from the enormous amount of sequence data available in the public databases. The book is non-technical with respect to the computer methods for genome analysis and discusses these methods from the user's viewpoint, without addressing mathematical and algorithmic details. Prior practical familiarity with the basic methods for sequence analysis is a major advantage, but a reader without such experience will be able to use the book as an introduction to these methods. This book is perfect for introductory level courses in computational methods for comparative and functional genomics.

This book reviews the current knowledge of the globally circulating SARS-CoV-2 variants, highlights their distinct genetic characteristics and associated conformational changes in the viral spike protein, and profoundly discusses the mechanisms of convergent evolution that led to the rise of these mutated strains at different geographic regions during the Covid-19 pandemic. Furthermore, the book explores how these variants do and may impact the efficacy of established neutralizing antibody-based (nAb) vaccines and therapeutics by analysing latest in vivo and in vitro clinical data. Finally, the author discusses ways on how nAb Covid-19 treatment derived immune escape of SARS-CoV-2 could be minimized in the future.