Evolution of proteins

White S H 1994 The evolution of proteins from random amino aoid sequenoes II. Evidenoe from the statistioal distributions of the lengths of modern protein sequenoes J. Mol. Evolution 38 383-94... 

SA Benner, GH Gonnet, MA Cohen. Empirical and stractural models for insertions and deletions m the divergent evolution of proteins. I Mol Biol 229 1065-1082, 1993. 

In order to make as much data on the structure and its determination available in the databases, approaches for automated data harvesting are being developed. Structure classification schemes, as implemented for example in the SCOP, CATH, andFSSP databases, elucidate the relationship between protein folds and function and shed light on the evolution of protein domains. 

Directed Enzyme Evolution Screening and Selection Methods, Humana Press, Totowa. Vol. 230. (b) Brakmann, S. and Johnsson, K. (eds)(2002) Directed Molecular Evolution of Proteins (or How to Improve Enzymes for Biocatalysis), Wdey-VCH Verlag GmbH, Weinheim. (c) Brakmann, S. and Schwienhorst, A. (eds)... 

Roodveldt, C., Aharoni, A. and Tawfik, D.S. (2005) Directed evolution of proteins for heterologous expression and stability. Current Opinion in Structural Biology, 15, 50-56. 

Kolkman, J.A. and Stemmer, W.P. (2001) Directed evolution of proteins by exon shuffling. Nature Biotechnology, 19, 423-428. 

Bittker, J.A., Le, B.V., Liu, J.M. and Liu, D.R. (2004) Directed evolution of protein enzymes using nonhomologous random recombination. Proceedings of the National Academy of Sciences of the United States of America, 101, 7011-7016. 

The use of sequence information to frame structural, functional, and evolutionary hypotheses represents a major challenge for the postgeno-mic era. Central to an understanding of the evolution of sequence families is the concept of the domain a structurally conserved, genetically mobile unit. When viewed at the three-dimensional level of protein structure, a domain is a compact arrangement of secondary structures connected by linker polypeptides. It usually folds independently and possesses a relatively hydrophobic core (Janin and Chothia, 1985). The importance of domains is that they cannot be divided into smaller units— they represent a fundamental building block that can be used to understand the evolution of proteins. 

Domains may be regarded as the basic units for the structure, function and evolution of proteins, but the definition of a domain remains fuzzy. They are most often treated as compact or connected areas that are apparent from a visual inspection of protein models. To avoid subjectivity and ambiguities of visual inspection, computer algorithms have been developed to localize domains. Rashin offered an alternative interpretation domains are stable globular fragments, generated in biochemical experiments that refold autonomously and retain specific functions. He proposed a method for localiz-... 

Moore, J.C., Jin, H.M., Kuchner, O. and Arnold, F.H. (1997) Strategies for the in vitro evolution of protein function enzyme evolution by random recombination of improved... 

The evolution of proteins in a modular fashion by fusion of segments of genes, each coding for a module of a compact structural unit of polypeptide, is thus a credible and attractive hypothesis for explaining the rapid generation of enzyme diversity. 

The book presented here is intended as a practical state-of-the-art compilation of methods related to the topic of directed evolution and hence is complementary to the recent successful book Directed Molecular Evolution of Proteins [5]. The methods are described in sufficient detail to serve as recipes in a cookbook . They are easy to follow by laboratory staff, from the technical assistant to the postdoctoral academic or industrial specialist. 

Brakmann, S., Johnsson, K., eds. Directed Molecular Evolution of Proteins or How to Improve Enzymes for Biocatalysis, Wiley-VCH, Weinheim, 2002. 

M. Ostermeier and S.). Benkovic, Evolution of protein function by domain swapping, Adv. Protein Chem. 2000, 55, 29-77. 

The evolution of protein structures shows conservation in recognition features for common binding sites. For example, the adenosine triphosphate (ATP)/ guanosine triphosphate (GTP) binding site contains an amino acid motif A (P-... 

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