TY - CHAP

T1 - Protein Engineering of DNA-Dependent Enzymes

AU - Yudkina, Anna V.

AU - Zharkov, Dmitry O.

N1 - Funding Information: Acknowledgments This research was supported by Russian Foundation for Basic Research (17-04-01761-a). Partial salary support from Russian Ministry of Science and Higher Education (Projects 6.5773.2017/6.7 and AAAA-A17-117020210023-1) is acknowledged. Publisher Copyright: © 2020, Springer Nature Switzerland AG.

PY - 2020/5/8

Y1 - 2020/5/8

N2 - Enzymes are extremely efficient natural catalysts of a variety of chemical reactions. Design of enzymes with new functions and properties has become one of the main goals of modern protein engineering. The field of protein engineering is growing intensively, and different strategies were developed for the creation of enzymes with new properties. While there is plenty of methods and instruments, all modern protein engineering strategies could be divided in two major groups, broadly based on the core ideas of rational design or directed evolution. DNA-dependent proteins present an important target of protein engineering due to their wide use in molecular cloning, bioanalytics, and genetic manipulations. Here we review examples of successful application of biochemical, structural and computational approaches belonging to both protein engineering strategies to create new proteins belonging to three important classes of DNA-dependent enzymes: CRISPR-associated nuclease Cas9, DNA polymerases, and DNA glycosylases. The review contains examples of successfully designed enzymes and discusses the most useful approaches in the engineering of these specific enzyme classes, problems restraining the development of this field, and future directions in the development and application of designed DNA-dependent enzymes.

AB - Enzymes are extremely efficient natural catalysts of a variety of chemical reactions. Design of enzymes with new functions and properties has become one of the main goals of modern protein engineering. The field of protein engineering is growing intensively, and different strategies were developed for the creation of enzymes with new properties. While there is plenty of methods and instruments, all modern protein engineering strategies could be divided in two major groups, broadly based on the core ideas of rational design or directed evolution. DNA-dependent proteins present an important target of protein engineering due to their wide use in molecular cloning, bioanalytics, and genetic manipulations. Here we review examples of successful application of biochemical, structural and computational approaches belonging to both protein engineering strategies to create new proteins belonging to three important classes of DNA-dependent enzymes: CRISPR-associated nuclease Cas9, DNA polymerases, and DNA glycosylases. The review contains examples of successfully designed enzymes and discusses the most useful approaches in the engineering of these specific enzyme classes, problems restraining the development of this field, and future directions in the development and application of designed DNA-dependent enzymes.

KW - CRISPR/Cas9

KW - Direct evolution

KW - DNA glycosylases

KW - DNA polymerases

KW - Protein design

KW - Protein engineering

KW - Random mutagenesis

KW - DNA Glycosylases/chemistry

KW - DNA/metabolism

KW - CRISPR-Associated Protein 9/chemistry

KW - Protein Engineering

KW - DNA-Directed DNA Polymerase/chemistry

UR - http://www.scopus.com/inward/record.url?scp=85084398367&partnerID=8YFLogxK

U2 - 10.1007/978-3-030-41283-8_2

DO - 10.1007/978-3-030-41283-8_2

M3 - Chapter

C2 - 32383113

AN - SCOPUS:85084398367

SN - 978-3-030-41282-1

SN - 978-3-030-41285-2

VL - 1241

T3 - Advances in experimental medicine and biology

SP - 19

EP - 33

BT - Mechanisms of Genome Protection and Repair

A2 - Zharkov, Dmitry O.

PB - Springer, Cham

ER -