Protein Engineering Techniques : Gateways to Synthetic Protein Universe

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Protein Engineering Techniques : Gateways to Synthetic Protein Universe

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http://libproxy.rpi.edu/login?url=https://ebookcentral.proquest.com/lib/rpi/detail.action?docID=4743127

Title remainder

Gateways to Synthetic Protein Universe

Instantiates

• Protein Engineering Techniques : Gateways to Synthetic Protein Universe

Publication

• Singapore, Springer Singapore, 2016
• Singapore, Springer, 2016

Copyright

• ©2017

Carrier category

online resource

Carrier category code

cr

Carrier MARC source

rdacarrier

Color

multicolored

Content category

text

Content type code

txt

Content type MARC source

rdacontent

Contents

• Preface -- Acknowledgements -- Contents -- 1 World of Proteins: Structure-Function Relationships and Engineering Techniques -- Abstract -- 1.1 Introduction -- 1.2 Functional Characteristics of Proteins -- 1.3 Transfer of Genetic Information: From DNA to Proteins -- 1.4 Amino Acids, Building Blocks of Proteins -- 1.4.1 Non Polar Amino Acids -- 1.4.2 Charged Polar Amino Acids -- 1.4.3 Uncharged Polar Amino Acids -- 1.5 Hydrophobicity Profiles of Amino Acids -- 1.6 Acidic and Basic Properties of Amino Acids -- 1.7 Structural Organization of Proteins -- 1.7.1 Primary Structure -- 1.7.2 Secondary Structure -- 1.7.3 Tertiary Structure -- 1.7.4 Quaternary Structure -- 1.8 Motifs/Super Secondary Structures -- 1.9 Protein Stability -- 1.9.1 Ionic Interactions -- 1.9.2 Van der Waal Interactions -- 1.9.2.1 Hydrogen Bonding -- 1.9.3 Hydrophobic Interactions -- 1.10 Protein Denaturation, Renaturation and Folding Energy Landscape -- 1.11 Structure Determination of Proteins -- 1.11.1 X-Ray Crystallography -- 1.11.2 Nuclear Magnetic Resonance Spectroscopy (NMR) -- 1.12 Concept of Biomolecular and Protein Engineering -- References -- 2 Expanding the Synthetic Protein Universe by Guided Evolutionary Concepts -- Abstract -- 2.1 Directed Evolution -- 2.2 Asexual Methods -- 2.3 Random Mutagenesis -- 2.3.1 Error Prone PCR -- 2.3.2 Chemical Mutagenesis -- 2.3.3 Mutator Strains -- 2.3.4 Dual Approach to Random Chemical Mutagenesis (DuARCheM) -- 2.3.5 Rolling Circle Error-Prone PCR -- 2.3.6 Targeting Glycosylases to Embedded Arrays for Mutagenesis (TaGTEAM) -- 2.3.7 Mutagenesis by Random Insertion and Deletion -- 2.3.8 Transposon Based Random Mutagenesis -- 2.3.9 Random Mutagenesis Methods Altering the Target DNA Length -- 2.4 Focused Mutagenesis -- 2.5 Site Saturation Mutagenesis (SSM) -- 2.5.1 Cassette Mutagenesis -- 2.5.2 Sequence Saturation Mutagenesis (SeSAM)
• 2.5.3 Single-Primer Reactions in Parallel (SPRINP) -- 2.5.4 Megaprimed and Ligase-Free -- 2.5.5 ]-PCR -- 2.5.6 PFunkel-Ominchange-OSCARR -- 2.5.7 Trimer-Dimer Mutagenesis -- 2.6 Sexual Methods -- 2.7 Homologous Recombination -- 2.8 In Vitro Homologous Recombination -- 2.8.1 DNA Shuffling -- 2.8.2 Random Priming In Vitro Recombination (RPR) -- 2.8.3 Truncated Metagenomic Gene-Specific PCR (TMGS-PCR) -- 2.8.4 Staggered Extension Process (StEP) -- 2.8.5 Random Chimeragenesis on Transient Templates (RACHITT) -- 2.8.6 Synthetic Shuffling -- 2.9 In Vivo Homologous Recombination -- 2.9.1 Cloning Performed in Yeast (CLERY) -- 2.9.2 Mutagenic Organized Recombination Process by Homologous In Vivo Grouping (MORPHING) -- 2.9.3 Phage Assisted Continuous Evolution (PACE) -- 2.10 In Vitro Non-homologous Recombination Methods -- 2.10.1 Exon Shuffling -- 2.10.2 Incremental Truncation for the Creation of Hybrid Enzymes (ITCHY) -- 2.10.3 SCRATCHY -- 2.10.4 Recombined Extension on Truncated Templates (RETT) -- 2.10.5 Sequence Homology-Independent Protein Recombination (SHIPREC) -- 2.10.6 Sequence Independent Site-Directed Chimeragenesis (SISDC) -- 2.10.7 Degenerate Homo-Duplex Recombination (DHR) -- 2.10.8 Random Multi-recombinant PCR (RM-PCR) -- 2.10.9 User Friendly DNA Recombination (USERec) -- 2.10.10 Golden Gate Shuffling (GGS) Recombination -- 2.10.11 PhosphoroThioate-Based DNA Recombination Method (PTRec) -- 2.10.12 Integron -- 2.10.13 Y-Ligation Based Shuffling (YLBS) -- 2.11 Screening and Selection Techniques -- 2.12 Proteins Designed Using Directed Evolution (DE) Methods -- References -- 3 Rational Designing of Novel Proteins Through Computational Approaches -- Abstract -- 3.1 Computational Designing of Proteins -- 3.2 Rational Designing of Proteins -- 3.3 Multiple Sequence Alignment (MSA) -- 3.3.1 Few Case Studies that Employed MSA Tools for Designing Proteins
• 3.4 Coevolutionary Analysis -- 3.5 Structure Based Designing of New Proteins -- 3.5.1 Ab Initio Methods -- 3.5.2 Fragment Based Methods -- 3.5.3 Homology Modeling -- 3.5.4 Protein Threading -- References -- 4 Generating the Fancy Protein Basket with De Novo and Combinatorial Approaches -- Abstract -- 4.1 De Novo Designing of Proteins -- 4.1.1 Building Backbone -- 4.1.2 Sequence Design and Optimization -- 4.1.3 In Silico and Experimental Validation -- 4.2 Negative Design Methods -- 4.3 Examples of De Novo Designed Proteins -- 4.4 Combinatorial/Semi-rational Approach for Protein Designing -- 4.5 Glimpse on Proteins Engineered by de Novo/Combinatorial Approaches -- References -- 5 Biotechnological and Biomedical Applications of Protein Engineering Methods -- Abstract -- 5.1 Diversified Applications of Protein Engineering Techniques -- 5.2 Industrial Applications -- 5.3 Environmental Applications -- 5.4 Biomaterial Applications -- 5.4.1 Elastin like Polypeptides (ELPs) -- 5.4.2 Silk Motifs -- 5.4.3 Coiled-Coil Motifs -- 5.4.4 Calmodulin Motifs -- 5.4.5 Ý-Sheet Forming Ionic Oligopeptides -- 5.5 Applications in Nanotechnology -- 5.6 Biosensors -- 5.7 Virus Engineering -- 5.8 Biomedical Applications -- 5.8.1 Engineered Proteins as Therapeutics -- 5.8.2 Protein Scaffolds as Therapeutics -- References

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unknown

Extent

1 online resource (144 pages)

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online

Isbn

9789811027321

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computer

Media MARC source

rdamedia

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c

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unknown sound

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remote