Protein Design

1. Front Matter

   Pages i-xiv

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2. Design of Structural Elementary Motifs

   1. Front Matter

      Pages 1-1

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   2. Structure and Stability of the α-Helix

      • Neil Errington, Teuku Iqbalsyah, Andrew J. Doig

      Pages 3-26

   3. De novo Design of Monomeric β-Hairpin and β-Sheet Peptides

      • David Pantoja-Uceda, Clara M. Santiveri, M. Angeles Jiménez

      Pages 27-51

   4. De novo Proteins From Binary-Patterned Combinatorial Libraries

      • Luke H. Bradley, Peter P. Thumfort, Michael H. Hecht

      Pages 53-69

   5. Non-Protein Amino Acids in the Design of Secondary Structure Scaffolds

      • Radhakrishnan Mahalakshmi, Padmanabhan Balaram

      Pages 71-94

   6. Design and Synthesis of β-Peptides With Biological Activity

      • Marc J. Koyack, Richard P. Cheng

      Pages 95-109

3. Design Of Entire Proteins And Protein Complexes

   1. Front Matter

      Pages 111-111

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   2. Design of Miniproteins by the Transfer of Active Sites Onto Small-Size Scaffolds

      • François Stricher, Loïc Martin, Claudio Vita

      Pages 113-149

   3. Consensus Design as a Tool for Engineering Repeat Proteins

      • Tommi Kajander, Aitziber L. Cortajarena, Lynne Regan

      Pages 151-170

   4. Multiple Sequence Alignment as a Guideline for Protein Engineering Strategies

      • Alan R. Davidson

      Pages 171-181

   5. Sequence Search Methods and Scoring Functions for the Design of Protein Structures

      • Hocine Madaoui, Emmanuelle Becker, Raphael Guerois

      Pages 183-206

   6. Prediction of Protein–Protein Interaction Based on Structure

      • Gregorio Fernandez-Ballester, Luis Serrano

      Pages 207-234

   7. Electrostatic Design of Protein–Protein Association Rates

      • Gideon Schreiber, Yossi Shaul, Kay E. Gottschalk

      Pages 235-249

4. Design of Amyloidogenic Polypeptides and Amyloid Inhibitors

   1. Front Matter

      Pages 251-251

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   2. Peptide Model Systems for Amyloid Fiber Formation Design Strategies and Validation Methods

      • Alexandra Esteras-Chopo, María Teresa Pastor, Manuela López de la Paz

      Pages 253-276

   3. Protein Misfolding Disorders and Rational Design of Antimisfolding Agents

      • Lisbell D. Estrada, June Yowtak, Claudio Soto

      Pages 277-293

5. Back Matter

   Pages 295-299

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Proteins have evolved through selective pressure to accomplish specific functions. The functional properties of proteins depend upon their thr- dimensional structures, which result from particular amino acid sequences folding into tightly packed domains. Thus, to understand and modulate protein function rationally, one definitely needs methods and algorithms to predict and decipher how amino acid sequences shape three-dimensional structures. Protein design aims precisely at providing the tools to achieve this goal. The predictive power of rational protein design methods has dramatically increased over the past five years. A broad range of studies now illustrate how the sequence of proteins and peptides can be tuned to engineer biological tools with intended properties (1–3). The extensive characterization of peptides and protein mutants has enormously benefited the understanding of protein sequence-to-structure relationships. Synergies between computational and experimental approaches have also added momentum to the advancing limits of design methods. The potential applications in fundamental biochemistry and in biotechnology justify the considerable excitement that this progress has generated within the research community. The field is probably mature enough so that expert knowledge can assist researchers of diverse disciplines to rationally create or modify their favorite protein. Thus, the aim of Protein Design: Methods and Protocols is to account for the most up-to-date protein design and engineering strategies so that readers can undertake their own projects with maximum confidence in a successful return. The basic concepts underlying rational design of proteins are intimately related to their three-dimensional structures.

• Amino acid
• Secondary structure
• protein complexes
• protein structure
• proteins

"...provides a comprehensive guide to the methods used at every stage of the protein-design process..." - ChemBioChem

"...combines a thorough theoretical foundation with detailed protocols and will be invaluable to all researchers in the area, from graduate students to senior investigators." -ChemBioChem

• Département de Biologie Joliot–Curie CEA Saclay, Gif-sur-Yvette, France

  Raphael Guerois

• Merz Pharmaceuticals GmbH, Frankfurt am Main, Germany

  Manuela López Paz

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