Protein DesignRaphael Guerois, Manuela López de la Paz 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. |
Contents
De novo Design of Monomeric Hairpin and Sheet Peptides | 27 |
De novo Proteins From BinaryPatterned Combinatorial Libraries | 53 |
NonProtein Amino Acids in the Design of Secondary | 71 |
Design and Synthesis of Peptides With Biological Activity | 95 |
Design of Miniproteins by the Transfer of Active Sites | 113 |
Consensus Design as a Tool for Engineering Repeat Proteins | 151 |
Multiple Sequence Alignment as a Guideline | 171 |
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Common terms and phrases
Acad activity affinity aggregation Alzheimer's amino acids amyloidogenic analysis antiparallel sheet backbone Balaram binary patterned binding bioactive Biochemistry Biol Biology C-terminal calculated cell charged charybdotoxin Chem circular dichroism codon conformational consensus CspB Curr database diazomethane disulfide bond edited electrostatic energy experimental Fmoc folding FoldX function gene hairpin hairpin peptide helical helical peptides helix homology hydrogen bonds hydrophobic HyPare inhibition inhibitor interactions interface ligand Methods mimic miniprotein molecular molecule motif mutant Mutant GB1_1 Natl nonpolar novo design nucleation oligonucleotides polar polypeptide positions prediction Proc protein design protein folding protein misfolding Protein Sci protein structure protein-protein Protocols region repeat proteins residues RosettaDesign scaffold scoring scyllatoxin secondary structure selected sequence alignment Serrano server SH3 domain side chains solubility solution solvent stability strand strategy Struct studies Subheading synthesis target teins template tion turn wild-type