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:''This article refers to rational protein design. For the broader engineering of proteins see protein engineering. Protein design is the rational design of new protein molecules to fold to a target protein structure, with the ultimate goal of designing novel function and/or behavior. Proteins can be designed from scratch (''de novo'' design) or by making calculated variations on a known protein structure and its sequence (known as ''protein redesign''). Rational protein design approaches make protein-sequence predictions that will fold to specific structures. These predicted sequences can then be validated experimentally through methods such as peptide synthesis, site-directed mutagenesis, or artificial gene synthesis. Rational protein design dates back to the mid-1970s, although initial protein design approaches were based mostly on sequence composition and did not account for specific interactions between side-chains at the atomic level. Recently, however, improvements in molecular force fields, protein design algorithms, and structural bioinformatics, such as libraries of amino acid conformations, have enabled the development of advanced computational protein design tools. These computational tools can make complex calculations on protein energetics and flexibility, and perform searches over enormous configuration spaces, which would be unfeasible to perform manually. Thanks to the development of computational protein design programs and important successes in the field (e.g., see examples below), rational protein design has become one of the most important tools in protein engineering. ==Overview and history== The goal in rational protein design is to predict amino acid sequences that will fold to a specific protein structure. Although the number of possible protein sequences is enormous, growing exponentially with the size of the protein chain, only a subset of them will fold reliably and quickly to a single native state. Protein design involves identifying novel sequences within this subset. The native state of a protein is the conformational free energy minimum for the chain. Therefore, protein design is the search for sequences that have the chosen structure as a free energy minimum. In a sense, it is the reverse of structure prediction: In design, a tertiary structure is specified, and a sequence that will fold to it is identified. Hence, it is also referred to as ''inverse folding''. Protein design is then an optimization problem: using some scoring criteria, an optimized sequence that will fold to the desired structure is chosen. When the first proteins were rationally designed during the 1970s and 1980s, the sequence for these was optimized manually based on analyses of other known proteins, the sequence composition, amino acid charges, and the geometry of the desired structure.〔 The first designed proteins are attributed to Bernd Gutte, who designed a reduced version of a known catalyst, bovine ribonuclease, as well as tertiary structures consisting of beta-sheets and alpha-helices, including a binder of DDT. Urry and colleagues later designed elastin-like fibrous peptides based on rules on sequence composition. Richardson and co-workers designed a 79-residue protein with no sequence homology to any known protein.〔 In the 1990s, the advent of powerful computers, libraries of amino acid conformations, and force fields developed primarily for molecular dynamics simulations enabled the development of structure-based computational protein design tools. Following the development of these computational tools, enormous success has been achieved over the last 30 years in protein design. The first protein successfully designed completely ''de novo'' was done by Stephen Mayo and co-workers in 1997,〔 and, shortly after, in 1999 Peter S. Kim and co-workers designed dimers, trimers, and tetramers of unnatural right-handed coiled coils. In 2003, David Baker's laboratory designed a full protein to a fold never seen before in nature.〔 Later, in 2008, Baker's group computationally designed enzymes for two different reactions. In 2010, one of the most powerful broadly neutralizing antibodies was isolated from patient serum using a computationally designed protein probe. Thanks to these and other successes (e.g., see examples below), protein design has become one of the most important tools available for protein engineering. There is great hope that the design of new proteins, small and large, will have applications in medicine and bioengineering. 抄文引用元・出典: フリー百科事典『 ウィキペディア（Wikipedia）』 ■ウィキペディアで「protein design」の詳細全文を読む スポンサード リンク
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