Protein design facts for kids

Protein design is the rational design of new protein molecules to design novel activity, behavior, or purpose, and to advance basic understanding of protein function. Proteins can be designed from scratch (de novo design) or by making calculated variants of a known protein structure and its sequence (termed 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. Recently, however, there were numerous examples of successful rational design of water-soluble and even transmembrane peptides and proteins, in part due to a better understanding of different factors contributing to protein structure stability and development of better computational methods.

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 vast, growing exponentially with the size of the protein chain, only a subset of them will fold reliably and quickly to one 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. Thus, 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 protein structure prediction. In design, a tertiary structure is specified, and a sequence that will fold to it is identified. Hence, it is also termed 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, and 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 coworkers designed a 79-residue protein with no sequence homology to a known protein. In the 1990s, the advent of powerful computers, libraries of amino acid conformations, and force fields developed mainly for molecular dynamics simulations enabled the development of structure-based computational protein design tools. Following the development of these computational tools, great 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 coworkers in 1997, and, shortly after, in 1999 Peter S. Kim and coworkers 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. Due 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 uses in biomedicine and bioengineering.

Images for kids

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  The Top7 protein was one of the first proteins designed for a fold that had never been seen before in nature

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  FSD-1 (shown in blue, PDB id: 1FSV) was the first de novo computational design of a full protein. The target fold was that of the zinc finger in residues 33–60 of the structure of protein Zif268 (shown in red, PDB id: 1ZAA). The designed sequence had very little sequence identity with any known protein sequence.

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  Common protein design programs use rotamer libraries to simplify the conformational space of protein side chains. This animation loops through all the rotamers of the isoleucine amino acid based on the Penultimate Rotamer Library (total of 7 rotamers).

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  Comparison of various potential energy functions. The most accurate energy are those that use quantum mechanical calculations, but these are too slow for protein design. On the other extreme, heuristic energy functions are based on statistical terms and are very fast. In the middle are molecular mechanics energy functions that are physically based but are not as computationally expensive as quantum mechanical simulations.

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  Water-mediated hydrogen bonds play a key role in protein–protein binding. One such interaction is shown between residues D457, S365 in the heavy chain of the HIV-broadly-neutralizing antibody VRC01 (green) and residues N58 and Y59 in the HIV envelope protein GP120 (purple).

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  This animation illustrates the complexity of a protein design search, which typically compares all the rotamer-conformations from all possible mutations at all residues. In this example, the residues Phe36 and His 106 are allowed to mutate to, respectively, the amino acids Tyr and Asn. Phe and Tyr have 4 rotamers each in the rotamer library, while Asn and His have 7 and 8 rotamers, respectively, in the rotamer library (from the Richardson's penultimate rotamer library). The animation loops through all (4 + 4) x (7 + 8) = 120 possibilities. The structure shown is that of myoglobin, PDB id: 1mbn.

See also

• Molecular design software
• Protein engineering
• Protein structure prediction software
• Comparison of software for molecular mechanics modeling