13 Facts About Protein design

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.

Rational protein design approaches make protein-sequence predictions that will fold to specific structures.

Goal in rational protein design is to predict amino acid sequences that will fold to a specific protein structure.

Protein design is then an optimization problem: using some scoring criteria, an optimized sequence that will fold to the desired structure is chosen.

Protein function is heavily dependent on protein structure, and rational protein design uses this relationship to design function by designing proteins that have a target structure or fold.

Many of the earliest attempts on protein design were heavily based on empiric rules on the sequence space.

One of the most challenging requirements for successful Protein design is an energy function that is both accurate and simple for computational calculations.

Protein design has requirements that can sometimes be limited in molecular mechanics force-fields.

Goal of protein design is to find a protein sequence that will fold to a target structure.

However protein design is a prerequisite of de novo enzyme design because, at the very least, the design of catalysts requires a scaffold in which the catalytic mechanism can be inserted.

Also, in the laboratory of Bruce Donald, computational protein design was used to switch the specificity of one of the protein domains of the nonribosomal peptide synthetase that produces Gramicidin S, from its natural substrate phenylalanine to other noncognate substrates including charged amino acids; the redesigned enzymes had activities close to those of the wild-type.

Protein design resurfacing is especially useful to alter the binding of a protein to other proteins.

One of the most desirable uses for protein design is for biosensors, proteins that will sense the presence of specific compounds.