The evolutionary capacity of protein structures

In nature, one finds large collections of different protein sequences exhibiting roughly the same three-dimensional structure, and this observation underpins the study of structural protein families. In studying such families at a global level, a natural question to ask is how close to "optimal" the native sequences are in terms of their energy. We therefore define and compute the evolutionary capacity of a protein structure as the total number of sequences whose energy in the structure is below that of the native sequence. An important aspect of our definition is that we consider the space of all possible protein sequences, i.e. the exponentially large set of all strings over the 20-letter amino acid alphabet, rather than just the set of sequences found in nature. In order to make our approach computationally feasible, we develop randomized algorithms that perform approximate enumeration in sequence space with provable performance guarantees. We draw on the area of rapidly ...

• Type: Conference
• Year: 2004
• Where: RECOMB
• Authors: Leonid Meyerguz, David Kempe, Jon M. Kleinberg, Ron Elber
• Keywords: Computational Biology, Evolutionary Capacity, Lucile Packard Foundation, Provable Performance Guarantees, RECOMB 2004