Tinkering with Protein Structure

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Science  08 Jun 2007:
Vol. 316, Issue 5830, pp. 1397
DOI: 10.1126/science.316.5830.1397a

A few years ago, a new protein (Top7) was made from scratch. A computational algorithm provided a sequence of amino acids that had been designed to fold into a stable structure unlike any previously deposited in the public databases; lo and behold, it did. Top7 consists of three substructures: a pair of two β-strand-one α-helix modules (A and C) separated in the sequence by a single β strand (module B), with the five β strands forming a hydrogen-bonded β sheet.

Using atomic force microscopy and steered molecular dynamics, Sharma et al. have assessed the mechanical resistance of Top7 to being pulled apart and compared these parameters to those of the canonical elastomeric module I27 of titin. They find that theory and experiment fit well, providing an average unfolding force of 155 pN that acts to strip off module A from B-C by breaking the hydrogen (and other) bonds between these substructures. Welding β-strands 1 and 3 with a disulfide revealed that 170 pN was needed to lever module C away from the A-B assembly, whereas interrupting one of the hydrogen bonds linking β-strands 3 and 5 was sufficient to lower the unfolding force to 125 pN. These results together illustrate the power of combining computational and biochemical approaches to the design and refinement of protein structure. — GJC

Proc. Natl. Acad. Sci. U.S.A. 104, 9278 (2007).

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