Slidel, Timothy Ward Featherstone; (1997) A Computational Study of Chirality in Protein Structure. Doctoral thesis (Ph.D), UCL (University College London).

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Abstract

This thesis discusses the development and use of computational methods to analyse the chirality that is found throughout protein structure. A computer program was written to investigate the chirality that occurs in the low-level twisting and coiling of the polypeptide chain using torsion angles. This approach was found to be useful for characterising the handedness of protein secondary structure as well as non-repetitive structures such as turns. To analyse the handedness of supersecondary structure motifs a computer program called ProSEC was written. A generic motif was defined that consists of two segments of secondary structure (i.e, helices or strands) and a central segment of chain that links them. In a βαβ motif, for example, the central segment contains an alpha helix and the flanking segments are 3-strands. The ProSEC program calculates the handedness of a motif by examining the path of the central segment relative to a frame of reference constructed from the two flanking segments. Using this program an analysis of the handedness of super-secondary structure motifs was performed. In general this analysis has established two main facts: 1) The majority of motifs (of any type) have connecting segments that join the flanking secondary structures by the most direct path, This is especially true for motifs that are more compact; 2) βαβ motifs have a high propensity for right-handedness. However, as several left-handed motifs were found this should no longer be viewed as a structural invariant. This handedness preference is a direct result of the well-defined packing that occurs between β-strands in β-sheets. All the left-handed βxβ motifs found were involved in protein function to some degree. Above all, this analysis has shown that it is possible to automatically determine structural motif handedness in a reliable and consistent manner using the algorithm implemented in the ProSEC program. Further analyses can therefore be routinely performed to establish the relationships between supersecondary structure chirality and other aspects of protein structure. Thereby furthering our knowledge of how protein secondary structures aggregate to form stable tertiary folds.

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