CLePAPS: FAST PAIR ALIGNMENT OF PROTEIN STRUCTURES BASED ON CONFORMATIONAL LETTERS

Fast, efficient, and reliable algorithms for pairwise alignment of protein structures are in ever-increasing demand for analyzing the rapidly growing data on protein structures. CLePAPS is a tool developed for this purpose. It distinguishes itself from other existing algorithms by the use of conformational letters, which are discretized states of 3D segmental structural states. A letter corresponds to a cluster of combinations of the three angles formed by Cα pseudobonds of four contiguous residues. A substitution matrix called CLESUM is available to measure the similarity between any two such letters. CLePAPS regards an aligned fragment pair (AFP) as an ungapped string pair with a high sum of pairwise CLESUM scores. Using CLESUM scores as the similarity measure, CLePAPS searches for AFPs by simple string comparison. The transformation which best superimposes a highly similar AFP can be used to superimpose the structure pairs under comparison. A highly scored AFP which is consistent with several other AFPs determines an initial alignment. CLePAPS then joins consistent AFPs guided by their similarity scores to extend the alignment by several "zoom-in" iteration steps. A follow-up refinement produces the final alignment. CLePAPS does not implement dynamic programming. The utility of CLePAPS is tested on various protein structure pairs.

Photofragment mapping of intramolecular motion

The intramolecular motion in selected rovibrational levels in HOOH and HOOD, populated by tunable, pulsed laser excitation in the third O-H overtone band, has been probed via ‘photofragment mapping’ following secondary photon absorption. Quantum state distributions, vector correlations and vibrational {vx, v2) and rotational jOC CZV2)) OH(D) fragment pair correlations have been obtained using polarized, Doppler resolved laser induced fluorescence techniques. The results provide quantitative estimates of the extensive intramolecular redistribution of energy among the overtone levels and highlight the role of a-axis rotation in promoting rotation—vibration coupling.