Archived Project: Protein Structures
Mentor: Nelson Max (Computer Science)
**This project is no longer offered**
The project I propose is to get statistics on the alignments of beta sheets in protein structures, for the purpose of predicting 3D protein structure from amino acid sequence. When two adjacent beta strands are aligned into a beta sheet, the probability of the alignment depends on the probabilities that each amino acid from one strand is opposite a particular amino acid type on the adjacent strand. These probabilities were investigated in a paper "Sequence specificity, statistical potentials, and three-dimensional structure prediction with self-correcting distance geometry calculations of beta-sheet formation in proteins" by Zhu and Braun in Protein Science, vol. 8, pp. 326 - 342 (1999) using statistics from 169 proteins known at that time from the Protein Data Bank (PDB), http://www.rcsb.org/pdb/home/home.do.
The goal of this project is to modernize these statistics using more recent data from the PDB, and also to take into account the four possible orientations of each beta strand, since Zhu and Braun only considered two more general classes of orientations, parallel and anti-parallel. Also, Zhu and Braun calculated the probability of an alignment as a simple product of probabilities of directly and diagonally opposite amino acid types, but more detailed joint distributions could also be considered.