From: Panchenko, Anna (NIH/NLM/NCBI) [E]
Sent: Tuesday, April 21, 2009 11:56 AM
To: NLM/NCBI List ncbi-seminar
Subject: Special seminar, April 24, 11am

Friday, April 24-th, 11 am
Bldg 38A, 8-th floor conference room

Protein sequence-structure relationship: sequence and folding patterns.

                    Alexander Kister
The University of Medicine and Dentistry of New Jersey (UMDNJ)

This work evaluates the hypothesis that proteins with an identical
supersecondary structure (SSS) share a unique set of residues  -
'SSS-determining residues' - even though they may belong to  different
protein families and have very low sequence similarities (below the
'twilight zone'). This hypothesis was tested on groups of sandwich-like
proteins. To find the SSS-determining residues a novel structure-based
algorithm of multiple sequences alignment was developed. The algorithm
is based on the alignment of residues that form hydrogen bonds.
Structure-based alignment revealed a unique set of SSS-determining
residues for each group of proteins with the same SSS. The set of
SSS-determining residues has very high sensitivity and specificity for
identifying proteins having a particular SSS. Thus, the sets of
SSS-determining residues can be used to classify proteins and to predict
SSS of a query amino acid sequence. An important corollary of this work
is that protein sequence/structure relationship is reciprocal: not only
does amino acid sequence determine the SSS of a protein, but also the
SSS determines residue content at key positions in sequences.

References:
1. PNAS (2006) vol. 103: 4107-4110; 
2. Proteins (2007) vol. 68: 915-921; 
3. PNAS (2008) vol. 105: 9233-9237; 
4. Springer Verlag Lecture Notes in Bioinformatics series, 2009 (in
press).