Relationship between amino acids sequences and protein structures

Alexander Kister
University of Medicine and Dentistry of New Jersey, SHRP, Department of
Health Informatics, Newark, NJ, 07107, USA
Relationship between amino acids sequences and protein
structures: folding patterns and sequence patterns.
To describe the main structural regularities - folding pattern we introduced
a supersecondary structure (SSS) unit of beta proteins called the
‘‘strandon’’. Analysis of sandwich-like proteins revealed two specific
folding patterns, which describe the arrangement of strandons and strands in
the protein domains. It enables us to construct a novel structural
classification scheme in the recently created SSS Protein database
The second goal of this study was to evaluate the hypothesis that proteins
from different families and with very low sequence similarities but with an
identical SSS have a common sequence pattern. To find common sequence
regularities a new algorithm of the multiple sequences alignment was
developed. The proposed method involves ‘projecting’ common
supersecondary structural characteristics onto the sequence to reveal key
residues. The results of the alignment revealed conserved positions. It was
shown that residues at these positions form an SSS-specific sequence pattern
and could be used for protein classification as an amino acid ‘tag’ that
brands a sequence as having a particular SSS. The important conclusion
follows from the results of this work: the protein sequence/structure
relationship cuts both ways. That is both the sequence of amino acids
determines the folding pattern and the structure defines key positions in
sequences and residues at these positions.
PNAS (2006) vol. 103: 4107-4110; Proteins (2007) vol. 68: 915–921; PNAS
(2008) vol. 105: 9233-9237; Protein Sci. (2008) the manuscript is submitted