Title:Sequence-Structure Similarity: Do Sequentially Identical Peptide Fragments have Similar Three-Dimensional Structures?
VOLUME: 7 ISSUE: 2
Author(s):Muthukumarasamy Uthayakumar, Sanjeev Patra, Raju Nagarajan and Kanagaraj Sekar
Affiliation:Bioinformatics Centre, Centre of Excellence in Structural Biology and Bio-computing, Indian Institute of Science, Bangalore 560012, India.
Keywords:Identical peptides, non-redundant structures, protein data bank, protein fragments, structural similarity, Plasmodium falciparum, Mycobacterium tuberculosis, fragments, organisms, parameters
Abstract:The rapidly growing structure databases enhance the probability of finding identical sequences sharing
structural similarity. Structure prediction methods are being used extensively to abridge the gap between known protein
sequences and the solved structures which is essential to understand its specific biochemical and cellular functions. In this
work, we plan to study the ambiguity between sequence-structure relationships and examine if sequentially identical
peptide fragments adopt similar three-dimensional structures. Fragments of varying lengths (five to ten residues) were
used to observe the behavior of sequence and its three-dimensional structures. The STAMP program was used to
superpose the three-dimensional structures and the two parameters (Sequence Structure Similarity Score (Sc) and Root
Mean Square Deviation value) were employed to classify them into three categories: similar, intermediate and dissimilar
structures. Furthermore, the same approach was carried out on all the three-dimensional protein structures solved in the
two organisms, Mycobacterium tuberculosis and Plasmodium falciparum to validate our results.
