In silico characterization and prediction of three-dimensional protein structures of Tenebrosin-C and Tenebrosin- X gene fragments from sea anemone (Actinia tenebrosa)

Date

4-2007

Degree

Bachelor of Science in Biology

College

College of Arts and Sciences (CAS)

Adviser/Committee Chair

Ivan Marcelo A. Duka

Abstract

Two gene fragments previously identified Tenebrosin-C (TN-C) and Tenebrosin-X (TN-X) were characterized for their sequence homology using gene and protein databases. Their physicochemical properties based on the protein primary sequence were computed and the three-dimensional structures of their proteins were predicted using different bioinformatics programs. Both sequences showed alignments with significantly high percent identity and similarity with Equinatoxin precursors from Actinic equines anemone using the BLAST and EMBOSS-Align programs. Their theoretical molecular weights and isoelectric points were predicted as 11.78 kDa and 9.16 pl for TN-C, and 11.70 kDa and 8.14 pl for TN-X using ProtParam program. Post-translational modifications sites of the proteins such as sites for glycosylation, phosphorylation, amidation and myristoylation were identified. Transmembrane helix was predicted in TN-X and none in TN-C using TMHMM program. Using comparative modeling methods, the 3-dimensional structures of the protein fragments were predicted using the 3DJIGSAW program and modeled in RasMol molecular viewer. Secondary structures and folding classes of the proteins were identified in the 3-D tertiary structures predicted. Alpha helix, beta-pleated sheet, beta strands, beta turns and gamma turns were present in both structures. The presence of chemical bonds and interactions were also identified since they primarily contribute to the overall protein tertiary structure. The characterizations of the biochemical and molecular properties of tenebrosin toxins which are reported to have cytolytic and cardiostimulatory activities on animals are essential in the production and development of new drugs and pesticides.

Language

English

Location

UPLB Main Library Special Collections Section (USCS)

Call Number

Thesis

Document Type

Thesis

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