Structural Elucidation of the Masp1 and Masp2 Protein from Nephila Pilipes Web Via Bioinformatics Approaches

Abstract

Major ampullate spidroin (MaSps) from orb-weaver spp spider has recently gained interest due to its exceptional characteristics. The biomechanical and biochemical properties from MaSps offer potential in harvesting and exploiting MaSps as a promising bio-based product. However, the current research on the structural elucidation focused more onto the Nephila clavipes spider web rather than the Nephila pilipes which are more common in this region. Herein, this study integrates the used of computational power and algorithm to elucidate the 3D protein morphology of MaSp1 and MaSp2 of Nephila pilipes dragline silk protein using nearly complete amino acid sequences obtained from the protein database. In silico homology modelling via Phyre2, SWISS-MODEL and RaptorX was adopted to predict the protein structure of MaSP-1 and 2 using proteins threading, automated comparative modelling of three-dimensional (3D) protein structures and deep learning approaches. Consequently, we described a thorough 3D protein models of MaSp1 and MaSp2 with a higher percentage of coils, α-helix and a low percentage of β-sheet on repetitive regions of MaSp1 and MaSp2. The results of this current work provide insights into Bioinformatics potentials in engineering spider silk-based biomaterial and bridging the most apparent gaps in the knowledge of MaSp1 and MaSp2.

Multi-epitopes vaccine design for surface glycoprotein against SARS-CoV-2 using immunoinformatic approach

“…The 3D structure was predicted by the Swiss model ( Fig. 1 b) [ 45 ]. The secondary structure showed that the S protein has 29.59 % α helixes, 4.08 % β sheets, and 44.30 % random coil, extended strand 22.07 % loops ( Fig.…”