Effects of thermal and electric fields on soybean trypsin inhibitor protein: A molecular modelling study. (June 2016)

• Record Type: Journal Article
• Authors: Harish Vagadia, Brinda; Vanga, Sai Kranthi; Singh, Ashutosh; Raghavan, Vijaya
• Is Part Of: Innovative food science & emerging technologies. Volume 35(2016)
• Page Start: 9
• Page End: 20
• Publication Date: 2016-06
• Subjects: MD molecular dynamics -- SASA Solvent Accessible Surface Area -- RMSD Root Mean Square Deviation -- STI Soybean Trypsin Inhibitor -- KTI Kunitz-type Trypsin Inhibitor -- NMR Nuclear Magnetic Resonance Imaging -- VMD Visual Molecular Dynamics -- FTIR Fourier Transformation Infrared Spectroscopy -- PDB Protein Data Base -- PME Particle Mesh Ewald -- NVT ensemble in which number of atoms, volume and temperature are constant -- NPT ensemble in which number of atoms, pressure and temperature are constant -- DSSP Define Secondary Structure of Protein; Soybean trypsin inhibitor -- Molecular dynamics -- GROMACS -- Solvent accessible area -- Ramachandran plot; Food -- Biotechnology -- Periodicals; Food industry and trade -- Technological innovations -- Periodicals; Aliments -- Biotechnologie -- Périodiques; Food -- Biotechnology; Periodicals; Electronic journals; 664.005
• DOI: 10.1016/j.ifset.2016.03.004
• Languages: English
• ISSNs: 1466-8564

Abstract

Abstract: This study uses molecular dynamics (MD) simulations in investigating the unusual stability of Soybean Trypsin Inhibitor (STI) protein. The effects of temperature and oscillating electric fields (0.5 V/nm and 2.45 GHz) have been used to perform simulations using GROMACS software. The conformational changes in the protein were studies using root mean square deviations and secondary structure analysis (STRIDE). It was found that significant rearrangements took place within the protein especially in 'turns' and 'coils', but the core structure was stable under external stresses because of the antiparallel β-sheet structure. This study also provides evidence that the aromatic residues play a major role in stabilizing the STI protein using Solvent Accessible Surface Area (SASA) analysis. Ramachandran plots were also used to analyze the stability of the molecules obtained on treatment with temperatures (300 K to 393 K) and oscillating electric fields. Industrial relevance: Molecular dynamics (MD) simulation techniques have been applied to visualize and predict the behaviour of proteins during food processing, and changes in their structure under the influence of external field stress. This study can be used to understand the changes at molecular level that could help industrialists to design processing methods with increased nutritive and sensory appeal of food products. This work can also contribute to the optimization of process parameters to enhance the functional properties of protein and increase protein digestibility. Highlights: Structural changes in Soybean Trypsin Inhibitor (STI) protein under the external field stress were visualized by Molecular Dynamics (MD) simulation techniques. Conformational changes in the STI protein structure were observed using secondary structure analysis (STRIDE) and Root Mean Square Deviation (RMSD) analysis. Solvent Accessible Surface Area (SASA) analysis showed visible changes in the secondary structure of the protein. Ramachandran plots were used to evaluate the stability of the molecules obtained on treatment with different processing conditions.