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Molecular dynamic (in silico) modeling of structure–function of glutelin type-B 5-like from proso millet storage protein: effects of temperature and pressure

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Abstract

Molecular dynamic (MD) simulation provides an insight into the behavior of a protein under applied processing at the molecular level. The behavior of glutelin type-B 5-like protein, a type of glutelin protein from proso millet was studied, in solution under different temperatures (300, 350, and 400 K) and pressure (1 bar, 3 kbar, and 6 kbar) levels using a molecular dynamics simulation approach. The combined treatment effect (400 K, 6 kbar) increased the compaction of the protein compared to the level at (300 K, 1 bar) as shown by the decreased radius of gyration values from 3.26 to 2.92 nm, decreased solvent accessibility surface area from 327.47 to 311.06 nm2 and decreased volume from 108.35 to 105.04 nm3. The root means square deviation increased with increasing temperature but decreased with increasing pressure while the root means square fluctuations increased significantly with increased in temperature and pressure. A snapshot of the three-dimensional structure of the protein revealed compression of its occluded cavities at higher pressure levels but no obvious disruption to the secondary structure elements of the protein was observed, except for the loss of a few amino acid residues that comprise the secondary structure element.

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Abbreviations

MD simulation:

Molecular dynamic simulation

GTB:

Glutelin type-B5-like

RMSD:

Root mean square deviation

RMSF:

Root mean square fluctuations

STI:

Soybean trypsin inhibitor

SASA:

Solvent accessibility surface area

LDL:

Low-density lipoprotein

NVT:

Number of particles, volume, and temperature

NPT:

Number of particles, pressure, and temperature

GROMACS:

Groningen machine for chemical structure

PMDB:

Protein model database

Rg:

Radius of gyration

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Acknowledgements

We thank Dr. Dipak Santra of the University of Nebraska for providing the proso millet cultivars used for this study.

Funding

This work was supported by the Kentucky Agricultural Experiment Station (KAES), and the National Institute of Food and Agriculture (NIFA), U.S. Department of Agriculture, Hatch- Multistate project #: 1024529.

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Authors and Affiliations

  1. Department of Biosystems and Agricultural Engineering, University of Kentucky, 128 Charles E. Barnhart Building, Lexington, KY, 40506, USA

    Felix Akharume & Akinbode Adedeji

Authors
  1. Felix Akharume
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  2. Akinbode Adedeji
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Contributions

Dr. FA was responsible for the design of experiment, data collection and analysis as well as writing the manuscript. Dr AA was responsible for ideation, supervision of the study and correcting the manuscript.

Corresponding author

Correspondence to Akinbode Adedeji.

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The authors declare no conflict of interest in the preparation, submission, and publication of this manuscript. All authors approved the submission and publication of this manuscript to the Journal of Food Science and Technology. Authors also acknowledge that this manuscript has not be previously published or being considered by other journal for publication.

Availability of Data and Materials

The dataset used for the protein model can be found in protein model database (PMDB) with the identity number of PM0083241. Additional data can be provided by the authors if requested.

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Akharume, F., Adedeji, A. Molecular dynamic (in silico) modeling of structure–function of glutelin type-B 5-like from proso millet storage protein: effects of temperature and pressure. J Food Sci Technol 60, 114–122 (2023). https://doi.org/10.1007/s13197-022-05594-y

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  • DOI: https://doi.org/10.1007/s13197-022-05594-y

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