The protein-protein interactions between SMPI and thermolysin studied by molecular dynamics and MM/PBSA calculations
Olayiwola A Adekoya1, Nils-Peder Willassen, Ingebrigt Sylte
1Department of Pharmacology, Institute of Medical Biology, Faculty of Medicine, University of Tromsø, N-9037 Tromsø, Norway.
Abstract:
Thermolysin is a zinc-metalloendopeptidase secreted by the gram-positive thermophilic bacterium Bacillus thermoproteolyticus. Thermolysin belongs to the gluzinicin family of enzymes, which is selectively inhibited by Steptomyces metalloproteinase inhibitor (SMPI). Very little is known about the interaction between SMPI and thermolysin. Knowledge about the protein-protein interactions is very important for designing new thermolysin inhibitors with possible industrial or pharmaceutical applications. In the present study, two binding modes between SMPI and thermolysin were studied by 2300 picoseconds (ps) of comparative molecular dynamics (MD) simulations and calculation of the free energy of binding using the molecular mechanics-Poisson-Boltmann surface area (MM/PBSA) method. One of the positions, the 'horizontal arrow head docking' (HAHD) was similar to the previously proposed binding mode by Tate et al. (Tate, S., Ohno, A., Seeram, S. S., Hiraga, K., Oda, K., and Kainosho, M. J. Mol. Biol. 282, 435-446 (1998)). The other position, the 'vertical arrow head docking' (VAHD) was obtained by a manual docking guided by the shape and charge distribution of SMPI and the binding pocket of thermolysin. The calculations showed that SMPI had stronger interactions with thermolysin in the VAHD than in the HAHD complex, and the VAHD complex was considered more realistic than the HAHD complex. SMPI interacted with thermolysin not only at the active site but had auxiliary binding sites contributing to proper interactions. The VAHD complex can be used for designing small molecule inhibitors mimicking the SMPI-thermolysin binding interfaces.
Insights
This study reveals that the vertical arrow head docking (VAHD) mode shows stronger interactions between thermolysin and its inhibitor (SMPI) than the horizontal mode. This finding aids in designing new inhibitors for thermolysin, a key enzyme.
Area of Science:
- Biochemistry
- Molecular Biology
- Enzymology
Background:
- Thermolysin, a zinc-metalloendopeptidase from Bacillus thermoproteolyticus, is inhibited by Streptomyces metalloproteinase inhibitor (SMPI).
- Understanding protein-protein interactions involving thermolysin is crucial for developing novel inhibitors for industrial and pharmaceutical applications.
- Limited information exists regarding the specific binding interactions between SMPI and thermolysin.
Purpose of the Study:
- To investigate and compare two distinct binding modes between SMPI and thermolysin.
- To determine the more energetically favorable and realistic binding conformation for inhibitor design.
- To elucidate the interaction sites beyond the active site that contribute to binding stability.
Main Methods:
- Comparative molecular dynamics (MD) simulations over 2300 picoseconds.
- Free energy of binding calculations using the molecular mechanics-Poisson-Boltzmann surface area (MM/PBSA) method.
- Analysis of two proposed binding modes: 'horizontal arrow head docking' (HAHD) and 'vertical arrow head docking' (VAHD).
Main Results:
- The VAHD complex exhibited significantly stronger interactions between SMPI and thermolysin compared to the HAHD complex.
- The VAHD complex was determined to be a more realistic representation of the SMPI-thermolysin interaction.
- SMPI binding involved both the active site and auxiliary binding sites on thermolysin.
Conclusions:
- The VAHD mode represents a more accurate binding conformation of SMPI to thermolysin.
- The identified binding interfaces, including auxiliary sites, provide a basis for designing targeted small molecule inhibitors.
- This research advances the understanding of thermolysin inhibition for potential therapeutic and biotechnological uses.
