THE EFFECT OF THE D185 MUTATION ON THE STABILITY AND FUNCTIONALITY OF RUBISCO LIKE PROTEIN (RLP) FROM CHROMOHALOBACTER SALEXIGEN BKL 5
Abstract
In the case of Rubisco Like Protein (RLP) Chromohalobacter salexigen BKL 5 (RLP CS), which is halophilic, the presence of salt bridges (SB) is not too numerous but efficient enough to maintain stability in high salt stress. This study was to determine the effect of mutations SB at position 185 (D185/WT) on the stability and activity of RLP CS through an in-silico approach by replacing aspartic acid with glutamic acid and alanine (D185E and D185A). The methods used were Molecular Dynamics Simulations (MDS) and Molecular Docking (MD). The MDS was used to study molecular characteristics at the atomic level, while MD was for the interaction patterns of proteins and ligands. The results of the MDS analysis carried out at 10ns showed that the mutation at position 185 with alanine and glutamic acid changed the size/dimensional of RLP CS and affected its overall geometric structure. Interestingly, even though the structure has changed, the activity of the protein remains relatively constant, which is indicated by the results of MD, and has a relatively similar binding energy value of around -6.3 Kcal/mol.
Keywords: Chromohalobacter salexigen BKL 5, molecular docking, molecular dynamic simulation, mutation, saltbridge
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Albeck, S., Unger, R., Schreiber, G. 2000. Evaluation of Direct and Cooperative Contributions Towards The Strength of Buried Hydrogen Bonds and Salt Bridges. Journal of Molecular Biology. 298(3): 503–520
Al-Karmalawy, A.A., Dahab, M.A., Metwaly, A.M., Elhady, S.S., Elkaeed, E.B., Eissa, I.H., Darwish, K.M. 2021. Molecular Docking and Dynamics Simulation Revealed the Potential Inhibitory Activity of ACEIs Against SARS-CoV-2 Targeting the hACE2 Receptor. Frontiers in Chemistry. 9
Bosshard, H. R., Marti, D. N., Jelesarov, I. 2004. Protein Stabilization by Salt Bridges: Concepts, Experimental Approaches and Clarification of Some Misunderstandings. Journal of Molecular Recognition. 17(1): 1–16
Guex, N., Peitsch, M.C. 1997. SWISS-MODEL and the Swiss-Pdb Viewer: An Environment for Comparative Protein Modeling. Electrophoresis. 18(15): 2714–2723
Hollingsworth, S.A., Dror, R.O. 2018. Molecular Dynamics Simulation for All. Neuron. 99(6): 1129–1143
Karplus, M., McCammon, J.A. 2002. Molecular Dynamics Simulations of Biomolecules. Nature Structural Biology. 9(9): 646–652
Kumar, S., Nussinov, R. 2002. Close-Range Electrostatic Interactions in Proteins. ChemBioChem. 3(7): 604-610
Meng, X.Y., Zhang, H.X., Mezei, M., Cui, M. 2011. Molecular Docking: A Powerful Approach for Structure-Based Drug Discovery. Current Computer Aided-Drug Design. 7(2): 146–157
Messaoudi, A., Belguith, H., Ben Hamida, J. 2013. Homology Modeling and Virtual Screening Approaches to Identify Potent Inhibitors of VEB-1 β-Lactamase. Theoretical Biology and Medical Modelling. 10(1)
Miyazono, K., Tanokura, M. 2022. New Era in Structural Biology with The Alphafold Program. Translational and Regulatory Sciences. 4(2): 48–52
Morris, G.M., Huey, R., Lindstrom, W., Sanner, M.F., Belew, R. K., Goodsell, D. S., Olson, A.J. 2009. AutoDock4 and AutoDockTools4: Automated Docking with Selective Receptor Flexibility. Journal of Computational Chemistry. 30(16): 2785–2791
Musafia, B., Buchner, V., Arad, D. 1995. Complex Salt Bridges in Proteins: Statistical Analysis of Structure and Function. Journal of Molecular Biology. 254(4): 761–770
Oostenbrink, C., Villa, A., Mark, A.E., Van Gunsteren, W.F. 2004. A Biomolecular Force Field Based on The Free Enthalpy of Hydration and Solvation: The GROMOS Force-Field Parameter Sets 53A5 and 53A6. Journal of Computational Chemistry. 25(13): 1656–1676
Pettersen, E.F., Goddard, T.D., Huang, C.C., Couch, G. S., Greenblatt, D.M., Meng, E.C., Ferrin, T.E. 2004. UCSF Chimera: A Visualization System for Exploratory Research and Analysis. Journal of Computational Chemistry. 25(13): 1605–1612
Rácz, A., Mihalovits, L.M., Bajusz, D., Héberger, K., & Miranda-Quintana, R.A. 2022. Molecular Dynamics Simulations and Diversity Selection by Extended Continuous Similarity Indices. Journal of Chemical Information and Modeling. 62(14): 3415–3425
Shukla, R., Shukla, H., Tripathi, T. 2018. Activity loss by H46A Mutation in Mycobacterium Tuberculosis Isocitrate Lyase is Due To Decrease in Structural Plasticity and Collective Motions of The Active Site. Tuberculosis. 108:143–150
Takano, K., Ogasahara, K., Kaneda, H., Yamagata, Y., Fujii, S., Kanaya, E., Kikuchi, M., Oobatake, M., Yutani, K. 1995. Contribution of Hydrophobic Residues to the Stability of Human Lysozyme: Calorimetric Studies and X-ray Structural Analysis of the Five Isoleucine to Valine Mutants. Journal of Molecular Biology. 254(1): 62–76
Takano, K., Tsuchimori, K., Yamagata, Y., Yutani, K. 2000. Contribution of Salt Bridges Near The Surface of A Protein to The Conformational Stability,. Biochemistry. 39(40): 12375–12381
Tian, W., Chen, C., Lei, X., Zhao, J., Liang, J. 2018. CASTp 3.0: Computed Atlas of Surface Topography of Proteins. Nucleic Acids Research. 46(W1): W363–W367
Walker, K. D., Causgrove, T. P. 2009. Contribution of Arginine-Glutamic Acid Salt Bridges to Helix Stability. Journal of Molecular Modeling. 15(10): 1213–1219
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