Abstract
This study characterises the interaction between the type IV pilus assembly PilB ATPase of a versatile electroactive microbe, Shewanella oneidensis MR-1, and ATP using in silico tools. PilB ATPase, which is associated with different cellular activities, is a protein subunit of type IV pili. A composite model of the protein was generated using the I-TASSER Web server and its stereochemical quality was evaluated using PROCHECK. Loop modeling was performed using the InteractiveRosetta tool to refine the structure of the model and the COACH server was used to identify the functional binding site. The nature of binding, with the native ligand ATP, was determined using Autodock Vina and Discovery Studio Visualizer. Molecular dynamics simulations were carried out, with the bound and unbound states of the protein, for a period of 100 ns using GROMACS. Favorable root mean square deviation (0.75±0.10 nm) and radius of gyration (2.78±0.05 nm) values pointed to the stability of the modeled protein structure. Root mean square fluctuation and solvent accessible surface area analyses indicated a conformational change upon the ligand binding which occurred without a corresponding reorganization of secondary structures as evidenced by definition of secondary protein analysis. Molecular mechanics/Poisson–Boltzmann surface area analysis revealed the presence of a loop critical to the formation of stable interactions with ATP.
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References
Aruleba RT, Adekiya TA, Oyinloye BE, et al. 2018 Structural studies of predicted ligand binding sites and molecular docking analysis of Slc2a4 as a therapeutic target for the treatment of cancer. Int. J. Mol. Sci. 19 386
Balaji S, Kalpana R and Shapshak P 2006 Paradigm development: Comparative and predictive 3D modeling of HIV-1 virion infectivity factor (vif). Bioinformation 1 290–309
Bhowmick S, Chorge RD, Jangam CS, et al. 2020 Identification of potential cruzain inhibitors using de novo design, molecular docking and dynamics simulations studies. J. Biomol. Struct. Dyn. 38 4005–4015
Bischof LF, Freidrich C, Harms A, et al. 2016 The type IV pilus assembly ATPase PilB of Myxococcus xanthus interacts with the inner membrane platform protein pilc and the nucleotide-binding protein PilM. J. Biol. Chem. 291 6946–6957
Black WP, Wang L, Jing X, et al. 2017 The type IV pilus assembly ATPase PilB functions as a signaling protein to regulate exopolysaccharide production in Myxococcus xanthus. Sci. Rep. 7 7263
Bulyha I, Schmidt C, Lenz P, et al. 2009 Regulation of the type IV pili molecular machine by dynamic localization of two motor proteins. Mol. Microbiol. 74 691–706
Chaudhury S, Lyskov S and Gray JJ 2010 PyRosetta: A script-based interface for implementing molecular modeling algorithms using Rosetta. Bioinformatics 26 689–691
Chiang P, Sampaleanu LM, Ayers M, et al. 2008 Functional role of conserved residues in the characteristic secretion NTPase motifs of the Pseudomonas aeruginosa type IV pilus motor proteins PilB, PilT and PilU. Microbiology 154 114–126
Craig L, Forest KT and Maier B 2019 Type IV pili: dynamics, biophysics and functional consequences. Nat. Rev. Microbiol. 17 429–440
Craig L and Li J 2008 Type IV pili: paradoxes in form and function. Curr. Opin. Struct. Biol. 18 267–277
Danielson ML and Lill MA 2012 Predicting flexible loop regions that interact with ligands: The challenge of accurate scoring. Proteins Struct. Funct. Bioinform. 80 246–260
Gorgel M, Ulstrup JJ, Bøggild A, et al. 2015 High-resolution structure of a type IV pilin from the metal-reducing bacterium Shewanella oneidensis. BMC Struct. Biol. 15 1–17
Hanwell MD, Curtis DE, Lonie DC, et al. 2012 Avogadro: an advanced semantic chemical editor, visualization, and analysis platform. J. Cheminform 4 17
Heidelberg JF, Paulsen IT, Nelson KE, et al. 2002 Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis. Nat. Biotechnol. 20 1118–1123
Humphrey W, Dalke A and Schulten K 1996 VMD: Visual molecular dynamics. J. Mol. Graph 14 33–38
Joshi T, Joshi T, Sharma P, et al. 2020 Molecular docking and molecular dynamics simulation approach to screen natural compounds for inhibition of Xanthomonas oryzae pv. Oryzae by targeting peptide deformylase. J. Biomol. Struct. Dyn. 39 823–840
Khor BY, Tye GJ, Lim TS, et al. 2015 General overview on structure prediction of twilight-zone proteins. Theor. Biol. Med. Model 12 15
Kumari R, Kumar R, Open Source Drug Discovery Consortium, et al. 2014 g-mmpbsa–A GROMACS tool for high-throughput MM-PBSA calculations. J. Chem. Inf. Model 54 1951–1962
Laskowski RA, MacArthur MW, Moss DS, et al. 1993 PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26 283–291
Lemkul J 2019 From proteins to perturbed Hamiltonians: a suite of tutorials for the GROMACS-2018 molecular simulation package [Article v1.0]. Living J. Comput. Mol. Sci. 1 5068
Lindahl E, Abraham MJ, Hess B, et al. 2020 GROMACS 2020.3 manual (https://doi.org/10.5281/ZENODO.3923644)
Lukaszczyk M, Pradhan B and Remaut H 2019 The biosynthesis and structures of bacterial pili. Subcell Biochem. 92 369–413
Mancl JM, Black WP, Robinson H, et al. 2016 Crystal structure of a Type IV pilus assembly ATPase: Insights into the molecular mechanism of PilB from Thermus thermophilus. Structure 24 1886–1897
Mattick JS 2002 Type IV pili and twitching motility. Annu. Rev. Microbiol. 56 289–314
McCallum M, Tammam S, Khan A, et al. 2017 The molecular mechanism of the type IVa pilus motors. Nat. Commun. 8 15091
Pandit S, Khilari S, Roy S, et al. 2014 Improvement of power generation using Shewanella putrefaciens mediated bioanode in a single chambered microbial fuel cell: Effect of different anodic operating conditions. Bioresour. Technol. 166 451–457
Qin S and Zhou HX 2007 Do electrostatic interactions destabilize protein–nucleic acid binding? Biopolymers 86 112–118
Rahman MS, Hossain MS, Saha SK, et al. 2021 Homology modeling and probable active site cavity prediction of uncharacterized arsenate reductase in bacterial spp. Appl. Biochem. Biotechnol. 193 1–18
Roy A, Kucukural A and Zhang Y 2010 I-TASSER: a unified platform for automated protein structure and function prediction. Nat. Protocols 5 725–738
Schenkelberg CD and Bystroff C 2015 InteractiveROSETTA: a graphical user interface for the PyRosetta protein modeling suite. Bioinformatics 31 4023–4025
Shu C, Xiao K, Cao C, et al. 2017 Predicting and interpreting the structure of type IV pilus of electricigens by molecular dynamics simulations. Molecules 22 1342
Solanki V, Kapoor S and Thakur KG 2018 Structural insights into the mechanism of Type IVa pilus extension and retraction ATPase motors. FEBS J. 285 3402–3421
Sousa Da Silva AW and Vranken WF 2012 ACPYPE – AnteChamber PYthon Parser interfacE. BMC Res. Notes 5 367
Sukmana A and Yang Z 2018 The type IV pilus assembly motor PilB is a robust hexameric ATPase with complex kinetics. Biochem. J. 475 1979–1993
Wink LH, Baker DL, Cole JA, et al. 2019 A benchmark study of loop modeling methods applied to G protein-coupled receptors. J. Comput. Aided Mol. Des. 33 573–595
Yang J, Roy A and Zhang Y 2013a Protein – ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment. Bioinformatics 29 2588–2595
Yang J, Roy A and Zhang Y 2013b BioLiP: a semi-manually curated database for biologically relevant ligand – protein interactions. Nucleic Acids Res. 41 1096–1103
Yang J, Yan R, Roy A, et al. 2015 The I-TASSER suite: protein structure and function prediction. Nat. Methods 12 7–8
Yang J and Zhang Y 2015 I-TASSER server: new development for protein structure and function predictions. Nucleic Acids Res. 43 W174–W181
Acknowledgements
This work is dedicated to the founder chancellor, Sri Sathya Sai Institute of Higher Learning. The authors thank Mr. Sahashransu Satyajeet Mahapatra for support in carrying out this study. Computational facilities provided by the Department of Mathematics and Computer Science, SSSIHL, and DBT-BIF, Government of India, are gratefully acknowledged.
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VVA: Conceptualization, formal analysis, methodology, validation, visualization, writing – original draft, writing – review and editing. MM: Formal analysis, methodology, validation, visualization, writing – original draft, writing – review and editing. ASV: Conceptualization, supervision, writing – original draft, writing – review and editing.
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Corresponding editor: Rajesh Vishwanathan
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Supplementary resource 1: Video showing the movements of the PilB–ATP complex during the 100 ns simulation. (MPG 20790 KB)
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Alluri, V.V., Mukhi, M. & Vishwanathan, A.S. Characterising ATP binding activity of PilB ATPase of Shewanella oneidensis MR-1 using a molecular modeling and simulations approach. J Biosci 48, 45 (2023). https://doi.org/10.1007/s12038-023-00371-1
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DOI: https://doi.org/10.1007/s12038-023-00371-1