IN SILICO STRUCTURAL CHARACTERIZATION OF L. lactis subsp. cremoris MG1363 FFH-FTSY COMPLEX IN PROTEIN TARGETING INTERACTION

Authors

  • Noor Izawati Alias Department of Bioprocess and Polymer Engineering, School of Chemical and Energy Engineering, Faculty of Engineering, Universiti Teknologi Malaysia, 81310 UTM Johor Bahru, Johor, Malaysia
  • Abdul Munir Abdul Murad School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor 43600, Malaysia
  • Farah Diba Abu Bakar School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor 43600, Malaysia
  • Rosli Md Illias Department of Bioprocess and Polymer Engineering, School of Chemical and Energy Engineering, Faculty of Engineering, Universiti Teknologi Malaysia, 81310 UTM Johor Bahru, Johor, Malaysia

DOI:

https://doi.org/10.11113/jt.v81.13424

Keywords:

Lactococcus lactis, signal recognition particle, homology modelling, protein docking, molecular dynamics simulationLactococcus lactis, molecular dynamics simulation

Abstract

In bacteria, gene conservation and experimental data show that Lactococcus lactis has the simplest version of protein secretion system compared to Escherichia coli and Bacillus subtilis whose systems are more complex. L. lactis only possess the signal recognition particle (SRP) pathway, where the specific interaction of Ffh and FtsY is known to be essential for the efficiency and fidelity of its protein targeting. Therefore, modelling and structural characterization study of Ffh and FtsY will give an idea of its crucial region and amino acids that are critical in Ffh-FtsY interaction during protein targeting. This work is the first attempt to model L. lactis Ffh-FtsY complex, which was derived by computational docking, where a blind dock was applied. Results showed that the complex interface was predominantly stabilized by four hydrophobic interactions and 17 hydrogen bonds, where these putative binding interfaces are mostly confined at the motifs II and III in each G domain of Ffh and FtsY. Several residues were expected to play important roles in initiating or regulating guanosine triphosphate hydrolysis, including residue R142. This structural information will allow for the rational design of L. lactis Ffh-FtsY association in the future.

References

Doudna, J. A., Batey, R. T. 2004. Structural Insights into the Signal Recognition Particle. Annual Review of Biochemistry. 73: 539-557. DOI:10.1146/annurev.biochem.73.011303.074048.

Matlin, K. S. 2002. The Strange Case of the Signal Recognition Particle. Nature Reviews Molecular Cell Biology. 3(7): 538-542. DOI:10.1038/nrm857.

Keenan, R. J., et al. 2001. The Signal Recognition Particle. Annual Review of Biochemistry. 70: 755-775. DOI:10.1146/annurev.biochem.70.1.755.

Zelazny, A., et al. 1997. The NG Domain of the Prokaryotic Signal Recognition Particle Receptor, FtsY, is Fully Functional when Fused to an Unrelated Integral Membrane Polypeptide. PNAS. 94(12): 6025-6029. DOI:10.1073/pnas.94.12.6025.

Shepotinovskaya, I. V., Focia, P. J., Freymann, D. M. 2003. Crystallization of the GMPPCP Complex of the NG Domains of Thermus aquaticus Ffh and FtsY. Acta Crystallographica Section D-Biological Crystallography. 59(10): 1834-1837. DOI:10.1107/S0907444903016573.

Cano-Garrido, O., Seras-Franzoso, J., Garcia-Fruitós, E. 2015. Lactic Acid Bacteria: Reviewing the Potential of a Promising Delivery Live Vector for Biomedical Purposes. Microbial Cell Factories. 14(1): 137-148. DOI:10.1186/s12934-015-0313-6.

Ferrer-Miralles, N., Villaverde, A. 2013. Bacterial Cell Factories for Recombinant Protein Production; Expanding the Catalogue. Microbial Cell Factories. 12(1): 113-116. DOI:10.1186/1475-2859-12-113.

García-Fruitós, E. 2012. Lactic Acid Bacteria: A Promising Alternative for Recombinant Protein Production. Microbial Cell Factories. 11(1): 157-159. DOI:10.1186/1475-2859-11-157.

Konings, W. N., et al. 2000. Lactic Acid Bacteria: The Bugs of the New Millennium. Current Opinion in Microbiology. 3(3): 276-282. DOI:10.1016/S1369-5274(00)00089-8.

Le Loir, Y., et al. 2005. Protein Secretion in Lactococcus lactis: An Efficient Way to Increase the Overall Heterologous Protein Production. Microbial Cell Factories. 4(1): 2. DOI:10.1186/1475-2859-4-2.

Liang, X., et al. 2007. Secretory Expression of a Heterologous Nattokinase in Lactococcus lactis. Applied Microbiology and Biotechnology. 75(1): 95-101. DOI:10.1007/s00253-006-0809-4.

Morello, E., Poquet, I., Langella, P. 2010. Secretion of Heterologous Proteins, Gram-positive Bacteria, Lactococcus lactis. Encyclopedia of Industrial Biotechnology, Bioprocess, Bioseparation and Cell Technology. M.C. Flickinger. USA, John Wiley & Sons, Inc.

Bolotin, A., et al. 2001. The Complete Genome Sequence of the Lactic Acid Bacterium Lactococcus lactis ssp. lactis IL1403. Genome Research. 11(5): 731-753. DOI:10.1101/gr.GR-1697R.

Chu, F., et al. 2004. Unraveling the Interface of Signal Recognition Particle and Its Receptor by Using Chemical Cross-linking and Tandem Mass Spectrometry. PNAS. 101(47): 16454-16459. DOI:10.1073/pnas.0407456101.

Tian, H., Beckwith, J. 2002. Genetic Screen Yields Mutations in Genes Encoding All Known Components of the Escherichia Coli Signal Recognition Particle Pathway. Journal of Bacteriology. 184(1): 111-118. DOI:10.1128/JB.184.1.111-118.2002.

The UniProt Consortium. 2017. UniProt: The Universal Protein Knowledgebase. Nucleic Acids Research. 45(D1): D158-D169. DOI:10.1093/nar/gkw1099.

Altschul, S. F., et al. 1997. Gapped BLAST and PSI-BLAST: A New Generation of Protein Database Search Programs. Nucleic Acids Research. 25(17): 3389-3402. DOI:10.1093/nar/25.17.3389.

Söding, J., Biegert, A., Lupas, A. N. 2005. The HHpred Interactive Server for Protein Homology Detection and Structure Prediction. Nucleic Acids Research. 33(SUPPL. 2): W244-W248. DOI:10.1093/nar/gki408.

Kelley, L. A., et al. 2015. The Phyre2 Web Portal for Protein Modeling, Prediction and Analysis. Nature Protocols. 10(6): 845-858. DOI:10.1038/nprot.2015.053.

Hunter, S., et al. 2012. InterPro in 2011: New Developments in the Family and Domain Prediction Database. Nucleic Acids Research. 40(Database Issue): D306-D312. DOI:10.1093/nar/gkr948.

Quevillon, E., et al. 2005. InterProScan: Protein Domains Identifier. Nucleic Acids Research. 33(SUPPL. 2): W116-W120. DOI:10.1093/nar/gki442.

Å ali, A., Blundell, T. L. 1993. Comparative Protein Modelling by Satisfaction of Spatial Restraints. Journal of Molecular Biology. 234(3): 779-815. DOI:10.1006/jmbi.1993.1626.

Laskowski, R. A., et al. 1993. PROCHECK: A Program to Check the Stereochemical Quality of Protein Structures. Journal of Applied Crystallography. 26(2): 283-291. DOI:10.1107/S0021889892009944.

Eisenberg, D., Lüthy, R., Bowie, J. U. 1997. VERIFY3D: Assessment of Protein Models with Three-dimensional Profiles. Methods in Enzymology. 277: 396-406. DOI:10.1016/S0076-6879(97)77022-8.

Colovos, C., Yeates, T.O. 1993. Verification of Protein Structures: Patterns of Nonbonded Atomic Interactions. Protein Science. 2(9): 1511-1519. DOI:10.1002/pro.5560020916.

Zhang, Y., Skolnick, J. 2005. TM-align: A Protein Structure Alignment Algorithm based on the TM-score. Nucleic Acids Research. 33(7): 2302-2309. DOI:10.1093/nar/gki524.

Van Der Spoel, D., et al. 2005. GROMACS: Fast, Flexible, and Free. Journal of Computational Chemistry. 26(16): 1701-1718. DOI:10.1002/jcc.20291.

Schrodinger, L. L. C. 2010. The PyMOL Molecular Graphics System, Version 1.3.

Kozakov, D., et al. 2017. The ClusPro Web Server for Protein-protein Docking. Nature Protocols. 12(2): 255-278. DOI:10.1038/nprot.2016.169.

Kozakov, D., et al. 2006. PIPER: An FFT-based Protein Docking Program with Pairwise Potentials. Proteins. 65(2): 392-406. DOI:10.1002/prot.21117.

Tina, K. G., Bhadra, R., Srinivasan, N. 2007. PIC: Protein Interactions Calculator. Nucleic Acids Research. 35(Web Server Issue): W473-476. DOI:10.1093/nar/gkm423.

Halic, M., et al. 2006. Following the Signal Sequence from Ribosomal Tunnel Exit to Signal Recognition Particle. Nature. 444(7118): 507-511. DOI:10.1038/nature05326.

Stjepanovic, G., et al. 2011. Lipids Trigger a Conformational Switch that Regulates Signal Recognition Particle (SRP)-mediated Protein Targeting. Journal of Biological Chemistry. 286(26): 23489-23497. DOI:10.1074/jbc.M110.212340.

Kaczanowski, S., Zielenkiewicz, P. 2010. Why Similar Protein Sequences Encode Similar Three-dimensional Structures? Theoretical Chemistry Accounts. 125(3-6): 643-650. DOI:10.1007/s00214-009-0656-3.

MacKerell, A. D.Jr., et al. 1998. All-atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins. Journal of Physical Chemistry B. 102(18): 3586-3616. DOI:10.1021/jp973084f.

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): 22. DOI:10.1186/1742-4682-10-22.

Bruce, A., et al. 2015. The Shape and Structure of Proteins, Molecular Biology of the Cell. Sixth Edition. Garland Science, Taylor & Francis Group, LLC.

Chaitanya, M., et al. 2010. Exploring the Molecular Basis for Selective Binding of Mycobacterium tuberculosis Asp Kinase Toward its Natural Substrates and Feedback Inhibitors: A Docking and Molecular Dynamics Study. Journal of Molecular Modeling. 16(8): 1357-1367. DOI:10.1007/s00894-010-0653-4.

Xu, J., Zhang, Y. 2010. How Significant is a Protein Structure Similarity with TM-score = 0.5? Bioinformatics. 26(7): 889-895. DOI:10.1093/bioinformatics/btq066.

Freymann, D. M., et al. 1997. Structure of the Conserved GTPase Domain of the Signal Recognition Particle. Nature. 385(6614): 361-364. DOI:10.1038/385361a0.

Montoya, G., et al. 1997. Crystal Structure of the NG Domain from the Signal-recognition Particle Receptor FtsY. Nature. 385(6614): 365-368. DOI:10.1038/385365a0.

Bourne, H. R., Sanders, D. A., McCormick, F. 1991. The GTPase Superfamily: Conserved Structure and Molecular Mechanism. Nature. 349(6305): 117-127. DOI:10.1038/349117a0.

Shan, S. O., Walter, P. 2005. Co-translational Protein Targeting by the Signal Recognition Particle. FEBS Letters. 579(4 SPEC. ISS.): 921-926. DOI:10.1016/j.febslet.2004.11.049.

Herskovits, A. A., et al. 2001. Evidence for Coupling of Membrane Targeting and Function of the Signal Recognition Particle (SRP) receptor FtsY. EMBO Reports. 2(11): 1040-1046. DOI:10.1093/embo-reports/kve226.

Gawronski-Salerno, J., Freymann, D. M. 2007. Structure of the GMPPNP-stabilized NG Domain Complex of the SRP GTPases Ffh and FtsY. Journal of Structural Biology. 158(1): 122-128. DOI:10.1016/j.jsb.2006.10.025.

Montoya, G., et al. 2000. The Crystal Structure of the Conserved GTPase of SRP54 from the Archaeon Acidianus ambivalens and its Comparison with Related Structures Suggests a Model for the SRP-SRP Receptor Complex. Structure. 8(5): 515-525. DOI:10.1016/S0969-2126(00)00131-3.

Focia, P. J., et al. 2004. Heterodimeric GTPase Core of the SRP Targeting Complex. Science. 303(5656): 373-377. DOI:10.1126/science.1090827.

Egea, P. F., et al. 2004. Substrate Twinning Activates the Signal Recognition Particle and its Receptor. Nature. 427(6971): 215-221. DOI:10.1038/nature02250.

Shan, S. O., Stroud, R. M., Walter, P. 2004. Mechanism of Association and Reciprocal Activation of two GTPases. PLoS Biology. 2(10): 1572-1581. DOI:10.1371/journal.pbio.0020320.

Chen, S., et al. 2008. A Molecular Modeling Study of the Interaction between SRP-receptor Complex and Peptide Translocon. Biochemical and Biophysical Research Communications. 377(2): 346-350. DOI:10.1016/j.bbrc.2008.09.119.

Dong, H. J., et al. 2006. Analysis of the GTPase Activity and Active Sites of the NG Domains of FtsY and Ffh from Streptomyces coelicolor. Acta Biochimica et Biophysica Sinica. 38(7): 467-476. DOI:10.1111/j.1745-7270.2006.00186.x.

Downloads

Published

2019-02-10

Issue

Section

Science and Engineering

How to Cite

IN SILICO STRUCTURAL CHARACTERIZATION OF L. lactis subsp. cremoris MG1363 FFH-FTSY COMPLEX IN PROTEIN TARGETING INTERACTION. (2019). Jurnal Teknologi, 81(2). https://doi.org/10.11113/jt.v81.13424