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Year 2024, Volume: 8 Issue: 1, 55 - 64, 15.01.2024

Ayşe Hümeyra Taşkın Kafa Rukiye Aslan Hanaou Ahamada Bydaa Atron

https://doi.org/10.33435/tcandtc.1191117

Abstract

References

  • [1] G.M. Cook, M. Berney, S. Gebhard, M. Heinemann, R.A. Cox, O. Danilchanka, M. Niederweis, Physiology of Mycobacteria, Advances in Microbial Physiology 55:81-182 (2009) 318-9.
  • [2] A. Aranaz, D. Cousins, A. Mateos, L. Domínguez, Elevation of Mycobacterium tuberculosis subsp. caprae Aranaz et al. 1999 to species rank as Mycobacterium caprae comb. nov., sp. nov, International Journal of Systematic and Evolutionary Microbiology 53 (2003) 1785-9.
  • [3] V. Briken, S.A. Porcelli, G.S. Besra, L. Kremer, Mycobacterial lipoarabinomannan and related lipoglycans: from biogenesis to modulation of the immune response, Molecular Microbiology 53 (2004) 391-403.
  • [4] M.A. Forrellad, L.I. Klepp, A. Gioffré, J. Sabio y García, H.R. Morbidoni, M. de la Paz Santangelo, A.A. Cataldi, F. Bigi, Virulence factors of the Mycobacterium tuberculosis complex, Virulence 4(3) (2013) 66.
  • [5] R.M. Donlan, Biofilms: microbial life on surfaces, Emerging Infectious Disease 8 (2002) 881-90.
  • [6] J. Recht, A. Martínez, S. Torello, R. Kolter, Genetic analysis of sliding motility in Mycobacterium smegmatis, Journal of Bacteriology 182 (2000) 4348-51.
  • [7] T.T. Aung, J.K. Yam, S. Lin, S.M. Salleh, M. Givskov, S. Liu, N.C. Lwin, L. Yang, R.W. Beuerman, biofilms of pathogenic nontuberculous Mycobacteria targeted by new therapeutic approaches, Antimicrobial Agents and Chemotheraphy 60 (2015) 24-35.
  • [8] M. Lescot, P. Déhais, G. Thijs, K. Marchal, Y. Moreau, Y. Van de Peer, R. Rouzé, S. Rombauts, PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences, Nucleic Acids Research 30 (2002) 325-7.
  • [9] R. Allen, R. Popat, S. Diggle, S. Brown, Targeting virulence: can we make evolution-proof drugs? Nature Reviews Microbiology, 12 (2014) 300-8.
  • [10] M. Rahbar, I. Rasooli, S. Mousavi Gargari, J. Amani, Y. Fattahian Y, In silico analysis of antibody triggering biofilm associated protein in Acinetobacter baumannii, Journal of Theoretical Biology 266 (2010) 275-90.
  • [11] S. Poux, M. Magrane, C. Arighi, A. Bridge, C. O'Donovan, K. Laiho, Expert curation in UniProtKB: a case study on dealing with conflicting and erroneous data, Database bau016 (2014).
  • [12] S. Altschul, Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Research 25 (1997) 3389-402.
  • [13] E. Gasteiger, ExPASy: the proteomics server for in-depth protein knowledge and analysis, Nucleic Acids Research 31 (2003) 3784-88.
  • [14] A. Krogh, B. Larsson, G. von Heijne, E.L. Sonnhammer, Predicting transmembrane protein topology with hidden Markov model: application to complete genomes, Journal of Molecular Biology 305(3) (2001) 567-80.
  • [15] T. Hirokawa, S. Boon-Chieng, S. Mitaku, SOSUI: classification and secondary structure prediction system for membrane proteins, Bioinformatics 14 (1998) 378-9.
  • [16] J.A. Siepen, S.E. Radford, D.R. Westhead, Beta edge strands in protein structure prediction and aggregation, Protein Science 12 (2003) 2348-59.
  • [17] M. Shapovalov, R.L. Dunbrack Jr, S. Vucetic, Multifaceted analysis of training and testing convolutional neural networks for protein secondary structure prediction, PLoS One 15 (2020) e0232528.
  • [18] M.E. Turanalp, T. Can, Discovering functional interaction patterns in protein-protein interaction networks, BMC Bioinformatics 9 (2008) 276.
  • [19] S. Saha, G.P. Raghava, VICMpred: an SVM-based method for the prediction of functional proteins of Gram-negative bacteria using amino acid patterns and composition, Genomics Proteomics Bioinformatics 4 (2006) 42-7.
  • [20] W. Qiu, C. Xu, X. Xiao, D. Xu, Computational prediction of ubiquitination proteins using evolutionary profiles and functional domain annotation, Current Genomics 20 (2019) 389-99.
  • [21] J. Prava, P. G, A. Pan, Functional assignment for essential hypothetical proteins of Staphylococcus aureus N315, International Journal of Biological Macromolecules 108 (2018) 765-74.
  • [22] A.S. Hauser, M.M Attwood, M. Rask-Andersen, H.B. Schiöth, D.E. Gloriam, Trends in GPCR drug discovery: new agents, targets and indications, National Reviews Drug Discovery 16 (2017) 829-42.
  • [23] J. Callis, The ubiquitination machinery of the ubiquitin system, Arabidopsis Book 6 (2014) 12.
  • [24] B. Wu, T. Skarina, A. Yee, M.C. Jobin, R. Dileo, A. Semesi, C. Fares, A. Lemak, B.K. Coombes, C.H. Arrowsmith, A.U. Singer, A. Savchenko, NleG Type 3 effectors from enterohaemorrhagic Escherichia coli are U-Box E3 ubiquitin ligases, PLoS Pathogens 6 (2010) e1000960.
  • [25] Y. Zhu, H. Li, L. Hu, J. Wang, Y. Zhou, Z. Pang, L. Liu, F. Shao, Structure of a Shigella effector reveals a new class of ubiquitin ligases, Nature Structural and Moleculer Biology 15 (2008) 1302-8.
  • [26] J. Jumper, R. Evans, A. Pritzel, T. Green, M. Figurnov, O. Ronneberger, et al, Highly accurate protein structure prediction with AlphaFold, Nature 596 (2021) 583-9.
  • [27] L.A. Kelley, S. Mezulis, C.M. Yates, M.N. Wass, M.J. Sternberg, The Phyre2 web portal for protein modeling, prediction and analysis, Nature Protocols 10 (2015) 845-58.
  • [28] B. Wallner, A. Elofsson, Identification of correct regions in protein models using structural, alignment, and consensus information, Protein Science 15 (2006) 900-13.
  • [29] J.C. Ranford, B. Henderson, Chaperonins in disease: mechanisms, models, and treatments, Molecular Pathology 55(4) (2002) 209-13.
  • [30] H. Kubota, G. Hynes, K. Willison, The Chaperonin Containing t-complex polypeptide 1 (TCP-1) multisubunit machinery assisting in protein folding and assembly in the eukaryotic cytosol, European Journal of Biochemistry 230 (1995) 3-16.
  • [31] K. Arita-Morioka, K. Yamanaka, Y. Mizunoe, T. Ogura, S. Sugimoto, Novel strategy for biofilm inhibition by using small molecules targeting molecular chaperone DnaK, Antimicrobial Agents and Chemotheraphy 59 (2015) 633-41.
  • [32] J. Amon, T. Bräu, A. Grimrath, E. Hänssler, K. Hasselt, M. Höller, N. Jessberger, L. Ott, J. Szököl, F. Titgemeyer, A. Burkovski, Nitrogen control in Mycobacterium smegmatis: nitrogen-dependent expression of ammonium transport and assimilation proteins depends on the OmpR-type regulator GlnR, Journal of Bacteriology 190 (2008) 7108-16.
  • [33] N. Pollock, R. Dhiman, N. Daifalla, M. Farhat, A. Campos-Neto, Discovery of a unique Mycobacterium tuberculosis protein through proteomic analysis of urine from patients with active tuberculosis, Microbes and Infection 20 (2018) 228-35.
  • [34] Q. Chai, L, Wang, C.H. Liu, B. Ge, New insights into the evasion of host innate immunity by Mycobacterium tuberculosis, Cellular and Molecular Immunology 17 (2020) 901-13.
  • [35] H, Öztürk, E. Ozkirimli, A. Özgür, Classification of Beta-lactamases and penicillin binding proteins using ligand-centric network models, PLoS One 10 (2015) e0117874.
  • [36] M. Oliva, O. Dideberg, M.J. Field, Understanding the acylation mechanisms of active-site serine penicillin-recognizing proteins: a molecular dynamics simulation study, Proteins 53 (2003) 88-100.
  • [37] D.J. Scheffers, M.G. Pinho, Bacterial cell wall synthesis: new insights from localization studies, Microbiology and Molecular Biology Reviews 69 (2005) 585-607.
  • [38] C.G. Marshall, G. Broadhead, B.K. Leskiw, G.D. Wright, D-Ala-D-Ala ligases from glycopeptide antibiotic-producing organisms are highly homologous to the enterococcal vancomycin-resistance ligases VanA and VanB, Comperative Study 94(12) (1997) 6480-3.
  • [39] C.R. Sanders, J.M. Hutchison, Membrane properties that shape the evolution of membrane enzymes, Current Opinion Structural Biology 51 (2018) 80-91.
  • [40] H.K. Gupta, S. Shrivastava, R. Sharma, A novel calcium uptake transporter of uncharacterized p-type ATPase family supplies calcium for cell surface integrity in Mycobacterium smegmatis, mBio 8 (2017) e01388-17.
  • [41] M. Guragain, D.L. Lenaburg, F.S. Moore, I. Reutlinger, M.A. Patrauchan, Calcium homeostasis in Pseudomonas aeruginosa requires multiple transporters and modulates swarming motility, Cell Calcium 54 (2013) 350-61.
  • [42] P. Gorla, R. Plocinska, K. Sarva, A.T. Satsangi, E. Pandeeti, R. Donnelly, J. Dziadek, M. Rajagopalan, M.V. Madiraju, MtrA response regulator controls cell division and cell wall metabolism and affects susceptibility of Mycobacteria to the first line antituberculosis drugs, Frontiers in Microbiology 9 (2018) 2839.
  • [43] S.K. Banerjee, S. Lata, A.K. Sharma, S. Bagchi, M. Kumar, S.K. Sahu, D. Sarkar, P. Gupta, K. Jana, U.D. Gupta, R. Singh, S. Saha, J. Basu, M. Kundu, The sensor kinase MtrB of Mycobacterium tuberculosis regulates hypoxic survival and establishment of infection, Journal of Biology and Chemistry 27(294) (2019) 19862-76.
  • [44] D. Lebeaux, J.M. Ghigo, C. Beloin, Biofilm-related infections: bridging the gap between clinical management and fundamental aspects of recalcitrance toward antibiotics, Microbiology and Molecular Biology Reviews 78 (2014) 510-43.
  • [45] S.A. Pacheco, F.F. Hsu, K.M. Powers, G.E. Purdy, MmpL11 protein transports mycolic acid-containing lipids to the mycobacterial cell wall and contributes to biofilm formation in Mycobacterium smegmatis, Journal of Biology and Chemistry 288 (2013) 24213-22.
  • [46] C.C. Wright, F.F. Hsu, E. Arnett, J.L. Dunaj, P.M. Davidson, S.A. Pacheco, M.J. Harriff, D.M. Lewinsohn, L.S. Schlesinger, G.E. Purdy, The Mycobacterium tuberculosis MmpL11 cell wall lipid transporter is important for biofilm formation, intracellular growth, and nonreplicating persistence, Infection and Immunity 85 (2017) e00131-17.
  • [47] A. Viljoen A, V. Dubois, F. Girard-Misguich, M. Blaise, J. Herrmann, L, Kremer, The diverse family of MmpL transporters in mycobacteria: from regulation to antimicrobial developments, Molecular Microbiology 104 (2017) 889-904.
  • [48] S. Brown, J.P. Santa Maria Jr, S. Walker, Wall teichoic acids of gram-positive bacteria, Annual Reviews in Microbiology 67 (2013) 313-36.
  • [49] A. Beceiro, M. Tomás, G. Bou, Antimicrobial resistance and virulence: a successful or deleterious association in the bacterial world? Clinical Microbiology Reviews, 26 (2013) 185-230.
  • [50] D.G. Biron, D. Nedelkov, D. Missé, P. Holzmuller, proteomics and host—pathogen interactions: a bright future? Genetics and Evolution of Infectious Disease (2011) 263–303.
  • [51] P. Kumar, K. Arora, J.R. Lloyd, I.Y. Lee, V. Nair, E. Fischer, H.I. Boshoff, C.E. Barry, 3rd. Meropenem inhibits D, D-carboxypeptidase activity in Mycobacterium tuberculosis, Moleculer Microbiology 86 (2012) 367-81.
  • [52] D. Prigozhin, I. Krieger, J. Huizar, D. Mavrici, G. Waldo, L. Hung, et al, subfamily-specific adaptations in the structures of two penicillin-binding proteins from Mycobacterium tuberculosis, PLoS One 9 (2014) e116249.
  • [53] G. Nicola, S. Peddi, M. Stefanova, R. Nicholas, W. Gutheil, C. Davies, Crystal structure of Escherichia coli penicillin-binding protein 5 bound to a tripeptide boronic acid inhibitor:  a role for ser-110 in diacylation, Biochemistry 44 (2005) 8207-17.
  • [54] L. Kelley, S. Mezulis, C. Yates, M.Wass, M. SternbergThe Phyre2 web portal for protein modeling, prediction and analysis, Nature protocols, 10 (2015)845–858.

Structural and Functional Characterization of Biofilm-Related Proteins of Mycobacterium spp: An in-silico Approach

Year 2024, Volume: 8 Issue: 1, 55 - 64, 15.01.2024

Ayşe Hümeyra Taşkın Kafa Rukiye Aslan Hanaou Ahamada Bydaa Atron

https://doi.org/10.33435/tcandtc.1191117

Abstract

Biofilm-associated infections are characterized by the chronicity, recurrence, and the requirement of a prolonged administration of multiple drugs. Several non-pathogenic and pathogenic species of microorganism including Mycobacteria spp form biofilm. Mycobacterial biofilms present a unique composition. Instead of exopolysaccharides in other bacteria, proteins are essential compounds of the biofilm matrix in mycobacteria. To tackle mycobacterial infections, a detailed understanding of the biofilm-forming mechanisms is crucial. In this present study, all available Mycobacterial proteins involved in the biofilm were selected. Their sequences were retrieved and characterized through the determination of their physicochemical properties, secondary structure, 3D structure, subcellular localization, conserved domain, ubiquitination sites, and virulence potentiality. Furthermore, druggability testing was undertaken after excluding proteins with homology to human proteins to identify possible drug targets. The results showed that they possess functionally important domains and families. All of the selected hypothetical proteins were stable. Six of them were classified as soluble and the remaining as transmembrane proteins. A sole protein was found to lack ubiquitination sites. Additionally, three of these were discovered to be virulent. Moreover, host non-homology results indicated eight pathogen-specific proteins that might be potential therapeutic targets. Among them, D-alanyl-D-alanine carboxypeptidase is a druggable target that is inhibited by beta-lactam antibiotics. The remainder of the proteins were categorized as new targets.
In conclusion, this study may increase our knowledge of pathogenesis and host adaptation, drug resistance, and identification of drug and vaccine targets against infections caused by Mycobacteria. It can also guide new research.

Keywords

Mycobacterium Biofilm protein characterization in-silico analysis

References

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  • [2] A. Aranaz, D. Cousins, A. Mateos, L. Domínguez, Elevation of Mycobacterium tuberculosis subsp. caprae Aranaz et al. 1999 to species rank as Mycobacterium caprae comb. nov., sp. nov, International Journal of Systematic and Evolutionary Microbiology 53 (2003) 1785-9.
  • [3] V. Briken, S.A. Porcelli, G.S. Besra, L. Kremer, Mycobacterial lipoarabinomannan and related lipoglycans: from biogenesis to modulation of the immune response, Molecular Microbiology 53 (2004) 391-403.
  • [4] M.A. Forrellad, L.I. Klepp, A. Gioffré, J. Sabio y García, H.R. Morbidoni, M. de la Paz Santangelo, A.A. Cataldi, F. Bigi, Virulence factors of the Mycobacterium tuberculosis complex, Virulence 4(3) (2013) 66.
  • [5] R.M. Donlan, Biofilms: microbial life on surfaces, Emerging Infectious Disease 8 (2002) 881-90.
  • [6] J. Recht, A. Martínez, S. Torello, R. Kolter, Genetic analysis of sliding motility in Mycobacterium smegmatis, Journal of Bacteriology 182 (2000) 4348-51.
  • [7] T.T. Aung, J.K. Yam, S. Lin, S.M. Salleh, M. Givskov, S. Liu, N.C. Lwin, L. Yang, R.W. Beuerman, biofilms of pathogenic nontuberculous Mycobacteria targeted by new therapeutic approaches, Antimicrobial Agents and Chemotheraphy 60 (2015) 24-35.
  • [8] M. Lescot, P. Déhais, G. Thijs, K. Marchal, Y. Moreau, Y. Van de Peer, R. Rouzé, S. Rombauts, PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences, Nucleic Acids Research 30 (2002) 325-7.
  • [9] R. Allen, R. Popat, S. Diggle, S. Brown, Targeting virulence: can we make evolution-proof drugs? Nature Reviews Microbiology, 12 (2014) 300-8.
  • [10] M. Rahbar, I. Rasooli, S. Mousavi Gargari, J. Amani, Y. Fattahian Y, In silico analysis of antibody triggering biofilm associated protein in Acinetobacter baumannii, Journal of Theoretical Biology 266 (2010) 275-90.
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  • [14] A. Krogh, B. Larsson, G. von Heijne, E.L. Sonnhammer, Predicting transmembrane protein topology with hidden Markov model: application to complete genomes, Journal of Molecular Biology 305(3) (2001) 567-80.
  • [15] T. Hirokawa, S. Boon-Chieng, S. Mitaku, SOSUI: classification and secondary structure prediction system for membrane proteins, Bioinformatics 14 (1998) 378-9.
  • [16] J.A. Siepen, S.E. Radford, D.R. Westhead, Beta edge strands in protein structure prediction and aggregation, Protein Science 12 (2003) 2348-59.
  • [17] M. Shapovalov, R.L. Dunbrack Jr, S. Vucetic, Multifaceted analysis of training and testing convolutional neural networks for protein secondary structure prediction, PLoS One 15 (2020) e0232528.
  • [18] M.E. Turanalp, T. Can, Discovering functional interaction patterns in protein-protein interaction networks, BMC Bioinformatics 9 (2008) 276.
  • [19] S. Saha, G.P. Raghava, VICMpred: an SVM-based method for the prediction of functional proteins of Gram-negative bacteria using amino acid patterns and composition, Genomics Proteomics Bioinformatics 4 (2006) 42-7.
  • [20] W. Qiu, C. Xu, X. Xiao, D. Xu, Computational prediction of ubiquitination proteins using evolutionary profiles and functional domain annotation, Current Genomics 20 (2019) 389-99.
  • [21] J. Prava, P. G, A. Pan, Functional assignment for essential hypothetical proteins of Staphylococcus aureus N315, International Journal of Biological Macromolecules 108 (2018) 765-74.
  • [22] A.S. Hauser, M.M Attwood, M. Rask-Andersen, H.B. Schiöth, D.E. Gloriam, Trends in GPCR drug discovery: new agents, targets and indications, National Reviews Drug Discovery 16 (2017) 829-42.
  • [23] J. Callis, The ubiquitination machinery of the ubiquitin system, Arabidopsis Book 6 (2014) 12.
  • [24] B. Wu, T. Skarina, A. Yee, M.C. Jobin, R. Dileo, A. Semesi, C. Fares, A. Lemak, B.K. Coombes, C.H. Arrowsmith, A.U. Singer, A. Savchenko, NleG Type 3 effectors from enterohaemorrhagic Escherichia coli are U-Box E3 ubiquitin ligases, PLoS Pathogens 6 (2010) e1000960.
  • [25] Y. Zhu, H. Li, L. Hu, J. Wang, Y. Zhou, Z. Pang, L. Liu, F. Shao, Structure of a Shigella effector reveals a new class of ubiquitin ligases, Nature Structural and Moleculer Biology 15 (2008) 1302-8.
  • [26] J. Jumper, R. Evans, A. Pritzel, T. Green, M. Figurnov, O. Ronneberger, et al, Highly accurate protein structure prediction with AlphaFold, Nature 596 (2021) 583-9.
  • [27] L.A. Kelley, S. Mezulis, C.M. Yates, M.N. Wass, M.J. Sternberg, The Phyre2 web portal for protein modeling, prediction and analysis, Nature Protocols 10 (2015) 845-58.
  • [28] B. Wallner, A. Elofsson, Identification of correct regions in protein models using structural, alignment, and consensus information, Protein Science 15 (2006) 900-13.
  • [29] J.C. Ranford, B. Henderson, Chaperonins in disease: mechanisms, models, and treatments, Molecular Pathology 55(4) (2002) 209-13.
  • [30] H. Kubota, G. Hynes, K. Willison, The Chaperonin Containing t-complex polypeptide 1 (TCP-1) multisubunit machinery assisting in protein folding and assembly in the eukaryotic cytosol, European Journal of Biochemistry 230 (1995) 3-16.
  • [31] K. Arita-Morioka, K. Yamanaka, Y. Mizunoe, T. Ogura, S. Sugimoto, Novel strategy for biofilm inhibition by using small molecules targeting molecular chaperone DnaK, Antimicrobial Agents and Chemotheraphy 59 (2015) 633-41.
  • [32] J. Amon, T. Bräu, A. Grimrath, E. Hänssler, K. Hasselt, M. Höller, N. Jessberger, L. Ott, J. Szököl, F. Titgemeyer, A. Burkovski, Nitrogen control in Mycobacterium smegmatis: nitrogen-dependent expression of ammonium transport and assimilation proteins depends on the OmpR-type regulator GlnR, Journal of Bacteriology 190 (2008) 7108-16.
  • [33] N. Pollock, R. Dhiman, N. Daifalla, M. Farhat, A. Campos-Neto, Discovery of a unique Mycobacterium tuberculosis protein through proteomic analysis of urine from patients with active tuberculosis, Microbes and Infection 20 (2018) 228-35.
  • [34] Q. Chai, L, Wang, C.H. Liu, B. Ge, New insights into the evasion of host innate immunity by Mycobacterium tuberculosis, Cellular and Molecular Immunology 17 (2020) 901-13.
  • [35] H, Öztürk, E. Ozkirimli, A. Özgür, Classification of Beta-lactamases and penicillin binding proteins using ligand-centric network models, PLoS One 10 (2015) e0117874.
  • [36] M. Oliva, O. Dideberg, M.J. Field, Understanding the acylation mechanisms of active-site serine penicillin-recognizing proteins: a molecular dynamics simulation study, Proteins 53 (2003) 88-100.
  • [37] D.J. Scheffers, M.G. Pinho, Bacterial cell wall synthesis: new insights from localization studies, Microbiology and Molecular Biology Reviews 69 (2005) 585-607.
  • [38] C.G. Marshall, G. Broadhead, B.K. Leskiw, G.D. Wright, D-Ala-D-Ala ligases from glycopeptide antibiotic-producing organisms are highly homologous to the enterococcal vancomycin-resistance ligases VanA and VanB, Comperative Study 94(12) (1997) 6480-3.
  • [39] C.R. Sanders, J.M. Hutchison, Membrane properties that shape the evolution of membrane enzymes, Current Opinion Structural Biology 51 (2018) 80-91.
  • [40] H.K. Gupta, S. Shrivastava, R. Sharma, A novel calcium uptake transporter of uncharacterized p-type ATPase family supplies calcium for cell surface integrity in Mycobacterium smegmatis, mBio 8 (2017) e01388-17.
  • [41] M. Guragain, D.L. Lenaburg, F.S. Moore, I. Reutlinger, M.A. Patrauchan, Calcium homeostasis in Pseudomonas aeruginosa requires multiple transporters and modulates swarming motility, Cell Calcium 54 (2013) 350-61.
  • [42] P. Gorla, R. Plocinska, K. Sarva, A.T. Satsangi, E. Pandeeti, R. Donnelly, J. Dziadek, M. Rajagopalan, M.V. Madiraju, MtrA response regulator controls cell division and cell wall metabolism and affects susceptibility of Mycobacteria to the first line antituberculosis drugs, Frontiers in Microbiology 9 (2018) 2839.
  • [43] S.K. Banerjee, S. Lata, A.K. Sharma, S. Bagchi, M. Kumar, S.K. Sahu, D. Sarkar, P. Gupta, K. Jana, U.D. Gupta, R. Singh, S. Saha, J. Basu, M. Kundu, The sensor kinase MtrB of Mycobacterium tuberculosis regulates hypoxic survival and establishment of infection, Journal of Biology and Chemistry 27(294) (2019) 19862-76.
  • [44] D. Lebeaux, J.M. Ghigo, C. Beloin, Biofilm-related infections: bridging the gap between clinical management and fundamental aspects of recalcitrance toward antibiotics, Microbiology and Molecular Biology Reviews 78 (2014) 510-43.
  • [45] S.A. Pacheco, F.F. Hsu, K.M. Powers, G.E. Purdy, MmpL11 protein transports mycolic acid-containing lipids to the mycobacterial cell wall and contributes to biofilm formation in Mycobacterium smegmatis, Journal of Biology and Chemistry 288 (2013) 24213-22.
  • [46] C.C. Wright, F.F. Hsu, E. Arnett, J.L. Dunaj, P.M. Davidson, S.A. Pacheco, M.J. Harriff, D.M. Lewinsohn, L.S. Schlesinger, G.E. Purdy, The Mycobacterium tuberculosis MmpL11 cell wall lipid transporter is important for biofilm formation, intracellular growth, and nonreplicating persistence, Infection and Immunity 85 (2017) e00131-17.
  • [47] A. Viljoen A, V. Dubois, F. Girard-Misguich, M. Blaise, J. Herrmann, L, Kremer, The diverse family of MmpL transporters in mycobacteria: from regulation to antimicrobial developments, Molecular Microbiology 104 (2017) 889-904.
  • [48] S. Brown, J.P. Santa Maria Jr, S. Walker, Wall teichoic acids of gram-positive bacteria, Annual Reviews in Microbiology 67 (2013) 313-36.
  • [49] A. Beceiro, M. Tomás, G. Bou, Antimicrobial resistance and virulence: a successful or deleterious association in the bacterial world? Clinical Microbiology Reviews, 26 (2013) 185-230.
  • [50] D.G. Biron, D. Nedelkov, D. Missé, P. Holzmuller, proteomics and host—pathogen interactions: a bright future? Genetics and Evolution of Infectious Disease (2011) 263–303.
  • [51] P. Kumar, K. Arora, J.R. Lloyd, I.Y. Lee, V. Nair, E. Fischer, H.I. Boshoff, C.E. Barry, 3rd. Meropenem inhibits D, D-carboxypeptidase activity in Mycobacterium tuberculosis, Moleculer Microbiology 86 (2012) 367-81.
  • [52] D. Prigozhin, I. Krieger, J. Huizar, D. Mavrici, G. Waldo, L. Hung, et al, subfamily-specific adaptations in the structures of two penicillin-binding proteins from Mycobacterium tuberculosis, PLoS One 9 (2014) e116249.
  • [53] G. Nicola, S. Peddi, M. Stefanova, R. Nicholas, W. Gutheil, C. Davies, Crystal structure of Escherichia coli penicillin-binding protein 5 bound to a tripeptide boronic acid inhibitor:  a role for ser-110 in diacylation, Biochemistry 44 (2005) 8207-17.
  • [54] L. Kelley, S. Mezulis, C. Yates, M.Wass, M. SternbergThe Phyre2 web portal for protein modeling, prediction and analysis, Nature protocols, 10 (2015)845–858.
There are 54 citations in total.

Details

Primary Language English
Subjects Chemical Engineering
Journal Section Research Article
Authors

Ayşe Hümeyra Taşkın Kafa 0000-0002-7282-4928

Rukiye Aslan 0000-0001-5843-626X

Hanaou Ahamada 0000-0002-0000-2239

Bydaa Atron 0000-0002-7571-9277

Early Pub Date May 26, 2023
Publication Date January 15, 2024
Submission Date October 18, 2022
Published in Issue Year 2024 Volume: 8 Issue: 1

Cite

APA Taşkın Kafa, A. H., Aslan, R., Ahamada, H., Atron, B. (2024). Structural and Functional Characterization of Biofilm-Related Proteins of Mycobacterium spp: An in-silico Approach. Turkish Computational and Theoretical Chemistry, 8(1), 55-64. https://doi.org/10.33435/tcandtc.1191117
AMA Taşkın Kafa AH, Aslan R, Ahamada H, Atron B. Structural and Functional Characterization of Biofilm-Related Proteins of Mycobacterium spp: An in-silico Approach. Turkish Comp Theo Chem (TC&TC). January 2024;8(1):55-64. doi:10.33435/tcandtc.1191117
Chicago Taşkın Kafa, Ayşe Hümeyra, Rukiye Aslan, Hanaou Ahamada, and Bydaa Atron. “Structural and Functional Characterization of Biofilm-Related Proteins of Mycobacterium Spp: An in-Silico Approach”. Turkish Computational and Theoretical Chemistry 8, no. 1 (January 2024): 55-64. https://doi.org/10.33435/tcandtc.1191117.
EndNote Taşkın Kafa AH, Aslan R, Ahamada H, Atron B (January 1, 2024) Structural and Functional Characterization of Biofilm-Related Proteins of Mycobacterium spp: An in-silico Approach. Turkish Computational and Theoretical Chemistry 8 1 55–64.
IEEE A. H. Taşkın Kafa, R. Aslan, H. Ahamada, and B. Atron, “Structural and Functional Characterization of Biofilm-Related Proteins of Mycobacterium spp: An in-silico Approach”, Turkish Comp Theo Chem (TC&TC), vol. 8, no. 1, pp. 55–64, 2024, doi: 10.33435/tcandtc.1191117.
ISNAD Taşkın Kafa, Ayşe Hümeyra et al. “Structural and Functional Characterization of Biofilm-Related Proteins of Mycobacterium Spp: An in-Silico Approach”. Turkish Computational and Theoretical Chemistry 8/1 (January 2024), 55-64. https://doi.org/10.33435/tcandtc.1191117.
JAMA Taşkın Kafa AH, Aslan R, Ahamada H, Atron B. Structural and Functional Characterization of Biofilm-Related Proteins of Mycobacterium spp: An in-silico Approach. Turkish Comp Theo Chem (TC&TC). 2024;8:55–64.
MLA Taşkın Kafa, Ayşe Hümeyra et al. “Structural and Functional Characterization of Biofilm-Related Proteins of Mycobacterium Spp: An in-Silico Approach”. Turkish Computational and Theoretical Chemistry, vol. 8, no. 1, 2024, pp. 55-64, doi:10.33435/tcandtc.1191117.
Vancouver Taşkın Kafa AH, Aslan R, Ahamada H, Atron B. Structural and Functional Characterization of Biofilm-Related Proteins of Mycobacterium spp: An in-silico Approach. Turkish Comp Theo Chem (TC&TC). 2024;8(1):55-64.

Journal Full Title: Turkish Computational and Theoretical Chemistry


Journal Abbreviated Title: Turkish Comp Theo Chem (TC&TC)