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Yee Siew Choong - One of the best experts on this subject based on the ideXlab platform.
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Integration of molecular dynamics simulation and hotspot residues grafting for de novo scFv design against Salmonella Typhi TolC Protein
Journal of molecular recognition : JMR, 2017Co-Authors: Siew Wen Leong, Theam Soon Lim, Asma Ismail, Yee Siew ChoongAbstract:With the development of de novo binders for Protein targets from non-related scaffolds, many possibilities for therapeutics and diagnostics have been created. In this study, we described the use of de novo design approach to create single-chain fragment variable (scFv) for Salmonella enterica subspecies enterica serovar Typhi TolC Protein. Typhoid fever is a global health concern in developing and underdeveloped countries. Rapid typhoid diagnostics will improve disease management and therapy. In this work, molecular dynamics simulation was first performed on a homology model of TolC Protein in POPE membrane bilayer to obtain the central structure that was subsequently used as the target for scFv design. Potential hotspot residues capable of anchoring the binders to the target were identified by docking "disembodied" amino acid residues against TolC surface. Next, scFv scaffolds were selected from Protein Data Bank to harbor the computed hotspot residues. The hotspot residues were then incorporated into the scFv scaffold complementarity determining regions. The designs recapitulated binding energy, shape complementarity, and interface surface area of natural Protein-antibody interfaces. This approach has yielded 5 designs with high binding affinity against TolC that may be beneficial for the future development of antigen-based detection agents for typhoid diagnostics.
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Assembly and stability of Salmonella enterica ser. Typhi TolC Protein in POPE and DMPE
Journal of Biological Physics, 2014Co-Authors: Siew Wen Leong, Theam Soon Lim, Gee Jun Tye, Asma Ismail, Ismail Aziah, Yee Siew ChoongAbstract:In this work we assessed the suitability of two different lipid membranes for the simulation of a TolC Protein from Salmonella enterica serovar Typhi. The TolC Protein family is found in many pathogenic Gram-negative bacteria including Vibrio cholera and Pseudomonas aeruginosa and acts as an outer membrane channel for expulsion of drug and toxin from the cell. In S. typhi , the causative agent for typhoid fever, the TolC outer membrane Protein is an antigen for the pathogen. The lipid environment is an important modulator of membrane Protein structure and function. We evaluated the conformation of the TolC Protein in the presence of DMPE and POPE bilayers using molecular dynamics simulation. The S. typhi TolC Protein exhibited similar conformational dynamics to TolC and its homologues. Conformational flexibility of the Protein is seen in the C-terminal, extracellular loops, and α-helical region. Despite differences in the two lipids, significant similarities in the motion of the Protein in POPE and DMPE were observed, including the rotational motion of the C-terminal residues and the partially open extracellular loops. However, analysis of the trajectories demonstrated effects of hydrophobic matching of the TolC Protein in the membrane, particularly in the lengthening of the lipids and subtle movements of the Protein’s β-barrel towards the lower leaflet in DMPE. The study exhibited the use of molecular dynamics simulation in revealing the differential effect of membrane Proteins and lipids on each other. In this study, POPE is potentially a more suitable model for future simulation of the S. typhi TolC Protein.
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Salmonella Typhi TolC Protein: A molecular dynamics investigation
Asian Pacific Journal of Tropical Disease, 2014Co-Authors: W. Leong, Theam Soon Lim, Aziah Ismail, Yee Siew ChoongAbstract:Abstract Introduction The TolC family of Proteins of Escherichia coli and other pathogenic Gram negative bacteria plays an important role as an outer membrane channel for the expulsion of drug and toxin from the cell. Typhoid fever, caused by Salmonella enterica serovar Typhi kills more than 200 000 lives annually. In S. Typhi, a TolC outer membrane Protein was found to be antigenic for this pathogen. Understanding the dynamics of the S. Typhi TolC Protein is essential towards development of diagnostics, therapeutics and vaccine towards typhoid fever. Therefore, molecular dynamics simulation has been performed on the Protein. Objective To refine homology structure of S. Typhi TolC Protein by molecular dynamics simulation. Methods: A homology model of the S. Typhi TolC Protein was embedded in phosphatidylethanolamine lipid bilayer. Water molecules were added and the system was subsequently neutralized. Minimization was performed by steepest descent method following which; temperature was equilibrated at 310.15K in the NVT ensemble. A 1 ns NPT run was performed with restraint on Protein atoms to maintain pressure at 1 bar. Finally, production simulation was performed for 20 ns without restraints in the NPT ensemble. The average structure of the Protein was generated by RMS fitting of all Protein atoms from the production run and averaging over the coordinates. Results & Discussion Results showed that the membrane simulation was energetically stable and reproduced experimental value. The Protein conformation was also stable in simulation. Conformational analysis showed that the Protein is highly mobile at the extracellular loops and periplasmic helices region. From Ramachandran plot and Errat analysis, the average structure showed improvements over the initial model. Conclusion The average structure could be advantageous in aiding design efforts for inhibitors and binders against the S. Typhi TolC Protein.
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Structural and functional studies of a 50 kDa antigenic Protein from Salmonella enterica serovar Typhi.
Journal of molecular graphics & modelling, 2011Co-Authors: Yee Siew Choong, Theam Soon Lim, Ismail Aziah, Ai Lan Chew, Asma IsmailAbstract:The high typhoid incidence rate in developing and under-developed countries emphasizes the need for a rapid, affordable and accessible diagnostic test for effective therapy and disease management. TYPHIDOT®, a rapid dot enzyme immunoassay test for typhoid, was developed from the discovery of a ∼50 kDa Protein specific for Salmonella enterica serovar Typhi. However, the structure of this antigen remains unknown till today. Studies on the structure of this antigen are important to elucidate its function, which will in turn increase the efficiency of the development and improvement of the typhoid detection test. This paper described the predictive structure and function of the antigenically specific Protein. The homology modeling approach was employed to construct the three-dimensional structure of the antigen. The built structure possesses the features of TolC-like outer membrane Protein. Molecular docking simulation was also performed to further probe the functionality of the antigen. Docking results showed that hexamminecobalt, Co(NH(3))(6)(3+), as an inhibitor of TolC Protein, formed favorable hydrogen bonds with D368 and D371 of the antigen. The single point (D368A, D371A) and double point (D368A and D371A) mutations of the antigen showed a decrease (single point mutation) and loss (double point mutations) of binding affinity towards hexamminecobalt. The architecture features of the built model and the docking simulation reinforced and supported that this antigen is indeed the variant of outer membrane Protein, TolC. As channel Proteins are important for the virulence and survival of bacteria, therefore this ∼50 kDa channel Protein is a good specific target for typhoid detection test.
Leonilde M Moreira - One of the best experts on this subject based on the ideXlab platform.
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Absence of functional TolC Protein causes increased stress response gene expression in Sinorhizobium meliloti
BMC Microbiology, 2010Co-Authors: Mário R Santos, Ana M Cosme, Jörg D Becker, João Mc Medeiros, Márcia F Mata, Leonilde M MoreiraAbstract:Background The TolC Protein from Sinorhizobium meliloti has previously been demonstrated to be required for establishing successful biological nitrogen fixation symbiosis with Medicago sativa . It is also needed in Protein and exopolysaccharide secretion and for protection against osmotic and oxidative stresses. Here, the transcriptional profile of free-living S. meliloti 1021 TolC mutant is described as a step toward understanding its role in the physiology of the cell. Results Comparison of TolC mutant and wild-type strains transcriptomes showed 1177 genes with significantly increased expression while 325 had significantly decreased expression levels. The genes with an increased expression suggest the activation of a cytoplasmic and extracytoplasmic stress responses possibly mediated by the sigma factor RpoH1 and Protein homologues of the CpxRA two-component regulatory system of Enterobacteria, respectively. Stress conditions are probably caused by perturbation of the cell envelope. Consistent with gene expression data, biochemical analysis indicates that the TolC mutant suffers from oxidative stress. This is illustrated by the elevated enzyme activity levels detected for catalase, superoxide dismutase and glutathione reductase. The observed increase in the expression of genes encoding products involved in central metabolism and transporters for nutrient uptake suggests a higher metabolic rate of the TolC mutant. We also demonstrated increased swarming motility in the TolC mutant strain. Absence of functional TolC caused decreased expression mainly of genes encoding products involved in nitrogen metabolism and transport. Conclusion This work shows how a mutation in the outer membrane Protein TolC, common to many bacterial transport systems, affects expression of a large number of genes that act in concert to restore cell homeostasis. This finding further underlines the fundamental role of this Protein in Sinorhizobium meliloti biology.
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The outer membrane Protein TolC from Sinorhizobium meliloti affects Protein secretion, polysaccharide biosynthesis, antimicrobial resistance, and symbiosis.
Molecular plant-microbe interactions : MPMI, 2008Co-Authors: Ana M Cosme, L. A. Sharypova, Anke Becker, Mário Santos, Pedro M. Santos, Leonilde M MoreiraAbstract:Sinorhizobium meliloti is capable of establishing a symbiotic nitrogen fixation relationship with Medicago sativa. During this process, it must cope with diverse environments and has evolved different types of transport systems that help its propagation in the plant roots. TolC Protein family members are the outer-membrane components of several transport systems involved in the export of diverse molecules, playing an important role in bacterial survival. In this work, we have characterized the Protein TolC from S. meliloti 2011. An insertional mutation in the TolC gene strongly affected the resistance phenotype to antimicrobial agents and induced higher susceptibility to osmotic and oxidative stresses. Immunodetection experiments and comparison of the extracellular Proteins present in the supernatant of the wild-type versus TolC mutant strains showed that the calcium-binding Protein ExpE1, the endoglycanase ExsH, and the product of open reading frame SMc04171, a putative hemolysin-type calcium-binding Protein, are secreted by a TolC-dependent secretion system. In the absence of TolC, neither succinoglycan nor galactoglucan were detected in the culture supernatant. Moreover, S. meliloti TolC mutant induced a reduced number of nonfixing nitrogen nodules in M. sativa roots. Taken together, our results confirm the importance of TolC in Protein secretion, exopolysaccharide biosynthesis, antimicrobials resistance, and symbiosis.
Theam Soon Lim - One of the best experts on this subject based on the ideXlab platform.
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Integration of molecular dynamics simulation and hotspot residues grafting for de novo scFv design against Salmonella Typhi TolC Protein
Journal of molecular recognition : JMR, 2017Co-Authors: Siew Wen Leong, Theam Soon Lim, Asma Ismail, Yee Siew ChoongAbstract:With the development of de novo binders for Protein targets from non-related scaffolds, many possibilities for therapeutics and diagnostics have been created. In this study, we described the use of de novo design approach to create single-chain fragment variable (scFv) for Salmonella enterica subspecies enterica serovar Typhi TolC Protein. Typhoid fever is a global health concern in developing and underdeveloped countries. Rapid typhoid diagnostics will improve disease management and therapy. In this work, molecular dynamics simulation was first performed on a homology model of TolC Protein in POPE membrane bilayer to obtain the central structure that was subsequently used as the target for scFv design. Potential hotspot residues capable of anchoring the binders to the target were identified by docking "disembodied" amino acid residues against TolC surface. Next, scFv scaffolds were selected from Protein Data Bank to harbor the computed hotspot residues. The hotspot residues were then incorporated into the scFv scaffold complementarity determining regions. The designs recapitulated binding energy, shape complementarity, and interface surface area of natural Protein-antibody interfaces. This approach has yielded 5 designs with high binding affinity against TolC that may be beneficial for the future development of antigen-based detection agents for typhoid diagnostics.
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Assembly and stability of Salmonella enterica ser. Typhi TolC Protein in POPE and DMPE
Journal of Biological Physics, 2014Co-Authors: Siew Wen Leong, Theam Soon Lim, Gee Jun Tye, Asma Ismail, Ismail Aziah, Yee Siew ChoongAbstract:In this work we assessed the suitability of two different lipid membranes for the simulation of a TolC Protein from Salmonella enterica serovar Typhi. The TolC Protein family is found in many pathogenic Gram-negative bacteria including Vibrio cholera and Pseudomonas aeruginosa and acts as an outer membrane channel for expulsion of drug and toxin from the cell. In S. typhi , the causative agent for typhoid fever, the TolC outer membrane Protein is an antigen for the pathogen. The lipid environment is an important modulator of membrane Protein structure and function. We evaluated the conformation of the TolC Protein in the presence of DMPE and POPE bilayers using molecular dynamics simulation. The S. typhi TolC Protein exhibited similar conformational dynamics to TolC and its homologues. Conformational flexibility of the Protein is seen in the C-terminal, extracellular loops, and α-helical region. Despite differences in the two lipids, significant similarities in the motion of the Protein in POPE and DMPE were observed, including the rotational motion of the C-terminal residues and the partially open extracellular loops. However, analysis of the trajectories demonstrated effects of hydrophobic matching of the TolC Protein in the membrane, particularly in the lengthening of the lipids and subtle movements of the Protein’s β-barrel towards the lower leaflet in DMPE. The study exhibited the use of molecular dynamics simulation in revealing the differential effect of membrane Proteins and lipids on each other. In this study, POPE is potentially a more suitable model for future simulation of the S. typhi TolC Protein.
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Salmonella Typhi TolC Protein: A molecular dynamics investigation
Asian Pacific Journal of Tropical Disease, 2014Co-Authors: W. Leong, Theam Soon Lim, Aziah Ismail, Yee Siew ChoongAbstract:Abstract Introduction The TolC family of Proteins of Escherichia coli and other pathogenic Gram negative bacteria plays an important role as an outer membrane channel for the expulsion of drug and toxin from the cell. Typhoid fever, caused by Salmonella enterica serovar Typhi kills more than 200 000 lives annually. In S. Typhi, a TolC outer membrane Protein was found to be antigenic for this pathogen. Understanding the dynamics of the S. Typhi TolC Protein is essential towards development of diagnostics, therapeutics and vaccine towards typhoid fever. Therefore, molecular dynamics simulation has been performed on the Protein. Objective To refine homology structure of S. Typhi TolC Protein by molecular dynamics simulation. Methods: A homology model of the S. Typhi TolC Protein was embedded in phosphatidylethanolamine lipid bilayer. Water molecules were added and the system was subsequently neutralized. Minimization was performed by steepest descent method following which; temperature was equilibrated at 310.15K in the NVT ensemble. A 1 ns NPT run was performed with restraint on Protein atoms to maintain pressure at 1 bar. Finally, production simulation was performed for 20 ns without restraints in the NPT ensemble. The average structure of the Protein was generated by RMS fitting of all Protein atoms from the production run and averaging over the coordinates. Results & Discussion Results showed that the membrane simulation was energetically stable and reproduced experimental value. The Protein conformation was also stable in simulation. Conformational analysis showed that the Protein is highly mobile at the extracellular loops and periplasmic helices region. From Ramachandran plot and Errat analysis, the average structure showed improvements over the initial model. Conclusion The average structure could be advantageous in aiding design efforts for inhibitors and binders against the S. Typhi TolC Protein.
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Structural and functional studies of a 50 kDa antigenic Protein from Salmonella enterica serovar Typhi.
Journal of molecular graphics & modelling, 2011Co-Authors: Yee Siew Choong, Theam Soon Lim, Ismail Aziah, Ai Lan Chew, Asma IsmailAbstract:The high typhoid incidence rate in developing and under-developed countries emphasizes the need for a rapid, affordable and accessible diagnostic test for effective therapy and disease management. TYPHIDOT®, a rapid dot enzyme immunoassay test for typhoid, was developed from the discovery of a ∼50 kDa Protein specific for Salmonella enterica serovar Typhi. However, the structure of this antigen remains unknown till today. Studies on the structure of this antigen are important to elucidate its function, which will in turn increase the efficiency of the development and improvement of the typhoid detection test. This paper described the predictive structure and function of the antigenically specific Protein. The homology modeling approach was employed to construct the three-dimensional structure of the antigen. The built structure possesses the features of TolC-like outer membrane Protein. Molecular docking simulation was also performed to further probe the functionality of the antigen. Docking results showed that hexamminecobalt, Co(NH(3))(6)(3+), as an inhibitor of TolC Protein, formed favorable hydrogen bonds with D368 and D371 of the antigen. The single point (D368A, D371A) and double point (D368A and D371A) mutations of the antigen showed a decrease (single point mutation) and loss (double point mutations) of binding affinity towards hexamminecobalt. The architecture features of the built model and the docking simulation reinforced and supported that this antigen is indeed the variant of outer membrane Protein, TolC. As channel Proteins are important for the virulence and survival of bacteria, therefore this ∼50 kDa channel Protein is a good specific target for typhoid detection test.
Cécile Wandersman - One of the best experts on this subject based on the ideXlab platform.
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Cloning of the Serratia marcescens hasF gene encoding the Has ABC exporter outer membrane component: a TolC analogue.
Molecular microbiology, 1996Co-Authors: Rachel Binet, Cécile WandersmanAbstract:The Serratia marcescens haemophore HasA is secreted by an ABC exporter comprising three envelope Proteins. The ABC Protein (ATP-binding cassette) HasD and the MFP Protein (membrane fusion Protein) HasE but not the outer membrane component have been isolated previously. In Escherichia coli, TolC, the outer membrane component of the haemolysin transporter, can form a hybrid exporter with HasD and HasE. This hybrid secretes HasA and the very similar metalloproteases from S. marcescens and Erwinia chrysanthemi. By analogy, the genuine exporter was predicted to secrete metalloproteases. The hasF gene was thus cloned from S. marcescens into an E. coli TolC mutant carrying hasD and hasE genes, by screening for a proteolytic phenotype on skimmed-milk plates. hasF encodes a Protein sharing 74% identity with the E. coli TolC Protein. Anti-TolC antibodies cross-reacted with a Protein with an apparent molecular weight of 53 kDa in E. coli expressing hasF and in S. marcescens. hasF is unlinked to the has cluster and, unlike the has operon, is not iron regulated. hasF complements some of the TolC phenotypes, including drug- and detergent sensitivities and haemolysin secretion but not colicin E1 uptake. This suggests that the various functions of TolC could correspond to distinct domains on the Protein.
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Secretion of the Serratia marcescens HasA Protein by an ABC transporter.
Journal of bacteriology, 1994Co-Authors: Sylvie Létoffé, J M Ghigo, Cécile WandersmanAbstract:We previously identified a Serratia marcescens extracellular Protein, HasA, able to bind heme and required for iron acquisition from heme and hemoglobin by the bacterium. This novel type of extracellular Protein does not have a signal peptide and does not show sequence similarities to other Proteins. HasA secretion was reconstituted in Escherichia coli, and we show here that like many Proteins lacking a signal peptide, HasA has a C-terminal targeting sequence and is secreted by a specific ATP binding cassette (ABC) transporter consisting of three Proteins, one inner membrane Protein with a conserved ATP binding domain, called the ABC; a second inner membrane Protein; and a third, outer membrane component. Since the three S. marcescens components of the HasA transporter have not yet been identified, the reconstituted HasA secretion system is a hybrid. It consists of the two S. marcescens inner membrane-specific components, HasD and HasE, associated with an outer membrane component coming from another bacterial ABC transporter, such as the E. coli TolC Protein, the outer membrane component of the hemolysin transporter, or the Erwinia chrysanthemi PrtF Protein, the outer membrane component of the protease transporter. This hybrid transporter was first shown to allow the secretion of the S. marcescens metalloprotease and the E. chrysanthemi metalloproteases B and C. On account of that, the two S. marcescens components HasD and HasE were previously named PrtDSM and PrtESM, respectively. However, HasA is secreted neither by the PrtD-PrtE-PrtF transporter (the genuine E. chrysanthemi protease transporter) nor by the HlyB-HlhD-TolC transporter (the hemolysin transporter). Moreover, HasA, coexpressed in the same cell, strongly inhibits the secretion of proteases B and C by their own transporter, indicating that the E. chrysanthemi transporter recognizes HasA. Since PrtF could replace TolC in the constitution of the HasA transporter, this indicates that the secretion block does not take place at the level of the outer membrane component but rather at an earlier step of interaction between HasA and the inner membrane components.
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Identification of two components of the Serratia marcescens metalloprotease transporter: protease SM secretion in Escherichia coli is TolC dependent.
Journal of bacteriology, 1993Co-Authors: S Létoffé, J M Ghigo, Cécile WandersmanAbstract:The Serratia marcescens metalloprotease (protease SM) belongs to a family of Proteins secreted from gram-negative bacteria by a signal peptide-independent pathway which requires a specific transporter consisting of three Proteins: two in the inner membrane and one in the outer membrane. The prtDSM and prtESM genes encoding the two S. marcescens inner membrane components were cloned and expressed in Escherichia coli. Their nucleotide sequence revealed high overall homology with the two analogous inner membrane components of the Erwinia chrysanthemi protease secretion apparatus and lower, but still significant, homology with the two analogous inner membrane components of the E. coli hemolysin transporter. When expressed in E. coli, these two Proteins, PrtDSM and PrtESM, allowed the secretion of protease SM only in the presence of TolC Protein, the outer membrane component of the hemolysin transporter.
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Involvement of lipopolysaccharide in the secretion of Escherichia coli α haemolysin and Erwinia chrysanthemi proteases
Molecular microbiology, 1993Co-Authors: Cécile Wandersman, Sylvie LétofféAbstract:The presence of the alpha-haemolysin secretion genes sensitizes Escherichia coli to vancomycin, a glycopeptide antibiotic that is normally excluded from the Gram-negative envelope (owing to its large size) (M(r) 1400). The selection of vancomycin mutants in strains carrying such genes was found to be a very powerful method for selecting non-haemolytic mutants. In this way, mutations in the known secretion genes, hlyB, hlyD and TolC, were obtained. However additional mutations mapped in genes rfaH and galU which are required for lipopolysaccharide (LPS) biosynthesis. Mutations in rfaH and galU strongly reduced alpha-haemolysin secretion as well as the secretion of Erwinia chrysanthemi proteases in E. coli without affecting their synthesis. These mutations markedly lowered the content of TolC Protein, required for haemolysin secretion and also of the PrtF Protein necessary for protease secretion. These results raise the possibility that LPS is involved in the correct incorporation of the TolC and PrtF Proteins into the cell envelope.
Asma Ismail - One of the best experts on this subject based on the ideXlab platform.
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Integration of molecular dynamics simulation and hotspot residues grafting for de novo scFv design against Salmonella Typhi TolC Protein
Journal of molecular recognition : JMR, 2017Co-Authors: Siew Wen Leong, Theam Soon Lim, Asma Ismail, Yee Siew ChoongAbstract:With the development of de novo binders for Protein targets from non-related scaffolds, many possibilities for therapeutics and diagnostics have been created. In this study, we described the use of de novo design approach to create single-chain fragment variable (scFv) for Salmonella enterica subspecies enterica serovar Typhi TolC Protein. Typhoid fever is a global health concern in developing and underdeveloped countries. Rapid typhoid diagnostics will improve disease management and therapy. In this work, molecular dynamics simulation was first performed on a homology model of TolC Protein in POPE membrane bilayer to obtain the central structure that was subsequently used as the target for scFv design. Potential hotspot residues capable of anchoring the binders to the target were identified by docking "disembodied" amino acid residues against TolC surface. Next, scFv scaffolds were selected from Protein Data Bank to harbor the computed hotspot residues. The hotspot residues were then incorporated into the scFv scaffold complementarity determining regions. The designs recapitulated binding energy, shape complementarity, and interface surface area of natural Protein-antibody interfaces. This approach has yielded 5 designs with high binding affinity against TolC that may be beneficial for the future development of antigen-based detection agents for typhoid diagnostics.
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Assembly and stability of Salmonella enterica ser. Typhi TolC Protein in POPE and DMPE
Journal of Biological Physics, 2014Co-Authors: Siew Wen Leong, Theam Soon Lim, Gee Jun Tye, Asma Ismail, Ismail Aziah, Yee Siew ChoongAbstract:In this work we assessed the suitability of two different lipid membranes for the simulation of a TolC Protein from Salmonella enterica serovar Typhi. The TolC Protein family is found in many pathogenic Gram-negative bacteria including Vibrio cholera and Pseudomonas aeruginosa and acts as an outer membrane channel for expulsion of drug and toxin from the cell. In S. typhi , the causative agent for typhoid fever, the TolC outer membrane Protein is an antigen for the pathogen. The lipid environment is an important modulator of membrane Protein structure and function. We evaluated the conformation of the TolC Protein in the presence of DMPE and POPE bilayers using molecular dynamics simulation. The S. typhi TolC Protein exhibited similar conformational dynamics to TolC and its homologues. Conformational flexibility of the Protein is seen in the C-terminal, extracellular loops, and α-helical region. Despite differences in the two lipids, significant similarities in the motion of the Protein in POPE and DMPE were observed, including the rotational motion of the C-terminal residues and the partially open extracellular loops. However, analysis of the trajectories demonstrated effects of hydrophobic matching of the TolC Protein in the membrane, particularly in the lengthening of the lipids and subtle movements of the Protein’s β-barrel towards the lower leaflet in DMPE. The study exhibited the use of molecular dynamics simulation in revealing the differential effect of membrane Proteins and lipids on each other. In this study, POPE is potentially a more suitable model for future simulation of the S. typhi TolC Protein.
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Structural and functional studies of a 50 kDa antigenic Protein from Salmonella enterica serovar Typhi.
Journal of molecular graphics & modelling, 2011Co-Authors: Yee Siew Choong, Theam Soon Lim, Ismail Aziah, Ai Lan Chew, Asma IsmailAbstract:The high typhoid incidence rate in developing and under-developed countries emphasizes the need for a rapid, affordable and accessible diagnostic test for effective therapy and disease management. TYPHIDOT®, a rapid dot enzyme immunoassay test for typhoid, was developed from the discovery of a ∼50 kDa Protein specific for Salmonella enterica serovar Typhi. However, the structure of this antigen remains unknown till today. Studies on the structure of this antigen are important to elucidate its function, which will in turn increase the efficiency of the development and improvement of the typhoid detection test. This paper described the predictive structure and function of the antigenically specific Protein. The homology modeling approach was employed to construct the three-dimensional structure of the antigen. The built structure possesses the features of TolC-like outer membrane Protein. Molecular docking simulation was also performed to further probe the functionality of the antigen. Docking results showed that hexamminecobalt, Co(NH(3))(6)(3+), as an inhibitor of TolC Protein, formed favorable hydrogen bonds with D368 and D371 of the antigen. The single point (D368A, D371A) and double point (D368A and D371A) mutations of the antigen showed a decrease (single point mutation) and loss (double point mutations) of binding affinity towards hexamminecobalt. The architecture features of the built model and the docking simulation reinforced and supported that this antigen is indeed the variant of outer membrane Protein, TolC. As channel Proteins are important for the virulence and survival of bacteria, therefore this ∼50 kDa channel Protein is a good specific target for typhoid detection test.