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Structure and mode of action of cyclic lipopeptide pseudofactin II with divalent metal ions. Colloids Surf B Biointerfaces 2016; 146:498-506. [PMID: 27416562 DOI: 10.1016/j.colsurfb.2016.06.055] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 06/22/2016] [Accepted: 06/27/2016] [Indexed: 12/21/2022]
Abstract
The interaction of natural lipopeptide pseudofactin II with a series of doubly charged metal cations was examined by matrix-assisted laser-desorption ionization-time of flight (MALDI-TOF) mass spectrometry and molecular modelling. The molecular modelling for metal-pseudofactin II provides information on the metal-peptide binding sites. Overall, Mg(2+), Ca(2+) and Zn(2+) favor the association with oxygen atoms spanning the peptide backbone, whereas Cu(2+) is coordinated by three nitrogens. Circular dichroism (CD) results confirmed that Zn(2+) and Cu(2+) can disrupt the secondary structure of pseudofactin II at high concentrations, while Ca(2+) and Mg(2+) did not essentially affect the structure of the lipopeptide. Interestingly, our results showed that the addition of Zn(2+) and Cu(2+) helped smaller micelles to form larger micellar aggregates. Since pseudofactin II binds metals, we tested whether this phenomena was somehow related to its antimicrobial activity against Staphylococcus epidermidis and Proteus mirabilis. We found that the antimicrobial effect of pseudofactin II was increased by supplementation of culture media with all tested divalent metal ions. Finally, by using Gram-positive and Gram-negative bacteria we showed that the higher antimicrobial activity of metal complexes of pseudofactin II is attributed to the disruption of the cytoplasmic membrane.
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Sawhney B, Chopra K, Misra R, Ranjan A. Identification of Plasmodium falciparum apicoplast-targeted tRNA-guanine transglycosylase and its potential inhibitors using comparative genomics, molecular modelling, docking and simulation studies. J Biomol Struct Dyn 2015; 33:2404-20. [PMID: 25869381 DOI: 10.1080/07391102.2015.1040074] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
tRNA modifications play an important role in the proper folding of tRNA and thereby determine its functionality as an adaptor molecule. Notwithstanding the centrality of this basic process in translation, a major gap in the genomics of Plasmodium falciparum is unambiguous identification of enzymes catalysing the various tRNA modifications. In this study, tRNA-modifying enzymes of P. falciparum were annotated using homology-based approach. Based on the presence of these identified enzymes, the modifications were compared with those of prokaryotic and eukaryotic organisms. Through sequence comparison and phylogenetic analysis, we have identified P. falciparum apicoplast tRNA-guanine 34 transglycosylase (TGT, EC: 2.4.2.29), which shows evidence of its prokaryotic origin. The docking analysis of the modelled TGT structures revealed that binding of quinazolinone derivatives is more favourable with P. falciparum apicoplast TGT as compared to human TGT. Molecular dynamic simulation and molecular mechanics/generalized Born surface area analysis of the complex confirmed the greater binding affinity of the ligand in the binding pocket of P. falciparum TGT protein. Further, evolutionary patterning analysis identified the amino acids of P. falciparum apicoplast TGT that are under purifying selection pressure and hence can be good inhibitor-targeting sites. Based on these computational studies, we suggest that P. falciparum apicoplast tRNA-guanine 34 transglycosylase can be a promising drug target.
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Affiliation(s)
- Bhavik Sawhney
- a Computational and Functional Genomics Group , Centre for DNA Fingerprinting and Diagnostics , Hyderabad , Telangana 500001 , India.,b Graduate School , Manipal University , Manipal, Karnataka 576104 , India
| | - Kriti Chopra
- a Computational and Functional Genomics Group , Centre for DNA Fingerprinting and Diagnostics , Hyderabad , Telangana 500001 , India.,c Department of Biotechnology and Bioinformatics, School of Life Sciences , University of Hyderabad , Gachibowli, Hyderabad , Telangana 500046 , India.,d National Centre for Cell Science, NCCS Complex , University of Pune Campus , Ganeshkhind, Pune , Maharashtra 411007 , India
| | - Rohan Misra
- a Computational and Functional Genomics Group , Centre for DNA Fingerprinting and Diagnostics , Hyderabad , Telangana 500001 , India.,b Graduate School , Manipal University , Manipal, Karnataka 576104 , India
| | - Akash Ranjan
- a Computational and Functional Genomics Group , Centre for DNA Fingerprinting and Diagnostics , Hyderabad , Telangana 500001 , India
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Reversible Conformational Change in the Plasmodium falciparum Circumsporozoite Protein Masks Its Adhesion Domains. Infect Immun 2015; 83:3771-80. [PMID: 26169272 DOI: 10.1128/iai.02676-14] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 07/02/2015] [Indexed: 11/20/2022] Open
Abstract
The extended rod-like Plasmodium falciparum circumsporozoite protein (CSP) is comprised of three primary domains: a charged N terminus that binds heparan sulfate proteoglycans, a central NANP repeat domain, and a C terminus containing a thrombospondin-like type I repeat (TSR) domain. Only the last two domains are incorporated in RTS,S, the leading malaria vaccine in phase 3 trials that, to date, protects about 50% of vaccinated children against clinical disease. A seroepidemiological study indicated that the N-terminal domain might improve the efficacy of a new CSP vaccine. Using a panel of CSP-specific monoclonal antibodies, well-characterized recombinant CSPs, label-free quantitative proteomics, and in vitro inhibition of sporozoite invasion, we show that native CSP is N-terminally processed in the mosquito host and undergoes a reversible conformational change to mask some epitopes in the N- and C-terminal domains until the sporozoite interacts with the liver hepatocyte. Our findings show the importance of understanding processing and the biophysical change in conformation, possibly due to a mechanical or molecular signal, and may aid in the development of a new CSP vaccine.
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Tedsana W, Tuntulani T, Ngeontae W. A circular dichroism sensor for Ni2+ and Co2+ based on l-cysteine capped cadmium sulfide quantum dots. Anal Chim Acta 2015; 867:1-8. [DOI: 10.1016/j.aca.2014.12.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Revised: 11/28/2014] [Accepted: 12/02/2014] [Indexed: 02/02/2023]
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