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Fields JL, Zhang H, Bellis NF, Petersen HA, Halder SK, Rich-New ST, Wu H, Wang F. Structural diversity and clustering of bacterial flagellar outer domains. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.18.585621. [PMID: 38562817 PMCID: PMC10983879 DOI: 10.1101/2024.03.18.585621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Supercoiled flagellar filaments function as mechanical propellers within the bacterial flagellum complex, playing a crucial role in motility. Flagellin, the building block of the filament, features a conserved inner D0/D1 core domain across different bacterial species. In contrast, approximately half of the flagellins possess additional, highly divergent outer domain(s), suggesting varied functional potential. In this study, we elucidate atomic structures of flagellar filaments from three distinct bacterial species: Cupriavidus gilardii , Stenotrophomonas maltophilia , and Geovibrio thiophilus . Our findings reveal that the flagella from the facultative anaerobic G. thiophilus possesses a significantly more negatively charged surface, potentially enabling adhesion to positively charged minerals. Furthermore, we analyzed all AlphaFold predicted structures for annotated bacterial flagellins, categorizing the flagellin outer domains into 682 structural clusters. This classification provides insights into the prevalence and experimental verification of these outer domains. Remarkably, two of the flagellar structures reported herein belong to a previously unexplored cluster, indicating new opportunities on the study of the functional diversity of flagellar outer domains. Our findings underscore the complexity of bacterial flagellins and open up possibilities for future studies into their varied roles beyond motility.
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2
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Nithichanon A, Kewcharoenwong C, Da-oh H, Surajinda S, Khongmee A, Koosakunwat S, Wren BW, Stabler RA, Brown JS, Lertmemongkolchai G. Acinetobacter nosocomialis Causes as Severe Disease as Acinetobacter baumannii in Northeast Thailand: Underestimated Role of A. nosocomialis in Infection. Microbiol Spectr 2022; 10:e0283622. [PMID: 36227120 PMCID: PMC9769887 DOI: 10.1128/spectrum.02836-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 09/21/2022] [Indexed: 01/09/2023] Open
Abstract
Infections by Acinetobacter species are recognized as a serious global threat due to causing severe disease and their high levels of antibiotic resistance. Acinetobacter baumannii is the most prevalent pathogen in the genus, but infection by Acinetobacter nosocomialis has been reported widely. Diagnosis of patients with A. baumannii infection is often misdiagnosed with other Acinetobacter species, especially A. nosocomialis. This study investigated whether there were significant differences in clinical outcomes between patients infected with A. baumannii versus A. nosocomialis in Northeast Thailand, and to characterize serological responses to infection with these pathogens. The results show that A. baumannii had higher levels of multidrug resistance. Despite this, clinical outcomes for infection with A. baumannii or A. nosocomialis were similar with mortalities of 33% and 36%, respectively. Both pathogens caused community-acquired infections (A. baumannii 35% and A. nosocomialis 29% of cases). Plasma from uninfected healthy controls contained IgG antibody that recognized both organisms, and infected patients did not show a significantly enhanced antibody response from the first week versus 2 weeks later. Finally, the patterns of antigen recognition for plasma IgG were similar for patients infected with A. baumannii or A. nosocomialis infection, and distinct to the pattern for patients infected with non-Acinetobacter. In conclusion, our data revealed that infection with A. nosocomialis was associated with a similarly high level of mortality as infection with A. baumannii, the high rate of community-acquired infection and antibodies in uninfected individuals suggesting that there is significant community exposure to both pathogens. IMPORTANCE Bacterial infections by Acinetobacter species are global threats due to their severity and high levels of antibiotic resistance. A. baumannii is the most common pathogen in the genus; however, infection by A. nosocomialis has also been widely reported but is thought to be less severe. In this study, we have prospectively investigated 48 reported cases of A. baumannii infection in Northeast Thailand, and characterized the serological responses to infection. We found that 14 (29%) of these infections were actually caused by A. nosocomialis. Furthermore, the incidence of antibiotic resistance among A. nosocomialis strains, APACHE II scores, and mortality for patients infected with A. nosocomialis were much higher than published data. Both A. baumannii and A. nosocomialis had unexpectedly mortality rates of over 30%, and both pathogens caused a high rate of community-acquired infections. Importantly, background antibodies in uninfected individuals suggest significant community exposure to both pathogens in the environment.
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Affiliation(s)
- Arnone Nithichanon
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
- Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Chidchamai Kewcharoenwong
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
- Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - Hudadini Da-oh
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
| | - Sirithorn Surajinda
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
| | - Aranya Khongmee
- Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | | | - Brendan W. Wren
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Infectious and Tropical Disease, London, United Kingdom
| | - Richard A. Stabler
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Infectious and Tropical Disease, London, United Kingdom
| | - Jeremy S. Brown
- Centre for Inflammation and Tissue Repair, UCL Respiratory, London, United Kingdom
| | - Ganjana Lertmemongkolchai
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
- Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
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3
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Kewcharoenwong C, Sein MM, Nithichanon A, Khongmee A, Wessells KR, Hinnouho GM, Barffour MA, Kounnavong S, Hess SY, Stephensen CB, Lertmemongkolchai G. Daily preventive zinc supplementation increases the antibody response against pathogenic Escherichia coli in children with zinc insufficiency: a randomised controlled trial. Sci Rep 2022; 12:16084. [PMID: 36167891 PMCID: PMC9515173 DOI: 10.1038/s41598-022-20445-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 09/13/2022] [Indexed: 12/03/2022] Open
Abstract
Zinc deficiency impairs the antibody-mediated immune response and is common in children from lower-income countries. This study aimed to investigate the impact of different zinc supplementation regimens (7, 10 or 20 mg/day elemental zinc)—therapeutic dispersible zinc tablets (TZ), daily multiple micronutrient powder (MNP), daily preventive zinc tablets (PZ) and placebo powder (control)—and compare between baseline and endline antibody production against pathogenic Escherichia coli in Laotian children (aged 6–23 months). Fifty representative plasma samples of each treatment group were randomly selected from 512 children to determine anti-E. coli IgG antibody levels and avidity. Of the 200 children, 78.5% had zinc deficiency (plasma zinc concentration < 65 µg/dL) and 40% had anaemia before receiving zinc supplementation. aAfter receiving the TZ, MNP or PZ regimen, the plasma anti-E. coli IgG levels were significantly increased compared with baseline; the effect on the antibody level was more pronounced in children with zinc deficiency. Interestingly, there was increased anti-E. coli IgG avidity in the control and PZ groups. This study suggests that PZ might be the optimal zinc supplementation regimen to increase both the quantity and quality of antibody responses in children with zinc deficiency. Clinical trial registration: https://clinicaltrials.gov/ct2/show/NCT02428647 (NCT02428647, 29/04/2015).
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Affiliation(s)
| | - Myint Myint Sein
- The Centre for Research & Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - Arnone Nithichanon
- Department of Microbiology, Faculty of Medicine, Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand
| | - Aranya Khongmee
- The Centre for Research & Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - K Ryan Wessells
- Department of Nutrition, Institute for Global Nutrition, University of California, Davis, CA, USA
| | - Guy-Marino Hinnouho
- Department of Nutrition, Institute for Global Nutrition, University of California, Davis, CA, USA.,Helen Keller International, Washington, DC, USA
| | - Maxwell A Barffour
- Department of Nutrition, Institute for Global Nutrition, University of California, Davis, CA, USA.,Public Health Program, College of Health and Human Services, Missouri State University, Springfield, MO, USA
| | - Sengchanh Kounnavong
- Lao Tropical and Public Health Institute, Vientiane, Lao People's Democratic Republic
| | - Sonja Y Hess
- Department of Nutrition, Institute for Global Nutrition, University of California, Davis, CA, USA
| | - Charles B Stephensen
- Department of Nutrition, Institute for Global Nutrition, University of California, Davis, CA, USA.,Agricultural Research Service, Western Human Nutrition Research Center, USDA, Davis, CA, USA
| | - Ganjana Lertmemongkolchai
- Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand. .,The Centre for Research & Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand.
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4
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Díaz-Dinamarca DA, Salazar ML, Castillo BN, Manubens A, Vasquez AE, Salazar F, Becker MI. Protein-Based Adjuvants for Vaccines as Immunomodulators of the Innate and Adaptive Immune Response: Current Knowledge, Challenges, and Future Opportunities. Pharmaceutics 2022; 14:1671. [PMID: 36015297 PMCID: PMC9414397 DOI: 10.3390/pharmaceutics14081671] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/05/2022] [Accepted: 08/07/2022] [Indexed: 12/03/2022] Open
Abstract
New-generation vaccines, formulated with subunits or nucleic acids, are less immunogenic than classical vaccines formulated with live-attenuated or inactivated pathogens. This difference has led to an intensified search for additional potent vaccine adjuvants that meet safety and efficacy criteria and confer long-term protection. This review provides an overview of protein-based adjuvants (PBAs) obtained from different organisms, including bacteria, mollusks, plants, and humans. Notably, despite structural differences, all PBAs show significant immunostimulatory properties, eliciting B-cell- and T-cell-mediated immune responses to administered antigens, providing advantages over many currently adopted adjuvant approaches. Furthermore, PBAs are natural biocompatible and biodegradable substances that induce minimal reactogenicity and toxicity and interact with innate immune receptors, enhancing their endocytosis and modulating subsequent adaptive immune responses. We propose that PBAs can contribute to the development of vaccines against complex pathogens, including intracellular pathogens such as Mycobacterium tuberculosis, those with complex life cycles such as Plasmodium falciparum, those that induce host immune dysfunction such as HIV, those that target immunocompromised individuals such as fungi, those with a latent disease phase such as Herpes, those that are antigenically variable such as SARS-CoV-2 and those that undergo continuous evolution, to reduce the likelihood of outbreaks.
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Affiliation(s)
- Diego A. Díaz-Dinamarca
- Fundación Ciencia y Tecnología para el Desarrollo (FUCITED), Santiago 7750000, Chile
- Sección de Biotecnología, Departamento Agencia Nacional de Dispositivos Médicos, Innovación y Desarrollo, Instituto de Salud Pública de Chile, Santiago 7750000, Chile
| | - Michelle L. Salazar
- Fundación Ciencia y Tecnología para el Desarrollo (FUCITED), Santiago 7750000, Chile
| | - Byron N. Castillo
- Fundación Ciencia y Tecnología para el Desarrollo (FUCITED), Santiago 7750000, Chile
| | - Augusto Manubens
- Fundación Ciencia y Tecnología para el Desarrollo (FUCITED), Santiago 7750000, Chile
- Biosonda Corporation, Santiago 7750000, Chile
| | - Abel E. Vasquez
- Sección de Biotecnología, Departamento Agencia Nacional de Dispositivos Médicos, Innovación y Desarrollo, Instituto de Salud Pública de Chile, Santiago 7750000, Chile
- Facultad de Ciencias para el Cuidado de la Salud, Universidad San Sebastián, Providencia, Santiago 8320000, Chile
| | - Fabián Salazar
- Fundación Ciencia y Tecnología para el Desarrollo (FUCITED), Santiago 7750000, Chile
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter EX4 4QD, UK
| | - María Inés Becker
- Fundación Ciencia y Tecnología para el Desarrollo (FUCITED), Santiago 7750000, Chile
- Biosonda Corporation, Santiago 7750000, Chile
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5
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Quilici G, Berardi A, Fabris C, Ghitti M, Punta M, Gourlay LJ, Bolognesi M, Musco G. Solution Structure of the BPSL1445 Protein of Burkholderia pseudomallei Reveals the SYLF Domain Three-Dimensional Fold. ACS Chem Biol 2022; 17:230-239. [PMID: 34968022 DOI: 10.1021/acschembio.1c00886] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The SYLF domain is an evolutionary conserved protein domain with phosphatidylinositol binding ability, whose three-dimensional structure is unknown. Here, we present the solution structure and the dynamics characterization of the SYLF domain of the bacterial BPSL1445 protein. BPSL1445 is a seroreactive antigen and a diagnostic marker of Burkholderia pseudomallei, the etiological agent of melioidosis, a severe infectious disease in the tropics. The BPSL1445 SYLF domain (BPSL1445-SYLF) consists of a β-barrel core, with two flexible loops protruding out of the barrel and three helices packing on its surface. Our structure allows for a more precise definition of the boundaries of the SYLF domain compared to the previously reported one and suggests common ancestry with bacterial EipA domains. We also demonstrate by phosphatidyl-inositol phosphate arrays and nuclear magnetic resonance titrations that BPSL1445-SYLF weakly interacts with phosphoinositides, thus supporting lipid binding abilities of this domain also in prokaryotes.
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Affiliation(s)
- Giacomo Quilici
- Biomolecular NMR Laboratory, I.R.C.C.S. Ospedale San Raffaele, Via Olgettina 58, 20132 Milan, Italy
| | - Andrea Berardi
- Biomolecular NMR Laboratory, I.R.C.C.S. Ospedale San Raffaele, Via Olgettina 58, 20132 Milan, Italy
| | - Chantal Fabris
- Biomolecular NMR Laboratory, I.R.C.C.S. Ospedale San Raffaele, Via Olgettina 58, 20132 Milan, Italy
| | - Michela Ghitti
- Biomolecular NMR Laboratory, I.R.C.C.S. Ospedale San Raffaele, Via Olgettina 58, 20132 Milan, Italy
| | - Marco Punta
- Unit of Immunogenetics, Leukemia Genomics and Immunobiology and Center for Omics Sciences, I.R.C.C.S. Ospedale San Raffaele, Via Olgettina 58, 20132 Milan, Italy
| | - Louise J. Gourlay
- Department of Biosciences, University of Milano, Via Celoria 26, 20133 Milan, Italy
- Centro di Ricerca Pediatrica Romeo ed Enrica Invernizzi, Università degli Studi di Milano, 20133 Milan, Italy
| | - Martino Bolognesi
- Department of Biosciences, University of Milano, Via Celoria 26, 20133 Milan, Italy
- Centro di Ricerca Pediatrica Romeo ed Enrica Invernizzi, Università degli Studi di Milano, 20133 Milan, Italy
| | - Giovanna Musco
- Biomolecular NMR Laboratory, I.R.C.C.S. Ospedale San Raffaele, Via Olgettina 58, 20132 Milan, Italy
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6
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Amemiya K, Dankmeyer JL, Bernhards RC, Fetterer DP, Waag DM, Worsham PL, DeShazer D. Activation of Toll-Like Receptors by Live Gram-Negative Bacterial Pathogens Reveals Mitigation of TLR4 Responses and Activation of TLR5 by Flagella. Front Cell Infect Microbiol 2021; 11:745325. [PMID: 34888257 PMCID: PMC8650638 DOI: 10.3389/fcimb.2021.745325] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 10/18/2021] [Indexed: 12/27/2022] Open
Abstract
Successful bacterial pathogens have evolved to avoid activating an innate immune system in the host that responds to the pathogen through distinct Toll-like receptors (TLRs). The general class of biochemical components that activate TLRs has been studied extensively, but less is known about how TLRs interact with the class of compounds that are still associated with the live pathogen. Accordingly, we examined the activation of surface assembled TLR 2, 4, and 5 with live Tier 1 Gram-negative pathogens that included Yersinia pestis (plague), Burkholderia mallei (glanders), Burkholderia pseudomallei (melioidosis), and Francisella tularensis (tularemia). We found that Y. pestis CO92 grown at 28°C activated TLR2 and TLR4, but at 37°C the pathogen activated primarily TLR2. Although B. mallei and B. pseudomallei are genetically related, the former microorganism activated predominately TLR4, while the latter activated predominately TLR2. The capsule of wild-type B. pseudomallei 1026b was found to mitigate the activation of TLR2 and TLR4 when compared to a capsule mutant. Live F. tularensis (Ft) Schu S4 did not activate TLR2 or 4, although the less virulent Ft LVS and F. novicida activated only TLR2. B. pseudomallei purified flagellin or flagella attached to the microorganism activated TLR5. Activation of TLR5 was abolished by an antibody to TLR5, or a mutation of fliC, or elimination of the pathogen by filtration. In conclusion, we have uncovered new properties of the Gram-negative pathogens, and their interaction with TLRs of the host. Further studies are needed to include other microorganism to extend our observations with their interaction with TLRs, and to the possibility of leading to new efforts in therapeutics against these pathogens.
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Affiliation(s)
- Kei Amemiya
- Bacteriology Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, United States
| | - Jennifer L Dankmeyer
- Bacteriology Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, United States
| | - Robert C Bernhards
- Edgewood Chemical Biological Centre, Aberdeen Proving Ground, Edgewood, MD, United States
| | - David P Fetterer
- Bacteriology Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, United States
| | - David M Waag
- Bacteriology Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, United States
| | - Patricia L Worsham
- Bacteriology Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, United States
| | - David DeShazer
- Bacteriology Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, United States
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7
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Triveri A, Serapian SA, Marchetti F, Doria F, Pavoni S, Cinquini F, Moroni E, Rasola A, Frigerio F, Colombo G. SARS-CoV-2 Spike Protein Mutations and Escape from Antibodies: A Computational Model of Epitope Loss in Variants of Concern. J Chem Inf Model 2021; 61:4687-4700. [PMID: 34468141 PMCID: PMC8479857 DOI: 10.1021/acs.jcim.1c00857] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Indexed: 12/30/2022]
Abstract
The SARS-CoV-2 spike (S) protein is exposed on the viral surface and is the first point of contact between the virus and the host. For these reasons it represents the prime target for Covid-19 vaccines. In recent months, variants of this protein have started to emerge. Their ability to reduce or evade recognition by S-targeting antibodies poses a threat to immunological treatments and raises concerns for their consequences on vaccine efficacy. To develop a model able to predict the potential impact of S-protein mutations on antibody binding sites, we performed unbiased multi-microsecond molecular dynamics of several glycosylated S-protein variants and applied a straightforward structure-dynamics-energy based strategy to predict potential changes in immunogenic regions on each variant. We recover known epitopes on the reference D614G sequence. By comparing our results, obtained on isolated S-proteins in solution, to recently published data on antibody binding and reactivity in new S variants, we directly show that modifications in the S-protein consistently translate into the loss of potentially immunoreactive regions. Our findings can thus be qualitatively reconnected to the experimentally characterized decreased ability of some of the Abs elicited against the dominant S-sequence to recognize variants. While based on the study of SARS-CoV-2 spike variants, our computational epitope-prediction strategy is portable and could be applied to study immunoreactivity in mutants of proteins of interest whose structures have been characterized, helping the development/selection of vaccines and antibodies able to control emerging variants.
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Affiliation(s)
- Alice Triveri
- Department
of Chemistry, University of Pavia, Via Taramelli 12, Pavia 27100, Italy
| | - Stefano A. Serapian
- Department
of Chemistry, University of Pavia, Via Taramelli 12, Pavia 27100, Italy
| | - Filippo Marchetti
- Department
of Chemistry, University of Pavia, Via Taramelli 12, Pavia 27100, Italy
| | - Filippo Doria
- Department
of Chemistry, University of Pavia, Via Taramelli 12, Pavia 27100, Italy
| | - Silvia Pavoni
- Department
of Physical Chemistry, R&D Eni SpA, Via Maritano 27, San Donato Milanese, Milan 20097, Italy
| | - Fabrizio Cinquini
- Upstream
& Technical Services—TECS/STES—Eni Spa, Via Emilia 1, San
Donato Milanese, Milan 20097, Italy
| | - Elisabetta Moroni
- Istituto
di Scienze e Tecnologie Chimiche “Giulio Natta”—SCITEC, CNR Via Mario Bianco 9, Milano 20131, Italy
| | - Andrea Rasola
- Department
of Biomedical Sciences, University of Padua, Viale G. Colombo 3, Padova 35131, Italy
| | - Francesco Frigerio
- Department
of Physical Chemistry, R&D Eni SpA, Via Maritano 27, San Donato Milanese, Milan 20097, Italy
| | - Giorgio Colombo
- Department
of Chemistry, University of Pavia, Via Taramelli 12, Pavia 27100, Italy
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8
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González-Ruiz A, López-Matas MÁ, Moya R, Carnés J. Immunoinformatic epitope prediction to select monoclonal antibodies for Phl p 1 quantification. Mol Immunol 2021; 136:1-7. [PMID: 34051631 DOI: 10.1016/j.molimm.2021.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/22/2021] [Accepted: 05/13/2021] [Indexed: 11/15/2022]
Abstract
BACKGROUND Allergen quantification has become a relevant parameter for allergen extract characterization and to guarantee the consistency of the manufacturing process at allergen immunotherapy. The aim of this study was to develop and validate a method to quantify the major allergen Phl p 1 based on a prediction of the antigenic regions by immunoinformatic strategies. METHODS Phl p 1 was purified from a Phleum pratense native extract by chromatographic methods. Immunoinformatic tools were used to predict B-cell epitopes. In silico predictions were verified by mapping linear epitopes with a peptide library and used to select the appropriate regions for producing the mAbs to develop an ELISA method, which was validated. Phl p 1 was quantified in 24 batches of P. pratense extracts. RESULTS Phl p 1 was purified with 95 % purity and completely functional. Eight B-cell epitopes in each of the two Phl p 1 isoforms were predicted. Two of the predicted B-cell epitopes overlapped with the experimentally determined peptides recognized by two mAbs selected for development of the kit. The quantification method demonstrated to be specific to Phl p 1, linear, accurate and precise in the range from 7.7 to 123.3 μg/mg. Mean Phl p 1 content was 28.95 μg of allergen/mg of lyophilized native extract and 44.23 μg of allergen/mg of lyophilized depigmented extract. CONCLUSIONS An ELISA method for measuring Phl p 1 in P. pratense extracts was developed and validated by producing the appropriate mAbs against epitopes selected by immunoinformatic tools.
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Affiliation(s)
| | | | - Raquel Moya
- R&D Allergy & Immunology Unit, LETI Pharma S.L.U, Madrid, Spain
| | - Jerónimo Carnés
- R&D Allergy & Immunology Unit, LETI Pharma S.L.U, Madrid, Spain.
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9
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Structural Conservation and Adaptation of the Bacterial Flagella Motor. Biomolecules 2020; 10:biom10111492. [PMID: 33138111 PMCID: PMC7693769 DOI: 10.3390/biom10111492] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 10/26/2020] [Accepted: 10/27/2020] [Indexed: 02/07/2023] Open
Abstract
Many bacteria require flagella for the ability to move, survive, and cause infection. The flagellum is a complex nanomachine that has evolved to increase the fitness of each bacterium to diverse environments. Over several decades, molecular, biochemical, and structural insights into the flagella have led to a comprehensive understanding of the structure and function of this fascinating nanomachine. Notably, X-ray crystallography, cryo-electron microscopy (cryo-EM), and cryo-electron tomography (cryo-ET) have elucidated the flagella and their components to unprecedented resolution, gleaning insights into their structural conservation and adaptation. In this review, we focus on recent structural studies that have led to a mechanistic understanding of flagellar assembly, function, and evolution.
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10
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Serapian S, Marchetti F, Triveri A, Morra G, Meli M, Moroni E, Sautto GA, Rasola A, Colombo G. The Answer Lies in the Energy: How Simple Atomistic Molecular Dynamics Simulations May Hold the Key to Epitope Prediction on the Fully Glycosylated SARS-CoV-2 Spike Protein. J Phys Chem Lett 2020; 11:8084-8093. [PMID: 32885971 PMCID: PMC7491317 DOI: 10.1021/acs.jpclett.0c02341] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 09/04/2020] [Indexed: 05/05/2023]
Abstract
SARS-CoV-2 is a health threat with dire socioeconomical consequences. As the crucial mediator of infection, the viral glycosylated spike protein (S) has attracted the most attention and is at the center of efforts to develop therapeutics and diagnostics. Herein, we use an original decomposition approach to identify energetically uncoupled substructures as antibody binding sites on the fully glycosylated S. Crucially, all that is required are unbiased MD simulations; no prior knowledge of binding properties or ad hoc parameter combinations is needed. Our results are validated by experimentally confirmed structures of S in complex with anti- or nanobodies. We identify poorly coupled subdomains that are poised to host (several) epitopes and potentially involved in large functional conformational transitions. Moreover, we detect two distinct behaviors for glycans: those with stronger energetic coupling are structurally relevant and protect underlying peptidic epitopes, and those with weaker coupling could themselves be prone to antibody recognition.
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Affiliation(s)
- Stefano
A. Serapian
- Department
of Chemistry, University of Pavia, viale Taramelli 12, 27100 Pavia, Italy
| | - Filippo Marchetti
- Department
of Chemistry, University of Pavia, viale Taramelli 12, 27100 Pavia, Italy
- Department
of Chemistry, University of Milan, via Venezian 21, 20133 Milano, Italy
| | - Alice Triveri
- Department
of Chemistry, University of Pavia, viale Taramelli 12, 27100 Pavia, Italy
| | - Giulia Morra
- SCITEC−CNR, via Mario Bianco 9, 20131 Milano, Italy
| | | | | | - Giuseppe A. Sautto
- Center
for Vaccines and Immunology, Department of Infectious Diseases, University of Georgia, 501 D. W. Brooks Drive, Athens, Georgia 30602, United States
| | - Andrea Rasola
- Dipartimento
di Scienze Biomediche, Università
di Padova, viale G. Colombo
3, 35131 Padova, Italy
| | - Giorgio Colombo
- Department
of Chemistry, University of Pavia, viale Taramelli 12, 27100 Pavia, Italy
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11
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A disclosure of hidden secrets in human cytomegalovirus: An in-silico study of identification of novel genes and their analysis for vaccine development. Meta Gene 2020. [DOI: 10.1016/j.mgene.2020.100754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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12
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Nithichanon A, Tussakhon I, Samer W, Kewcharoenwong C, Ato M, Bancroft GJ, Lertmemongkolchai G. Immune responses in beta-thalassaemia: heme oxygenase 1 reduces cytokine production and bactericidal activity of human leucocytes. Sci Rep 2020; 10:10297. [PMID: 32581238 PMCID: PMC7314746 DOI: 10.1038/s41598-020-67346-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 06/08/2020] [Indexed: 12/17/2022] Open
Abstract
Patients with beta-thalassaemia increase the risk of bacterial infections, particularly Burkholderia pseudomallei (Bp), the causative agent of melioidosis in Thailand. Impaired immune cell functions may be the cause of this susceptibility, but detailed mechanisms have not been defined. In this study, we observed impaired production of IFN-gamma and IL-10 by whole blood from beta-thalassaemia patients upon stimulation with a range of bacteria-derived stimuli. In contrast, IFN-gamma response via TCR and plasma IgG specific for Bp were still intact. Importantly, mRNA expression of heme oxygenase 1 (HO-1), a potential modulator of immune function, was increased in whole blood from beta-thalassaemia patients, either with or without stimulation with Bp in vitro. Induction of HO-1 by hemin or CoPP in vitro reduced production of IFN-gamma and IL-10 from healthy human PBMCs and decreased bacterial clearance activity of whole blood from healthy controls and beta-thalassaemia, while inhibition of HO-1 by SnPP enhanced both functions in healthy controls. These results were confirmed to some extent in purified human monocytes of healthy controls. Our results suggest a mechanism that excess hemin of beta-thalassaemia patients is a significant cause of immune suppression via HO-1 induction and may underlie the susceptibility of these individuals to severe bacterial infection.
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Affiliation(s)
- Arnone Nithichanon
- The Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Inthira Tussakhon
- The Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Waraporn Samer
- The Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Chidchamai Kewcharoenwong
- The Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Manabu Ato
- Department of Immunology, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Gregory J Bancroft
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Ganjana Lertmemongkolchai
- The Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, 40002, Thailand.
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13
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Cretich M, Gori A, D'Annessa I, Chiari M, Colombo G. Peptides for Infectious Diseases: From Probe Design to Diagnostic Microarrays. Antibodies (Basel) 2019; 8:E23. [PMID: 31544829 PMCID: PMC6640701 DOI: 10.3390/antib8010023] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 02/28/2019] [Accepted: 03/04/2019] [Indexed: 01/03/2023] Open
Abstract
Peptides and peptidomimetics have attracted revived interest regarding their applications in chemical biology over the last few years. Their chemical versatility, synthetic accessibility and the ease of storage and management compared to full proteins have made peptides particularly interesting in diagnostic applications, where they proved to efficiently recapitulate the molecular recognition properties of larger protein antigens, and were proven to be able to capture antibodies circulating in the plasma and serum of patients previously exposed to bacterial or viral infections. Here, we describe the development, integration and application of strategies for computational prediction and design, advanced chemical synthesis, and diagnostic deployment in multiplexed assays of peptide-based materials which are able to bind antibodies of diagnostic as well as therapeutic interest. By presenting successful applications of such an integrated strategy, we argue that they will have an ever-increasing role in both basic and clinical realms of research, where important advances can be expected in the next few years.
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Affiliation(s)
- Marina Cretich
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco 9, 20131 Milano, Italy.
| | - Alessandro Gori
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco 9, 20131 Milano, Italy.
| | - Ilda D'Annessa
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco 9, 20131 Milano, Italy.
| | - Marcella Chiari
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco 9, 20131 Milano, Italy.
| | - Giorgio Colombo
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco 9, 20131 Milano, Italy.
- Dipartimento di Chimica, Università di Pavia, V.le Taramelli 12, 27100 Pavia, Italy.
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14
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Kim JH, Namgung B, Jeon YJ, Song WS, Lee J, Kang SG, Yoon SI. Helicobacter pylori flagellin: TLR5 evasion and fusion-based conversion into a TLR5 agonist. Biochem Biophys Res Commun 2018; 505:872-878. [PMID: 30301528 DOI: 10.1016/j.bbrc.2018.09.179] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 09/28/2018] [Indexed: 12/31/2022]
Abstract
Helicobacter pylori is a flagellated bacterium of the Epsilonproteobacteria class that causes peptic ulcers. Flagellin is a primary structural protein that assembles into the flagellar filament. Flagellins from bacteria that belong to the Gammaproteobacteria and Firmicutes groups are detected by Toll-like receptor 5 (TLR5) in the host, triggering the innate immune response, and thus have been studied for the development of vaccines against diverse infections through fusion with protein antigens. However, H. pylori flagellin (hFlg) does not stimulate TLR5, allowing H. pylori to evade TLR5-mediated immune surveillance. The unresponsiveness of TLR5 to hFlg, along with the tendency of the hFlg protein to precipitate, limits the utility of hFlg for H. pylori vaccine development. Here, we report a soluble hFlg derivative protein that activates TLR5. We performed expression and purification screens with full-length and fragment hFlg proteins and identified the hypervariable domains as the soluble part of hFlg. The hypervariable domains of hFlg were engineered into a TLR5 agonist through fusion with the TLR5-activating Bacillus subtilis flagellin. Furthermore, based on comparative sequence and mutation analyses, we reveal that hFlg evolved to evade TLR5 detection by modifying residues that correspond to a TLR5-activation hot spot.
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Affiliation(s)
- Jee-Hyeon Kim
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Byeol Namgung
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Ye Ji Jeon
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Wan Seok Song
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Jeonghyun Lee
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Seung Goo Kang
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, 24341, Republic of Korea.
| | - Sung-Il Yoon
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, 24341, Republic of Korea.
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15
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Ferraro M, Colombo G. Targeting Difficult Protein-Protein Interactions with Plain and General Computational Approaches. Molecules 2018; 23:molecules23092256. [PMID: 30181519 PMCID: PMC6225287 DOI: 10.3390/molecules23092256] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 08/27/2018] [Accepted: 08/31/2018] [Indexed: 11/21/2022] Open
Abstract
Investigating protein-protein interactions (PPIs) holds great potential for therapeutic applications, since they mediate intricate cell signaling networks in physiological and disease states. However, their complex and multifaceted nature poses a major challenge for biochemistry and medicinal chemistry, thereby limiting the druggability of biological partners participating in PPIs. Molecular Dynamics (MD) provides a solid framework to study the reciprocal shaping of proteins’ interacting surfaces. Here, we review successful applications of MD-based methods developed in our group to predict interfacial areas involved in PPIs of pharmaceutical interest. We report two interesting examples of how structural, dynamic and energetic information can be combined into efficient strategies which, complemented by experiments, can lead to the design of new small molecules with promising activities against cancer and infections. Our advances in targeting key PPIs in angiogenic pathways and antigen-antibody recognition events will be discussed for their role in drug discovery and chemical biology.
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Affiliation(s)
- Mariarosaria Ferraro
- Istituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco 9, 20131 Milano, Italy.
| | - Giorgio Colombo
- Istituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco 9, 20131 Milano, Italy.
- Dipartimento di Chimica, Università di Pavia, V.le Taramelli 10, 27100 Pavia, Italy.
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16
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Echazarreta MA, Kepple JL, Yen LH, Chen Y, Klose KE. A Critical Region in the FlaA Flagellin Facilitates Filament Formation of the Vibrio cholerae Flagellum. J Bacteriol 2018; 200:e00029-18. [PMID: 29581407 PMCID: PMC6040194 DOI: 10.1128/jb.00029-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 03/10/2018] [Indexed: 11/20/2022] Open
Abstract
Vibrio cholerae is a Gram-negative bacterium with a monotrichous flagellum that causes the human disease cholera. Flagellum-mediated motility is an integral part of the bacterial life cycle inside the host and in the aquatic environment. The V. cholerae flagellar filament is composed of five flagellin subunits (FlaA, FlaB, FlaC, FlaD, and FlaE); however, only FlaA is necessary and sufficient for filament synthesis. flaA is transcribed from a class III flagellar promoter, whereas the other four flagellins are transcribed from class IV promoters. However, expressing flaA from a class IV promoter still facilitated motility in a strain that was otherwise lacking all five flagellins (ΔflaA-E). Furthermore, FlaA from V. parahaemolyticus (FlaAVP; 77% identity) supported motility of the V. cholerae ΔflaA-E strain, whereas FlaA from V. vulnificus (FlaAVV; 75% identity) did not, indicating that FlaA amino acid sequence is responsible for its critical role in flagellar synthesis. Chimeric proteins composed of different domains of FlaAVC and FlaD or FlaAVV revealed that the N-terminal D1 domain (D1N) contains an important region required for FlaA function. Further analyses of chimeric FlaAVC-FlaD proteins identified a lysine residue present at position 145 of the other flagellins but absent from FlaAVC that can prevent monofilament formation. Moreover, the D1N region of amino acids 87 to 153 of FlaAVV inserted into FlaAVC allows monofilament formation but not motility, apparently due to the lack of filament curvature. These results identify residues within the D1N domain that allow FlaAVC to fold into a functional filament structure and suggest that FlaAVC assists correct folding of the other flagellins.IMPORTANCEV. cholerae causes the severe diarrheal disease cholera. Its ability to swim is mediated by rotation of a polar flagellum, and this motility is integral to its ability to cause disease and persist in the environment. The current studies illuminate how one specific flagellin (FlaA) within a multiflagellin structure mediates formation of the flagellar filament, thus allowing V. cholerae to swim. This knowledge can lead to safer vaccines and potential therapeutics to inhibit cholera.
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Affiliation(s)
- Mylea A Echazarreta
- South Texas Center for Emerging Infectious Diseases, Department of Biology, The University of Texas at San Antonio, San Antonio, Texas, USA
| | - Johnathan L Kepple
- South Texas Center for Emerging Infectious Diseases, Department of Biology, The University of Texas at San Antonio, San Antonio, Texas, USA
| | - Li-Hua Yen
- South Texas Center for Emerging Infectious Diseases, Department of Biology, The University of Texas at San Antonio, San Antonio, Texas, USA
| | - Yue Chen
- South Texas Center for Emerging Infectious Diseases, Department of Biology, The University of Texas at San Antonio, San Antonio, Texas, USA
| | - Karl E Klose
- South Texas Center for Emerging Infectious Diseases, Department of Biology, The University of Texas at San Antonio, San Antonio, Texas, USA
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17
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Capelli R, Peri C, Villa R, Nithichanon A, Conchillo-Solé O, Yero D, Gagni P, Chiari M, Lertmemongkolchai G, Cretich M, Daura X, Bolognesi M, Colombo G, Gourlay LJ. BPSL1626: Reverse and Structural Vaccinology Reveal a Novel Candidate for Vaccine Design against Burkholderia pseudomallei. Antibodies (Basel) 2018; 7:antib7030026. [PMID: 31544878 PMCID: PMC6640674 DOI: 10.3390/antib7030026] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/16/2018] [Accepted: 07/17/2018] [Indexed: 11/24/2022] Open
Abstract
Due to significant advances in computational biology, protein prediction, together with antigen and epitope design, have rapidly moved from conventional methods, based on experimental approaches, to in silico-based bioinformatics methods. In this context, we report a reverse vaccinology study that identified a panel of 104 candidate antigens from the Gram-negative bacterial pathogen Burkholderia pseudomallei, which is responsible for the disease melioidosis. B. pseudomallei can cause fatal sepsis in endemic populations in the tropical regions of the world and treatment with antibiotics is mostly ineffective. With the aim of identifying potential vaccine candidates, we report the experimental validation of predicted antigen and type I fimbrial subunit, BPSL1626, which we show is able to recognize and bind human antibodies from the sera of Burkholderia infected patients and to stimulate T-lymphocytes in vitro. The prerequisite for a melioidosis vaccine, in fact, is that both antibody- and cell-mediated immune responses must be triggered. In order to reveal potential antigenic regions of the protein that may aid immunogen re-design, we also report the crystal structure of BPSL1626 at 1.9 Å resolution on which structure-based epitope predictions were based. Overall, our data suggest that BPSL1626 and three epitope regions here-identified can represent viable candidates as potential antigenic molecules.
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Affiliation(s)
- Riccardo Capelli
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Via Mario Bianco 9, 20131 Milano, Italy.
- Center for Complexity and Biosystems and Dipartimento di Fisica, Università degli Studi di Milano and INFN, 20133 Milano, Italy.
- Computational Biomedicine Section, Institute of Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9 Forschungszentrum Jülich, 52425 Jülich, Germany.
| | - Claudio Peri
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Via Mario Bianco 9, 20131 Milano, Italy.
| | - Riccardo Villa
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy.
| | - Arnone Nithichanon
- Center for Research and Development of Medical Diagnostic Laboratories (CMDL), Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen 40002, Thailand.
| | - Oscar Conchillo-Solé
- Institute of Biotechnology and Biomedicine (IBB), Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Spain.
| | - Daniel Yero
- Institute of Biotechnology and Biomedicine (IBB), Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Spain.
| | - Paola Gagni
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Via Mario Bianco 9, 20131 Milano, Italy.
| | - Marcella Chiari
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Via Mario Bianco 9, 20131 Milano, Italy.
| | - Ganjana Lertmemongkolchai
- Center for Research and Development of Medical Diagnostic Laboratories (CMDL), Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen 40002, Thailand.
| | - Marina Cretich
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Via Mario Bianco 9, 20131 Milano, Italy.
| | - Xavier Daura
- Institute of Biotechnology and Biomedicine (IBB), Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Spain.
- Catalan Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Spain.
| | - Martino Bolognesi
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy.
- Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi", Cryo Electron-Microscopy Laboratory, Università degli Studi di Milano, 20133 Milano, Italy.
| | - Giorgio Colombo
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Via Mario Bianco 9, 20131 Milano, Italy.
- Department of Chemistry, Università di Pavia, 27100 Pavia, Italy.
| | - Louise J Gourlay
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy.
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18
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Koosakulnirand S, Phokrai P, Jenjaroen K, Roberts RA, Utaisincharoen P, Dunachie SJ, Brett PJ, Burtnick MN, Chantratita N. Immune response to recombinant Burkholderia pseudomallei FliC. PLoS One 2018; 13:e0198906. [PMID: 29902230 PMCID: PMC6002054 DOI: 10.1371/journal.pone.0198906] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Accepted: 05/29/2018] [Indexed: 11/22/2022] Open
Abstract
Burkholderia pseudomallei is a flagellated Gram-negative bacterium which is the causative agent of melioidosis. The disease poses a major public health problem in tropical regions and diabetes is a major risk factor. The high mortality rate of melioidosis is associated with severe sepsis which involves the overwhelming production of pro-inflammatory cytokines. Bacterial flagellar protein (flagellin) activates Toll-like receptor 5 (TLR5)-mediated innate immune signaling pathways and induces adaptive immune response. However, previous studies of TLR5 signaling in melioidosis have been performed using recombinant flagellin from Salmonella Typhimurium instead of B. pseudomallei. This study aimed to investigate human innate immune response and antibody response against a recombinant B. pseudomallei flagellin (rFliC). We prepared B. pseudomallei rFliC and used it to stimulate HEK-BlueTM-hTLR5 and THP1-DualTM cells to assess TLR5 activation. Subsequently, whole blood stimulation assays with rFliC were performed ex vivo. TLR5-flagellin interactions trigger activation of transcription factor NF-κB in HEK-BlueTM-hTLR5 cells. Pro-inflammatory cytokine (IL-1β, IL-6, and TNF-α) productions from whole blood in response to rFliC differed between fourteen healthy individuals. The levels of these cytokines changed in a dose and time-dependent manner. ELISA was used to determine rFliC-specific antibodies in serum samples from different groups of melioidosis patients and healthy subjects. IgG antibody to rFliC in melioidosis patients with diabetes were higher compared with non-diabetic patients. Our results show that B. pseudomallei flagellin is a potent immune stimulator and that the immune responses to rFliC are different among individuals. This may provide valuable insights toward the potential use of rFliC in vaccine development.
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Affiliation(s)
- Sirikamon Koosakulnirand
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Phornpun Phokrai
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Kemajittra Jenjaroen
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Rosemary A. Roberts
- Department of Microbiology and Immunology, University of South Alabama, Mobile, AL, United States of America
| | | | - Susanna J. Dunachie
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
- Center for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Paul J. Brett
- Department of Microbiology and Immunology, University of South Alabama, Mobile, AL, United States of America
| | - Mary N. Burtnick
- Department of Microbiology and Immunology, University of South Alabama, Mobile, AL, United States of America
| | - Narisara Chantratita
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
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19
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Sola L, Gagni P, D’Annessa I, Capelli R, Bertino C, Romanato A, Damin F, Bergamaschi G, Marchisio E, Cuzzocrea A, Bombaci M, Grifantini R, Chiari M, Colombo G, Gori A, Cretich M. Enhancing Antibody Serodiagnosis Using a Controlled Peptide Coimmobilization Strategy. ACS Infect Dis 2018; 4:998-1006. [PMID: 29570266 DOI: 10.1021/acsinfecdis.8b00014] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Antigen immunoreactivity is often determined by surface regions defined by the 3D juxtapositions of amino acids stretches that are not continuous in the linear sequence. As such, mimicking an antigen immunoreactivity by means of putative linear peptide epitopes for diagnostic purposes is not trivial. Here we present a straightforward and robust method to extend the reach of immune-diagnostic probes design by copresenting peptides belonging to the same antigenic surface. In this case study focused on a computationally predicted Zika virus NS1 protein putative antigenic region, we reached a diagnostic confidence by the oriented and spatially controlled coimmobilization of peptide sequences found adjacent within the protein fold, that cooperatively interacted to provide enhanced immunoreactivity with respect to single linear epitopes. Through our method, we were able to differentiate Zika infected individuals from healthy controls. Remarkably, our strategy fits well with the requirements to build high-throughput screening platforms of linear and mixed peptide libraries, and it could possibly facilitate the rapid identification of conformational immunoreactive regions.
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Affiliation(s)
- Laura Sola
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco, 9, 20131 Milano, Italy
| | - Paola Gagni
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco, 9, 20131 Milano, Italy
| | - Ilda D’Annessa
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco, 9, 20131 Milano, Italy
| | - Riccardo Capelli
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco, 9, 20131 Milano, Italy
| | - Camilla Bertino
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco, 9, 20131 Milano, Italy
| | - Alessandro Romanato
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco, 9, 20131 Milano, Italy
| | - Francesco Damin
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco, 9, 20131 Milano, Italy
| | - Greta Bergamaschi
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco, 9, 20131 Milano, Italy
| | - Edoardo Marchisio
- Diagnostic Bioprobes s.r.l. (DiaPro), via G. Carducci 27, 20090 Sesto San Giovanni, Italy
| | - Angela Cuzzocrea
- Diagnostic Bioprobes s.r.l. (DiaPro), via G. Carducci 27, 20090 Sesto San Giovanni, Italy
| | - Mauro Bombaci
- Istituto Nazionale di Genetica Molecolare “Romeo ed Enrica Invernizzi” (INGM), Via Francesco Sforza. 35, 20122 Milano, Italy
| | - Renata Grifantini
- Istituto Nazionale di Genetica Molecolare “Romeo ed Enrica Invernizzi” (INGM), Via Francesco Sforza. 35, 20122 Milano, Italy
| | - Marcella Chiari
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco, 9, 20131 Milano, Italy
| | - Giorgio Colombo
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco, 9, 20131 Milano, Italy
- Dipartimento di Chimica, Università di Pavia, V.le Taramelli 12, 27100 Pavia, Italy
| | - Alessandro Gori
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco, 9, 20131 Milano, Italy
| | - Marina Cretich
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco, 9, 20131 Milano, Italy
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20
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Nithichanon A, Rinchai D, Buddhisa S, Saenmuang P, Kewcharoenwong C, Kessler B, Khaenam P, Chetchotisakd P, Maillere B, Robinson J, Reynolds CJ, Boyton RJ, Altmann DM, Lertmemongkolchai G. Immune Control of Burkholderia pseudomallei--Common, High-Frequency T-Cell Responses to a Broad Repertoire of Immunoprevalent Epitopes. Front Immunol 2018; 9:484. [PMID: 29616023 PMCID: PMC5869189 DOI: 10.3389/fimmu.2018.00484] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 02/23/2018] [Indexed: 12/03/2022] Open
Abstract
Burkholderia pseudomallei (Bp) is an environmental bacterial pathogen that causes potentially lethal sepsis in susceptible individuals and is considered a Category B, Tier-1 biothreat agent. As such, it is crucial to gain an improved understanding of protective immunity and potential vaccine candidates. The nature of immune correlates dictating why most exposed individuals in endemic regions undergo asymptomatic seroconversion while others succumb to life-threatening sepsis is largely uncharted. Bp seroreactive, immunogenic proteins have previously been identified by antigen microarray. We here set out to conduct an analysis of T-cell recognition of the Bp immunome using serodominant antigens represented in the original antigen microarray, examining immune correlates of disease in healthy seropositive individuals and those with acute disease or in convalescence. By screening a library of 739 overlapping peptides representing the sequences of 20 different Bp antigens, we aimed to define immune correlates of protection at the level of immunoprevalent T-cell epitopes. Responses to a large number of epitopes were common in healthy seropositive individuals: we found remarkably broad responsiveness to Bp epitopes, with 235 of 739 peptides recognized by ≥80% of all tested donors. The cumulative response to Bp epitopes in healthy, seropositive, donors from this endemic region were of the order of thousands of spot forming cells per million cells, making Bp recognition a significant component of the T-cell repertoire. Noteworthy among our findings, analysis revealed 10 highly immunoprevalent T-cell epitopes, able to induce Bp-specific IFNγ responses that were high in responding T-cell frequency within the repertoire, and also common across individuals with different human leukocyte antigen types. Acute melioidosis patients showed poor T-cell responses to the immunoprevalent epitopes, but acquired responsiveness following recovery from infection. Our findings suggest that a large repertoire of CD4 T cells, high in frequency and with broad coverage of antigens and epitopes, is important in controlling Bp infection. This offers an attractive potential strategy for subunit or epitope-based vaccines.
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Affiliation(s)
- Arnone Nithichanon
- Centre for Research & Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Mekong Health Science Research Institute, Khon Kaen University, Khon Kaen, Thailand
| | - Darawan Rinchai
- Centre for Research & Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Mekong Health Science Research Institute, Khon Kaen University, Khon Kaen, Thailand
| | - Surachat Buddhisa
- Centre for Research & Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Mekong Health Science Research Institute, Khon Kaen University, Khon Kaen, Thailand
| | - Pornpun Saenmuang
- Centre for Research & Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Mekong Health Science Research Institute, Khon Kaen University, Khon Kaen, Thailand
| | - Chidchamai Kewcharoenwong
- Centre for Research & Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Mekong Health Science Research Institute, Khon Kaen University, Khon Kaen, Thailand
| | - Bianca Kessler
- Centre for Research & Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Mekong Health Science Research Institute, Khon Kaen University, Khon Kaen, Thailand
| | - Prasong Khaenam
- Centre for Research & Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Mekong Health Science Research Institute, Khon Kaen University, Khon Kaen, Thailand
| | | | - Bernard Maillere
- Protein Engineering and Research Department, CEA Saclay, Gif-sur-Yvette, France
| | - John Robinson
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | | | | | - Daniel M. Altmann
- Department of Medicine, Imperial College London, London, United Kingdom
| | - Ganjana Lertmemongkolchai
- Centre for Research & Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Mekong Health Science Research Institute, Khon Kaen University, Khon Kaen, Thailand
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21
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Bacterial flagellar axial structure and its construction. Biophys Rev 2017; 10:559-570. [PMID: 29235079 DOI: 10.1007/s12551-017-0378-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 11/26/2017] [Indexed: 12/19/2022] Open
Abstract
The bacterial flagellum is a motile organelle composed of thousands of protein subunits. The filamentous part that extends from the cell membrane is called the axial structure and consists of three major parts, the filament, hook, and rod, and other minor components. Each of the three main parts shares a similar self-assembly mechanism and a common basic architecture of subunit arrangement while showing quite distinct mechanical properties to achieve its specific function. Structural and molecular mechanisms to produce these various mechanical properties of the axial structure, such as the filament, the hook, and the rod, have been revealed by the complementary use of X-ray crystallography and cryo-electron microscopy. In addition, the mechanism of growth of the axial structure is beginning to be revealed based on the molecular structure.
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22
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Titball RW, Burtnick MN, Bancroft GJ, Brett P. Burkholderia pseudomallei and Burkholderia mallei vaccines: Are we close to clinical trials? Vaccine 2017; 35:5981-5989. [DOI: 10.1016/j.vaccine.2017.03.022] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 02/17/2017] [Accepted: 03/07/2017] [Indexed: 10/19/2022]
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23
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Gori A, Bolognesi M, Colombo G, Gourlay LJ. Structural Vaccinology for Melioidosis Vaccine Design and Immunodiagnostics. CURRENT TROPICAL MEDICINE REPORTS 2017. [DOI: 10.1007/s40475-017-0117-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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24
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Paladino A, Marchetti F, Rinaldi S, Colombo G. Protein design: from computer models to artificial intelligence. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2017. [DOI: 10.1002/wcms.1318] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Antonella Paladino
- Biomolecular Simulations & Computational Chemistry Group; Istituto Istituto di Chimica del Riconoscimento Molecolare, CNR; Milano Italy
| | - Filippo Marchetti
- Biomolecular Simulations & Computational Chemistry Group; Istituto Istituto di Chimica del Riconoscimento Molecolare, CNR; Milano Italy
| | - Silvia Rinaldi
- Biomolecular Simulations & Computational Chemistry Group; Istituto Istituto di Chimica del Riconoscimento Molecolare, CNR; Milano Italy
| | - Giorgio Colombo
- Biomolecular Simulations & Computational Chemistry Group; Istituto Istituto di Chimica del Riconoscimento Molecolare, CNR; Milano Italy
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25
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Nithichanon A, Gourlay LJ, Bancroft GJ, Ato M, Takahashi Y, Lertmemongkolchai G. Boosting of post-exposure human T-cell and B-cell recall responses in vivo by Burkholderia pseudomallei-related proteins. Immunology 2017; 151:98-109. [PMID: 28066900 DOI: 10.1111/imm.12709] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2016] [Revised: 12/30/2016] [Accepted: 01/04/2017] [Indexed: 12/20/2022] Open
Abstract
Burkholderia pseudomallei is the causative agent of melioidosis, an infectious disease with high incidence and mortality in South East Asia and northern Australia. To date there is no protective vaccine and antibiotic treatment is prolonged and not always effective. Most people living in endemic areas have been exposed to the bacteria and have developed some immunity, which may have helped to prevent disease. Here, we used a humanized mouse model (hu-PBL-SCID), reconstituted with human peripheral blood mononuclear cells from seropositive donors, to illustrate the potential of three known antigens (FliC, OmpA and N-PilO2) for boosting both T-cell and B-cell immune responses. All three antigens boosted the production of specific antibodies in vivo, and increased the number of antibody and interferon-γ-secreting cells, and induced antibody affinity maturation. Moreover, antigen-specific antibodies isolated from either seropositive individuals or boosted mice, were found to enhance phagocytosis and oxidative burst activities from human polymorphonuclear cells. Our study demonstrates that FliC, OmpA and N-PilO2 can stimulate human memory T and B cells and highlight the potential of the hu-PBL-SCID system for screening and evaluation of novel protein antigens for inclusion in future vaccine trials against melioidosis.
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Affiliation(s)
- Arnone Nithichanon
- The Centre for Research and Development of Medical Diagnostic Laboratories, Khon Kaen University, Khon Kaen, Thailand
| | | | | | - Manabu Ato
- Department of Immunology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yoshimasa Takahashi
- Department of Immunology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Ganjana Lertmemongkolchai
- The Centre for Research and Development of Medical Diagnostic Laboratories, Khon Kaen University, Khon Kaen, Thailand
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26
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Song WS, Cho SY, Hong HJ, Park SC, Yoon SI. Self-Oligomerizing Structure of the Flagellar Cap Protein FliD and Its Implication in Filament Assembly. J Mol Biol 2017; 429:847-857. [PMID: 28179186 DOI: 10.1016/j.jmb.2017.02.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 02/01/2017] [Accepted: 02/01/2017] [Indexed: 12/30/2022]
Abstract
FliD is a self-oligomerizing structural protein that caps the growing end of the bacterial flagellar filament. FliD also plays a key role in the flagellar system by continuously adding a new flagellin protein to the tip of the filament. To structurally characterize FliD oligomerization and to provide a FliD-mediated flagellin polymerization mechanism, we have determined the crystal structures of FliD proteins from Escherichia coli and Salmonella enterica serovar Typhimurium (ecFliD and stFliD, respectively). ecFliD consists of three domains (D1, D2, and D3) and forms a hexamer plate of the D2 and D3 domains that resembles a six-pointed star with legs consisting of the D1 domain. In contrast, the D2 and D3 domains of stFliD assemble into a pentamer as a five-pointed star plate. Despite their distinct oligomeric states, ecFliD and stFliD engage a common molecular surface for oligomerization. FliD also features interdomain and intersubunit flexibility, suggesting that FliD reorganizes its domains and adjacent subunits depending on the FliD binding partner. The similarity of the FliD shape to flagellin and the structural dynamics of FliD led us to propose a FliD-catalyzed filament elongation mechanism. In this model, FliD occupies a position in place of a nascent flagellin until the flagellin reaches the growing end of the filament, and then, FliD moves aside to repeat the positional replacement.
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Affiliation(s)
- Wan Seok Song
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - So Yeon Cho
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Ho Jeong Hong
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Sun Cheol Park
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Sung-Il Yoon
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea; Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon 24341, Republic of Korea.
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27
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Peri C, Gori A, Gagni P, Sola L, Girelli D, Sottotetti S, Cariani L, Chiari M, Cretich M, Colombo G. Evolving serodiagnostics by rationally designed peptide arrays: the Burkholderia paradigm in Cystic Fibrosis. Sci Rep 2016; 6:32873. [PMID: 27615705 PMCID: PMC5018727 DOI: 10.1038/srep32873] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 08/16/2016] [Indexed: 01/05/2023] Open
Abstract
Efficient diagnosis of emerging and novel bacterial infections is fundamental to guide decisions on therapeutic treatments. Here, we engineered a novel rational strategy to design peptide microarray platforms, which combines structural and genomic analyses to predict the binding interfaces between diverse protein antigens and antibodies against Burkholderia cepacia complex infections present in the sera of Cystic Fibrosis (CF) patients. The predicted binding interfaces on the antigens are synthesized in the form of isolated peptides and chemically optimized for controlled orientation on the surface. Our platform displays multiple Burkholderia-related epitopes and is shown to diagnose infected individuals even in presence of superinfections caused by other prevalent CF pathogens, with limited cost and time requirements. Moreover, our data point out that the specific patterns determined by combined probe responses might provide a characterization of Burkholderia infections even at the subtype level (genomovars). The method is general and immediately applicable to other bacteria.
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Affiliation(s)
- Claudio Peri
- Istituto di Chimica del Riconoscimento Molecolare, ICRM, CNR. Via Mario Bianco 9, 20131, Milano (Italy)
| | - Alessandro Gori
- Istituto di Chimica del Riconoscimento Molecolare, ICRM, CNR. Via Mario Bianco 9, 20131, Milano (Italy)
| | - Paola Gagni
- Istituto di Chimica del Riconoscimento Molecolare, ICRM, CNR. Via Mario Bianco 9, 20131, Milano (Italy)
| | - Laura Sola
- Istituto di Chimica del Riconoscimento Molecolare, ICRM, CNR. Via Mario Bianco 9, 20131, Milano (Italy)
| | - Daniela Girelli
- Cystic Fibrosis Microbiology Laboratory, Fondazione IRCCS Cà Granda, Ospedale Maggiore Policlinico, via San Barnaba 8, 20122, Milano (Italy)
| | - Samantha Sottotetti
- Cystic Fibrosis Microbiology Laboratory, Fondazione IRCCS Cà Granda, Ospedale Maggiore Policlinico, via San Barnaba 8, 20122, Milano (Italy)
| | - Lisa Cariani
- Cystic Fibrosis Microbiology Laboratory, Fondazione IRCCS Cà Granda, Ospedale Maggiore Policlinico, via San Barnaba 8, 20122, Milano (Italy)
| | - Marcella Chiari
- Istituto di Chimica del Riconoscimento Molecolare, ICRM, CNR. Via Mario Bianco 9, 20131, Milano (Italy)
| | - Marina Cretich
- Istituto di Chimica del Riconoscimento Molecolare, ICRM, CNR. Via Mario Bianco 9, 20131, Milano (Italy)
| | - Giorgio Colombo
- Istituto di Chimica del Riconoscimento Molecolare, ICRM, CNR. Via Mario Bianco 9, 20131, Milano (Italy)
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28
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Swetha RG, Sandhya M, Ramaiah S, Anbarasu A. Identification of CD4+ T-cell epitope and investigation of HLA distribution for the immunogenic proteins of Burkholderia pseudomallei using in silico approaches - A key vaccine development strategy for melioidosis. J Theor Biol 2016; 400:11-8. [PMID: 27086038 DOI: 10.1016/j.jtbi.2016.04.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 03/18/2016] [Accepted: 04/08/2016] [Indexed: 10/21/2022]
Abstract
Melioidosis is a serious infectious diseases affecting multi-organ system in humans with high mortality rate. The disease is caused by the bacterium, Burkholderia pseudomallei and it is intrinsically resistant to many antibiotics. Thus, there is an urgent need for protective vaccine against B. pseudomallei; which may reduce morbidity and mortality in endemic areas. The identification of peptides that bind to major histocompatibility complex II class helps in understanding the nature of immune response and identifying T-cell epitopes for the design of new vaccines. Previous studies indicate that, ompA, bipB, fliC and groEL proteins of B. pseudomallei stimulate CD4+ T-cell immune response and act as protective immunogens. However, the data for CD4+ T-cell epitopes of these immunogenic proteins are very limited. Hence, in this present study we attempted to identify CD4+ T-cell epitopes in B. pseudomallei immunogenic proteins using in silico approaches. We did population coverage analysis for these identified epitopic core sequences to identify individuals in endemic areas expected to respond to a given set of these epitopes on the basis of HLA genotype frequencies. We observed that eight epitopic core sequences, two from each immunogenic protein, were associated with the maximum number of HLA-DR binding alleles. These eight peptides are found to be immunogenic in more than 90% of population in endemic areas considered. Thus, these eight peptides containing epitopic core sequences may act as probable vaccine candidates and they may be considered for the development of epitope-based vaccines for melioidosis.
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Affiliation(s)
- Rayapadi G Swetha
- Medical & Biological Computing Laboratory, School of BioSciences and Technology, VIT University, Vellore 632014, India
| | - Madangopal Sandhya
- Medical & Biological Computing Laboratory, School of BioSciences and Technology, VIT University, Vellore 632014, India
| | - Sudha Ramaiah
- Medical & Biological Computing Laboratory, School of BioSciences and Technology, VIT University, Vellore 632014, India
| | - Anand Anbarasu
- Medical & Biological Computing Laboratory, School of BioSciences and Technology, VIT University, Vellore 632014, India.
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29
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Peri C, Morra G, Colombo G. Surface energetics and protein-protein interactions: analysis and mechanistic implications. Sci Rep 2016; 6:24035. [PMID: 27050828 PMCID: PMC4822145 DOI: 10.1038/srep24035] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 03/16/2016] [Indexed: 12/17/2022] Open
Abstract
Understanding protein-protein interactions (PPI) at the molecular level is a fundamental task in the design of new drugs, the prediction of protein function and the clarification of the mechanisms of (dis)regulation of biochemical pathways. In this study, we use a novel computational approach to investigate the energetics of aminoacid networks located on the surface of proteins, isolated and in complex with their respective partners. Interestingly, the analysis of individual proteins identifies patches of surface residues that, when mapped on the structure of their respective complexes, reveal regions of residue-pair couplings that extend across the binding interfaces, forming continuous motifs. An enhanced effect is visible across the proteins of the dataset forming larger quaternary assemblies. The method indicates the presence of energetic signatures in the isolated proteins that are retained in the bound form, which we hypothesize to determine binding orientation upon complex formation. We propose our method, BLUEPRINT, as a complement to different approaches ranging from the ab-initio characterization of PPIs, to protein-protein docking algorithms, for the physico-chemical and functional investigation of protein-protein interactions.
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Affiliation(s)
- Claudio Peri
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, via Mario Bianco, 9, 20131, Milan, Italy
| | - Giulia Morra
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, via Mario Bianco, 9, 20131, Milan, Italy
| | - Giorgio Colombo
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, via Mario Bianco, 9, 20131, Milan, Italy
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