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Widdicombe M, Coff L, Nowak BF, Ramsland PA, Bott NJ. Understanding the host response of farmed fish to blood flukes (Trematoda: Aporocotylidae) for developing new treatment strategies. Fish Shellfish Immunol 2024; 149:109613. [PMID: 38710341 DOI: 10.1016/j.fsi.2024.109613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/29/2024] [Accepted: 05/03/2024] [Indexed: 05/08/2024]
Abstract
Aporocotylids (Trematoda: Digenea), also known as fish blood flukes infect the circulatory system of fish leading to serious health problems and mortality. Aporocotylids are a particular concern for farmed fish as infection intensity can increase within the farming environment and lead to mortalities. In the context of managing these infections, one of the most crucial aspects to consider is the host response of the infected fish against these blood flukes. Understanding the response is essential to improving current treatment strategies that are largely based on the use of anthelmintic praziquantel to manage infections in aquaculture. This review focuses on the current knowledge of farmed fish host responses against the different life stages of aporocotylids. New treatment strategies that are able to provide protection against reinfections should be a long-term goal and is not possible without understanding the fish response to infection and the interactions between host and parasite.
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Affiliation(s)
- Maree Widdicombe
- School of Science, STEM College, RMIT University, Bundoora, Victoria, 3083, Australia
| | - Lachlan Coff
- School of Science, STEM College, RMIT University, Bundoora, Victoria, 3083, Australia; Australian Centre for Disease Preparedness, CSIRO, East Geelong, Victoria, 3219, Australia
| | - Barbara F Nowak
- School of Science, STEM College, RMIT University, Bundoora, Victoria, 3083, Australia; Institute for Marine and Antarctic Studies, University of Tasmania, Locked Bag 1370, Launceston, Tasmania, 7250, Australia
| | - Paul A Ramsland
- School of Science, STEM College, RMIT University, Bundoora, Victoria, 3083, Australia; Department of Immunology, Monash University, Melbourne, Victoria, 3004. Australia; Department of Surgery, Austin Health, University of Melbourne, Heidelberg, Victoria, 3084, Australia
| | - Nathan J Bott
- School of Science, STEM College, RMIT University, Bundoora, Victoria, 3083, Australia.
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Sijmons D, Collett S, Soliman C, Guy AJ, Scott AM, Durrant LG, Elbourne A, Walduck AK, Ramsland PA. Probing the expression and adhesion of glycans involved in Helicobacter pylori infection. Sci Rep 2024; 14:8587. [PMID: 38615147 PMCID: PMC11016089 DOI: 10.1038/s41598-024-59234-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 04/08/2024] [Indexed: 04/15/2024] Open
Abstract
Helicobacter pylori infects approximately half the human population and has an unusual infective niche of the human stomach. Helicobacter pylori is a major cause of gastritis and has been classified as a group 1 carcinogen by the WHO. Treatment involves triple or quadruple antibiotic therapy, but antibiotic resistance is becoming increasingly prevalent. Helicobacter pylori expresses certain blood group related antigens (Lewis system) as a part of its lipopolysaccharide (LPS), which is thought to assist in immune evasion. Additionally, H. pylori LPS participates in adhesion to host cells alongside several adhesion proteins. This study profiled the carbohydrates of H. pylori reference strains (SS1 and 26695) using monoclonal antibodies (mAbs) and lectins, identifying interactions between two carbohydrate-targeting mAbs and multiple lectins. Atomic force microscopy (AFM) scans were used to probe lectin and antibody interactions with the bacterial surfaces. The selected mAb and lectins displayed an increased adhesive force over the surface of the curved H. pylori rods. Furthermore, this study demonstrates the ability of anti-carbohydrate antibodies to reduce the adhesion of H. pylori 26695 to human gastric adenocarcinoma cells via AFM. Targeting bacterial carbohydrates to disrupt crucial adhesion and immune evasion mechanisms represents a promising strategy for combating H. pylori infection.
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Affiliation(s)
- Daniel Sijmons
- School of Science, RMIT University, Melbourne, VIC, 3000, Australia
| | - Simon Collett
- School of Science, RMIT University, Melbourne, VIC, 3000, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Caroline Soliman
- School of Science, RMIT University, Melbourne, VIC, 3000, Australia
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Andrew J Guy
- School of Science, RMIT University, Melbourne, VIC, 3000, Australia
- ZiP Diagnostics, Collingwood, VIC, 3066, Australia
| | - Andrew M Scott
- Olivia Newton-John Cancer Research Institute and School of Cancer Medicine, La Trobe University, Melbourne, VIC, Australia
- Department of Molecular Imaging and Therapy, Austin Health and Faculty of Medicine, The University of Melbourne, Melbourne, VIC, Australia
| | - Lindy G Durrant
- Scancell Limited, University of Nottingham Biodiscovery Institute, Nottingham, UK
- Division of Cancer and Stem Cells, School of Medicine, University of Nottingham Biodiscovery Institute, Nottingham, UK
| | - Aaron Elbourne
- School of Science, RMIT University, Melbourne, VIC, 3000, Australia
| | - Anna K Walduck
- School of Science, RMIT University, Melbourne, VIC, 3000, Australia.
- Rural Health Research Institute, Charles Sturt University, Orange, NSW, 2800, Australia.
| | - Paul A Ramsland
- School of Science, RMIT University, Melbourne, VIC, 3000, Australia.
- Department of Immunology, Monash University, Melbourne, VIC, 3004, Australia.
- Department of Surgery, Austin Health, The University of Melbourne, Heidelberg, VIC, 3084, Australia.
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Skakic I, Taki AC, Francis JE, Dekiwadia C, Van TTH, Joe CCD, Phan T, Lovrecz G, Gorry PR, Ramsland PA, Walduck AK, Smooker PM. Nanocapsules Comprised of Purified Protein: Construction and Applications in Vaccine Research. Vaccines (Basel) 2024; 12:410. [PMID: 38675791 PMCID: PMC11053559 DOI: 10.3390/vaccines12040410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/03/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
Nanoparticles show great promise as a platform for developing vaccines for the prevention of infectious disease. We have been investigating a method whereby nanocapsules can be formulated from protein, such that the final capsules contain only the cross-linked protein itself. Such nanocapsules are made using a silica templating system and can be customised in terms of size and porosity. Here we compare the construction and characteristics of nanocapsules from four different proteins: one a model protein (ovalbumin) and three from infectious disease pathogens, namely the influenza virus, Helicobacter pylori and HIV. Two of the nanocapsules were assessed further. We confirm that nanocapsules constructed from the urease A subunit of H. pylori can reduce subsequent infection in a vaccinated mouse model. Further, we show that capsules constructed from the HIV gp120 protein can be taken up by dendritic cells in tissue culture and can be recognised by antibodies raised against the virus. These results point to the utility of this method in constructing protein-only nanocapsules from proteins of varying sizes and isoelectric points.
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Affiliation(s)
- Ivana Skakic
- School of Science, RMIT University, 264 Plenty Road, Bundoora, VIC 3083, Australia; (I.S.); (J.E.F.); (T.T.H.V.); (P.A.R.)
| | - Aya C. Taki
- Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia;
| | - Jasmine E. Francis
- School of Science, RMIT University, 264 Plenty Road, Bundoora, VIC 3083, Australia; (I.S.); (J.E.F.); (T.T.H.V.); (P.A.R.)
| | - Chaitali Dekiwadia
- RMIT Microscopy & Microanalysis Facility, School of Science, RMIT University, Melbourne, VIC 3001, Australia;
| | - Thi Thu Hao Van
- School of Science, RMIT University, 264 Plenty Road, Bundoora, VIC 3083, Australia; (I.S.); (J.E.F.); (T.T.H.V.); (P.A.R.)
| | - Carina C. D. Joe
- CSIRO Manufacturing, Clayton, VIC 3169, Australia; (C.C.D.J.); (T.P.); (G.L.)
| | - Tram Phan
- CSIRO Manufacturing, Clayton, VIC 3169, Australia; (C.C.D.J.); (T.P.); (G.L.)
| | - George Lovrecz
- CSIRO Manufacturing, Clayton, VIC 3169, Australia; (C.C.D.J.); (T.P.); (G.L.)
| | - Paul R. Gorry
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute of Infection and Immunity, Parkville, VIC 3010, Australia;
| | - Paul A. Ramsland
- School of Science, RMIT University, 264 Plenty Road, Bundoora, VIC 3083, Australia; (I.S.); (J.E.F.); (T.T.H.V.); (P.A.R.)
- Department of Immunology, Monash University, Melbourne, VIC 3004, Australia
- Department of Surgery, Austin Health, The University of Melbourne, Heidelberg, VIC 3084, Australia
| | - Anna K. Walduck
- School of Science, RMIT University, 264 Plenty Road, Bundoora, VIC 3083, Australia; (I.S.); (J.E.F.); (T.T.H.V.); (P.A.R.)
| | - Peter M. Smooker
- School of Science, RMIT University, 264 Plenty Road, Bundoora, VIC 3083, Australia; (I.S.); (J.E.F.); (T.T.H.V.); (P.A.R.)
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Collett S, Earnest L, Carrera Montoya J, Edeling MA, Yap A, Wong CY, Christiansen D, Roberts J, Mumford J, Lecouturier V, Pavot V, Marco S, Loi JK, Simmons C, Gulab SA, Mackenzie JM, Elbourne A, Ramsland PA, Cameron G, Hans D, Godfrey DI, Torresi J. Development of virus-like particles with inbuilt immunostimulatory properties as vaccine candidates. Front Microbiol 2023; 14:1065609. [PMID: 37350788 PMCID: PMC10282183 DOI: 10.3389/fmicb.2023.1065609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 05/17/2023] [Indexed: 06/24/2023] Open
Abstract
The development of virus-like particle (VLP) based vaccines for human papillomavirus, hepatitis B and hepatitis E viruses represented a breakthrough in vaccine development. However, for dengue and COVID-19, technical complications, such as an incomplete understanding of the requirements for protective immunity, but also limitations in processes to manufacture VLP vaccines for enveloped viruses to large scale, have hampered VLP vaccine development. Selecting the right adjuvant is also an important consideration to ensure that a VLP vaccine induces protective antibody and T cell responses. For diseases like COVID-19 and dengue fever caused by RNA viruses that exist as families of viral variants with the potential to escape vaccine-induced immunity, the development of more efficacious vaccines is also necessary. Here, we describe the development and characterisation of novel VLP vaccine candidates using SARS-CoV-2 and dengue virus (DENV), containing the major viral structural proteins, as protypes for a novel approach to produce VLP vaccines. The VLPs were characterised by Western immunoblot, enzyme immunoassay, electron and atomic force microscopy, and in vitro and in vivo immunogenicity studies. Microscopy techniques showed proteins self-assemble to form VLPs authentic to native viruses. The inclusion of the glycolipid adjuvant, α-galactosylceramide (α-GalCer) in the vaccine formulation led to high levels of natural killer T (NKT) cell stimulation in vitro, and strong antibody and memory CD8+ T cell responses in vivo, demonstrated with SARS-CoV-2, hepatitis C virus (HCV) and DEN VLPs. This study shows our unique vaccine formulation presents a promising, and much needed, new vaccine platform in the fight against infections caused by enveloped RNA viruses.
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Affiliation(s)
- Simon Collett
- School of Science, College of Science, Engineering and Health, RMIT University, Melbourne, VIC, Australia
| | - Linda Earnest
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC, Australia
| | - Julio Carrera Montoya
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC, Australia
| | - Melissa A. Edeling
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC, Australia
| | - Ashley Yap
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC, Australia
| | - Chinn Yi Wong
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC, Australia
| | - Dale Christiansen
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC, Australia
| | - Jason Roberts
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Department of Infectious Diseases, The University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Jamie Mumford
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | | | | | | | - Joon Keit Loi
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC, Australia
| | - Cameron Simmons
- Institute of Vector-Borne Disease, Monash University, Clayton, VIC, Australia
| | - Shivali A. Gulab
- Avalia Immunotherapies Limited, Wellington, New Zealand
- Vaccine Alliance Aotearoa New Zealand, Wellington, New Zealand
| | - Jason M. Mackenzie
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC, Australia
| | - Aaron Elbourne
- School of Science, College of Science, Engineering and Health, RMIT University, Melbourne, VIC, Australia
| | - Paul A. Ramsland
- School of Science, College of Science, Engineering and Health, RMIT University, Melbourne, VIC, Australia
- Department of Surgery Austin Health, University of Melbourne, Heidelberg, VIC, Australia
- Department of Immunology, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Garth Cameron
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC, Australia
| | - Dhiraj Hans
- Research, Innovation and Commercialisation, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, Australia
| | - Dale I. Godfrey
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC, Australia
| | - Joseph Torresi
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC, Australia
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Sijmons D, Guy AJ, Walduck AK, Ramsland PA. Helicobacter pylori and the Role of Lipopolysaccharide Variation in Innate Immune Evasion. Front Immunol 2022; 13:868225. [PMID: 35634347 PMCID: PMC9136243 DOI: 10.3389/fimmu.2022.868225] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 04/04/2022] [Indexed: 11/30/2022] Open
Abstract
Helicobacter pylori is an important human pathogen that infects half the human population and can lead to significant clinical outcomes such as acute and chronic gastritis, duodenal ulcer, and gastric adenocarcinoma. To establish infection, H. pylori employs several mechanisms to overcome the innate and adaptive immune systems. H. pylori can modulate interleukin (IL) secretion and innate immune cell function by the action of several virulence factors such as VacA, CagA and the type IV secretion system. Additionally, H. pylori can modulate local dendritic cells (DC) negatively impacting the function of these cells, reducing the secretion of immune signaling molecules, and influencing the differentiation of CD4+ T helper cells causing a bias to Th1 type cells. Furthermore, the lipopolysaccharide (LPS) of H. pylori displays a high degree of phase variation and contains human blood group carbohydrate determinants such as the Lewis system antigens, which are proposed to be involved in molecular mimicry of the host. Lastly, the H. pylori group of outer membrane proteins such as BabA play an important role in attachment and interaction with host Lewis and other carbohydrate antigens. This review examines the various mechanisms that H. pylori utilises to evade the innate immune system as well as discussing how the structure of the H. pylori LPS plays a role in immune evasion.
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Affiliation(s)
- Daniel Sijmons
- School of Science, RMIT University, Melbourne, VIC, Australia
| | - Andrew J. Guy
- School of Science, RMIT University, Melbourne, VIC, Australia
- ZiP Diagnostics, Collingwood, VIC, Australia
| | - Anna K. Walduck
- School of Science, RMIT University, Melbourne, VIC, Australia
| | - Paul A. Ramsland
- School of Science, RMIT University, Melbourne, VIC, Australia
- Department of Immunology, Monash University, Melbourne, VIC, Australia
- Department of Surgery, Austin Health, University of Melbourne, Heidelberg, VIC, Australia
- *Correspondence: Paul A. Ramsland,
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Irani V, Soliman C, Raftis MA, Guy AJ, Elbourne A, Ramsland PA. Expression of monoclonal antibodies for functional and structural studies. Methods in Microbiology 2022. [DOI: 10.1016/bs.mim.2022.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Coff L, Abrahams JL, Collett S, Power C, Nowak BF, Kolarich D, Bott NJ, Ramsland PA. Profiling the glycome of Cardicola forsteri, a blood fluke parasitic to bluefin tuna. Int J Parasitol 2021; 52:1-12. [PMID: 34391752 DOI: 10.1016/j.ijpara.2021.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 06/16/2021] [Accepted: 06/17/2021] [Indexed: 11/05/2022]
Abstract
Infections by blood flukes (Cardicola spp.) are considered the most significant health issue for ranched bluefin tuna, a major aquaculture industry in Japan and Australia. The host-parasite interfaces of trematodes, namely their teguments, are particularly rich in carbohydrates, which function both in evasion and modulation of the host immune system, while some are primary antigenic targets. In this study, histochemistry and mass spectrometry techniques were used to profile the glycans of Cardicola forsteri. Fluorescent lectin staining of adult flukes indicates the presence of oligomannose (Concanavalin A-reactive) and fucosylated (Pisum sativum agglutinin-reactive) N-glycans. Additionally, reactivity of succinylated wheat germ agglutinin (s-WGA) was localised to several internal organs of the digestive and monoecious reproductive systems. Glycan structures were further investigated with tandem mass spectrometry, which revealed structures indicated by lectin reactivity. While O-glycans from these adult specimens were not detectable by mass spectrometry, several oligomannose, paucimannosidic, and complex-type N-glycans were identified, including some carrying hexuronic acid and many carrying core xylose. This is, to our knowledge, the first glycomic characterisation of a marine platyhelminth, with broader implications for research into other trematodes.
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Affiliation(s)
- Lachlan Coff
- School of Science, STEM College, RMIT University, Bundoora, VIC 3083, Australia
| | - Jodie L Abrahams
- Institute for Glycomics, Griffith University, Southport, QLD 4215, Australia
| | - Simon Collett
- School of Science, STEM College, RMIT University, Bundoora, VIC 3083, Australia
| | - Cecilia Power
- School of Science, STEM College, RMIT University, Bundoora, VIC 3083, Australia
| | - Barbara F Nowak
- School of Science, STEM College, RMIT University, Bundoora, VIC 3083, Australia; Institute for Marine and Antarctic Studies, University of Tasmania, Locked Bag 1370, Launceston, TAS 7250, Australia
| | - Daniel Kolarich
- Institute for Glycomics, Griffith University, Southport, QLD 4215, Australia; ARC Centre of Excellence for Nanoscale BioPhotonics, Griffith University, Southport, QLD 4215, Australia
| | - Nathan J Bott
- School of Science, STEM College, RMIT University, Bundoora, VIC 3083, Australia.
| | - Paul A Ramsland
- School of Science, STEM College, RMIT University, Bundoora, VIC 3083, Australia; Department of Immunology, Monash University, Melbourne, VIC 3004, Australia; Department of Surgery, Austin Health, University of Melbourne, Heidelberg, VIC 3084, Australia.
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Kamath SD, Scheiblhofer S, Johnson CM, Machado Y, McLean T, Taki AC, Ramsland PA, Iyer S, Joubert I, Hofer H, Wallner M, Thalhamer J, Rolland J, O’Hehir R, Briza P, Ferreira F, Weiss R, Lopata AL. Effect of structural stability on endolysosomal degradation and T-cell reactivity of major shrimp allergen tropomyosin. Allergy 2020; 75:2909-2919. [PMID: 32436591 PMCID: PMC7687109 DOI: 10.1111/all.14410] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/21/2020] [Accepted: 04/30/2020] [Indexed: 12/17/2022]
Abstract
BACKGROUND Tropomyosins are highly conserved proteins, an attribute that forms the molecular basis for their IgE antibody cross-reactivity. Despite sequence similarities, their allergenicity varies greatly between ingested and inhaled invertebrate sources. In this study, we investigated the relationship between the structural stability of different tropomyosins, their endolysosomal degradation patterns, and T-cell reactivity. METHODS We investigated the differences between four tropomyosins-the major shrimp allergen Pen m 1 and the minor allergens Der p 10 (dust mite), Bla g 7 (cockroach), and Ani s 3 (fish parasite)-in terms of IgE binding, structural stability, endolysosomal degradation and subsequent peptide generation, and T-cell cross-reactivity in a BALB/c murine model. RESULTS Tropomyosins displayed different melting temperatures, which did not correlate with amino acid sequence similarities. Endolysosomal degradation experiments demonstrated differential proteolytic digestion, as a function of thermal stability, generating different peptide repertoires. Pen m 1 (Tm 42°C) and Der p 10 (Tm 44°C) elicited similar patterns of endolysosomal degradation, but not Bla g 7 (Tm 63°C) or Ani s 3 (Tm 33°C). Pen m 1-specific T-cell clones, with specificity for regions highly conserved in all four tropomyosins, proliferated weakly to Der p 10, but did not proliferate to Bla g 7 and Ani s 3, indicating lack of T-cell epitope cross-reactivity. CONCLUSIONS Tropomyosin T-cell cross-reactivity, unlike IgE cross-reactivity, is dependent on structural stability rather than amino acid sequence similarity. These findings contribute to our understanding of cross-sensitization among different invertebrates and design of suitable T-cell peptide-based immunotherapies for shrimp and related allergies.
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Affiliation(s)
- Sandip D. Kamath
- Australian Institute of Tropical Health and MedicineJames Cook UniversityTownsvilleQldAustralia
| | | | | | - Yoan Machado
- Department of BiosciencesUniversity of SalzburgSalzburgAustria
- Centre of Blood ResearchUniversity of British ColumbiaVancouverBCCanada
| | - Thomas McLean
- School of ScienceRMIT UniversityMelbourneVic.Australia
| | - Aya C. Taki
- Faculty of Veterinary and Agricultural SciencesUniversity of MelbourneMelbourneVic.Australia
| | | | - Swati Iyer
- Department of PhysiologyUniversity of MelbourneMelbourneVic.Australia
| | | | - Heidi Hofer
- Department of BiosciencesUniversity of SalzburgSalzburgAustria
| | - Michael Wallner
- Department of BiosciencesUniversity of SalzburgSalzburgAustria
| | - Josef Thalhamer
- Department of BiosciencesUniversity of SalzburgSalzburgAustria
| | - Jennifer Rolland
- Department of Immunology and PathologyCentral Clinical SchoolMonash UniversityMelbourneVic.Australia
- Department of Allergy, Immunology and Respiratory MedicineCentral Clinical SchoolMonash UniversityMelbourneVic.Australia
- Alfred HospitalMelbourneVic.Australia
| | - Robyn O’Hehir
- Department of Immunology and PathologyCentral Clinical SchoolMonash UniversityMelbourneVic.Australia
- Department of Allergy, Immunology and Respiratory MedicineCentral Clinical SchoolMonash UniversityMelbourneVic.Australia
- Alfred HospitalMelbourneVic.Australia
| | - Peter Briza
- Department of BiosciencesUniversity of SalzburgSalzburgAustria
| | - Fatima Ferreira
- Department of BiosciencesUniversity of SalzburgSalzburgAustria
| | - Richard Weiss
- Department of BiosciencesUniversity of SalzburgSalzburgAustria
| | - Andreas L. Lopata
- Australian Institute of Tropical Health and MedicineJames Cook UniversityTownsvilleQldAustralia
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Affiliation(s)
- Sony Malhotra
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, University of London, Malet Street, London, WC1E 7HX, United Kingdom.
| | - Paul A Ramsland
- Biosciences & Food Technology, School of Science, College of Science, Engineering & Health, RMIT University, Plenty Road, Bundoora, Melbourne, VIC 3083, Australia.
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10
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Abstract
Background Glycans are complex sugar chains, crucial to many biological processes. By participating in binding interactions with proteins, glycans often play key roles in host–pathogen interactions. The specificities of glycan-binding proteins, such as lectins and antibodies, are governed by motifs within larger glycan structures, and improved characterisations of these determinants would aid research into human diseases. Identification of motifs has previously been approached as a frequent subtree mining problem, and we extend these approaches with a glycan notation that allows recognition of terminal motifs. Results In this work, we customised a frequent subtree mining approach by altering the glycan notation to include information on terminal connections. This allows specific identification of terminal residues as potential motifs, better capturing the complexity of glycan-binding interactions. We achieved this by including additional nodes in a graph representation of the glycan structure to indicate the presence or absence of a linkage at particular backbone carbon positions. Combining this frequent subtree mining approach with a state-of-the-art feature selection algorithm termed minimum-redundancy, maximum-relevance (mRMR), we have generated a classification pipeline that is trained on data from a glycan microarray. When applied to a set of commonly used lectins, the identified motifs were consistent with known binding determinants. Furthermore, logistic regression classifiers trained using these motifs performed well across most lectins examined, with a median AUC value of 0.89. Conclusions We present here a new subtree mining approach for the classification of glycan binding and identification of potential binding motifs. The Carbohydrate Classification Accounting for Restricted Linkages (CCARL) method will assist in the interpretation of glycan microarray experiments and will aid in the discovery of novel binding motifs for further experimental characterisation.
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Affiliation(s)
- Lachlan Coff
- School of Science, College of Science, Engineering and Health, RMIT University, 3000, Melbourne, Australia
| | - Jeffrey Chan
- School of Science, College of Science, Engineering and Health, RMIT University, 3000, Melbourne, Australia
| | - Paul A Ramsland
- School of Science, College of Science, Engineering and Health, RMIT University, 3000, Melbourne, Australia.,Department of Immunology, Monash University, 3004, Melbourne, Australia.,Department of Surgery Austin Health, University of Melbourne, 3084, Heidelberg, Australia
| | - Andrew J Guy
- School of Science, College of Science, Engineering and Health, RMIT University, 3000, Melbourne, Australia.
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Soliman C, Chua JX, Vankemmelbeke M, McIntosh RS, Guy AJ, Spendlove I, Durrant LG, Ramsland PA. The terminal sialic acid of stage-specific embryonic antigen-4 has a crucial role in binding to a cancer-targeting antibody. J Biol Chem 2020. [DOI: 10.1016/s0021-9258(17)49911-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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12
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Soliman C, Chua JX, Vankemmelbeke M, McIntosh RS, Guy AJ, Spendlove I, Durrant LG, Ramsland PA. The terminal sialic acid of stage-specific embryonic antigen-4 has a crucial role in binding to a cancer-targeting antibody. J Biol Chem 2019; 295:1009-1020. [PMID: 31831622 DOI: 10.1074/jbc.ra119.011518] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 12/05/2019] [Indexed: 01/06/2023] Open
Abstract
Cancer remains a leading cause of morbidity and mortality worldwide, requiring ongoing development of targeted therapeutics such as monoclonal antibodies. Carbohydrates on embryonic cells are often highly expressed in cancer and are therefore attractive targets for antibodies. Stage-specific embryonic antigen-4 (SSEA-4) is one such glycolipid target expressed in many cancers, including breast and ovarian carcinomas. Here, we defined the structural basis for recognition of SSEA-4 by a novel monospecific chimeric antibody (ch28/11). Five X-ray structures of ch28/11 Fab complexes with the SSEA-4 glycan headgroup, determined at 1.5-2.7 Å resolutions, displayed highly similar three-dimensional structures indicating a stable binding mode. The structures also revealed that by adopting a horseshoe-shaped conformation in a deep groove, the glycan headgroup likely sits flat against the membrane to allow the antibody to interact with SSEA-4 on cancer cells. Moreover, we found that the terminal sialic acid of SSEA-4 plays a dominant role in dictating the exquisite specificity of the ch28/11 antibody. This observation was further supported by molecular dynamics simulations of the ch28/11-glycan complex, which show that SSEA-4 is stabilized by its terminal sialic acid, unlike SSEA-3, which lacks this sialic acid modification. These high-resolution views of how a glycolipid interacts with an antibody may help to advance a new class of cancer-targeting immunotherapy.
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Affiliation(s)
- Caroline Soliman
- School of Science, RMIT University, Melbourne, Victoria 3083, Australia
| | - Jia Xin Chua
- Academic Department of Clinical Oncology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, City Hospital Campus, Nottingham NG7 2RD, United Kingdom.,Scancell Ltd., Academic Department of Clinical Oncology, University of Nottingham, City Hospital Campus, Nottingham NG7 2RD, United Kingdom
| | - Mireille Vankemmelbeke
- Academic Department of Clinical Oncology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, City Hospital Campus, Nottingham NG7 2RD, United Kingdom.,Scancell Ltd., Academic Department of Clinical Oncology, University of Nottingham, City Hospital Campus, Nottingham NG7 2RD, United Kingdom
| | - Richard S McIntosh
- Academic Department of Clinical Oncology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, City Hospital Campus, Nottingham NG7 2RD, United Kingdom
| | - Andrew J Guy
- School of Science, RMIT University, Melbourne, Victoria 3083, Australia
| | - Ian Spendlove
- Academic Department of Clinical Oncology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, City Hospital Campus, Nottingham NG7 2RD, United Kingdom
| | - Lindy G Durrant
- Academic Department of Clinical Oncology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, City Hospital Campus, Nottingham NG7 2RD, United Kingdom.,Scancell Ltd., Academic Department of Clinical Oncology, University of Nottingham, City Hospital Campus, Nottingham NG7 2RD, United Kingdom
| | - Paul A Ramsland
- School of Science, RMIT University, Melbourne, Victoria 3083, Australia .,Department of Immunology, Central Clinical School, Monash University, Melbourne, Victoria 3800, Australia.,Department of Surgery Austin Health, University of Melbourne, Heidelberg, Victoria 3084, Australia
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13
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Guy AJ, Irani V, Richards JS, Ramsland PA. BioStructMap: a Python tool for integration of protein structure and sequence-based features. Bioinformatics 2019; 34:3942-3944. [PMID: 29931276 PMCID: PMC6223362 DOI: 10.1093/bioinformatics/bty474] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 06/18/2018] [Indexed: 12/22/2022] Open
Abstract
Summary A sliding window analysis over a protein or genomic sequence is commonly performed, and we present a Python tool, BioStructMap, that extends this concept to three-dimensional (3D) space, allowing the application of a 3D sliding window analysis over a protein structure. BioStructMap is easily extensible, allowing the user to apply custom functions to spatially aggregated data. BioStructMap also allows mapping of underlying genomic sequences to protein structures, allowing the user to perform genetic-based analysis over spatially linked codons-this has applications when selection pressures arise at the level of protein structure. Availability and implementation The Python BioStructMap package is available at https://github.com/andrewguy/biostructmap and released under the MIT License. An online server implementing standard functionality is available at https://biostructmap.burnet.edu.au. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Andrew J Guy
- Life Sciences, Burnet Institute, Melbourne, VIC, Australia.,Department of Immunology, Monash University, Melbourne, VIC, Australia
| | - Vashti Irani
- Life Sciences, Burnet Institute, Melbourne, VIC, Australia.,Department of Medicine, University of Melbourne, Melbourne, VIC, Australia
| | - Jack S Richards
- Life Sciences, Burnet Institute, Melbourne, VIC, Australia.,Department of Medicine, University of Melbourne, Melbourne, VIC, Australia.,Department of Infectious Diseases, Monash University, Melbourne, VIC, Australia.,Victorian Infectious Diseases Service, Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - Paul A Ramsland
- Life Sciences, Burnet Institute, Melbourne, VIC, Australia.,Department of Immunology, Monash University, Melbourne, VIC, Australia.,Department of Surgery, Austin Health, University of Melbourne, Heidelberg, VIC, Australia.,School of Science, RMIT University, Bundoora, VIC, Australia
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14
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Soliman C, Eastwood S, Truong VK, Ramsland PA, Elbourne A. The membrane effects of melittin on gastric and colorectal cancer. PLoS One 2019; 14:e0224028. [PMID: 31622415 PMCID: PMC6797111 DOI: 10.1371/journal.pone.0224028] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 10/03/2019] [Indexed: 01/30/2023] Open
Abstract
The cytotoxic effects of melittin, a bee-venom peptide, have been widely studied towards cancer cells. Typically, these studies have examined the effect of melittin over extended-time courses (6-24 hours), meaning that immediate cellular interactions have been overlooked. In this work, we demonstrate the rapid effects of melittin on both gastric and colorectal cancer, specifically AGS, COLO205 and HCT-15 cell lines, over a period of 15 minutes. Melittin exhibited a dose dependent effect at 4 hours of treatment, with complete cellular death occurring at the highest dose of 20 μg/mL. Interestingly, when observed at shorter time points, melittin induced cellular changes within seconds; membrane damage was observed as swelling, breakage or blebbing. High-resolution imaging revealed treated cells to be compromised, showing clear change in cellular morphology. After 1 minute of melittin treatment, membrane changes were observed, and intracellular material could be seen expelled from the cells. Overall, these results enhance our understanding of the fast acting anti-cancer effects of melittin.
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Affiliation(s)
- Caroline Soliman
- School of Science, RMIT University, Bundoora West Campusm Bundoora, Victoria, Australia
| | - Sarah Eastwood
- School of Science, RMIT University, Bundoora West Campusm Bundoora, Victoria, Australia
| | - Vi Khanh Truong
- School of Science, RMIT University, Bundoora West Campusm Bundoora, Victoria, Australia
- Nanobiotechnology Laboratory, RMIT University, Melbourne City Campus, Melbourne, Victoria, Australia
| | - Paul A. Ramsland
- School of Science, RMIT University, Bundoora West Campusm Bundoora, Victoria, Australia
- Department of Immunology, Central Clinical School (Monash University), Alfred Medical Research and Education Precinct, Melbourne, Victoria, Australia
- Department of Surgery Austin Health (University of Melbourne), Austin Health, Heidelberg, Victoria, Australia
| | - Aaron Elbourne
- School of Science, RMIT University, Bundoora West Campusm Bundoora, Victoria, Australia
- Nanobiotechnology Laboratory, RMIT University, Melbourne City Campus, Melbourne, Victoria, Australia
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15
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Collett S, Torresi J, Earnest-Silveira L, Christiansen D, Elbourne A, Ramsland PA. Probing and pressing surfaces of hepatitis C virus-like particles. J Colloid Interface Sci 2019; 545:259-268. [DOI: 10.1016/j.jcis.2019.03.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 03/07/2019] [Accepted: 03/09/2019] [Indexed: 02/09/2023]
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16
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Soliman C, Walduck AK, Yuriev E, Richards JS, Cywes‐Bentley C, Pier GB, Ramsland PA. Antibody Recognition of a Polysaccharide Common to many Microbes and Biofilms. FASEB J 2019. [DOI: 10.1096/fasebj.2019.33.1_supplement.351.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Caroline Soliman
- School of ScienceRoyal Melbourne Institute of Technology UniversityBundooraAustralia
| | - Anna K. Walduck
- School of ScienceRoyal Melbourne Institute of Technology UniversityBundooraAustralia
| | - Elizabeth Yuriev
- Medicinal ChemistryMonash Institute of Pharmaceutical Sciences, Monash UniversityParkvilleAustralia
| | | | - Colette Cywes‐Bentley
- Division of Infectious Diseases, Department of MedicineBrigham and Women's Hospital/Harvard Medical SchoolBostonMA
| | - Gerald B. Pier
- Division of Infectious Diseases, Department of MedicineBrigham and Women's Hospital/Harvard Medical SchoolBostonMA
| | - Paul A. Ramsland
- School of ScienceRoyal Melbourne Institute of Technology UniversityBundooraAustralia
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17
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Sanders PR, Dickerman BK, Charnaud SC, Ramsland PA, Crabb BS, Gilson PR. The N-terminus of EXP2 forms the membrane-associated pore of the protein exporting translocon PTEX in Plasmodium falciparum. J Biochem 2018; 165:239-248. [DOI: 10.1093/jb/mvy099] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 11/20/2018] [Indexed: 12/12/2022] Open
Affiliation(s)
| | | | | | - Paul A Ramsland
- Burnet Institute, Melbourne, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
- RMIT University, Bundoora, VIC, Australia
- Monash University, Melbourne, VIC, Australia
| | - Brendan S Crabb
- Burnet Institute, Melbourne, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
- Monash University, Melbourne, VIC, Australia
| | - Paul R Gilson
- Burnet Institute, Melbourne, VIC, Australia
- Monash University, Melbourne, VIC, Australia
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18
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Dingjan T, Gillon É, Imberty A, Pérez S, Titz A, Ramsland PA, Yuriev E. Virtual Screening Against Carbohydrate-Binding Proteins: Evaluation and Application to Bacterial Burkholderia ambifaria Lectin. J Chem Inf Model 2018; 58:1976-1989. [DOI: 10.1021/acs.jcim.8b00185] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Tamir Dingjan
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Émilie Gillon
- University Grenoble Alpes, CNRS, CERMAV, 38000 Grenoble, France
| | - Anne Imberty
- University Grenoble Alpes, CNRS, CERMAV, 38000 Grenoble, France
| | - Serge Pérez
- University Grenoble Alpes, CNRS, DPM, 38000 Grenoble, France
| | - Alexander Titz
- Chemical Biology of Carbohydrates, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, D-66123 Saarbrücken, Germany
- Deutsches Zentrum für Infektionsforschung (DZIF), Standort Hannover-Braunschweig, Germany
- Department of Pharmacy, Saarland University, D-66123 Saarbrücken, Germany
| | - Paul A. Ramsland
- School of Science, RMIT University, Bundoora, Victoria 3083, Australia
- Department of Surgery Austin Health, University of Melbourne, Heidelberg, Victoria 3084, Australia
- Department of Immunology, Monash University, Alfred Medical Research and Education Precinct, Melbourne, Victoria 3004, Australia
- Burnet Institute, Melbourne, Victoria 3004, Australia
| | - Elizabeth Yuriev
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
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19
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Guy AJ, Irani V, Richards JS, Ramsland PA. Structural patterns of selection and diversity for Plasmodium vivax antigens DBP and AMA1. Malar J 2018; 17:183. [PMID: 29720179 PMCID: PMC5930944 DOI: 10.1186/s12936-018-2324-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 04/18/2018] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Plasmodium vivax is a significant contributor to the global malaria burden, and a vaccine targeting vivax malaria is urgently needed. An understanding of the targets of functional immune responses during the course of natural infection will aid in the development of a vaccine. Antibodies play a key role in this process, with responses against particular epitopes leading to immune selection pressure on these epitopes. A number of techniques exist to estimate levels of immune selection pressure on particular epitopes, with a sliding window analysis often used to determine particular regions likely to be under immune pressure. However, such analysis neglects protein three-dimensional structural information. With this in mind, a newly developed tool, BioStructMap, was applied to two key antigens from Plasmodium vivax: PvAMA1 and PvDBP Region II. This tool incorporates structural information into tests of selection pressure. RESULTS Sequences from a number of populations were analysed, examining spatially-derived nucleotide diversity and Tajima's D over protein structures for PvAMA1 and PvDBP. Structural patterns of nucleotide diversity were similar across all populations examined, with Domain I of PvAMA1 having the highest nucleotide diversity and displaying significant signatures of immune selection pressure (Tajima's D > 0). Nucleotide diversity for PvDBP was highest bordering the dimerization and DARC-binding interface, although there was less evidence of immune selection pressure on PvDBP compared with PvAMA1. This study supports previous work that has identified Domain I as the main target of immune-mediated selection pressure for PvAMA1, and also supports studies that have identified functional epitopes within PvDBP Region II. CONCLUSIONS The BioStructMap tool was applied to leading vaccine candidates from P. vivax, to examine structural patterns of selection and diversity across a number of geographic populations. There were striking similarities in structural patterns of diversity across multiple populations. Furthermore, whilst regions of high diversity tended to surround conserved binding interfaces, a number of protein regions with very low diversity were also identified, and these may be useful targets for further vaccine development, given previous evidence of functional antibody responses against these regions.
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Affiliation(s)
- Andrew J Guy
- Life Sciences, Burnet Institute, 85 Commercial Road, Melbourne, VIC, 3004, Australia.,Department of Immunology, Monash University, Melbourne, Australia
| | - Vashti Irani
- Life Sciences, Burnet Institute, 85 Commercial Road, Melbourne, VIC, 3004, Australia.,Department of Medicine, University of Melbourne, Melbourne, Australia
| | - Jack S Richards
- Life Sciences, Burnet Institute, 85 Commercial Road, Melbourne, VIC, 3004, Australia. .,Department of Medicine, University of Melbourne, Melbourne, Australia. .,Department of Infectious Diseases, Monash University, Melbourne, Australia. .,Victorian Infectious Diseases Service, Royal Melbourne Hospital, Melbourne, Australia.
| | - Paul A Ramsland
- Life Sciences, Burnet Institute, 85 Commercial Road, Melbourne, VIC, 3004, Australia. .,Department of Immunology, Monash University, Melbourne, Australia. .,School of Science, RMIT University, Plenty Road, Bundoora, VIC, 3083, Australia. .,Department of Surgery Austin Health, University of Melbourne, Heidelberg, Australia.
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20
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Soliman C, Walduck AK, Yuriev E, Richards JS, Cywes-Bentley C, Pier GB, Ramsland PA. Structural basis for antibody targeting of the broadly expressed microbial polysaccharide poly- N-acetylglucosamine. J Biol Chem 2018; 293:5079-5089. [PMID: 29449370 DOI: 10.1074/jbc.ra117.001170] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 02/08/2018] [Indexed: 01/19/2023] Open
Abstract
In response to the widespread emergence of antibiotic-resistant microbes, new therapeutic agents are required for many human pathogens. A non-mammalian polysaccharide, poly-N-acetyl-d-glucosamine (PNAG), is produced by bacteria, fungi, and protozoan parasites. Antibodies that bind to PNAG and its deacetylated form (dPNAG) exhibit promising in vitro and in vivo activities against many microbes. A human IgG1 mAb (F598) that binds both PNAG and dPNAG has opsonic and protective activities against multiple microbial pathogens and is undergoing preclinical and clinical assessments as a broad-spectrum antimicrobial therapy. Here, to understand how F598 targets PNAG, we determined crystal structures of the unliganded F598 antigen-binding fragment (Fab) and its complexes with N-acetyl-d-glucosamine (GlcNAc) and a PNAG oligosaccharide. We found that F598 recognizes PNAG through a large groove-shaped binding site that traverses the entire light- and heavy-chain interface and accommodates at least five GlcNAc residues. The Fab-GlcNAc complex revealed a deep binding pocket in which the monosaccharide and a core GlcNAc of the oligosaccharide were almost identically positioned, suggesting an anchored binding mechanism of PNAG by F598. The Fab used in our structural analyses retained binding to PNAG on the surface of an antibiotic-resistant, biofilm-forming strain of Staphylococcus aureus Additionally, a model of intact F598 binding to two pentasaccharide epitopes indicates that the Fab arms can span at least 40 GlcNAc residues on an extended PNAG chain. Our findings unravel the structural basis for F598 binding to PNAG on microbial surfaces and biofilms.
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Affiliation(s)
- Caroline Soliman
- From the School of Science, Royal Melbourne Institute of Technology (RMIT) University, Bundoora, Victoria 3083, Australia
| | - Anna K Walduck
- From the School of Science, Royal Melbourne Institute of Technology (RMIT) University, Bundoora, Victoria 3083, Australia
| | - Elizabeth Yuriev
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Jack S Richards
- Disease Elimination Program, Burnet Institute, Melbourne, Victoria 3004, Australia.,Victorian Infectious Diseases Service, Royal Melbourne Hospital, Parkville, Victoria 3052, Australia.,Department of Medicine, University of Melbourne, Parkville, Victoria 3052, Australia.,Department of Infectious Diseases, Central Clinical School, Alfred Hospital, Melbourne, Victoria 3004, Australia
| | - Colette Cywes-Bentley
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital/Harvard Medical School, Boston, Massachusetts 02115
| | - Gerald B Pier
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital/Harvard Medical School, Boston, Massachusetts 02115
| | - Paul A Ramsland
- From the School of Science, Royal Melbourne Institute of Technology (RMIT) University, Bundoora, Victoria 3083, Australia, .,Disease Elimination Program, Burnet Institute, Melbourne, Victoria 3004, Australia.,Department of Immunology, Central Clinical School, Monash University, Victoria 3004, Melbourne, Australia, and.,Department of Surgery Austin Health, University of Melbourne, Heidelberg, Victoria 3084
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21
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Dingjan T, Imberty A, Pérez S, Yuriev E, Ramsland PA. Molecular Simulations of Carbohydrates with a Fucose-Binding Burkholderia ambifaria Lectin Suggest Modulation by Surface Residues Outside the Fucose-Binding Pocket. Front Pharmacol 2017; 8:393. [PMID: 28680402 PMCID: PMC5478714 DOI: 10.3389/fphar.2017.00393] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Accepted: 06/06/2017] [Indexed: 12/22/2022] Open
Abstract
Burkholderia ambifaria is an opportunistic respiratory pathogen belonging to the Burkholderia cepacia complex, a collection of species responsible for the rapidly fatal cepacia syndrome in cystic fibrosis patients. A fucose-binding lectin identified in the B. ambifaria genome, BambL, is able to adhere to lung tissue, and may play a role in respiratory infection. X-ray crystallography has revealed the bound complex structures for four fucosylated human blood group epitopes (blood group B, H type 1, H type 2, and Lex determinants). The present study employed computational approaches, including docking and molecular dynamics (MD), to extend the structural analysis of BambL-oligosaccharide complexes to include four additional blood group saccharides (A, Lea, Leb, and Ley) and a library of blood-group-related carbohydrates. Carbohydrate recognition is dominated by interactions with fucose via a hydrogen-bonding network involving Arg15, Glu26, Ala38, and Trp79 and a stacking interaction with Trp74. Additional hydrogen bonds to non-fucose residues are formed with Asp30, Tyr35, Thr36, and Trp74. BambL recognition is dominated by interactions with fucose, but also features interactions with other parts of the ligands that may modulate specificity or affinity. The detailed computational characterization of the BambL carbohydrate-binding site provides guidelines for the future design of lectin inhibitors.
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Affiliation(s)
- Tamir Dingjan
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash UniversityMelbourne, VIC, Australia
| | - Anne Imberty
- Centre de Recherches sur les Macromolécules Végétales, Centre National de la Recherche Scientifique UPR5301, Université Grenoble AlpesGrenoble, France
| | - Serge Pérez
- Département de Pharmacochimie Moléculaire, Centre National de la Recherche Scientifique, UMR5063, Université Grenoble AlpesGrenoble, France
| | - Elizabeth Yuriev
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash UniversityMelbourne, VIC, Australia
| | - Paul A Ramsland
- School of Science, RMIT UniversityMelbourne, VIC, Australia.,Department of Surgery Austin Health, University of MelbourneMelbourne, VIC, Australia.,Department of Immunology, Central Clinical School, Monash UniversityMelbourne, VIC, Australia.,Burnet InstituteMelbourne, VIC, Australia
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22
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Molloy CP, Yao Y, Kammoun H, Bonnard T, Hoefer T, Alt K, Tovar-Lopez F, Rosengarten G, Ramsland PA, van der Meer AD, van den Berg A, Murphy AJ, Hagemeyer CE, Peter K, Westein E. Shear-sensitive nanocapsule drug release for site-specific inhibition of occlusive thrombus formation. J Thromb Haemost 2017; 15:972-982. [PMID: 28267256 DOI: 10.1111/jth.13666] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Indexed: 11/29/2022]
Abstract
Essentials Vessel stenosis due to large thrombus formation increases local shear 1-2 orders of magnitude. High shear at stenotic sites was exploited to trigger eptifibatide release from nanocapsules. Local delivery of eptifibatide prevented vessel occlusion without increased tail bleeding times. Local nanocapsule delivery of eptifibatide may be safer than systemic antiplatelet therapies. SUMMARY Background Myocardial infarction and stroke remain the leading causes of mortality and morbidity. The major limitation of current antiplatelet therapy is that the effective concentrations are limited because of bleeding complications. Targeted delivery of antiplatelet drug to sites of thrombosis would overcome these limitations. Objectives Here, we have exploited a key biomechanical feature specific to thrombosis, i.e. significantly increased blood shear stress resulting from a reduction in the lumen of the vessel, to achieve site-directed delivery of the clinically used antiplatelet agent eptifibatide by using shear-sensitive phosphatidylcholine (PC)-based nanocapsules. Methods PC-based nanocapsules (2.8 × 1012 ) with high-dose encapsulated eptifibatide were introduced into microfluidic blood perfusion assays and into in vivo models of thrombosis and tail bleeding. Results Shear-triggered nanocapsule delivery of eptifibatide inhibited in vitro thrombus formation selectively under stenotic and high shear flow conditions above a shear rate of 1000 s-1 while leaving thrombus formation under physiologic shear rates unaffected. Thrombosis was effectively prevented in in vivo models of vessel wall damage. Importantly, mice infused with shear-sensitive antiplatelet nanocapsules did not show prolonged bleeding times. Conclusions Targeted delivery of eptifibatide by shear-sensitive nanocapsules offers site-specific antiplatelet potential, and may form a basis for developing more potent and safer antiplatelet drugs.
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Affiliation(s)
- C P Molloy
- Atherothrombosis and Vascular Biology, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Y Yao
- Atherothrombosis and Vascular Biology, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - H Kammoun
- Haematopoiesis and Leukocyte Biology, Baker Heart & Diabetes Institute, Melbourne, Victoria, Australia
| | - T Bonnard
- Nano Biotechnology Laboratory, Australian Centre for Blood Diseases, Monash University, Melbourne, Victoria, Australia
| | - T Hoefer
- Atherothrombosis and Vascular Biology, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - K Alt
- Nano Biotechnology Laboratory, Australian Centre for Blood Diseases, Monash University, Melbourne, Victoria, Australia
| | - F Tovar-Lopez
- School of Engineering, RMIT University, Melbourne, Victoria, Australia
| | - G Rosengarten
- School of Engineering, RMIT University, Melbourne, Victoria, Australia
| | - P A Ramsland
- School of Science, RMIT University, Bundoora, Victoria, Australia
- Centre for Biomedical Research, Burnet Institute, Melbourne, Victoria, Australia
- Department of Immunology, Monash University, Melbourne, Victoria, Australia
- Department of Surgery at Austin Health, University of Melbourne, Heidelberg, Victoria, Australia
| | - A D van der Meer
- MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, Enschede, the Netherlands
| | - A van den Berg
- MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, Enschede, the Netherlands
| | - A J Murphy
- Haematopoiesis and Leukocyte Biology, Baker Heart & Diabetes Institute, Melbourne, Victoria, Australia
| | - C E Hagemeyer
- Nano Biotechnology Laboratory, Australian Centre for Blood Diseases, Monash University, Melbourne, Victoria, Australia
| | - K Peter
- Atherothrombosis and Vascular Biology, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - E Westein
- Atherothrombosis and Vascular Biology, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
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23
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Vuckovic S, Vandyke K, Rickards DA, McCauley Winter P, Brown SHJ, Mitchell TW, Liu J, Lu J, Askenase PW, Yuriev E, Capuano B, Ramsland PA, Hill GR, Zannettino ACW, Hutchinson AT. The cationic small molecule GW4869 is cytotoxic to high phosphatidylserine-expressing myeloma cells. Br J Haematol 2017; 177:423-440. [PMID: 28211573 DOI: 10.1111/bjh.14561] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Accepted: 12/01/2016] [Indexed: 12/19/2022]
Abstract
We have discovered that a small cationic molecule, GW4869, is cytotoxic to a subset of myeloma cell lines and primary myeloma plasma cells. Biochemical analysis revealed that GW4869 binds to anionic phospholipids such as phosphatidylserine - a lipid normally confined to the intracellular side of the cell membrane. However, interestingly, phosphatidylserine was expressed on the surface of all myeloma cell lines tested (n = 12) and 9/15 primary myeloma samples. Notably, the level of phosphatidylserine expression correlated well with sensitivity to GW4869. Inhibition of cell surface phosphatidylserine exposure with brefeldin A resulted in resistance to GW4869. Finally, GW4869 was shown to delay the growth of phosphatidylserine-high myeloma cells in vivo. To the best of our knowledge, this is the first example of using a small molecule to target phosphatidylserine on malignant cells. This study may provide the rationale for the development of phosphatidylserine-targeting small molecules for the treatment of surface phosphatidylserine-expressing cancers.
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Affiliation(s)
- Slavica Vuckovic
- The Bone Marrow Transplantation Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Qld, Australia.,School of Medicine, University of Queensland, Brisbane, Qld, Australia.,Mater Research, Translational Research Institute, Brisbane, Qld, Australia
| | - Kate Vandyke
- Faculty of Health and Medical Sciences, SA Pathology, The University of Adelaide, Adelaide, SA.,Cancer Theme, South Australian Health and Medical Research Institute, SA Pathology, Adelaide, SA, Australia
| | - David A Rickards
- School of Life Sciences, Centre for Health Technologies and the iThree Institute, University of Technology Sydney, Ultimo, NSW, Australia
| | - Padraig McCauley Winter
- School of Life Sciences, Centre for Health Technologies and the iThree Institute, University of Technology Sydney, Ultimo, NSW, Australia
| | - Simon H J Brown
- School of Biology and Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, Australia
| | - Todd W Mitchell
- School of Biology and Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, Australia
| | - Jun Liu
- Department of Genetics, Yale Stem Cell Center, Yale Cancer Center and Yale Center for RNA Science and Medicine, New Haven, CT, USA
| | - Jun Lu
- Department of Genetics, Yale Stem Cell Center, Yale Cancer Center and Yale Center for RNA Science and Medicine, New Haven, CT, USA
| | - Philip W Askenase
- Section of Allergy and Clinical Immunology, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Elizabeth Yuriev
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
| | - Ben Capuano
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
| | - Paul A Ramsland
- School of Science, RMIT University, Bundoora, VIC, Australia.,Centre for Biomedical Research, Burnet Institute, Melbourne, VIC, Australia.,Department of Immunology, Monash University, Alfred Medical Research and Education Precinct, Melbourne, VIC, Australia.,Department of Surgery Austin Health, University of Melbourne, Heidelberg, Vic, Australia
| | - Geoffrey R Hill
- The Bone Marrow Transplantation Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Qld, Australia.,Department of Bone Marrow Transplantation, The Royal Brisbane and Women's Hospital, Herston, Qld, Australia
| | - Andrew C W Zannettino
- Faculty of Health and Medical Sciences, SA Pathology, The University of Adelaide, Adelaide, SA.,Cancer Theme, South Australian Health and Medical Research Institute, SA Pathology, Adelaide, SA, Australia
| | - Andrew T Hutchinson
- School of Life Sciences, Centre for Health Technologies and the iThree Institute, University of Technology Sydney, Ultimo, NSW, Australia.,Section of Allergy and Clinical Immunology, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA.,Centre for Biomedical Research, Burnet Institute, Melbourne, VIC, Australia
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Pasman Y, Soliman C, Ramsland PA, Kaushik AK. Exceptionally long CDR3H of bovine scFv antigenized with BoHV-1 B-epitope generates specific immune response against the targeted epitope. Mol Immunol 2016; 77:113-25. [PMID: 27497190 DOI: 10.1016/j.molimm.2016.07.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 07/13/2016] [Accepted: 07/20/2016] [Indexed: 11/18/2022]
Abstract
We discovered that some bovine antibodies are amongst the largest known to exist due to the presence of an exceptionally long CDR3H (≥49 amino acids) with multiple cysteines that provide a unique knob and stalk structure to the antigen binding site. The large CDR3H size, unlike mouse and human, provides a suitable platform for antigenization with large configurational B-epitopes. Here we report the identification of a B-epitope on the gC envelope protein of bovine herpes virus type-1 (BoHV-1) recognized by a bovine IgG1 antibody. The identified 156 amino acid long gC fragment (gC156) was expressed as a recombinant protein. Subsequently, a functional scFv fragment with a 61 amino-acid long CDR3H (scFv1H12) was expressed such that gC156 was grafted into the CDR3H, replacing the "knob" region (gC156scFv1H12 or Ag-scFv). Importantly, the Ag-scFv could be recognized by a neutralizing antibody fragment (scFv3-18L), which suggests that the engraftment of gC156 into the CDR3H of 1H12 maintained the native conformation of the BoHV-1 B-epitope. A 3D model of gC156 was generated using fold-recognition approaches and this was grafted onto the CDR3H stalk of the 1H12 Fab crystal structure to predict the 3D structure of the Ag-scFv. The grafted antigen in Ag-scFv is predicted to have a compact conformation with the ability to protrude into the solvent. Upon immunization of bovine calves, the antigenized scFv (gC156scFv1H12) induced a higher antibody response as compared to free recombinant gC156. These observations suggest that antigenization of bovine scFv with an exceptionally long CDR3H provides a novel approach to developing the next generation of vaccines against infectious agents that require induction of protective humoral immunity.
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Affiliation(s)
- Yfke Pasman
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Caroline Soliman
- School of Science, RMIT University, Bundoora, VIC 3083, Australia
| | - Paul A Ramsland
- School of Science, RMIT University, Bundoora, VIC 3083, Australia; Centre for Biomedical Research, Burnet Institute, Melbourne, VIC 3004, Australia; Department of Immunology, Alfred Medical Research and Education Precinct, Monash University, Melbourne, VIC 3004, Australia; Department of Surgery Austin Health, University of Melbourne, Heidelberg, VIC 3084, Australia
| | - Azad K Kaushik
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada.
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Agostino M, Mancera RL, Ramsland PA, Fernández-Recio J. Optimization of protein-protein docking for predicting Fc-protein interactions. J Mol Recognit 2016; 29:555-568. [PMID: 27445195 DOI: 10.1002/jmr.2555] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 06/12/2016] [Accepted: 06/14/2016] [Indexed: 01/08/2023]
Abstract
The antibody crystallizable fragment (Fc) is recognized by effector proteins as part of the immune system. Pathogens produce proteins that bind Fc in order to subvert or evade the immune response. The structural characterization of the determinants of Fc-protein association is essential to improve our understanding of the immune system at the molecular level and to develop new therapeutic agents. Furthermore, Fc-binding peptides and proteins are frequently used to purify therapeutic antibodies. Although several structures of Fc-protein complexes are available, numerous others have not yet been determined. Protein-protein docking could be used to investigate Fc-protein complexes; however, improved approaches are necessary to efficiently model such cases. In this study, a docking-based structural bioinformatics approach is developed for predicting the structures of Fc-protein complexes. Based on the available set of X-ray structures of Fc-protein complexes, three regions of the Fc, loosely corresponding to three turns within the structure, were defined as containing the essential features for protein recognition and used as restraints to filter the initial docking search. Rescoring the filtered poses with an optimal scoring strategy provided a success rate of approximately 80% of the test cases examined within the top ranked 20 poses, compared to approximately 20% by the initial unrestrained docking. The developed docking protocol provides a significant improvement over the initial unrestrained docking and will be valuable for predicting the structures of currently undetermined Fc-protein complexes, as well as in the design of peptides and proteins that target Fc.
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Affiliation(s)
- Mark Agostino
- School of Biomedical Sciences, Curtin Health Innovation Research Institute and Curtin Institute for Computation, Curtin University, Perth, Australia.,Joint BSC-CRG-IRB Research Program in Computational Biology, Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Spain.,Centre for Biomedical Research, Burnet Institute, Melbourne, Australia
| | - Ricardo L Mancera
- School of Biomedical Sciences, Curtin Health Innovation Research Institute and Curtin Institute for Computation, Curtin University, Perth, Australia
| | - Paul A Ramsland
- Centre for Biomedical Research, Burnet Institute, Melbourne, Australia. .,School of Science, RMIT University, Bundoora, Australia. .,Department of Surgery Austin Health, University of Melbourne, Heidelberg, Australia. .,Department of Immunology, Monash University, Alfred Medical Research and Education Precinct, Melbourne, Australia.
| | - Juan Fernández-Recio
- Joint BSC-CRG-IRB Research Program in Computational Biology, Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Spain.
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Abstract
Carbohydrate-protein recognition is vital to many processes in health and disease. In particular, elucidation of the structural basis of carbohydrate binding is important to the development of oligosaccharides and oligosaccharide mimetics as vaccines for infectious diseases and cancer. Computational structural techniques are valuable for the study of carbohydrate-protein recognition due to the challenges associated with experimental determination of carbohydrate-protein complexes. AutoMap is a computer program that we have developed to study protein-ligand recognition. AutoMap determines the interactions taking place in a set of highly ranked poses obtained from molecular docking and processes these to identify the protein residues most likely to be involved in interactions. In this protocol, we describe the use of AutoMap and illustrate its suitability for studying antibody recognition of the Lewis Y tetrasaccharide, which is a potential cancer vaccine antigen.
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Affiliation(s)
- Tamir Dingjan
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
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27
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Burvenich IJG, Farrugia W, Lee FT, Catimel B, Liu Z, Makris D, Cao D, O'Keefe GJ, Brechbiel MW, King D, Spirkoska V, Allan LC, Ramsland PA, Scott AM. Cross-species analysis of Fc engineered anti-Lewis-Y human IgG1 variants in human neonatal receptor transgenic mice reveal importance of S254 and Y436 in binding human neonatal Fc receptor. MAbs 2016; 8:775-86. [PMID: 27030023 DOI: 10.1080/19420862.2016.1156285] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
IgG has a long half-life through engagement of its Fc region with the neonatal Fc receptor (FcRn). The FcRn binding site on IgG1 has been shown to contain I253 and H310 in the CH2 domain and H435 in the CH3 domain. Altering the half-life of IgG has been pursued with the aim to prolong or reduce the half-life of therapeutic IgGs. More recent studies have shown that IgGs bind differently to mouse and human FcRn. In this study we characterize a set of hu3S193 IgG1 variants with mutations in the FcRn binding site. A double mutation in the binding site is necessary to abrogate binding to murine FcRn, whereas a single mutation in the FcRn binding site is sufficient to no longer detect binding to human FcRn and create hu3S193 IgG1 variants with a half-life similar to previously studied hu3S193 F(ab')2 (t1/2β, I253A, 12.23 h; H310A, 12.94; H435A, 12.57; F(ab')2, 12.6 h). Alanine substitutions in S254 in the CH2 domain and Y436 in the CH3 domain showed reduced binding in vitro to human FcRn and reduced elimination half-lives in huFcRn transgenic mice (t1/2β, S254A, 37.43 h; Y436A, 39.53 h; wild-type, 83.15 h). These variants had minimal effect on half-life in BALB/c nu/nu mice (t1/2β, S254A, 119.9 h; Y436A, 162.1 h; wild-type, 163.1 h). These results provide insight into the interaction of human Fc by human FcRn, and are important for antibody-based therapeutics with optimal pharmacokinetics for payload strategies used in the clinic.
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Affiliation(s)
- Ingrid J G Burvenich
- a Tumour Targeting Laboratory, Ludwig Institute for Cancer Research and Olivia Newton-John Cancer Research Institute , Melbourne , VIC , Australia.,b School of Cancer Medicine, La Trobe University , Melbourne , VIC , Australia
| | - William Farrugia
- c Centre for Biomedical Research, Burnet Institute , Melbourne , VIC , Australia
| | - Fook T Lee
- a Tumour Targeting Laboratory, Ludwig Institute for Cancer Research and Olivia Newton-John Cancer Research Institute , Melbourne , VIC , Australia
| | - Bruno Catimel
- a Tumour Targeting Laboratory, Ludwig Institute for Cancer Research and Olivia Newton-John Cancer Research Institute , Melbourne , VIC , Australia
| | - Zhanqi Liu
- a Tumour Targeting Laboratory, Ludwig Institute for Cancer Research and Olivia Newton-John Cancer Research Institute , Melbourne , VIC , Australia
| | - Dahna Makris
- a Tumour Targeting Laboratory, Ludwig Institute for Cancer Research and Olivia Newton-John Cancer Research Institute , Melbourne , VIC , Australia
| | - Diana Cao
- a Tumour Targeting Laboratory, Ludwig Institute for Cancer Research and Olivia Newton-John Cancer Research Institute , Melbourne , VIC , Australia
| | - Graeme J O'Keefe
- b School of Cancer Medicine, La Trobe University , Melbourne , VIC , Australia.,d Department of Molecular Imaging and Therapy, Austin Health , Melbourne , Australia
| | - Martin W Brechbiel
- e Radioimmune Inorganic Chemistry Section, Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute , Bethesda , MD , USA
| | - Dylan King
- a Tumour Targeting Laboratory, Ludwig Institute for Cancer Research and Olivia Newton-John Cancer Research Institute , Melbourne , VIC , Australia
| | - Violeta Spirkoska
- a Tumour Targeting Laboratory, Ludwig Institute for Cancer Research and Olivia Newton-John Cancer Research Institute , Melbourne , VIC , Australia
| | - Laura C Allan
- a Tumour Targeting Laboratory, Ludwig Institute for Cancer Research and Olivia Newton-John Cancer Research Institute , Melbourne , VIC , Australia
| | - Paul A Ramsland
- c Centre for Biomedical Research, Burnet Institute , Melbourne , VIC , Australia.,f School of Science, RMIT University , Bundoora , VIC , Australia.,g Department of Immunology , Monash University , Melbourne , VIC , Australia.,h Department of Surgery Austin Health , University of Melbourne , Heidelberg , VIC , Australia
| | - Andrew M Scott
- a Tumour Targeting Laboratory, Ludwig Institute for Cancer Research and Olivia Newton-John Cancer Research Institute , Melbourne , VIC , Australia.,b School of Cancer Medicine, La Trobe University , Melbourne , VIC , Australia.,d Department of Molecular Imaging and Therapy, Austin Health , Melbourne , Australia.,i Faculty of Medicine, University of Melbourne , Melbourne , VIC , Australia
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28
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Burvenich IJG, Lee FT, O'Keefe GJ, Makris D, Cao D, Gong S, Rigopoulos A, Allan LC, Brechbiel MW, Liu Z, Ramsland PA, Scott AM. Engineering anti-Lewis-Y hu3S193 antibodies with improved therapeutic ratio for radioimmunotherapy of epithelial cancers. EJNMMI Res 2016; 6:26. [PMID: 26983636 PMCID: PMC4796444 DOI: 10.1186/s13550-016-0180-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 03/03/2016] [Indexed: 08/23/2023] Open
Abstract
Background The aim of the study was to explore Fc mutations of a humanised anti-Lewis-Y antibody (IgG1) hu3S193 as a strategy to improve therapeutic ratios for therapeutic payload delivery. Methods Four hu3S193 variants (I253A, H310A, H435A and I253A/H310A) were generated via site-directed mutagenesis and radiolabelled with diagnostic isotopes iodine-125 or indium-111. Biodistribution studies in Lewis-Y-positive tumour-bearing mice were used to calculate the dose in tumours and organs for therapeutic isotopes (iodine-131, yttrium-90 and lutetium-177). Results 111In-labelled I253A and H435A showed similar slow kinetics (t1/2β, 63.2 and 62.2 h, respectively) and a maximum tumour uptake of 33.11 ± 4.05 and 33.69 ± 3.77 percentage injected dose per gramme (%ID/g), respectively. 111In-labelled I253A/H310A cleared fastest (t1/2β, 9.1 h) with the lowest maximum tumour uptake (23.72 ± 0.85 %ID/g). The highest increase in tumour-to-blood area under the curve (AUC) ratio was observed with the metal-labelled mutants (90Y and 177Lu). 177Lu-CHX-A" DTPA-hu3S193 I253A/H310A (6:1) showed the highest tumour-to-blood AUC ratio compared to wild type (3:1) and other variants and doubling of calculated dose to tumour based on red marrow dose constraints. Conclusions These results suggest that hu3S193 Fc can be engineered with improved therapeutic ratios for 90Y- and 177Lu-based therapy, with the best candidate being hu3S193 I253A/H310A for 177Lu-based therapy. Electronic supplementary material The online version of this article (doi:10.1186/s13550-016-0180-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ingrid J G Burvenich
- Tumour Targeting Laboratory, Ludwig Institute for Cancer Research and Olivia Newton-John Cancer Research Institute, Melbourne, VIC, Australia.,School of Cancer Medicine, La Trobe University, Melbourne, VIC, Australia
| | - Fook-Thean Lee
- Tumour Targeting Laboratory, Ludwig Institute for Cancer Research and Olivia Newton-John Cancer Research Institute, Melbourne, VIC, Australia
| | - Graeme J O'Keefe
- School of Cancer Medicine, La Trobe University, Melbourne, VIC, Australia.,Department of Molecular Imaging and Therapy, Austin Health, Melbourne, Australia
| | - Dahna Makris
- Tumour Targeting Laboratory, Ludwig Institute for Cancer Research and Olivia Newton-John Cancer Research Institute, Melbourne, VIC, Australia
| | - Diana Cao
- Tumour Targeting Laboratory, Ludwig Institute for Cancer Research and Olivia Newton-John Cancer Research Institute, Melbourne, VIC, Australia
| | - Sylvia Gong
- Department of Molecular Imaging and Therapy, Austin Health, Melbourne, Australia
| | - Angela Rigopoulos
- Tumour Targeting Laboratory, Ludwig Institute for Cancer Research and Olivia Newton-John Cancer Research Institute, Melbourne, VIC, Australia
| | - Laura C Allan
- Tumour Targeting Laboratory, Ludwig Institute for Cancer Research and Olivia Newton-John Cancer Research Institute, Melbourne, VIC, Australia
| | - Martin W Brechbiel
- Radioimmune and Inorganic Chemistry Section, Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Zhanqi Liu
- Tumour Targeting Laboratory, Ludwig Institute for Cancer Research and Olivia Newton-John Cancer Research Institute, Melbourne, VIC, Australia
| | - Paul A Ramsland
- School of Science, RMIT University, Bundoora, VIC, Australia.,Centre for Biomedical Research, Burnet Institute, Melbourne, VIC, Australia.,Department of Immunology, Monash University, Melbourne, VIC, Australia.,Department of Surgery Austin Health, University of Melbourne, Heidelberg, VIC, Australia
| | - Andrew M Scott
- Tumour Targeting Laboratory, Ludwig Institute for Cancer Research and Olivia Newton-John Cancer Research Institute, Melbourne, VIC, Australia. .,School of Cancer Medicine, La Trobe University, Melbourne, VIC, Australia. .,Department of Molecular Imaging and Therapy, Austin Health, Melbourne, Australia. .,Faculty of Medicine, University of Melbourne, Melbourne, VIC, Australia. .,Olivia Newton-John Cancer Research Institute, 145-163 Studley Road, Heidelberg, VIC, 3084, Australia.
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29
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Guy AJ, Irani V, MacRaild CA, Anders RF, Norton RS, Beeson JG, Richards JS, Ramsland PA. Insights into the Immunological Properties of Intrinsically Disordered Malaria Proteins Using Proteome Scale Predictions. PLoS One 2015; 10:e0141729. [PMID: 26513658 PMCID: PMC4626106 DOI: 10.1371/journal.pone.0141729] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 10/12/2015] [Indexed: 12/31/2022] Open
Abstract
Malaria remains a significant global health burden. The development of an effective malaria vaccine remains as a major challenge with the potential to significantly reduce morbidity and mortality. While Plasmodium spp. have been shown to contain a large number of intrinsically disordered proteins (IDPs) or disordered protein regions, the relationship of protein structure to subcellular localisation and adaptive immune responses remains unclear. In this study, we employed several computational prediction algorithms to identify IDPs at the proteome level of six Plasmodium spp. and to investigate the potential impact of protein disorder on adaptive immunity against P. falciparum parasites. IDPs were shown to be particularly enriched within nuclear proteins, apical proteins, exported proteins and proteins localised to the parasitophorous vacuole. Furthermore, several leading vaccine candidates, and proteins with known roles in host-cell invasion, have extensive regions of disorder. Presentation of peptides by MHC molecules plays an important role in adaptive immune responses, and we show that IDP regions are predicted to contain relatively few MHC class I and II binding peptides owing to inherent differences in amino acid composition compared to structured domains. In contrast, linear B-cell epitopes were predicted to be enriched in IDPs. Tandem repeat regions and non-synonymous single nucleotide polymorphisms were found to be strongly associated with regions of disorder. In summary, immune responses against IDPs appear to have characteristics distinct from those against structured protein domains, with increased antibody recognition of linear epitopes but some constraints for MHC presentation and issues of polymorphisms. These findings have major implications for vaccine design, and understanding immunity to malaria.
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Affiliation(s)
- Andrew J. Guy
- Centre for Biomedical Research, Burnet Institute, Melbourne, Australia
- Department of Immunology, Monash University, Melbourne, Australia
| | - Vashti Irani
- Centre for Biomedical Research, Burnet Institute, Melbourne, Australia
- Department of Medicine, University of Melbourne, Melbourne, Australia
| | - Christopher A. MacRaild
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Robin F. Anders
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Raymond S. Norton
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - James G. Beeson
- Centre for Biomedical Research, Burnet Institute, Melbourne, Australia
- Department of Medicine, University of Melbourne, Melbourne, Australia
- Department of Microbiology, Monash University, Melbourne, Australia
| | - Jack S. Richards
- Centre for Biomedical Research, Burnet Institute, Melbourne, Australia
- Department of Medicine, University of Melbourne, Melbourne, Australia
- Department of Microbiology, Monash University, Melbourne, Australia
- Victorian Infectious Diseases Service, Royal Melbourne Hospital, Melbourne, Australia
- * E-mail: (JSR); (PAR)
| | - Paul A. Ramsland
- Centre for Biomedical Research, Burnet Institute, Melbourne, Australia
- Department of Immunology, Monash University, Melbourne, Australia
- Department of Surgery Austin Health, University of Melbourne, Heidelberg, Australia
- School of Biomedical Sciences, CHIRI Biosciences, Faculty of Health Sciences, Curtin University, Perth, Australia
- * E-mail: (JSR); (PAR)
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30
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Irani V, Guy AJ, Andrew D, Beeson JG, Ramsland PA, Richards JS. Molecular properties of human IgG subclasses and their implications for designing therapeutic monoclonal antibodies against infectious diseases. Mol Immunol 2015; 67:171-82. [DOI: 10.1016/j.molimm.2015.03.255] [Citation(s) in RCA: 181] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 03/25/2015] [Accepted: 03/25/2015] [Indexed: 12/31/2022]
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31
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Irani V, Ramsland PA, Guy AJ, Siba PM, Mueller I, Richards JS, Beeson JG. Acquisition of Functional Antibodies That Block the Binding of Erythrocyte-Binding Antigen 175 and Protection Against Plasmodium falciparum Malaria in Children. Clin Infect Dis 2015; 61:1244-52. [PMID: 26136391 DOI: 10.1093/cid/civ525] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 05/22/2015] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The targets and mechanisms of human immunity to malaria are poorly understood, which poses a major barrier to malaria vaccine development. Antibodies play a key role in human immunity and may act by inhibiting receptor-binding functions of key merozoite invasion ligands. Antibodies to the major invasion ligand and vaccine candidate, erythrocyte-binding antigen 175 (EBA-175), have been linked with protection, but how these antibodies function has not been established. METHODS We developed 2 new assays that quantify the ability of antibodies to inhibit binding of EBA-175 to its erythrocyte receptor, glycophorin A, using either native or recombinant EBA-175. Binding-inhibitory antibodies were evaluated in a longitudinal cohort study of Papua New Guinean children and related to risk of malaria, age, infection status, and markers of parasite exposure. RESULTS Binding-inhibition assays (BIAs) were reproducible, and the 2 assays had a high level of agreement. Inhibitory antibodies were common among children, acquired in association with markers of increasing parasite exposure, and high in those children with active infection. Inhibitory antibodies correlated with total immunoglobulin G levels to the EBA-175 binding domain (region II). Importantly, binding-inhibitory antibodies were significantly associated with protection from symptomatic malaria when measured using either BIA. CONCLUSIONS Findings suggest that naturally acquired binding-inhibitory antibodies are an important functional mechanism that contributes to protection against malaria and further supports the potential of EBA-175 as a vaccine candidate. Identifying vaccines and approaches that induce potent binding-inhibitory antibodies may be a valuable strategy in the development of highly efficacious malaria vaccines.
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Affiliation(s)
- Vashti Irani
- Centre for Biomedical Research, Burnet Institute, Melbourne Department of Medicine, University of Melbourne, Parkville Department of Immunology, Monash University, Melbourne
| | - Paul A Ramsland
- Centre for Biomedical Research, Burnet Institute, Melbourne Department of Immunology, Monash University, Melbourne Department of Surgery, Austin Health, University of Melbourne, Heidelberg, Victoria School of Biomedical Sciences, Curtin Health Innovation Research Institute-Biosciences, Curtin University, Perth, Western Australia, Australia
| | - Andrew J Guy
- Centre for Biomedical Research, Burnet Institute, Melbourne Department of Immunology, Monash University, Melbourne
| | - Peter M Siba
- Papua New Guinea Institute of Medical Research, Goroka
| | - Ivo Mueller
- Infection and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia Barcelona Centre for International Health Research, Spain
| | - Jack S Richards
- Centre for Biomedical Research, Burnet Institute, Melbourne Department of Medicine, University of Melbourne, Parkville Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - James G Beeson
- Centre for Biomedical Research, Burnet Institute, Melbourne Department of Medicine, University of Melbourne, Parkville Department of Microbiology, Monash University, Clayton, Victoria, Australia
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32
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Affiliation(s)
- Elizabeth Yuriev
- Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, VIC , Australia
| | - Paul A Ramsland
- Centre for Biomedical Research, Burnet Institute , Melbourne, VIC , Australia ; Department of Immunology, Alfred Medical Research and Education Precinct, Monash University , Melbourne, VIC , Australia ; Department of Surgery Austin Health, University of Melbourne , Heidelberg, VIC , Australia ; CHIRI Biosciences, School of Biomedical Sciences, Curtin University , Perth, WA , Australia
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33
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Aldunate M, Srbinovski D, Hearps AC, Latham CF, Ramsland PA, Gugasyan R, Cone RA, Tachedjian G. Antimicrobial and immune modulatory effects of lactic acid and short chain fatty acids produced by vaginal microbiota associated with eubiosis and bacterial vaginosis. Front Physiol 2015; 6:164. [PMID: 26082720 PMCID: PMC4451362 DOI: 10.3389/fphys.2015.00164] [Citation(s) in RCA: 201] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 05/12/2015] [Indexed: 12/14/2022] Open
Abstract
Lactic acid and short chain fatty acids (SCFAs) produced by vaginal microbiota have reported antimicrobial and immune modulatory activities indicating their potential as biomarkers of disease and/or disease susceptibility. In asymptomatic women of reproductive-age the vaginal microbiota is comprised of lactic acid-producing bacteria that are primarily responsible for the production of lactic acid present at ~110 mM and acidifying the vaginal milieu to pH ~3.5. In contrast, bacterial vaginosis (BV), a dysbiosis of the vaginal microbiota, is characterized by decreased lactic acid-producing microbiota and increased diverse anaerobic bacteria accompanied by an elevated pH>4.5. BV is also characterized by a dramatic loss of lactic acid and greater concentrations of mixed SCFAs including acetate, propionate, butyrate, and succinate. Notably women with lactic acid-producing microbiota have more favorable reproductive and sexual health outcomes compared to women with BV. Regarding the latter, BV is associated with increased susceptibility to sexually transmitted infections (STIs) including HIV. In vitro studies demonstrate that lactic acid produced by vaginal microbiota has microbicidal and virucidal activities that may protect against STIs and endogenous opportunistic bacteria as well as immune modulatory properties that require further characterization with regard to their effects on the vaginal mucosa. In contrast, BV-associated SCFAs have far less antimicrobial activity with the potential to contribute to a pro-inflammatory vaginal environment. Here we review the composition of lactic acid and SCFAs in respective states of eubiosis (non-BV) or dysbiosis (BV), their effects on susceptibility to bacterial/viral STIs and whether they have inherent microbicidal/virucidal and immune modulatory properties. We also explore their potential as biomarkers for the presence and/or increased susceptibility to STIs.
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Affiliation(s)
- Muriel Aldunate
- Centre for Biomedical Research, Burnet Institute Melbourne, VIC, Australia ; Department of Microbiology, Nursing and Health, Faculty of Medicine, Monash University Clayton, VIC, Australia
| | - Daniela Srbinovski
- Centre for Biomedical Research, Burnet Institute Melbourne, VIC, Australia ; Department of Microbiology, Nursing and Health, Faculty of Medicine, Monash University Clayton, VIC, Australia
| | - Anna C Hearps
- Centre for Biomedical Research, Burnet Institute Melbourne, VIC, Australia ; Department of Infectious Disease, Monash University Melbourne, VIC, Australia
| | - Catherine F Latham
- Centre for Biomedical Research, Burnet Institute Melbourne, VIC, Australia
| | - Paul A Ramsland
- Centre for Biomedical Research, Burnet Institute Melbourne, VIC, Australia ; Department of Immunology, Monash University Melbourne, VIC, Australia ; Department of Surgery Austin Health, The University of Melbourne Heidelberg, VIC, Australia ; School of Biomedical Sciences, CHIRI Biosciences, Curtin University Perth, WA, Australia
| | - Raffi Gugasyan
- Centre for Biomedical Research, Burnet Institute Melbourne, VIC, Australia ; Department of Immunology, Monash University Melbourne, VIC, Australia
| | - Richard A Cone
- Department of Biophysics, Johns Hopkins University Baltimore, MD, USA
| | - Gilda Tachedjian
- Centre for Biomedical Research, Burnet Institute Melbourne, VIC, Australia ; Department of Microbiology, Nursing and Health, Faculty of Medicine, Monash University Clayton, VIC, Australia ; Department of Infectious Disease, Monash University Melbourne, VIC, Australia ; Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity Parkville, VIC, Australia
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Abstract
Therapeutic antibodies have come of age with major progress being made in cancer, autoimmunity and chronic inflammation, as well as a wide range of other human diseases. Antibody engineering is further driving development of novel antibody formats and genetically modified cell-based therapies that harness the power of the immune system to progress cures in otherwise intractable human diseases. Nevertheless, there are still significant challenges ahead for basic and applied research relating to therapeutic antibodies. This special issue of the journal provides reviews and opinions that relate to the discovery, design and deployment of antibodies as therapeutics.
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Affiliation(s)
- Paul A Ramsland
- Centre for Biomedical Research, Burnet Institute, Melbourne, VIC 3004, Australia; Department of Immunology, Monash University, Alfred Medical Research and Education Precinct, Melbourne, VIC 3004, Australia; Department of Surgery Austin Health, University of Melbourne, Heidelberg, VIC 3084, Australia; School of Biomedical Sciences, CHIRI Biosciences, Curtin University, Perth, WA 6845, Australia.
| | - Andrew T Hutchinson
- Centre for Biomedical Research, Burnet Institute, Melbourne, VIC 3004, Australia; School of Life Sciences, Centre for Health Technologies, University of Technology Sydney, Ultimo, NSW 2007, Australia; Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT 06520, USA
| | - Paul J Carter
- Department of Antibody Engineering, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
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Pereira LA, Hugo HJ, Malaterre J, Huiling X, Sonza S, Cures A, Purcell DFJ, Ramsland PA, Gerondakis S, Gonda TJ, Ramsay RG. MYB elongation is regulated by the nucleic acid binding of NFκB p50 to the intronic stem-loop region. PLoS One 2015; 10:e0122919. [PMID: 25853889 PMCID: PMC4390348 DOI: 10.1371/journal.pone.0122919] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 02/23/2015] [Indexed: 11/30/2022] Open
Abstract
MYB transcriptional elongation is regulated by an attenuator sequence within intron 1 that has been proposed to encode a RNA stem loop (SLR) followed by a polyU tract. We report that NFκBp50 can bind the SLR polyU RNA and promote MYB transcriptional elongation together with NFκBp65. We identified a conserved lysine-rich motif within the Rel homology domain (RHD) of NFκBp50, mutation of which abrogated the interaction of NFκBp50 with the SLR polyU and impaired NFκBp50 mediated MYB elongation. We observed that the TAR RNA-binding region of Tat is homologous to the NFκBp50 RHD lysine-rich motif, a finding consistent with HIV Tat acting as an effector of MYB transcriptional elongation in an SLR dependent manner. Furthermore, we identify the DNA binding activity of NFκBp50 as a key component required for the SLR polyU mediated regulation of MYB. Collectively these results suggest that the MYB SLR polyU provides a platform for proteins to regulate MYB and reveals novel nucleic acid binding properties of NFκBp50 required for MYB regulation.
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Affiliation(s)
- Lloyd A. Pereira
- Differentiation and Transcription Laboratory, Peter MacCallum Cancer Centre, Locked Bag #1, Melbourne, Victoria, 8006, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Honor J. Hugo
- Victorian Breast Cancer Consortium, Invasion and Metastasis Unit, St Vincent’s Institute of Medical Research, Melbourne, Victoria, 3065, Australia
| | - Jordane Malaterre
- Differentiation and Transcription Laboratory, Peter MacCallum Cancer Centre, Locked Bag #1, Melbourne, Victoria, 8006, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Xu Huiling
- Differentiation and Transcription Laboratory, Peter MacCallum Cancer Centre, Locked Bag #1, Melbourne, Victoria, 8006, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, 3010, Australia
- The Department of Pathology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Secondo Sonza
- The Department of Microbiology and Immunology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Alina Cures
- Differentiation and Transcription Laboratory, Peter MacCallum Cancer Centre, Locked Bag #1, Melbourne, Victoria, 8006, Australia
| | - Damian F. J. Purcell
- The Department of Microbiology and Immunology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Paul A. Ramsland
- Centre for Immunology, Burnet Institute, Melbourne, Victoria, 3004, Australia
- Department of Surgery (Austin Health), The University of Melbourne, Heidelberg, Victoria, 3084, Australia
- Department of Immunology, Monash University, Alfred Medical Research and Education Precinct, Melbourne, Victoria, 3004, Australia
| | - Steven Gerondakis
- Australian Centre for Blood Diseases, Monash University, Prahran, Victoria 3004, Australia
| | - Thomas J. Gonda
- School of Pharmacy University of Queensland, Woolloongabba, Queensland, 4102, Australia
| | - Robert G. Ramsay
- Differentiation and Transcription Laboratory, Peter MacCallum Cancer Centre, Locked Bag #1, Melbourne, Victoria, 8006, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, 3010, Australia
- The Department of Pathology, The University of Melbourne, Parkville, Victoria, 3010, Australia
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Yuriev E, Holien J, Ramsland PA. Improvements, trends, and new ideas in molecular docking: 2012-2013 in review. J Mol Recognit 2015; 28:581-604. [PMID: 25808539 DOI: 10.1002/jmr.2471] [Citation(s) in RCA: 159] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Revised: 01/16/2015] [Accepted: 02/05/2015] [Indexed: 12/11/2022]
Abstract
Molecular docking is a computational method for predicting the placement of ligands in the binding sites of their receptor(s). In this review, we discuss the methodological developments that occurred in the docking field in 2012 and 2013, with a particular focus on the more difficult aspects of this computational discipline. The main challenges and therefore focal points for developments in docking, covered in this review, are receptor flexibility, solvation, scoring, and virtual screening. We specifically deal with such aspects of molecular docking and its applications as selection criteria for constructing receptor ensembles, target dependence of scoring functions, integration of higher-level theory into scoring, implicit and explicit handling of solvation in the binding process, and comparison and evaluation of docking and scoring methods.
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Affiliation(s)
- Elizabeth Yuriev
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia
| | - Jessica Holien
- ACRF Rational Drug Discovery Centre and Structural Biology Laboratory, St. Vincent's Institute of Medical Research, Fitzroy, Victoria, 3065, Australia
| | - Paul A Ramsland
- Centre for Biomedical Research, Burnet Institute, Melbourne, Victoria, 3004, Australia.,Department of Surgery Austin Health, University of Melbourne, Melbourne, Victoria, 3084, Australia.,Department of Immunology, Monash University, Alfred Medical Research and Education Precinct, Melbourne, Victoria, 3004, Australia.,School of Biomedical Sciences, CHIRI Biosciences, Curtin University, Perth, Western Australia, 6845, Australia
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Dingjan T, Spendlove I, Durrant LG, Scott AM, Yuriev E, Ramsland PA. Structural biology of antibody recognition of carbohydrate epitopes and potential uses for targeted cancer immunotherapies. Mol Immunol 2015; 67:75-88. [PMID: 25757815 DOI: 10.1016/j.molimm.2015.02.028] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 02/16/2015] [Accepted: 02/19/2015] [Indexed: 11/18/2022]
Abstract
Monoclonal antibodies represent the most successful class of biopharmaceuticals for the treatment of cancer. Mechanisms of action of therapeutic antibodies are very diverse and reflect their ability to engage in antibody-dependent effector mechanisms, internalize to deliver cytotoxic payloads, and display direct effects on cells by lysis or by modulating the biological pathways of their target antigens. Importantly, one of the universal changes in cancer is glycosylation and carbohydrate-binding antibodies can be produced to selectively recognize tumor cells over normal tissues. A promising group of cell surface antibody targets consists of carbohydrates presented as glycolipids or glycoproteins. In this review, we outline the basic principles of antibody-based targeting of carbohydrate antigens in cancer. We also present a detailed structural view of antibody recognition and the conformational properties of a series of related tissue-blood group (Lewis) carbohydrates that are being pursued as potential targets of cancer immunotherapy.
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Affiliation(s)
- Tamir Dingjan
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Ian Spendlove
- Academic Department of Clinical Oncology, Division of Cancer and Stem cells, University of Nottingham, City Hospital, Nottingham NG5 1PB, United Kingdom
| | - Lindy G Durrant
- Academic Department of Clinical Oncology, Division of Cancer and Stem cells, University of Nottingham, City Hospital, Nottingham NG5 1PB, United Kingdom
| | - Andrew M Scott
- Tumour Targeting Laboratory, Olivia Newton-John Cancer Research Institute, Melbourne, VIC, Australia; Faculty of Medicine, University of Melbourne, Melbourne, VIC, Australia; School of Cancer Medicine, La Trobe University, Melbourne, VIC, Australia
| | - Elizabeth Yuriev
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia.
| | - Paul A Ramsland
- Centre for Biomedical Research, Burnet Institute, Melbourne, VIC 3004, Australia; Department of Immunology, Monash University, Alfred Medical Research and Education Precinct, Melbourne, VIC 3004, Australia; Department of Surgery Austin Health, University of Melbourne, Heidelberg, VIC 3084, Australia; School of Biomedical Sciences, CHIRI Biosciences, Curtin University, Perth, WA 6845, Australia.
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Apostolopoulos V, Yuriev E, Lazoura E, Yu M, Ramsland PA. MHC and MHC‑like molecules: Structural perspectives on the design of molecular vaccines. Human Vaccines 2014; 4:400-9. [DOI: 10.4161/hv.4.6.6690] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Cashin K, Sterjovski J, Harvey KL, Ramsland PA, Churchill MJ, Gorry PR. Covariance of charged amino acids at positions 322 and 440 of HIV-1 Env contributes to coreceptor specificity of subtype B viruses, and can be used to improve the performance of V3 sequence-based coreceptor usage prediction algorithms. PLoS One 2014; 9:e109771. [PMID: 25313689 PMCID: PMC4196930 DOI: 10.1371/journal.pone.0109771] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 09/05/2014] [Indexed: 11/18/2022] Open
Abstract
The ability to determine coreceptor usage of patient-derived human immunodeficiency virus type 1 (HIV-1) strains is clinically important, particularly for the administration of the CCR5 antagonist maraviroc. The envelope glycoprotein (Env) determinants of coreceptor specificity lie primarily within the gp120 V3 loop region, although other Env determinants have been shown to influence gp120-coreceptor interactions. Here, we determined whether conserved amino acid alterations outside the V3 loop that contribute to coreceptor usage exist, and whether these alterations improve the performance of V3 sequence-based coreceptor usage prediction algorithms. We demonstrate a significant covariant association between charged amino acids at position 322 in V3 and position 440 in the C4 Env region that contributes to the specificity of HIV-1 subtype B strains for CCR5 or CXCR4. Specifically, positively charged Lys/Arg at position 322 and negatively charged Asp/Glu at position 440 occurred more frequently in CXCR4-using viruses, whereas negatively charged Asp/Glu at position 322 and positively charged Arg at position 440 occurred more frequently in R5 strains. In the context of CD4-bound gp120, structural models suggest that covariation of amino acids at Env positions 322 and 440 has the potential to alter electrostatic interactions that are formed between gp120 and charged amino acids in the CCR5 N-terminus. We further demonstrate that inclusion of a "440 rule" can improve the sensitivity of several V3 sequence-based genotypic algorithms for predicting coreceptor usage of subtype B HIV-1 strains, without compromising specificity, and significantly improves the AUROC of the geno2pheno algorithm when set to its recommended false positive rate of 5.75%. Together, our results provide further mechanistic insights into the intra-molecular interactions within Env that contribute to coreceptor specificity of subtype B HIV-1 strains, and demonstrate that incorporation of Env determinants outside V3 can improve the reliability of coreceptor usage prediction algorithms.
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Affiliation(s)
- Kieran Cashin
- Center for Biomedical Research, Burnet Institute, Melbourne, Australia
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Australia
| | | | - Katherine L. Harvey
- Center for Biomedical Research, Burnet Institute, Melbourne, Australia
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Australia
| | - Paul A. Ramsland
- Center for Biomedical Research, Burnet Institute, Melbourne, Australia
- Department of Surgery (Austin Health), University of Melbourne, Melbourne, Australia
- Department of Immunology, Monash University, Melbourne, Australia
- School of Biomedical Sciences, CHIRI Biosciences, Faculty of Health Sciences, Curtin University, Perth, Australia
| | - Melissa J. Churchill
- Center for Biomedical Research, Burnet Institute, Melbourne, Australia
- Department of Microbiology, Monash University, Melbourne, Australia
- Department of Medicine, Monash University, Melbourne, Australia
| | - Paul R. Gorry
- Center for Biomedical Research, Burnet Institute, Melbourne, Australia
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Australia
- Department of Infectious Diseases, Monash University, Melbourne, Australia
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Agostino M, Velkov T, Dingjan T, Williams SJ, Yuriev E, Ramsland PA. The carbohydrate-binding promiscuity of Euonymus europaeus lectin is predicted to involve a single binding site. Glycobiology 2014; 25:101-14. [PMID: 25209582 DOI: 10.1093/glycob/cwu095] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Euonymus europaeus lectin (EEL) is a carbohydrate-binding protein derived from the fruit of the European spindle tree. EEL was first identified for its erythrocyte agglutinating properties and specificity for B and H blood groups. However, a detailed molecular picture of the structural basis of carbohydrate recognition by EEL remains to be developed. In this study, we performed fluorescence titrations of a range of carbohydrates against EEL. Binding of EEL to a wide range of carbohydrates was observed, including a series of blood group-related carbohydrates, mannosides, chitotriose and sialic acid. Affinity was strongest for carbohydrates with H-related structures and the B trisaccharide. A homology model of EEL was produced from templates identified using the HHPred server, which employs hidden Markov models (HMMs) to identify templates. The HMM approach identified that the best templates for EEL were proteins featuring a ricin B-like (R-type) fold. Separate templates were used to model the core and binding site regions of the lectin. Through the use of constrained docking and spatial comparison with a template ligand, binding modes for the carbohydrate ligands were predicted. A relationship between the experimental binding energies and the computed binding energies of the selected docked poses was determined and optimized. Collectively, our results suggest that EEL utilizes a single site for recognition of carbohydrates terminating in a variety of monosaccharides.
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Affiliation(s)
- Mark Agostino
- School of Biomedical Sciences, CHIRI Biosciences, Curtin University, Perth, WA 6845, Australia Joint BSC-IRB Research Program in Computational Biology, Life Science Department, Barcelona Supercomputing Centre, Barcelona 08034, Spain Centre for Biomedical Research, Burnet Institute, Melbourne, VIC 3004, Australia Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Tony Velkov
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Tamir Dingjan
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Spencer J Williams
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia
| | - Elizabeth Yuriev
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Paul A Ramsland
- School of Biomedical Sciences, CHIRI Biosciences, Curtin University, Perth, WA 6845, Australia Centre for Biomedical Research, Burnet Institute, Melbourne, VIC 3004, Australia Department of Surgery Austin Health, University of Melbourne, Heidelberg, VIC 3084, Australia Department of Immunology, Alfred Medical Research and Education Precinct, Monash University, Melbourne, VIC 3004, Australia
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Arnott A, Wapling J, Mueller I, Ramsland PA, Siba PM, Reeder JC, Barry AE. Distinct patterns of diversity, population structure and evolution in the AMA1 genes of sympatric Plasmodium falciparum and Plasmodium vivax populations of Papua New Guinea from an area of similarly high transmission. Malar J 2014; 13:233. [PMID: 24930015 PMCID: PMC4085730 DOI: 10.1186/1475-2875-13-233] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 05/22/2014] [Indexed: 12/19/2022] Open
Abstract
Background As Plasmodium falciparum and Plasmodium vivax co-exist in most malaria-endemic regions outside sub-Saharan Africa, malaria control strategies in these areas must target both species in order to succeed. Population genetic analyses can predict the effectiveness of interventions including vaccines, by providing insight into patterns of diversity and evolution. The aim of this study was to investigate the population genetics of leading malaria vaccine candidate AMA1 in sympatric P. falciparum and P. vivax populations of Papua New Guinea (PNG), an area of similarly high prevalence (Pf = 22.3 to 38.8%, Pv = 15.3 to 31.8%). Methods A total of 72 Pfama1 and 102 Pvama1 sequences were collected from two distinct areas, Madang and Wosera, on the highly endemic PNG north coast. Results Despite a greater number of polymorphic sites in the AMA1 genes of P. falciparum (Madang = 52; Wosera = 56) compared to P. vivax (Madang = 36, Wosera = 34), the number of AMA1 haplotypes, haplotype diversity (Hd) and recombination (R) was far lower for P. falciparum (Madang = 12, Wosera = 20; Hd ≤0.92, R ≤45.8) than for P. vivax (Madang = 50, Wosera = 38; Hd = 0.99, R = ≤70.9). Balancing selection was detected only within domain I of AMA1 for P. vivax, and in both domains I and III for P. falciparum. Conclusions Higher diversity in the genes encoding P. vivax AMA1 than in P. falciparum AMA1 in this highly endemic area has important implications for development of AMA1-based vaccines in PNG and beyond. These results also suggest a smaller effective population size of P. falciparum compared to P. vivax, a finding that warrants further investigation. Differing patterns of selection on the AMA1 genes indicate that critical antigenic sites may differ between the species, highlighting the need for independent investigations of these two leading vaccine candidates.
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Affiliation(s)
| | | | | | | | | | | | - Alyssa E Barry
- Division of Infection and Immunity, Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia.
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Trist HM, Tan PS, Wines BD, Ramsland PA, Orlowski E, Stubbs J, Gardiner EE, Pietersz GA, Kent SJ, Stratov I, Burton DR, Hogarth PM. Polymorphisms and interspecies differences of the activating and inhibitory FcγRII of Macaca nemestrina influence the binding of human IgG subclasses. J Immunol 2013; 192:792-803. [PMID: 24342805 DOI: 10.4049/jimmunol.1301554] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Little is known of the impact of Fc receptor (FcR) polymorphism in macaques on the binding of human (hu)IgG, and nothing is known of this interaction in the pig-tailed macaque (Macaca nemestrina), which is used in preclinical evaluation of vaccines and therapeutic Abs. We defined the sequence and huIgG binding characteristics of the M. nemestrina activating FcγRIIa (mnFcγRIIa) and inhibitory FcγRIIb (mnFcγRIIb) and predicted their structures using the huIgGFc/huFcγRIIa crystal structure. Large differences were observed in the binding of huIgG by mnFcγRIIa and mnFcγRIIb compared with their human FcR counterparts. MnFcγRIIa has markedly impaired binding of huIgG1 and huIgG2 immune complexes compared with huFcγRIIa (His(131)). In contrast, mnFcγRIIb has enhanced binding of huIgG1 and broader specificity, as, unlike huFcγRIIb, it avidly binds IgG2. Mutagenesis and molecular modeling of mnFcγRIIa showed that Pro(159) and Tyr(160) impair the critical FG loop interaction with huIgG. The enhanced binding of huIgG1 and huIgG2 by mnFcγRIIb was shown to be dependent on His(131) and Met(132). Significantly, both His(131) and Met(132) are conserved across FcγRIIb of rhesus and cynomolgus macaques. We identified functionally significant polymorphism of mnFcγRIIa wherein proline at position 131, also an important polymorphic site in huFcγRIIa, almost abolished binding of huIgG2 and huIgG1 and reduced binding of huIgG3 compared with mnFcγRIIa His(131). These marked interspecies differences in IgG binding between human and macaque FcRs and polymorphisms within species have implications for preclinical evaluation of Abs and vaccines in macaques.
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Affiliation(s)
- Halina M Trist
- Centre for Biomedical Research, Burnet Institute, Melbourne, Victoria 3004, Australia
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Arnott A, Mueller I, Ramsland PA, Siba PM, Reeder JC, Barry AE. Global Population Structure of the Genes Encoding the Malaria Vaccine Candidate, Plasmodium vivax Apical Membrane Antigen 1 (PvAMA1). PLoS Negl Trop Dis 2013; 7:e2506. [PMID: 24205419 PMCID: PMC3814406 DOI: 10.1371/journal.pntd.0002506] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 09/16/2013] [Indexed: 12/22/2022] Open
Abstract
Background The Plasmodium vivax Apical Membrane Antigen 1 (PvAMA1) is a promising malaria vaccine candidate, however it remains unclear which regions are naturally targeted by host immunity and whether its high genetic diversity will preclude coverage by a monovalent vaccine. To assess its feasibility as a vaccine candidate, we investigated the global population structure of PvAMA1. Methodology and Principal Findings New sequences from Papua New Guinea (PNG, n = 102) were analysed together with published sequences from Thailand (n = 158), India (n = 8), Sri Lanka (n = 23), Venezuela (n = 74) and a collection of isolates from disparate geographic locations (n = 8). A total of 92 single nucleotide polymorphisms (SNPs) were identified including 22 synonymous SNPs and 70 non-synonymous (NS) SNPs. Polymorphisms and signatures of balancing (positive Tajima's D and low FST values) selection were predominantly clustered in domain I, suggesting it is a dominant target of protective immune responses. To estimate global antigenic diversity, haplotypes comprised of (i) non-singleton (n = 40) and (ii) common (≥10% minor allele frequency, n = 23) polymorphic amino acid sites were then analysed revealing a total of 219 and 210 distinct haplotypes, respectively. Although highly diverse, the 210 haplotypes comprised of only common polymorphisms were grouped into eleven clusters, however substantial geographic differentiation was observed, and this may have implications for the efficacy of PvAMA1 vaccines in different malaria-endemic areas. The PNG haplotypes form a distinct group of clusters not found in any other geographic region. Vaccine haplotypes were rare and geographically restricted, suggesting potentially poor efficacy of candidate PvAMA1 vaccines. Conclusions It may be possible to cover the existing global PvAMA1 diversity by selection of diverse alleles based on these analyses however it will be important to first define the relationships between the genetic and antigenic diversity of this molecule. Traditionally misclassified as benign and neglected as a research priority, it is now understood that P. vivax is an increasingly important cause of human malaria. This important human pathogen poses an enormous obstacle to malaria control and elimination efforts due its broad geographic distribution, ability to cause recurring episodes of malaria after long periods of inactivity and extreme biodiversity. Vaccines are an essential component of global malaria control and elimination campaigns but the diversity of malaria antigens is thought to be a major cause of vaccine failure. Furthermore, at present the majority of current vaccine research is directed toward P. falciparum. The aims of this study were to investigate the global diversity of the P. vivax vaccine candidate, Apical Membrane Antigen 1 (PvAMA1), to determine the feasibility of designing a globally effective PvAMA1 vaccine and to determine which region of PvAMA1 is targeted by host immune responses, in order to identify the most promising vaccine candidates. We report that PvAMA1 diversity is extremely high, and that PvAMA1 domain I is a dominant target of host immune responses. These analyses of PvAMA1 diversity from several geographic regions provide a framework to guide development of a broadly efficacious P. vivax vaccine.
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Affiliation(s)
- Alicia Arnott
- Centre for Biomedical Research, Burnet Institute, Melbourne, Australia
| | - Ivo Mueller
- Barcelona Centre for International Health Research, Barcelona, Spain
- Division of Infection and Immunity, Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Paul A. Ramsland
- Centre for Biomedical Research, Burnet Institute, Melbourne, Australia
- Department of Immunology, Monash University, Melbourne, Australia
- Department of Surgery Austin Health, University of Melbourne, Heidelberg, Australia
- School of Biomedical Sciences, CHIRI Biosciences, Faculty of Health Sciences, Curtin University, Perth, Australia
| | - Peter M. Siba
- Papua New Guinea Institute for Medical Research, Goroka, Papua New Guinea
| | - John C. Reeder
- Centre for Population Health, Burnet Institute, Melbourne, Australia
- Department of Epidemiology and Preventative Medicine, Monash University, Melbourne, Australia
| | - Alyssa E. Barry
- Division of Infection and Immunity, Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Australia
- * E-mail:
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Roche M, Salimi H, Duncan R, Wilkinson BL, Chikere K, Moore MS, Webb NE, Zappi H, Sterjovski J, Flynn JK, Ellett A, Gray LR, Lee B, Jubb B, Westby M, Ramsland PA, Lewin SR, Payne RJ, Churchill MJ, Gorry PR. A common mechanism of clinical HIV-1 resistance to the CCR5 antagonist maraviroc despite divergent resistance levels and lack of common gp120 resistance mutations. Retrovirology 2013; 10:43. [PMID: 23602046 PMCID: PMC3648390 DOI: 10.1186/1742-4690-10-43] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2012] [Accepted: 04/17/2013] [Indexed: 12/02/2022] Open
Abstract
Background The CCR5 antagonist maraviroc (MVC) inhibits human immunodeficiency virus type 1 (HIV-1) entry by altering the CCR5 extracellular loops (ECL), such that the gp120 envelope glycoproteins (Env) no longer recognize CCR5. The mechanisms of HIV-1 resistance to MVC, the only CCR5 antagonist licensed for clinical use are poorly understood, with insights into MVC resistance almost exclusively limited to knowledge obtained from in vitro studies or from studies of resistance to other CCR5 antagonists. To more precisely understand mechanisms of resistance to MVC in vivo, we characterized Envs isolated from 2 subjects who experienced virologic failure on MVC. Results Envs were cloned from subjects 17 and 24 before commencement of MVC (17-Sens and 24-Sens) and after virologic failure (17-Res and 24-Res). The Envs cloned during virologic failure showed broad divergence in resistance levels, with 17-Res Env exhibiting a relatively high maximal percent inhibition (MPI) of ~90% in NP2-CD4/CCR5 cells and peripheral blood mononuclear cells (PBMC), and 24-Res Env exhibiting a very low MPI of ~0 to 12% in both cell types, indicating relatively “weak” and “strong” resistance, respectively. Resistance mutations were strain-specific and mapped to the gp120 V3 loop. Affinity profiling by the 293-Affinofile assay and mathematical modeling using VERSA (Viral Entry Receptor Sensitivity Analysis) metrics revealed that 17-Res and 24-Res Envs engaged MVC-bound CCR5 inefficiently or very efficiently, respectively. Despite highly divergent phenotypes, and a lack of common gp120 resistance mutations, both resistant Envs exhibited an almost superimposable pattern of dramatically increased reliance on sulfated tyrosine residues in the CCR5 N-terminus, and on histidine residues in the CCR5 ECLs. This altered mechanism of CCR5 engagement rendered both the resistant Envs susceptible to neutralization by a sulfated peptide fragment of the CCR5 N-terminus. Conclusions Clinical resistance to MVC may involve divergent Env phenotypes and different genetic alterations in gp120, but the molecular mechanism of resistance of the Envs studied here appears to be related. The increased reliance on sulfated CCR5 N-terminus residues suggests a new avenue to block HIV-1 entry by CCR5 N-terminus sulfopeptidomimetic drugs.
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Affiliation(s)
- Michael Roche
- Center for Virology, Monash University, Melbourne, Victoria, Australia
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Drummer HE, Hill MK, Maerz AL, Wood S, Ramsland PA, Mak J, Poumbourios P. Allosteric modulation of the HIV-1 gp120-gp41 association site by adjacent gp120 variable region 1 (V1) N-glycans linked to neutralization sensitivity. PLoS Pathog 2013; 9:e1003218. [PMID: 23592978 PMCID: PMC3616969 DOI: 10.1371/journal.ppat.1003218] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Accepted: 01/15/2013] [Indexed: 12/28/2022] Open
Abstract
The HIV-1 gp120-gp41 complex, which mediates viral fusion and cellular entry, undergoes rapid evolution within its external glycan shield to enable escape from neutralizing antibody (NAb). Understanding how conserved protein determinants retain functionality in the context of such evolution is important for their evaluation and exploitation as potential drug and/or vaccine targets. In this study, we examined how the conserved gp120-gp41 association site, formed by the N- and C-terminal segments of gp120 and the disulfide-bonded region (DSR) of gp41, adapts to glycan changes that are linked to neutralization sensitivity. To this end, a DSR mutant virus (K601D) with defective gp120-association was sequentially passaged in peripheral blood mononuclear cells to select suppressor mutations. We reasoned that the locations of suppressors point to structural elements that are functionally linked to the gp120-gp41 association site. In culture 1, gp120 association and viral replication was restored by loss of the conserved glycan at Asn136 in V1 (T138N mutation) in conjunction with the L494I substitution in C5 within the association site. In culture 2, replication was restored with deletion of the N139INN sequence, which ablates the overlapping Asn141-Asn142-Ser-Ser potential N-linked glycosylation sequons in V1, in conjunction with D601N in the DSR. The 136 and 142 glycan mutations appeared to exert their suppressive effects by altering the dependence of gp120-gp41 interactions on the DSR residues, Leu593, Trp596 and Lys601. The 136 and/or 142 glycan mutations increased the sensitivity of HIV-1 pseudovirions to the glycan-dependent NAbs 2G12 and PG16, and also pooled IgG obtained from HIV-1-infected individuals. Thus adjacent V1 glycans allosterically modulate the distal gp120-gp41 association site. We propose that this represents a mechanism for functional adaptation of the gp120-gp41 association site to an evolving glycan shield in a setting of NAb selection. The envelope glycoprotein gp120-gp41 complex of HIV-1 mediates receptor attachment and virus-cell membrane fusion, leading to cellular entry. A shield of asparagine-linked oligosaccharides occludes the gp120-gp41 protein surface and evolution of this glycan shield provides a means for evading circulating neutralizing antibody. Here we examined how conserved structural elements of the glycoprotein complex, in particular the gp120-gp41 association site, retain functionality in the context of glycan shield evolution. This information is important for the evaluation and exploitation of such conserved functional determinants as potential drug and/or vaccine targets. Our data indicate that the loss of either of 2 adjacent glycans in variable region 1 of gp120 leads to changes in local and remote glycan-dependent epitopes and that this is linked to a remodelling of gp120-gp41 interactions in order to maintain a functional gp120-gp41 complex. We propose that this represents a mechanism for the functional adaptation of the gp120-gp41 association site to an evolving glycan shield in a setting of neutralizing antibody selection.
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Affiliation(s)
- Heidi E. Drummer
- Macfarlane Burnet Institute for Medical Research and Public Health, Melbourne, Victoria, Australia
- Department of Microbiology, Monash University, Clayton, Victoria, Australia
- Department of Microbiology and Immunology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Melissa K. Hill
- Macfarlane Burnet Institute for Medical Research and Public Health, Melbourne, Victoria, Australia
| | - Anne L. Maerz
- Macfarlane Burnet Institute for Medical Research and Public Health, Melbourne, Victoria, Australia
| | - Stephanie Wood
- Macfarlane Burnet Institute for Medical Research and Public Health, Melbourne, Victoria, Australia
| | - Paul A. Ramsland
- Macfarlane Burnet Institute for Medical Research and Public Health, Melbourne, Victoria, Australia
- Department of Immunology, Monash University, Alfred Medical Research and Education Precinct, Melbourne, Victoria, Australia
- Department of Surgery, Austin Health, The University of Melbourne, Heidelberg, Victoria, Australia
| | - Johnson Mak
- Macfarlane Burnet Institute for Medical Research and Public Health, Melbourne, Victoria, Australia
- Department of Microbiology, Monash University, Clayton, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
- Deakin University School of Medicine, Geelong, Victoria, Australia
| | - Pantelis Poumbourios
- Macfarlane Burnet Institute for Medical Research and Public Health, Melbourne, Victoria, Australia
- Department of Microbiology, Monash University, Clayton, Victoria, Australia
- * E-mail:
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Yuriev E, Ramsland PA. Latest developments in molecular docking: 2010-2011 in review. J Mol Recognit 2013; 26:215-39. [PMID: 23526775 DOI: 10.1002/jmr.2266] [Citation(s) in RCA: 193] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2012] [Revised: 01/16/2013] [Accepted: 01/19/2013] [Indexed: 12/28/2022]
Affiliation(s)
- Elizabeth Yuriev
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences; Monash University; Parkville; VIC; 3052; Australia
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Agostino M, Mancera RL, Ramsland PA, Yuriev E. AutoMap: A tool for analyzing protein–ligand recognition using multiple ligand binding modes. J Mol Graph Model 2013; 40:80-90. [DOI: 10.1016/j.jmgm.2013.01.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Accepted: 01/01/2013] [Indexed: 10/27/2022]
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Meliga SC, Farrugia W, Ramsland PA, Falconer RJ. Cold-Induced Precipitation of a Monoclonal IgM: A Negative Activation Enthalpy Reaction. J Phys Chem B 2013; 117:490-4. [DOI: 10.1021/jp309109k] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Stefano C. Meliga
- Australian Institute for Bioengineering
and Nanotechnology, University of Queensland, St. Lucia, Qld 4072, Australia
| | - William Farrugia
- Centre for Immunology, Burnet Institute, Melbourne, Vic 3004, Australia
| | - Paul A. Ramsland
- Centre for Immunology, Burnet Institute, Melbourne, Vic 3004, Australia
- Department of Surgery
Austin Health, University of Melbourne, Heidelberg, Vic 3084, Australia
- Department of Immunology, Monash University, Alfred Medical Research
and Education Precinct, Melbourne, Vic 3004, Australia
| | - Robert J. Falconer
- Department of Chemical & Biological Engineering, ChELSI Institute, University of Sheffield, Sheffield S1 3JD, England
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Salimi H, Roche M, Webb N, Gray LR, Chikere K, Sterjovski J, Ellett A, Wesselingh SL, Ramsland PA, Lee B, Churchill MJ, Gorry PR. Macrophage-tropic HIV-1 variants from brain demonstrate alterations in the way gp120 engages both CD4 and CCR5. J Leukoc Biol 2012; 93:113-26. [PMID: 23077246 DOI: 10.1189/jlb.0612308] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
BR-derived HIV-1 strains have an exceptional ability to enter macrophages via mechanisms involving their gp120 Env that remain incompletely understood. Here, we used cell-based affinity-profiling methods and mathematical modeling to generate quantitative VERSA metrics that simultaneously measure Env-CD4 and Env-CCR5 interactions. These metrics were analyzed to distinguish the phenotypes of M-tropic and non-M-tropic CCR5-using HIV-1 variants derived from autopsy BRs and LNs, respectively. We show that highly M-tropic Env variants derived from brain can be defined by two distinct and simultaneously occurring phenotypes. First, BR-derived Envs demonstrated an enhanced ability to interact with CD4 compared with LN-derived Envs, permitting entry into cells expressing scant levels of CD4. Second, BR-derived Envs displayed an altered mechanism of engagement between CD4-bound gp120 and CCR5 occurring in tandem. With the use of epitope mapping, mutagenesis, and structural studies, we show that this altered mechanism is characterized by increased exposure of CD4-induced epitopes in gp120 and by a more critical interaction between BR-derived Envs and the CCR5 N-terminus, which was associated with the predicted presence of additional atomic contacts formed at the gp120-CCR5 N-terminus interface. Our results suggest that BR-derived HIV-1 variants with highly efficient macrophage entry adopt conformations in gp120 that simultaneously alter the way in which the Env interacts with CD4 and CCR5.
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Affiliation(s)
- Hamid Salimi
- Center for Virology, Burnet Institute, Melbourne, Victoria, Australia
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Sterjovski J, Churchill MJ, Ellett A, Wesselingh SL, Ramsland PA, Gorry PR. Structural elements of primary CCR5-using HIV-1 gp120 proteins influencing sensitivity and resistance to the broadly neutralizing monoclonal antibody b12. Virology 2012; 432:394-404. [PMID: 22818780 DOI: 10.1016/j.virol.2012.06.024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Revised: 06/18/2012] [Accepted: 06/26/2012] [Indexed: 11/18/2022]
Abstract
Structure-guided approaches to HIV-1 vaccine design depend on knowledge of the presentation of neutralizing epitopes on gp120, such as the epitope for the broadly neutralizing mAb b12. Here, we characterized predicted three-dimensional structures of functionally diverse gp120 proteins in their b12-bound conformation, to better understand the gp120 determinants that expose or occlude the b12 epitope. Mapping the gp120-b12 binding interface identified amino acid polymorphisms within the C2, C3, C4 and V5 regions of gp120 associated with augmented b12 binding, and importantly, identified residues in the b12-exclusive binding domain of gp120 that are important for b12 neutralization resistance. Structural studies suggest that these b12 resistance variants promote reduced conformational flexibility in the b12 recognition site, which we show involves structural alterations within the gp120 CD4 binding loop and the V4 loop. Together, our studies provide new mechanistic insights into the gp120 determinants influencing sensitivity and resistance to HIV-1 neutralization by b12.
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