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Ruiz J, Gomes C. In silico analysis of Pap31 from Bartonella bacilliformis and other Bartonella spp. INFECTION GENETICS AND EVOLUTION 2020; 84:104482. [PMID: 32738366 DOI: 10.1016/j.meegid.2020.104482] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 07/18/2020] [Accepted: 07/23/2020] [Indexed: 01/01/2023]
Abstract
Pap31 is an outer membrane protein of Bartonella bacilliformis which is considered to be a potential antigenic candidate for the development of diagnostic tools. The present study aimed to compare Pap31 from B. bacilliformis with that of other Bartonella spp. The results showed the presence of at least 5 different B. bacilliformis Pap31 alleles, with the strain Ver097 being the most divergent (89.7% of identity with the reference strain KC583). The most significant finding was the presence of a variable number (1 to 3) of 6 amino acid tandem repeats (GTEGGG) in the different B. bacilliformis Pap31 alleles, with no similar structure in other established Bartonella spp., except for Bartonella ancashensis, another Bartonella spp. isolated from chronic cases of Carrion's disease. In both B. bacilliformis and B. ancashensis this repetitive region was coincident with the most predicted immunogenic region of the protein. In other microorganisms, the presence of amino acid tandem repeats has been related to the development of poorly functional antibodies. The findings of this study also suggest a utility of Pap31 amino acid tandem repeats as potential contributors to the immune evasion of Carrion's disease-related Bartonella spp. and the establishment of asymptomatic B. bacilliformis / B. ancashensis infections.
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Affiliation(s)
- Joaquim Ruiz
- Laboratorio de Microbiología Molecular y Genómica Bacteriana, Universidad Científica del Sur, Lima, Peru.
| | - Cláudia Gomes
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
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2
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A disordered acidic domain in GPIHBP1 harboring a sulfated tyrosine regulates lipoprotein lipase. Proc Natl Acad Sci U S A 2018; 115:E6020-E6029. [PMID: 29899144 DOI: 10.1073/pnas.1806774115] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The intravascular processing of triglyceride-rich lipoproteins depends on lipoprotein lipase (LPL) and GPIHBP1, a membrane protein of endothelial cells that binds LPL within the subendothelial spaces and shuttles it to the capillary lumen. In the absence of GPIHBP1, LPL remains mislocalized within the subendothelial spaces, causing severe hypertriglyceridemia (chylomicronemia). The N-terminal domain of GPIHBP1, an intrinsically disordered region (IDR) rich in acidic residues, is important for stabilizing LPL's catalytic domain against spontaneous and ANGPTL4-catalyzed unfolding. Here, we define several important properties of GPIHBP1's IDR. First, a conserved tyrosine in the middle of the IDR is posttranslationally modified by O-sulfation; this modification increases both the affinity of GPIHBP1-LPL interactions and the ability of GPIHBP1 to protect LPL against ANGPTL4-catalyzed unfolding. Second, the acidic IDR of GPIHBP1 increases the probability of a GPIHBP1-LPL encounter via electrostatic steering, increasing the association rate constant (kon) for LPL binding by >250-fold. Third, we show that LPL accumulates near capillary endothelial cells even in the absence of GPIHBP1. In wild-type mice, we expect that the accumulation of LPL in close proximity to capillaries would increase interactions with GPIHBP1. Fourth, we found that GPIHBP1's IDR is not a key factor in the pathogenicity of chylomicronemia in patients with the GPIHBP1 autoimmune syndrome. Finally, based on biophysical studies, we propose that the negatively charged IDR of GPIHBP1 traverses a vast space, facilitating capture of LPL by capillary endothelial cells and simultaneously contributing to GPIHBP1's ability to preserve LPL structure and activity.
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Yruela I, Contreras-Moreira B, Magalhães C, Osório NS, Gonzalo-Asensio J. Mycobacterium tuberculosis Complex Exhibits Lineage-Specific Variations Affecting Protein Ductility and Epitope Recognition. Genome Biol Evol 2017; 8:3751-3764. [PMID: 28062754 PMCID: PMC5521731 DOI: 10.1093/gbe/evw279] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/18/2016] [Indexed: 12/19/2022] Open
Abstract
The advent of whole-genome sequencing has provided an unprecedented detail about the evolution and genetic significance of species-specific variations across the whole Mycobacterium tuberculosis Complex. However, little attention has been focused on understanding the functional roles of these variations in the protein coding sequences. In this work, we compare the coding sequences from 74 sequenced mycobacterial species including M. africanum, M. bovis, M. canettii, M. caprae, M. orygis, and M. tuberculosis. Results show that albeit protein variations affect all functional classes, those proteins involved in lipid and intermediary metabolism and respiration have accumulated mutations during evolution. To understand the impact of these mutations on protein functionality, we explored their implications on protein ductility/disorder, a yet unexplored feature of mycobacterial proteomes. In agreement with previous studies, we found that a Gly71Ile substitution in the PhoPR virulence system severely affects the ductility of its nearby region in M. africanum and animal-adapted species. In the same line of evidence, the SmtB transcriptional regulator shows amino acid variations specific to the Beijing lineage, which affects the flexibility of the N-terminal trans-activation domain. Furthermore, despite the fact that MTBC epitopes are evolutionary hyperconserved, we identify strain- and lineage-specific amino acid mutations affecting previously known T-cell epitopes such as EsxH and FbpA (Ag85A). Interestingly, in silico studies reveal that these variations result in differential interaction of epitopes with the main HLA haplogroups.
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Affiliation(s)
- Inmaculada Yruela
- Estación Experimental de Aula Dei-Consejo Superior de Investigaciones Científicas (EEAD-CSIC), Zaragoza, Spain.,Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada I+D+i al CSIC, Zaragoza, Spain
| | - Bruno Contreras-Moreira
- Estación Experimental de Aula Dei-Consejo Superior de Investigaciones Científicas (EEAD-CSIC), Zaragoza, Spain.,Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada I+D+i al CSIC, Zaragoza, Spain.,Fundación ARAID, Aragón, Spain
| | - Carlos Magalhães
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Nuno S Osório
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Jesús Gonzalo-Asensio
- Grupo de Genética de Micobacterias, Departamento de Microbiología y Medicina Preventiva, Facultad de Medicina, Universidad de Zaragoza, Zaragoza, Spain.,CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain.,Instituto de Biocomputación y Física de Sistemas Complejos (BIFI-UNIZAR), Zaragoza, Spain.,Servicio de Microbiología Hospital Universitario Miguel Servet, ISS Aragón, Zaragoza, Spain
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DeForte S, Uversky VN. Quarterly intrinsic disorder digest (April-May-June, 2014). INTRINSICALLY DISORDERED PROTEINS 2017; 5:e1287505. [PMID: 28321370 DOI: 10.1080/21690707.2017.1287505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
This is the 6th issue of the Digested Disorder series that continues to use only 2 criteria for inclusion of a paper to this digest: The publication date (a paper should be published within the covered time frame) and the topic (a paper should be dedicated to any aspect of protein intrinsic disorder). The current digest issue covers papers published during the second quarter of 2014; i.e., during the period of April, May, and June of 2014. Similar to previous issues, the papers are grouped hierarchically by topics they cover, and for each of the included papers a short description is given on its major findings.
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Affiliation(s)
- Shelly DeForte
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA; Département De Biochimie and Centre Robert-Cedergren, Bio-Informatique et Génomique, Université de Montréal, Succursale Centre-Ville, Montreal, Quebec, Canada
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA; USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA; Laboratory of New Methods in Biology, Institute of Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region, Russia; Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
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Jandrlić DR. SVM and SVR-based MHC-binding prediction using a mathematical presentation of peptide sequences. Comput Biol Chem 2016; 65:117-127. [PMID: 27816828 DOI: 10.1016/j.compbiolchem.2016.10.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 09/16/2016] [Accepted: 10/24/2016] [Indexed: 11/16/2022]
Abstract
At present, there are a number of methods for the prediction of T-cell epitopes and major histocompatibility complex (MHC)-binding peptides. Despite numerous methods for predicting T-cell epitopes, there still exist limitations that affect the reliability of prevailing methods. For this reason, the development of models with high accuracy are crucial. An accurate prediction of the peptides that bind to specific major histocompatibility complex class I and II (MHC-I and MHC-II) molecules is important for an understanding of the functioning of the immune system and the development of peptide-based vaccines. Peptide binding is the most selective step in identifying T-cell epitopes. In this paper, we present a new approach to predicting MHC-binding ligands that takes into account new weighting schemes for position-based amino acid frequencies, BLOSUM and VOGG substitution of amino acids, and the physicochemical and molecular properties of amino acids. We have made models for quantitatively and qualitatively predicting MHC-binding ligands. Our models are based on two machine learning methods support vector machine (SVM) and support vector regression (SVR), where our models have used for feature selection, several different encoding and weighting schemes for peptides. The resulting models showed comparable, and in some cases better, performance than the best existing predictors. The obtained results indicate that the physicochemical and molecular properties of amino acids (AA) contribute significantly to the peptide-binding affinity.
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Affiliation(s)
- Davorka R Jandrlić
- University of Belgrade, Faculty of Mechanical Engineering, Kraljice Marije 16, Belgrade, Serbia.
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Jandrlić DR, Lazić GM, Mitić NS, Pavlović MD. Software tools for simultaneous data visualization and T cell epitopes and disorder prediction in proteins. J Biomed Inform 2016; 60:120-31. [PMID: 26851400 DOI: 10.1016/j.jbi.2016.01.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Revised: 01/15/2016] [Accepted: 01/28/2016] [Indexed: 11/16/2022]
Abstract
We have developed EpDis and MassPred, extendable open source software tools that support bioinformatic research and enable parallel use of different methods for the prediction of T cell epitopes, disorder and disordered binding regions and hydropathy calculation. These tools offer a semi-automated installation of chosen sets of external predictors and an interface allowing for easy application of the prediction methods, which can be applied either to individual proteins or to datasets of a large number of proteins. In addition to access to prediction methods, the tools also provide visualization of the obtained results, calculation of consensus from results of different methods, as well as import of experimental data and their comparison with results obtained with different predictors. The tools also offer a graphical user interface and the possibility to store data and the results obtained using all of the integrated methods in the relational database or flat file for further analysis. The MassPred part enables a massive parallel application of all integrated predictors to the set of proteins. Both tools can be downloaded from http://bioinfo.matf.bg.ac.rs/home/downloads.wafl?cat=Software. Appendix A includes the technical description of the created tools and a list of supported predictors.
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Affiliation(s)
- Davorka R Jandrlić
- University of Belgrade, Faculty of Mechanical Engineering, Kraljice Marije 16, Belgrade, Serbia.
| | - Goran M Lazić
- University of Belgrade, Faculty of Mathematics, P.O.B. 550, Studentski trg 16/IV, Belgrade, Serbia.
| | - Nenad S Mitić
- University of Belgrade, Faculty of Mathematics, P.O.B. 550, Studentski trg 16/IV, Belgrade, Serbia.
| | - Mirjana D Pavlović
- University of Belgrade, Institute of General and Physical Chemistry, Studentski trg 12/V, Belgrade, Serbia.
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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] [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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Abidin RS, Lua LHL, Middelberg APJ, Sainsbury F. Insert engineering and solubility screening improves recovery of virus-like particle subunits displaying hydrophobic epitopes. Protein Sci 2015; 24:1820-8. [PMID: 26401641 DOI: 10.1002/pro.2775] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 08/20/2015] [Indexed: 11/09/2022]
Abstract
The Polyomavirus coat protein, VP1 has been developed as an epitope presentation system able to provoke humoral immunity against a variety of pathogens, such as Influenza and Group A Streptococcus. The ability of the system to carry cytotoxic T cell epitopes on a surface-exposed loop and the impact on protein solubility has not been examined. Four variations of three selected epitopes were cloned into surface-exposed loops of VP1, and expressed in Escherichia coli. VP1 pentamers, also known as capsomeres, were purified via a glutathione-S-transferase tag. Size exclusion chromatography indicated severe aggregation of the recombinant VP1 during enzymatic tag removal resulting from the introduction the hydrophobic epitopes. Inserts were modified to possess double aspartic acid residues at each end of the hydrophobic epitopes and a high-throughput buffer condition screen was implemented with protein aggregation monitored during tag removal by spectrophotometry and dynamic light scattering. These analyses showed that the insertion of charged residues at the extremities of epitopes could improve solubility of capsomeres and revealed multiple windows of opportunity for further condition optimization. A combination of epitope design, pH optimization, and the additive l-arginine permitted the recovery of soluble VP1 pentamers presenting hydrophobic epitopes and their subsequent assembly into virus-like particles.
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Affiliation(s)
- R S Abidin
- The University of Queensland, Australian Institute for Bioengineering and Nanotechnology Centre for Biomolecular Engineering, St Lucia, Queensland, 4072, Australia
| | - L H L Lua
- Protein Expression Facility, The University of Queensland, St Lucia, Queensland, 4072, Australia
| | - A P J Middelberg
- The University of Queensland, Australian Institute for Bioengineering and Nanotechnology Centre for Biomolecular Engineering, St Lucia, Queensland, 4072, Australia
| | - F Sainsbury
- The University of Queensland, Australian Institute for Bioengineering and Nanotechnology Centre for Biomolecular Engineering, St Lucia, Queensland, 4072, Australia
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Pavlović MD, Jandrlić DR, Mitić NS. Epitope distribution in ordered and disordered protein regions. Part B — Ordered regions and disordered binding sites are targets of T- and B-cell immunity. J Immunol Methods 2014; 407:90-107. [DOI: 10.1016/j.jim.2014.03.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 03/31/2014] [Accepted: 03/31/2014] [Indexed: 01/04/2023]
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