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McKenna S, Aylward F, Miliara X, Lau RJ, Huemer CB, Giblin SP, Huse KK, Liang M, Reeves L, Pearson M, Xu Y, Rouse SL, Pease JE, Sriskandan S, Kagawa TF, Cooney J, Matthews S. The protease associated (PA) domain in ScpA from Streptococcus pyogenes plays a role in substrate recruitment. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2023; 1871:140946. [PMID: 37562488 DOI: 10.1016/j.bbapap.2023.140946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/28/2023] [Accepted: 08/06/2023] [Indexed: 08/12/2023]
Abstract
Annually, over 18 million disease cases and half a million deaths worldwide are estimated to be caused by Group A Streptococcus. ScpA (or C5a peptidase) is a well characterised member of the cell enveleope protease family, which possess a S8 subtilisin-like catalytic domain and a shared multi-domain architecture. ScpA cleaves complement factors C5a and C3a, impairing the function of these critical anaphylatoxins and disrupts complement-mediated innate immunity. Although the high resolution structure of ScpA is known, the details of how it recognises its substrate are only just emerging. Previous studies have identified a distant exosite on the 2nd fibronectin domain that plays an important role in recruitment via an interaction with the substrate core. Here, using a combination of solution NMR spectroscopy, mutagenesis with functional assays and computational approaches we identify a second exosite within the protease-associated (PA) domain. We propose a model in which the PA domain assists optimal delivery of the substrate's C terminus to the active site for cleavage.
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Affiliation(s)
- Sophie McKenna
- Department of Life Sciences, Imperial College London, South Kensington Campus SW7 2AZ, UK
| | - Frances Aylward
- Department of Life Sciences, Imperial College London, South Kensington Campus SW7 2AZ, UK
| | - Xeni Miliara
- Department of Life Sciences, Imperial College London, South Kensington Campus SW7 2AZ, UK
| | - Rikin J Lau
- Department of Life Sciences, Imperial College London, South Kensington Campus SW7 2AZ, UK
| | - Camilla Berg Huemer
- Department of Life Sciences, Imperial College London, South Kensington Campus SW7 2AZ, UK
| | - Sean P Giblin
- National Heart and Lung Institute, Imperial College London, London SW7 2AZ, UK
| | - Kristin K Huse
- Department of Infectious Disease, Imperial College London, London W12 0NN, UK; Centre for Bacterial Resistance Biology, Imperial College London, London SW7 2AZ, UK
| | - Mingyang Liang
- Department of Life Sciences, Imperial College London, South Kensington Campus SW7 2AZ, UK
| | - Lucy Reeves
- Department of Life Sciences, Imperial College London, South Kensington Campus SW7 2AZ, UK
| | - Max Pearson
- Department of Infectious Disease, Imperial College London, London W12 0NN, UK
| | - Yingqi Xu
- Department of Life Sciences, Imperial College London, South Kensington Campus SW7 2AZ, UK
| | - Sarah L Rouse
- Department of Life Sciences, Imperial College London, South Kensington Campus SW7 2AZ, UK
| | - James E Pease
- National Heart and Lung Institute, Imperial College London, London SW7 2AZ, UK
| | - Shiranee Sriskandan
- Department of Infectious Disease, Imperial College London, London W12 0NN, UK; Centre for Bacterial Resistance Biology, Imperial College London, London SW7 2AZ, UK
| | - Todd F Kagawa
- Department of Biological Sciences, University of Limerick, Limerick, Ireland; Bernal Institute, University of Limerick, Limerick, Ireland
| | - Jakki Cooney
- Department of Biological Sciences, University of Limerick, Limerick, Ireland; Bernal Institute, University of Limerick, Limerick, Ireland
| | - Stephen Matthews
- Department of Life Sciences, Imperial College London, South Kensington Campus SW7 2AZ, UK; Centre for Bacterial Resistance Biology, Imperial College London, London SW7 2AZ, UK.
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2
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Perkins SJ, Smith KF, Nealis AS, Lachmann PJ, Harrison RA. Structural homologies of component C5 of human complement with components C3 and C4 by neutron scattering. Biochemistry 2002. [DOI: 10.1021/bi00457a012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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3
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Anderson CY, Kellogg GE, Freer RJ. C5aR ligand peptide 3D QSAR study performed with an applied linear conformation. THE JOURNAL OF PEPTIDE RESEARCH : OFFICIAL JOURNAL OF THE AMERICAN PEPTIDE SOCIETY 1997; 49:476-83. [PMID: 9266474 DOI: 10.1111/j.1399-3011.1997.tb01154.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A 3D quantitative structure-activity relationship study (QSAR) of binding and activation of the human C5a receptor by peptide analogs of the C-terminal binding domain of C5a anaphylatoxin is reported. Using published C5a analog affinity and activity data, this paper seeks to elucidate the pharmacophore for the high affinity C-terminal binding domain of the C5a peptide with the molecular modeling technique of comparative molecular field analysis (CoMFA). In order to model peptides for which there was incomplete conformational data, an arbitrary linear conformation was imposed upon the highly flexible C5a analogs. The resulting models yield a crossvalidated q2 of 0.889 and 0.787, for receptor-ligand affinity and EC50 calcium release activity, respectively, suggesting these models have good predictive ability for other test peptides.
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Affiliation(s)
- C Y Anderson
- Biomedical Engineering Program, Virginia Commonwealth University, Richmond, USA
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4
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Federwisch M, Wollmer A, Emde M, Stühmer T, Melcher T, Klos A, Köhl J, Bautsch W. Tryptophan mutants of human C5a anaphylatoxin: a fluorescence anisotropy decay and energy transfer study. Biophys Chem 1993; 46:237-48. [PMID: 8343570 DOI: 10.1016/0301-4622(93)80017-d] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Three mutants of the anaphylatoxin C5a were prepared with positions 2, 64 and 70, respectively, substituted by tryptophan. The last mutant was additionally labelled at Cys27 for fluorescence energy transfer (FET) measurements. The structural integrity and biological activity of the molecules were not affected. Fluorescence anisotropy decay (FAD) measurements showed that the rotational correlation time for tryptophan decreases in the order: [Trp2]rhC5a > [Trp64]rhC5a > [Trp70]rhC5a, indicating an increasing mobility of the side chain. Measurements of the fluorescence energy transfer from Trp70 to the 1,5-AEDANS group at Cys27 yielded a distance distribution of 2.4 +/- 0.8 nm. This value is compatible with the C-terminal chain being arranged as a slightly stretched helix pointing away from the body of the molecule.
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Affiliation(s)
- M Federwisch
- Institut für Biochemie, Rheinisch-Westfälische Technische Hochschule Aachen, Klinikum, Germany
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5
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Ring CS, Sun E, McKerrow JH, Lee GK, Rosenthal PJ, Kuntz ID, Cohen FE. Structure-based inhibitor design by using protein models for the development of antiparasitic agents. Proc Natl Acad Sci U S A 1993; 90:3583-7. [PMID: 8475107 PMCID: PMC46345 DOI: 10.1073/pnas.90.8.3583] [Citation(s) in RCA: 194] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The lack of an experimentally determined structure of a target protein frequently limits the application of structure-based drug design methods. In an effort to overcome this limitation, we have investigated the use of computer model-built structures for the identification of previously unknown inhibitors of enzymes from two major protease families, serine and cysteine proteases. We have successfully used our model-built structures to identify computationally and to confirm experimentally the activity of nonpeptidic inhibitors directed against important enzymes in the schistosome [2-(4-methoxybenzoyl)-1-naphthoic acid, Ki = 3 microM] and malaria (oxalic bis[(2-hydroxy-1-naphthylmethylene)hydrazide], IC50 = 6 microM) parasite life cycles.
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Affiliation(s)
- C S Ring
- Department of Pharmaceutical Chemistry, University of California, San Francisco 94143-0446
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6
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Köhl J, Lübbers B, Klos A, Bautsch W, Casaretto M. Evaluation of the C-terminal C5a effector site with short synthetic C5a analog peptides. Eur J Immunol 1993; 23:646-52. [PMID: 8383599 DOI: 10.1002/eji.1830230311] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Biological activities have been determined for a series of 18 peptides based on the C-terminal sequence of human or rat C5a. Lysosomal enzyme release was tested in two cell types, the promyelotic leukemia cell line U937 and polymorphonuclear leukocytes. In addition, an ATP-release assay with guinea pig platelets was performed. It was demonstrated that the C-terminal octapeptide 67-74 of human C5a represents the minimal sequence required to induce a measurable biological signal in all assays. Extending this peptide to a length of 21 amino acids produced at best only a slight enhancement of potency. Amino acid replacements with either tryptophanyl or phenylalanyl residues in positions between 65-69 either increased potency (at position 67), or abrogated potency (at position 66) in the two lysosomal enzyme assays. N-terminal acylation with the fluorenylmethoxy-carbonyl-aminohexanoyl group slightly enhanced C5a potency. In desensitization experiments with guinea pig platelets all peptides with a C5a activity were able to desensitize not only the C5a but also the C3a responses.
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Affiliation(s)
- J Köhl
- Institut für Medizinische Mikrobiologie, Medizinische Hochschule Hannover, FRG
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7
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Federwisch M, Casaretto M, Gerardy-Schahn R, Bitter-Suermann D, Wollmer A. Enhanced biopotency of synthetic C3a analogues by membrane binding. A fluorescence anisotropy decay study. Biophys Chem 1992; 44:151-61. [PMID: 1420945 DOI: 10.1016/0301-4622(92)80048-a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The biological activity of oligopeptide analogues of C3a is markedly increased by N-terminal attachment of a hydrophobic group as, for instance, 9-fluorenylmethoxycarbonyl (Fmoc), either direct or via a flexible 6-aminohexanoyl (Ahx) spacer. This study presents evidence from fluorescence anisotropy decay measurements that the hydrophobic appendix mediates non-specific binding of the synthetic peptide analogues to phospholipid vesicles. According to quantitative considerations no alternative or additional rate-enhancing mechanisms other than surface diffusion are required to account for the gain in biopotency.
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Affiliation(s)
- M Federwisch
- Institut für Biochemie, Rheinisch-Westfälische Technische Hochschule Aachen, Germany
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8
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Chapter 21. Potentlal Therapeutic Modifiers of the Complement Cascade. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 1992. [DOI: 10.1016/s0065-7743(08)60419-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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9
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10
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Braun W. Distance geometry in distance and torsion angle space: Flexibility, convergence and sampling properties. Proteins 1991. [DOI: 10.1007/978-94-010-9063-6_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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11
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Abstract
Comparative modeling methods are described that can be used to construct a three-dimensional model structure of a new protein from knowledge of its sequence and of the experimental structures and sequences of other members of its homology family. The methods are illustrated with the mammalian serine protease family, for which seven experimental structures have been reported in the literature, and the sequences for over 35 different protein members of the family are available. The strategy for modeling these proteins is presented, and criteria are developed for determining and assigning the reliability of the modeled structure. Criteria are described that are specially designed to help detect cases in which it is likely that the local structure diverges significantly from the usual conformation of the family.
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Affiliation(s)
- J Greer
- Pharmaceutical Products Division, Abbott Laboratories, Abbott Park, Illinois 60064
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12
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Abstract
The four-alpha-helix bundle, a common structural motif in globular proteins, provides an excellent forum for the examination of predictive constraints for protein backbone topology. An exhaustive examination of the Brookhaven Crystallographic Protein Data Bank and other literature sources has lead to the discovery of 20 putative four-alpha-helix bundles. Application of an analytical method that examines the difference between solvent-accessible surface areas in packed and partially unpacked bundles reduced the number of structures to 16. Angular requirements further reduced the list of bundles to 13. In 12 of these bundles, all pairs of neighboring helices were oriented in an anti-parallel fashion. This distribution is in accordance with structure types expected if the helix macro dipole effect makes a substantial contribution to the stability of the native structure. The characterizations and classifications made in this study prompt a reevaluation of constraints used in structure prediction efforts.
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Affiliation(s)
- S R Presnell
- Department of Pharmaceutical Chemistry, University of California, San Francisco 94143-0446
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13
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Williamson MP. 1H nuclear magnetic resonance assignments and secondary structure of porcine C5ades Arg. J Mol Biol 1989; 206:407-10. [PMID: 2716054 DOI: 10.1016/0022-2836(89)90489-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Sequence-specific assignments of the 1H nuclear magnetic resonance spectrum of porcine C5ades Arg are described. Assignments were facilitated by comparison of spectra obtained in H2O with partially exchanged spectra obtained in 2H2O. The sequence-specific assignments thus obtained were used to characterized the regular secondary structure in the protein, which is helical in the regions 2 to 11, 16 to 27, 35 to 41 and 45 to 64. The structure is very similar to that of human and bovine C5a.
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14
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Mollison KW, Mandecki W, Zuiderweg ER, Fayer L, Fey TA, Krause RA, Conway RG, Miller L, Edalji RP, Shallcross MA. Identification of receptor-binding residues in the inflammatory complement protein C5a by site-directed mutagenesis. Proc Natl Acad Sci U S A 1989; 86:292-6. [PMID: 2643101 PMCID: PMC286450 DOI: 10.1073/pnas.86.1.292] [Citation(s) in RCA: 99] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
C5a is an inflammatory mediator potentially involved in a number of diseases. To help define which of its 74 residues are important for receptor binding and response triggering, changes in the amino acid sequence of C5a were introduced by site-directed mutagenesis. Synthetic C5a-encoding genes incorporating point mutations were expressed in Escherichia coli, and the mutant proteins were purified to homogeneity. Modifications of the C5a molecule causing parallel reductions in binding to polymorphonuclear leukocyte membranes and in stimulation of polymorphonuclear leukocyte locomotion (chemokinesis) suggest that carboxyl-terminal residues Lys-68, Leu-72, and Arg-74 interact with the receptor. Substitutions in the disulfide-linked core of C5a revealed involvement of Arg-40 or nearby residues, because potency losses were associated with only localized conformational changes as detected by NMR. Surprisingly, a substitution at core residue Ala-26, which did not alter C5a core structure, appeared from NMR results to reduce potency by causing a long-distance conformational change centered on residue His-15. Thus, at least three discontinuous regions of the C5a molecule appear to act in concert to achieve full potency.
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Affiliation(s)
- K W Mollison
- Immunoscience Research Area, Abbott Laboratories, Abbott Park, IL 60064
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15
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McDonald JJ, Rein R. Molecular modeling of calmodulin: a comparison with crystallographic data. INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY. QUANTUM BIOLOGY SYMPOSIUM : PROCEEDINGS OF THE INTERNATIONAL SYMPOSIUM ON QUANTUM BIOLOGY AND QUANTUM PHARMACOLOGY. INTERNATIONAL SYMPOSIUM ON QUANTUM BIOLOGY AND QUANTUM PHARMACOLOGY 1989; 16:57-72. [PMID: 11542153 DOI: 10.1002/qua.560360707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2023]
Abstract
Two methods of side-chain placement on a modeled protein have been examined. Two molecular models of calmodulin were constructed that differ in the treatment of side chains prior to optimization of the molecule. A virtual bond analysis program developed by Purisima and Scheraga was used to determine the backbone conformation based on 2.2 angstroms resolution C alpha coordinates for the molecules. In the first model, side chains were initially constructed in an extended conformation. In the second model, a conformational grid search technique was employed. Calcium ions were treated explicitly during energy optimization using CHARMM. The models are compared to a recently published refined crystal structure of calmodulin. The results indicate that the initial choices for side-chains, but also significant effects on the main-chain conformation and supersecondary structure. The conformational differences are discussed. Analysis of these and other methods makes possible the formulation of a methodology for more appropriate side-chain placement in modeled proteins.
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Affiliation(s)
- J J McDonald
- Roswell Park Memorial Institute, Buffalo, New York 14263, USA
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16
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Zarbock J, Gennaro R, Romeo D, Clore GM, Gronenborn AM. A proton nuclear magnetic resonance study of the conformation of bovine anaphylatoxin C5a in solution. FEBS Lett 1988; 238:289-94. [PMID: 3262536 DOI: 10.1016/0014-5793(88)80499-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The solution conformation of bovine anaphylatoxin C5a has been investigated by nuclear magnetic resonance (NMR) spectroscopy. The 1H-NMR spectrum is assigned in a sequential manner using a variety of two-dimensional NMR techniques. A qualitative interpretation of the short range nuclear Overhauser enhancement data involving the NH, C alpha H and C beta H protons suggests that C5a has four helices comprising residues 5-11, 15-25, 33-39 and 46-61, and is composed of a globular head (residues 5-61) and a C-terminal tail. The polypeptide fold was determined by hybrid distance geometry-dynamical simulated annealing calculations on the basis of 203 approximate interproton distance restraints, 22 distance restraints for 11 intrahelical hydrogen bonds (identified on the basis of the pattern of short range NOEs and slowly exchanging backbone amide protons) and restraints for the 3 disulfide bridges. The overall polypeptide fold is similar to that of the sequence related human recombinant anaphylatoxin C5a [(1988) Proteins 3, 139-145].
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Affiliation(s)
- J Zarbock
- Max-Planck Institut für Biochemie, Martinsried bei München, FRG
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