1
|
Fatehi S, Herdendorf TJ, Ploscariu NT, Geisbrecht BV. Staphylococcal peroxidase inhibitor (SPIN): Residue-level investigation of the helical bundle domain. Arch Biochem Biophys 2024; 756:110023. [PMID: 38705227 DOI: 10.1016/j.abb.2024.110023] [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: 03/20/2024] [Revised: 04/22/2024] [Accepted: 04/30/2024] [Indexed: 05/07/2024]
Abstract
Myeloperoxidase is a critical component of the antibacterial arsenal of neutrophils, whereby it consumes H2O2 as an oxidant to convert halogen and pseudohalogen anions into cytotoxic hypohalous acids. Following phagocytosis by neutrophils, the human pathogen Staphylococcus aureus secretes a potent myeloperoxidase inhibitory protein, called SPIN, as part of its immune evasion repertoire. The matured S. aureus SPIN polypeptide consists of only 73 residues yet contains two functional domains: whereas the 60 residue C-terminal helical bundle domain is responsible for MPO binding, the 13 residue N-terminal domain is required to inhibit MPO. Previous studies have informed understanding of the SPIN N-terminal domain, but comparatively little is known about the helical domain insofar as the contribution of individual residues is concerned. To address this limitation, we carried out a residue-level structure/function investigation on the helical bundle domain of S. aureus SPIN. Using sequence conservation and existing structures of SPIN bound to human MPO as a guide, we selected residues L49, E50, H51, E52, Y55, and Y75 for interrogation by site-directed mutagenesis. We found that loss of L49 or E52 reduced SPIN activity by roughly an order of magnitude, but that loss of Y55 or H51 caused progressively greater loss of inhibitory potency. Direct binding studies by SPR showed that loss of inhibitory potency in these SPIN mutants resulted from a diminished initial interaction between the inhibitor and MPO. Together, our studies provide new insights into the structure/function relationships of SPIN and identify positions Y55 and H51 as critical determinants of SPIN function.
Collapse
Affiliation(s)
- Soheila Fatehi
- Department of Biochemistry & Molecular Biophysics, Kansas State University, Manhattan, KS, 66506, USA
| | - Timothy J Herdendorf
- Department of Biochemistry & Molecular Biophysics, Kansas State University, Manhattan, KS, 66506, USA
| | - Nicoleta T Ploscariu
- Department of Biochemistry & Molecular Biophysics, Kansas State University, Manhattan, KS, 66506, USA
| | - Brian V Geisbrecht
- Department of Biochemistry & Molecular Biophysics, Kansas State University, Manhattan, KS, 66506, USA.
| |
Collapse
|
2
|
Weber JJ, Geisbrecht BV, Kanost MR, Gorman MJ. A conserved asparagine residue stabilizes iron binding in Manduca sexta transferrin-1. Insect Biochem Mol Biol 2024; 168:104109. [PMID: 38494145 PMCID: PMC11018507 DOI: 10.1016/j.ibmb.2024.104109] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 02/21/2024] [Accepted: 03/14/2024] [Indexed: 03/19/2024]
Abstract
Transferrin 1 (Tsf1) is an insect-specific iron-binding protein that is abundant in hemolymph and other extracellular fluids. It binds iron tightly at neutral pH and releases iron under acidic conditions. Tsf1 influences the distribution of iron in the body and protects against infection. Elucidating the mechanisms by which Tsf1 achieves these functions will require an understanding of how Tsf1 binds and releases iron. Previously, crystallized Tsf1 from Manduca sexta was shown to have a novel type of iron coordination that involves four iron-binding ligands: two tyrosine residues (Tyr90 and Tyr204), a buried carbonate anion, and a solvent-exposed carbonate anion. The solvent-exposed carbonate anion was bound by a single amino acid residue, a highly conserved asparagine at position 121 (Asn121); thus, we predicted that Asn121 would be essential for high-affinity iron binding. To test this hypothesis, we analyzed the iron-binding and -release properties of five forms of recombinant Tsf1: wild-type, a Y90F/Y204F double mutant (negative control), and three Asn121 mutants (N121A, N121D and N121S). Each of the Asn121 mutants exhibited altered spectral properties, confirming that Asn121 contributes to iron coordination. The N121D and N121S mutations resulted in slightly lower affinity for iron, especially at acidic pH, while iron binding and release by the N121A mutant was indistinguishable from that of the wild-type protein. The surprisingly minor consequences of mutating Asn121, despite its high degree of conservation in diverse insect species, suggest that Asn121 may play a role that is essential in vivo but non-essential for high affinity iron binding in vitro.
Collapse
Affiliation(s)
- Jacob J Weber
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, 66506, USA.
| | - Brian V Geisbrecht
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, 66506, USA.
| | - Michael R Kanost
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, 66506, USA.
| | - Maureen J Gorman
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, 66506, USA.
| |
Collapse
|
3
|
Wallach I, Bernard D, Nguyen K, Ho G, Morrison A, Stecula A, Rosnik A, O’Sullivan AM, Davtyan A, Samudio B, Thomas B, Worley B, Butler B, Laggner C, Thayer D, Moharreri E, Friedland G, Truong H, van den Bedem H, Ng HL, Stafford K, Sarangapani K, Giesler K, Ngo L, Mysinger M, Ahmed M, Anthis NJ, Henriksen N, Gniewek P, Eckert S, de Oliveira S, Suterwala S, PrasadPrasad SVK, Shek S, Contreras S, Hare S, Palazzo T, O’Brien TE, Van Grack T, Williams T, Chern TR, Kenyon V, Lee AH, Cann AB, Bergman B, Anderson BM, Cox BD, Warrington JM, Sorenson JM, Goldenberg JM, Young MA, DeHaan N, Pemberton RP, Schroedl S, Abramyan TM, Gupta T, Mysore V, Presser AG, Ferrando AA, Andricopulo AD, Ghosh A, Ayachi AG, Mushtaq A, Shaqra AM, Toh AKL, Smrcka AV, Ciccia A, de Oliveira AS, Sverzhinsky A, de Sousa AM, Agoulnik AI, Kushnir A, Freiberg AN, Statsyuk AV, Gingras AR, Degterev A, Tomilov A, Vrielink A, Garaeva AA, Bryant-Friedrich A, Caflisch A, Patel AK, Rangarajan AV, Matheeussen A, Battistoni A, Caporali A, Chini A, Ilari A, Mattevi A, Foote AT, Trabocchi A, Stahl A, Herr AB, Berti A, Freywald A, Reidenbach AG, Lam A, Cuddihy AR, White A, Taglialatela A, Ojha AK, Cathcart AM, Motyl AAL, Borowska A, D’Antuono A, Hirsch AKH, Porcelli AM, Minakova A, Montanaro A, Müller A, Fiorillo A, Virtanen A, O’Donoghue AJ, Del Rio Flores A, Garmendia AE, Pineda-Lucena A, Panganiban AT, Samantha A, Chatterjee AK, Haas AL, Paparella AS, John ALS, Prince A, ElSheikh A, Apfel AM, Colomba A, O’Dea A, Diallo BN, Ribeiro BMRM, Bailey-Elkin BA, Edelman BL, Liou B, Perry B, Chua BSK, Kováts B, Englinger B, Balakrishnan B, Gong B, Agianian B, Pressly B, Salas BPM, Duggan BM, Geisbrecht BV, Dymock BW, Morten BC, Hammock BD, Mota BEF, Dickinson BC, Fraser C, Lempicki C, Novina CD, Torner C, Ballatore C, Bon C, Chapman CJ, Partch CL, Chaton CT, Huang C, Yang CY, Kahler CM, Karan C, Keller C, Dieck CL, Huimei C, Liu C, Peltier C, Mantri CK, Kemet CM, Müller CE, Weber C, Zeina CM, Muli CS, Morisseau C, Alkan C, Reglero C, Loy CA, Wilson CM, Myhr C, Arrigoni C, Paulino C, Santiago C, Luo D, Tumes DJ, Keedy DA, Lawrence DA, Chen D, Manor D, Trader DJ, Hildeman DA, Drewry DH, Dowling DJ, Hosfield DJ, Smith DM, Moreira D, Siderovski DP, Shum D, Krist DT, Riches DWH, Ferraris DM, Anderson DH, Coombe DR, Welsbie DS, Hu D, Ortiz D, Alramadhani D, Zhang D, Chaudhuri D, Slotboom DJ, Ronning DR, Lee D, Dirksen D, Shoue DA, Zochodne DW, Krishnamurthy D, Duncan D, Glubb DM, Gelardi ELM, Hsiao EC, Lynn EG, Silva EB, Aguilera E, Lenci E, Abraham ET, Lama E, Mameli E, Leung E, Christensen EM, Mason ER, Petretto E, Trakhtenberg EF, Rubin EJ, Strauss E, Thompson EW, Cione E, Lisabeth EM, Fan E, Kroon EG, Jo E, García-Cuesta EM, Glukhov E, Gavathiotis E, Yu F, Xiang F, Leng F, Wang F, Ingoglia F, van den Akker F, Borriello F, Vizeacoumar FJ, Luh F, Buckner FS, Vizeacoumar FS, Bdira FB, Svensson F, Rodriguez GM, Bognár G, Lembo G, Zhang G, Dempsey G, Eitzen G, Mayer G, Greene GL, Garcia GA, Lukacs GL, Prikler G, Parico GCG, Colotti G, De Keulenaer G, Cortopassi G, Roti G, Girolimetti G, Fiermonte G, Gasparre G, Leuzzi G, Dahal G, Michlewski G, Conn GL, Stuchbury GD, Bowman GR, Popowicz GM, Veit G, de Souza GE, Akk G, Caljon G, Alvarez G, Rucinski G, Lee G, Cildir G, Li H, Breton HE, Jafar-Nejad H, Zhou H, Moore HP, Tilford H, Yuan H, Shim H, Wulff H, Hoppe H, Chaytow H, Tam HK, Van Remmen H, Xu H, Debonsi HM, Lieberman HB, Jung H, Fan HY, Feng H, Zhou H, Kim HJ, Greig IR, Caliandro I, Corvo I, Arozarena I, Mungrue IN, Verhamme IM, Qureshi IA, Lotsaris I, Cakir I, Perry JJP, Kwiatkowski J, Boorman J, Ferreira J, Fries J, Kratz JM, Miner J, Siqueira-Neto JL, Granneman JG, Ng J, Shorter J, Voss JH, Gebauer JM, Chuah J, Mousa JJ, Maynes JT, Evans JD, Dickhout J, MacKeigan JP, Jossart JN, Zhou J, Lin J, Xu J, Wang J, Zhu J, Liao J, Xu J, Zhao J, Lin J, Lee J, Reis J, Stetefeld J, Bruning JB, Bruning JB, Coles JG, Tanner JJ, Pascal JM, So J, Pederick JL, Costoya JA, Rayman JB, Maciag JJ, Nasburg JA, Gruber JJ, Finkelstein JM, Watkins J, Rodríguez-Frade JM, Arias JAS, Lasarte JJ, Oyarzabal J, Milosavljevic J, Cools J, Lescar J, Bogomolovas J, Wang J, Kee JM, Kee JM, Liao J, Sistla JC, Abrahão JS, Sishtla K, Francisco KR, Hansen KB, Molyneaux KA, Cunningham KA, Martin KR, Gadar K, Ojo KK, Wong KS, Wentworth KL, Lai K, Lobb KA, Hopkins KM, Parang K, Machaca K, Pham K, Ghilarducci K, Sugamori KS, McManus KJ, Musta K, Faller KME, Nagamori K, Mostert KJ, Korotkov KV, Liu K, Smith KS, Sarosiek K, Rohde KH, Kim KK, Lee KH, Pusztai L, Lehtiö L, Haupt LM, Cowen LE, Byrne LJ, Su L, Wert-Lamas L, Puchades-Carrasco L, Chen L, Malkas LH, Zhuo L, Hedstrom L, Hedstrom L, Walensky LD, Antonelli L, Iommarini L, Whitesell L, Randall LM, Fathallah MD, Nagai MH, Kilkenny ML, Ben-Johny M, Lussier MP, Windisch MP, Lolicato M, Lolli ML, Vleminckx M, Caroleo MC, Macias MJ, Valli M, Barghash MM, Mellado M, Tye MA, Wilson MA, Hannink M, Ashton MR, Cerna MVC, Giorgis M, Safo MK, Maurice MS, McDowell MA, Pasquali M, Mehedi M, Serafim MSM, Soellner MB, Alteen MG, Champion MM, Skorodinsky M, O’Mara ML, Bedi M, Rizzi M, Levin M, Mowat M, Jackson MR, Paige M, Al-Yozbaki M, Giardini MA, Maksimainen MM, De Luise M, Hussain MS, Christodoulides M, Stec N, Zelinskaya N, Van Pelt N, Merrill NM, Singh N, Kootstra NA, Singh N, Gandhi NS, Chan NL, Trinh NM, Schneider NO, Matovic N, Horstmann N, Longo N, Bharambe N, Rouzbeh N, Mahmoodi N, Gumede NJ, Anastasio NC, Khalaf NB, Rabal O, Kandror O, Escaffre O, Silvennoinen O, Bishop OT, Iglesias P, Sobrado P, Chuong P, O’Connell P, Martin-Malpartida P, Mellor P, Fish PV, Moreira POL, Zhou P, Liu P, Liu P, Wu P, Agogo-Mawuli P, Jones PL, Ngoi P, Toogood P, Ip P, von Hundelshausen P, Lee PH, Rowswell-Turner RB, Balaña-Fouce R, Rocha REO, Guido RVC, Ferreira RS, Agrawal RK, Harijan RK, Ramachandran R, Verma R, Singh RK, Tiwari RK, Mazitschek R, Koppisetti RK, Dame RT, Douville RN, Austin RC, Taylor RE, Moore RG, Ebright RH, Angell RM, Yan R, Kejriwal R, Batey RA, Blelloch R, Vandenberg RJ, Hickey RJ, Kelm RJ, Lake RJ, Bradley RK, Blumenthal RM, Solano R, Gierse RM, Viola RE, McCarthy RR, Reguera RM, Uribe RV, do Monte-Neto RL, Gorgoglione R, Cullinane RT, Katyal S, Hossain S, Phadke S, Shelburne SA, Geden SE, Johannsen S, Wazir S, Legare S, Landfear SM, Radhakrishnan SK, Ammendola S, Dzhumaev S, Seo SY, Li S, Zhou S, Chu S, Chauhan S, Maruta S, Ashkar SR, Shyng SL, Conticello SG, Buroni S, Garavaglia S, White SJ, Zhu S, Tsimbalyuk S, Chadni SH, Byun SY, Park S, Xu SQ, Banerjee S, Zahler S, Espinoza S, Gustincich S, Sainas S, Celano SL, Capuzzi SJ, Waggoner SN, Poirier S, Olson SH, Marx SO, Van Doren SR, Sarilla S, Brady-Kalnay SM, Dallman S, Azeem SM, Teramoto T, Mehlman T, Swart T, Abaffy T, Akopian T, Haikarainen T, Moreda TL, Ikegami T, Teixeira TR, Jayasinghe TD, Gillingwater TH, Kampourakis T, Richardson TI, Herdendorf TJ, Kotzé TJ, O’Meara TR, Corson TW, Hermle T, Ogunwa TH, Lan T, Su T, Banjo T, O’Mara TA, Chou T, Chou TF, Baumann U, Desai UR, Pai VP, Thai VC, Tandon V, Banerji V, Robinson VL, Gunasekharan V, Namasivayam V, Segers VFM, Maranda V, Dolce V, Maltarollo VG, Scoffone VC, Woods VA, Ronchi VP, Van Hung Le V, Clayton WB, Lowther WT, Houry WA, Li W, Tang W, Zhang W, Van Voorhis WC, Donaldson WA, Hahn WC, Kerr WG, Gerwick WH, Bradshaw WJ, Foong WE, Blanchet X, Wu X, Lu X, Qi X, Xu X, Yu X, Qin X, Wang X, Yuan X, Zhang X, Zhang YJ, Hu Y, Aldhamen YA, Chen Y, Li Y, Sun Y, Zhu Y, Gupta YK, Pérez-Pertejo Y, Li Y, Tang Y, He Y, Tse-Dinh YC, Sidorova YA, Yen Y, Li Y, Frangos ZJ, Chung Z, Su Z, Wang Z, Zhang Z, Liu Z, Inde Z, Artía Z, Heifets A. AI is a viable alternative to high throughput screening: a 318-target study. Sci Rep 2024; 14:7526. [PMID: 38565852 PMCID: PMC10987645 DOI: 10.1038/s41598-024-54655-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 02/15/2024] [Indexed: 04/04/2024] Open
Abstract
High throughput screening (HTS) is routinely used to identify bioactive small molecules. This requires physical compounds, which limits coverage of accessible chemical space. Computational approaches combined with vast on-demand chemical libraries can access far greater chemical space, provided that the predictive accuracy is sufficient to identify useful molecules. Through the largest and most diverse virtual HTS campaign reported to date, comprising 318 individual projects, we demonstrate that our AtomNet® convolutional neural network successfully finds novel hits across every major therapeutic area and protein class. We address historical limitations of computational screening by demonstrating success for target proteins without known binders, high-quality X-ray crystal structures, or manual cherry-picking of compounds. We show that the molecules selected by the AtomNet® model are novel drug-like scaffolds rather than minor modifications to known bioactive compounds. Our empirical results suggest that computational methods can substantially replace HTS as the first step of small-molecule drug discovery.
Collapse
|
4
|
Xu X, Herdendorf TJ, Duan H, Rohlik DL, Roy S, Zhou H, Alkhateeb H, Khandelwal S, Zhou Q, Li P, Arepally GM, Walker JK, Garcia BL, Geisbrecht BV. Inhibition of the C1s Protease and the Classical Complement Pathway by 6-(4-Phenylpiperazin-1-yl)Pyridine-3-Carboximidamide and Chemical Analogs. J Immunol 2024; 212:689-701. [PMID: 38149922 PMCID: PMC10872613 DOI: 10.4049/jimmunol.2300630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 12/05/2023] [Indexed: 12/28/2023]
Abstract
The classical pathway (CP) is a potent mechanism for initiating complement activity and is a driver of pathology in many complement-mediated diseases. The CP is initiated via activation of complement component C1, which consists of the pattern recognition molecule C1q bound to a tetrameric assembly of proteases C1r and C1s. Enzymatically active C1s provides the catalytic basis for cleavage of the downstream CP components, C4 and C2, and is therefore an attractive target for therapeutic intervention in CP-driven diseases. Although an anti-C1s mAb has been Food and Drug Administration approved, identifying small-molecule C1s inhibitors remains a priority. In this study, we describe 6-(4-phenylpiperazin-1-yl)pyridine-3-carboximidamide (A1) as a selective, competitive inhibitor of C1s. A1 was identified through a virtual screen for small molecules that interact with the C1s substrate recognition site. Subsequent functional studies revealed that A1 dose-dependently inhibits CP activation by heparin-induced immune complexes, CP-driven lysis of Ab-sensitized sheep erythrocytes, CP activation in a pathway-specific ELISA, and cleavage of C2 by C1s. Biochemical experiments demonstrated that A1 binds directly to C1s with a Kd of ∼9.8 μM and competitively inhibits its activity with an inhibition constant (Ki) of ∼5.8 μM. A 1.8-Å-resolution crystal structure revealed the physical basis for C1s inhibition by A1 and provided information on the structure-activity relationship of the A1 scaffold, which was supported by evaluating a panel of A1 analogs. Taken together, our work identifies A1 as a new class of small-molecule C1s inhibitor and lays the foundation for development of increasingly potent and selective A1 analogs for both research and therapeutic purposes.
Collapse
Affiliation(s)
- Xin Xu
- Department of Biochemistry & Molecular Biophysics, Kansas State University; Manhattan, KS 66506 U.S.A
| | - Timothy J. Herdendorf
- Department of Biochemistry & Molecular Biophysics, Kansas State University; Manhattan, KS 66506 U.S.A
| | - Huiquan Duan
- Department of Biochemistry & Molecular Biophysics, Kansas State University; Manhattan, KS 66506 U.S.A
| | - Denise L. Rohlik
- Department of Microbiology & Immunology, Brody School of Medicine East Carolina University; Greenville, NC 27834 U.S.A
| | - Sourav Roy
- Department of Microbiology & Immunology, Brody School of Medicine East Carolina University; Greenville, NC 27834 U.S.A
| | - Hinman Zhou
- Department of Pharmacology, School of Medicine, St. Louis University; St. Louis, MO 63104 U.S.A
| | - Haya Alkhateeb
- Department of Pharmacology, School of Medicine, St. Louis University; St. Louis, MO 63104 U.S.A
| | - Sanjay Khandelwal
- Division of Hematology, Duke University Medical Center; Durham, NC 27710 U.S.A
| | - Qilong Zhou
- Department of Chemistry, Kansas State University; Manhattan, KS 66506 U.S.A
| | - Ping Li
- Department of Chemistry, Kansas State University; Manhattan, KS 66506 U.S.A
| | | | - John K. Walker
- Department of Pharmacology, School of Medicine, St. Louis University; St. Louis, MO 63104 U.S.A
- Department of Chemistry, St. Louis University; St. Louis, MO 63103 U.S.A
| | - Brandon L. Garcia
- Department of Microbiology & Immunology, Brody School of Medicine East Carolina University; Greenville, NC 27834 U.S.A
| | - Brian V. Geisbrecht
- Department of Biochemistry & Molecular Biophysics, Kansas State University; Manhattan, KS 66506 U.S.A
| |
Collapse
|
5
|
Duan H, Abram TG, Cruz AR, Rooijakkers SHM, Geisbrecht BV. New Insights into the Complement Receptor of the Ig Superfamily Obtained from Structural and Functional Studies on Two Mutants. Immunohorizons 2023; 7:806-818. [PMID: 38032267 PMCID: PMC10696418 DOI: 10.4049/immunohorizons.2300064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 11/03/2023] [Indexed: 12/01/2023] Open
Abstract
The extracellular region of the complement receptor of the Ig superfamily (CRIg) binds to certain C3 cleavage products (C3b, iC3b, C3c) and inhibits the alternative pathway (AP) of complement. In this study, we provide further insight into the CRIg protein and describe two CRIg mutants that lack multiple lysine residues as a means of facilitating chemical modifications of the protein. Structural analyses confirmed preservation of the native CRIg architecture in both mutants. In contrast to earlier reports suggesting that CRIg binds to C3b with an affinity of ∼1 μM, we found that wild-type CRIg binds to C3b and iC3b with affinities <100 nM, but to C3c with an affinity closer to 1 μM. We observed this same trend for both lysine substitution mutants, albeit with an apparent ∼2- to 3-fold loss of affinity when compared with wild-type CRIg. Using flow cytometry, we confirmed binding to C3 fragment-opsonized Staphylococcus aureus cells by each mutant, again with an ∼2- to 3-fold decrease when compared with wild-type. Whereas wild-type CRIg inhibits AP-driven lysis of rabbit erythrocytes with an IC50 of 1.6 μM, we observed an ∼3-fold reduction in inhibition for both mutants. Interestingly, we found that amine-reactive crosslinking of the CRIg mutant containing only a single lysine results in a significant improvement in inhibitory potency across all concentrations examined when compared with the unmodified mutant, but in a manner sensitive to the length of the crosslinker. Collectively, our findings provide new insights into the CRIg protein and suggest an approach for engineering increasingly potent CRIg-based inhibitors of the AP.
Collapse
Affiliation(s)
- Huiquan Duan
- Department of Biochemistry and Molecular Biophysics, Kansas State University; Manhattan, KS
| | - Troy G. Abram
- Department of Biochemistry and Molecular Biophysics, Kansas State University; Manhattan, KS
| | - Ana Rita Cruz
- Department of Medical Microbiology and Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Suzan H. M. Rooijakkers
- Department of Medical Microbiology and Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Brian V. Geisbrecht
- Department of Biochemistry and Molecular Biophysics, Kansas State University; Manhattan, KS
| |
Collapse
|
6
|
Paterson NM, Al-Zubieri H, Ragona J, Kohler KM, Tirado J, Geisbrecht BV, Barber MF. Dynamic Evolution of Bacterial Ligand Recognition by Formyl Peptide Receptors. Genome Biol Evol 2023; 15:evad175. [PMID: 37776517 PMCID: PMC10566242 DOI: 10.1093/gbe/evad175] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 09/13/2023] [Indexed: 10/02/2023] Open
Abstract
The detection of invasive pathogens is critical for host immune defense. Cell surface receptors play a key role in the recognition of diverse microbe-associated molecules, triggering leukocyte recruitment, phagocytosis, release of antimicrobial compounds, and cytokine production. The intense evolutionary forces acting on innate immune receptor genes have contributed to their rapid diversification across plants and animals. However, the functional consequences of immune receptor divergence are often unclear. Formyl peptide receptors (FPRs) comprise a family of animal G protein-coupled receptors which are activated in response to a variety of ligands including formylated bacterial peptides, pathogen virulence factors, and host-derived antimicrobial peptides. FPR activation in turn promotes inflammatory signaling and leukocyte migration to sites of infection. Here we investigate patterns of gene loss, diversification, and ligand recognition among FPRs in primates and carnivores. We find that FPR1, which plays a critical role in innate immune defense in humans, has been lost in New World primates. Amino acid variation in FPR1 and FPR2 among primates and carnivores is consistent with a history of repeated positive selection acting on extracellular domains involved in ligand recognition. To assess the consequences of FPR divergence on bacterial ligand interactions, we measured binding between primate FPRs and the FPR agonist Staphylococcus aureus enterotoxin B, as well as S. aureus FLIPr-like, an FPR inhibitor. We found that few rapidly evolving sites in primate FPRs are sufficient to modulate recognition of bacterial proteins, demonstrating how natural selection may serve to tune FPR activation in response to diverse microbial ligands.
Collapse
Affiliation(s)
- Nicole M Paterson
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Hussein Al-Zubieri
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | - Joseph Ragona
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, USA
| | - Kristin M Kohler
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | - Juan Tirado
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | - Brian V Geisbrecht
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, USA
| | - Matthew F Barber
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
- Department of Biology, University of Oregon, Eugene, Oregon, USA
| |
Collapse
|
7
|
Mishra N, Herdendorf TJ, Prakash O, Geisbrecht BV. Correction: Simultaneous inhibition of two neutrophil serine proteases by the S. aureus innate immune evasion protein EapH2. J Biol Chem 2023; 299:105113. [PMID: 37544055 PMCID: PMC10413344 DOI: 10.1016/j.jbc.2023.105113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/08/2023] Open
|
8
|
Mishra N, Herdendorf TJ, Prakash O, Geisbrecht BV. Simultaneous inhibition of two neutrophil serine proteases by the S. aureus innate immune evasion protein EapH2. J Biol Chem 2023; 299:104878. [PMID: 37269950 PMCID: PMC10339191 DOI: 10.1016/j.jbc.2023.104878] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 05/06/2023] [Accepted: 05/26/2023] [Indexed: 06/05/2023] Open
Abstract
Extracellular adherence protein domain (EAP) proteins are high-affinity, selective inhibitors of neutrophil serine proteases (NSP), including cathepsin-G (CG) and neutrophil elastase (NE). Most Staphylococcus aureus isolates encode for two EAPs, EapH1 and EapH2, that contain a single functional domain and share 43% identity with one another. Although structure/function investigations from our group have shown that EapH1 uses a globally similar binding mode to inhibit CG and NE, NSP inhibition by EapH2 is incompletely understood due to a lack of NSP/EapH2 cocrystal structures. To address this limitation, we further studied NSP inhibition by EapH2 in comparison with EapH1. Like its effects on NE, we found that EapH2 is a reversible, time-dependent, and low nanomolar affinity inhibitor of CG. We characterized an EapH2 mutant which suggested that the CG binding mode of EapH2 is comparable to EapH1. To test this directly, we used NMR chemical shift perturbation to study EapH1 and EapH2 binding to CG and NE in solution. Although we found that overlapping regions of EapH1 and EapH2 were involved in CG binding, we found that altogether distinct regions of EapH1 and EapH2 experienced changes upon binding to NE. An important implication of this observation is that EapH2 might be capable of binding and inhibiting CG and NE simultaneously. We confirmed this unexpected feature by solving crystal structures of the CG/EapH2/NE complex and demonstrating their functional relevance through enzyme inhibition assays. Together, our work defines a new mechanism of simultaneous inhibition of two serine proteases by a single EAP protein.
Collapse
Affiliation(s)
- Nitin Mishra
- Department of Biochemistry & Molecular Biophysics, Kansas State University, Manhattan, Kansas, USA
| | - Timothy J Herdendorf
- Department of Biochemistry & Molecular Biophysics, Kansas State University, Manhattan, Kansas, USA
| | - Om Prakash
- Department of Biochemistry & Molecular Biophysics, Kansas State University, Manhattan, Kansas, USA
| | - Brian V Geisbrecht
- Department of Biochemistry & Molecular Biophysics, Kansas State University, Manhattan, Kansas, USA.
| |
Collapse
|
9
|
Mishra N, Pal I, Herrera AI, Dubey A, Arthanari H, Geisbrecht BV, Prakash O. Complete non-proline backbone resonance assignments of the S. aureus neutrophil serine protease inhibitor, EapH1. Biomol NMR Assign 2023; 17:129-134. [PMID: 37160842 PMCID: PMC10823442 DOI: 10.1007/s12104-023-10131-9] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 04/24/2023] [Indexed: 05/11/2023]
Abstract
The S. aureus extracellular adherence protein (Eap) and its homologs, EapH1 and EapH2, serve roles in evasion of the human innate immune system. EapH1 binds with high-affinity and inhibits the neutrophil azurophilic granule proteases neutrophil elastase, cathepsin-G and proteinase-3. Previous structural studies using X-ray crystallography have shown that EapH1 binds to neutrophil elastase and cathepsin-G using a globally similar binding mode. However, whether the same holds true in solution is unknown and whether the inhibitor experiences dynamic changes following binding remains uncertain. To facilitate solution-phase structural and biochemical studies of EapH1 and its complexes with neutrophil granule proteases, we have characterized EapH1 by multidimensional NMR spectroscopy. Here we report a total of 100% of the non-proline backbone resonance assignments of EapH1 with BMRB accession number 50,304.
Collapse
Affiliation(s)
- Nitin Mishra
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, 66506, USA
| | - Indrani Pal
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, 66506, USA
| | - Alvaro I Herrera
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, 66506, USA
| | - Abhinav Dubey
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Haribabu Arthanari
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Brian V Geisbrecht
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, 66506, USA.
| | - Om Prakash
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, 66506, USA.
| |
Collapse
|
10
|
Gido CD, Herdendorf TJ, Geisbrecht BV. Characterization of two distinct neutrophil serine protease-binding modes within a Staphylococcus aureus innate immune evasion protein family. J Biol Chem 2023; 299:102969. [PMID: 36736422 PMCID: PMC9996362 DOI: 10.1016/j.jbc.2023.102969] [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: 11/28/2022] [Revised: 01/25/2023] [Accepted: 01/27/2023] [Indexed: 02/03/2023] Open
Abstract
Extracellular adherence protein domain (EAPs) proteins are a class of innate immune evasion proteins secreted by the human pathogen Staphylococcus aureus. EAPs are potent and selective inhibitors of cathepsin-G (CG) and neutrophil elastase (NE), which are the two most abundant neutrophil serine proteases (NSPs). Previous work from our group has shown that the prototypical EAP, EapH1, relies on plasticity within a single inhibitory site to block the activities of CG and NE. However, whether other EAPs follow similar structure-function relationships is unclear. To address this question, we studied the inhibitory properties of the first (Eap1) and second (Eap2) domains of the modular extracellular adherence protein of S. aureus and determined their structures when bound to CG and NE, respectively. We observed that both Eap1 and Eap2 displayed time-dependent inhibition of CG (on the order of 10-9 M) and of NE (on the order of 10-10 M). We also found that whereas the structures of Eap1 and Eap2 bound to CG showed an overall inhibitory mode like that seen previously for EapH1, the structures of Eap1 and Eap2 bound to NE revealed a new inhibitory mode involving a distal region of the EAP domain. Using site-directed mutagenesis of Eap1 and Eap2, along with enzyme assays, we confirmed the roles of interfacial residues in NSP inhibition. Taken together, our work demonstrates that EAPs can form structurally divergent complexes with two closely related serine proteases and further suggests that certain EAPs may be capable of inhibiting two NSPs simultaneously.
Collapse
Affiliation(s)
- Carson D Gido
- Department of Biochemistry & Molecular Biophysics, Kansas State University, Manhattan, Kansas, USA
| | - Timothy J Herdendorf
- Department of Biochemistry & Molecular Biophysics, Kansas State University, Manhattan, Kansas, USA
| | - Brian V Geisbrecht
- Department of Biochemistry & Molecular Biophysics, Kansas State University, Manhattan, Kansas, USA.
| |
Collapse
|
11
|
Dobó J, Gál P, Geisbrecht BV. Editorial: Complement: Latest developments regarding structure, mechanism, and connections to other proteolytic pathways. Front Immunol 2023; 14:1144038. [PMID: 36761776 PMCID: PMC9903131 DOI: 10.3389/fimmu.2023.1144038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 01/17/2023] [Indexed: 01/26/2023] Open
Affiliation(s)
- József Dobó
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Péter Gál
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Brian V. Geisbrecht
- Department of Biochemistry & Molecular Biophysics, Kansas State University, Manhattan, KS, United States,*Correspondence: Brian V. Geisbrecht,
| |
Collapse
|
12
|
Gamage SST, Pahattuge TN, Wijerathne H, Childers K, Vaidyanathan S, Athapattu US, Zhang L, Zhao Z, Hupert ML, Muller RM, Muller-Cohn J, Dickerson J, Dufek D, Geisbrecht BV, Pathak H, Pessetto Z, Gan GN, Choi J, Park S, Godwin AK, Witek MA, Soper SA. Microfluidic affinity selection of active SARS-CoV-2 virus particles. Sci Adv 2022; 8:eabn9665. [PMID: 36170362 PMCID: PMC9519043 DOI: 10.1126/sciadv.abn9665] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 08/10/2022] [Indexed: 06/07/2023]
Abstract
We report a microfluidic assay to select active severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral particles (VPs), which were defined as intact particles with an accessible angiotensin-converting enzyme 2 receptor binding domain (RBD) on the spike (S) protein, from clinical samples. Affinity selection of SARS-CoV-2 particles was carried out using injection molded microfluidic chips, which allow for high-scale production to accommodate large-scale screening. The microfluidic contained a surface-bound aptamer directed against the virus's S protein RBD to affinity select SARS-CoV-2 VPs. Following selection (~94% recovery), the VPs were released from the chip's surface using a blue light light-emitting diode (89% efficiency). Selected SARS-CoV-2 VP enumeration was carried out using reverse transcription quantitative polymerase chain reaction. The VP selection assay successfully identified healthy donors (clinical specificity = 100%) and 19 of 20 patients with coronavirus disease 2019 (COVID-19) (95% sensitivity). In 15 patients with COVID-19, the presence of active SARS-CoV-2 VPs was found. The chip can be reprogrammed for any VP or exosomes by simply changing the affinity agent.
Collapse
Affiliation(s)
- Sachindra S. T. Gamage
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045, USA
| | - Thilanga N. Pahattuge
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045, USA
| | - Harshani Wijerathne
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045, USA
| | - Katie Childers
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045, USA
- Bioengineering Program, The University of Kansas, Lawrence, KS 66045, USA
| | - Swarnagowri Vaidyanathan
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045, USA
- Bioengineering Program, The University of Kansas, Lawrence, KS 66045, USA
| | - Uditha S. Athapattu
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045, USA
| | - Lulu Zhang
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045, USA
- Bioengineering Program, The University of Kansas, Lawrence, KS 66045, USA
| | - Zheng Zhao
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045, USA
| | | | | | | | | | | | - Brian V. Geisbrecht
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506, USA
| | - Harsh Pathak
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | | | - Gregory N. Gan
- Department of Radiation Oncology, University of Kansas Medical Center, Kansas City, KS 66160, USA
- University of Kansas Cancer Center, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Junseo Choi
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045, USA
- Department of Industrial and Mechanical Engineering, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Sunggook Park
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045, USA
- Department of Industrial and Mechanical Engineering, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Andrew K. Godwin
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045, USA
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
- University of Kansas Cancer Center, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Malgorzata A. Witek
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045, USA
| | - Steven A. Soper
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045, USA
- Bioengineering Program, The University of Kansas, Lawrence, KS 66045, USA
- University of Kansas Cancer Center, University of Kansas Medical Center, Kansas City, KS 66160, USA
- Department of Mechanical Engineering, The University of Kansas, Lawrence, KS 66045, USA
| |
Collapse
|
13
|
Zhang Y, Vontz AJ, Kallenberger EM, Xu X, Ploscariu NT, Ramyar KX, Garcia BL, Ghebrehiwet B, Geisbrecht BV. gC1qR/C1qBP/HABP-1: Structural Analysis of the Trimeric Core Region, Interactions With a Novel Panel of Monoclonal Antibodies, and Their Influence on Binding to FXII. Front Immunol 2022; 13:887742. [PMID: 35865516 PMCID: PMC9294231 DOI: 10.3389/fimmu.2022.887742] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 06/06/2022] [Indexed: 01/01/2023] Open
Abstract
The protein gC1qR/C1qBP/HABP-1 plays an essential role in mitochondrial biogenesis, but becomes localized at the cellular surface in numerous pathophysiological states. When this occurs on endothelial cells, surface-exposed gC1qR activates the classical pathway of complement. It also promotes assembly of a multi-protein complex comprised of coagulation factor XII (FXII), pre-kallikrein (PK), and high-molecular weight kininogen (HMWK) that activates the contact system and the kinin-generating system. Since surface-exposed gC1qR triggers intravascular inflammatory pathways, there is interest in identifying molecules that block gC1qR function. Here we further that objective by reporting the outcome of a structure/function investigation of gC1qR, its interactions with FXII, and the impact of a panel of monoclonal anti-gC1qR antibodies on FXII binding to gC1qR. Although deletion mutants have been used extensively to assess gC1qR function, none of these proteins have been characterized structurally. To that end, we determined a 2.2 Å resolution crystal structure of a gC1qR mutant lacking both of its acidic loops, but which retained nanomolar-affinity binding to FXII and FXIIa. This structure revealed that the trimeric gC1qR assembly was maintained despite loss of roughly thirty residues. Characterization of a novel panel of anti-gC1qR monoclonal antibodies identified several with biochemical properties distinct from previously described antibodies, as well as one which bound to the first acidic loop of gC1qR. Intriguingly, we found that each of these antibodies could partly inhibit binding of FXII and FXIIa to gC1qR. Based on these results and previously published studies, we offer new perspectives for developing gC1qR inhibitors.
Collapse
Affiliation(s)
- Ying Zhang
- Department of Biochemistry & Molecular Biophysics, Kansas State University, Manhattan, KS, United States
| | - Alexander J. Vontz
- Department of Biochemistry & Molecular Biophysics, Kansas State University, Manhattan, KS, United States
| | - Ethan M. Kallenberger
- Department of Biochemistry & Molecular Biophysics, Kansas State University, Manhattan, KS, United States
| | - Xin Xu
- Department of Biochemistry & Molecular Biophysics, Kansas State University, Manhattan, KS, United States
| | - Nicoleta T. Ploscariu
- Department of Biochemistry & Molecular Biophysics, Kansas State University, Manhattan, KS, United States
| | - Kasra X. Ramyar
- Department of Biochemistry & Molecular Biophysics, Kansas State University, Manhattan, KS, United States
| | - Brandon L. Garcia
- Department of Biochemistry & Molecular Biophysics, Kansas State University, Manhattan, KS, United States
| | - Berhane Ghebrehiwet
- Department of Medicine, Stony Brook University, Stony Brook, NY, United States,*Correspondence: Berhane Ghebrehiwet, ; Brian V. Geisbrecht,
| | - Brian V. Geisbrecht
- Department of Biochemistry & Molecular Biophysics, Kansas State University, Manhattan, KS, United States,*Correspondence: Berhane Ghebrehiwet, ; Brian V. Geisbrecht,
| |
Collapse
|
14
|
Xu X, Marffy ALL, Keightley A, McCarthy AJ, Geisbrecht BV. Group B Streptococcus Surface Protein β: Structural Characterization of a Complement Factor H-Binding Motif and Its Contribution to Immune Evasion. J Immunol 2022; 208:1232-1247. [PMID: 35110419 PMCID: PMC8881398 DOI: 10.4049/jimmunol.2101078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 12/10/2021] [Indexed: 11/19/2022]
Abstract
The β protein from group B Streptococcus (GBS) is a ∼132-kDa, cell-surface exposed molecule that binds to multiple host-derived ligands, including complement factor H (FH). Many details regarding this interaction and its significance to immune evasion by GBS remain unclear. In this study, we identified a three-helix bundle domain within the C-terminal half of the B75KN region of β as the major FH-binding determinant and determined its crystal structure at 2.5 Å resolution. Analysis of this structure suggested a role in FH binding for a loop region connecting helices α1 and α2, which we confirmed by mutagenesis and direct binding studies. Using a combination of protein cross-linking and mass spectrometry, we observed that B75KN bound to complement control protein (CCP)3 and CCP4 domains of FH. Although this binding site lies within a complement regulatory region of FH, we determined that FH bound by β retained its decay acceleration and cofactor activities. Heterologous expression of β by Lactococcus lactis resulted in recruitment of FH to the bacterial surface and a significant reduction of C3b deposition following exposure to human serum. Surprisingly, we found that FH binding by β was not required for bacterial resistance to phagocytosis by neutrophils or killing of bacteria by whole human blood. However, loss of the B75KN region significantly diminished bacterial survival in both assays. Although our results show that FH recruited to the bacterial surface through a high-affinity interaction maintains key complement-regulatory functions, they raise questions about the importance of FH binding to immune evasion by GBS as a whole.
Collapse
Affiliation(s)
- Xin Xu
- Department of Biochemistry & Molecular Biophysics, Kansas State University; Manhattan, KS U.S.A
| | - Alexander L. Lewis Marffy
- Department of Infectious Diseases, Section of Molecular Microbiology, MRC Centre for Molecular Bacteriology & Infection, Imperial College London; London, U.K
| | - Andrew Keightley
- Department of Opthamology, School of Medicine, University of Missouri-Kansas City; Kansas City, MO U.S.A
| | - Alex J. McCarthy
- Department of Infectious Diseases, Section of Molecular Microbiology, MRC Centre for Molecular Bacteriology & Infection, Imperial College London; London, U.K
| | - Brian V. Geisbrecht
- Department of Biochemistry & Molecular Biophysics, Kansas State University; Manhattan, KS U.S.A.,To whom correspondence should be addressed: Brian V. Geisbrecht, Ph.D., Kansas State University, 141 Chalmers Hall, 1711 Claflin Road, Manhattan, KS 66506, PH: 785.532.3154,
| |
Collapse
|
15
|
Savitt AG, Manimala S, White T, Fandaros M, Yin W, Duan H, Xu X, Geisbrecht BV, Rubenstein DA, Kaplan AP, Peerschke EI, Ghebrehiwet B. SARS-CoV-2 Exacerbates COVID-19 Pathology Through Activation of the Complement and Kinin Systems. Front Immunol 2021; 12:767347. [PMID: 34804054 PMCID: PMC8602850 DOI: 10.3389/fimmu.2021.767347] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [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: 08/30/2021] [Accepted: 10/19/2021] [Indexed: 11/13/2022] Open
Abstract
Infection with SARS-CoV-2 triggers the simultaneous activation of innate inflammatory pathways including the complement system and the kallikrein-kinin system (KKS) generating in the process potent vasoactive peptides that contribute to severe acute respiratory syndrome (SARS) and multi-organ failure. The genome of SARS-CoV-2 encodes four major structural proteins - the spike (S) protein, nucleocapsid (N) protein, membrane (M) protein, and the envelope (E) protein. However, the role of these proteins in either binding to or activation of the complement system and/or the KKS is still incompletely understood. In these studies, we used: solid phase ELISA, hemolytic assay and surface plasmon resonance (SPR) techniques to examine if recombinant proteins corresponding to S1, N, M and E: (a) bind to C1q, gC1qR, FXII and high molecular weight kininogen (HK), and (b) activate complement and/or the KKS. Our data show that the viral proteins: (a) bind C1q and activate the classical pathway of complement, (b) bind FXII and HK, and activate the KKS in normal human plasma to generate bradykinin and (c) bind to gC1qR, the receptor for the globular heads of C1q (gC1q) which in turn could serve as a platform for the activation of both the complement system and KKS. Collectively, our data indicate that the SARS-CoV-2 viral particle can independently activate major innate inflammatory pathways for maximal damage and efficiency. Therefore, if efficient therapeutic modalities for the treatment of COVID-19 are to be designed, a strategy that includes blockade of the four major structural proteins may provide the best option.
Collapse
Affiliation(s)
- Anne G Savitt
- Department of Microbiology & Immunology, Renaissance School of Medicine of Stony Brook University, Stony Brook, NY, United States.,Department of Medicine, Renaissance School of Medicine of Stony Brook University, Stony Brook, NY, United States
| | - Samantha Manimala
- Department of Medicine, Renaissance School of Medicine of Stony Brook University, Stony Brook, NY, United States
| | - Tiara White
- Department of Microbiology & Immunology, Renaissance School of Medicine of Stony Brook University, Stony Brook, NY, United States.,Department of Medicine, Renaissance School of Medicine of Stony Brook University, Stony Brook, NY, United States
| | - Marina Fandaros
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, United States
| | - Wei Yin
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, United States
| | - Huiquan Duan
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, United States
| | - Xin Xu
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, United States
| | - Brian V Geisbrecht
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, United States
| | - David A Rubenstein
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, United States
| | - Allen P Kaplan
- Pulmonary and Critical Care Division, The Medical University of South Carolina, Charleston, SC, United States
| | - Ellinor I Peerschke
- The Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Berhane Ghebrehiwet
- Department of Microbiology & Immunology, Renaissance School of Medicine of Stony Brook University, Stony Brook, NY, United States
| |
Collapse
|
16
|
Pal I, Mishra N, Herrera AI, Dubey A, Arthanari H, Geisbrecht BV, Prakash O. 1H, 15N, and 13C backbone resonance assignments of the C4b-binding region from the S. aureus extracellular adherence protein. Biomol NMR Assign 2021; 15:183-186. [PMID: 33423171 PMCID: PMC7979526 DOI: 10.1007/s12104-020-10003-6] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 12/26/2020] [Indexed: 06/12/2023]
Abstract
The Extracellular Adherence Protein (Eap) from Staphylococcus aureus is a potent inhibitor of the classical and lectin pathways of the complement system. Previous studies have shown that Eap binds with nanomolar affinity to complement component C4b and prevents C4b binding the pro-protease, C2, thereby inhibiting formation of the pro-C3 convertase shared by the classical and lectin pathways (Woehl et al. in J Immunol 193:6161-6171, 2014). The C4b-binding and complement-inhibitory properties of Eap from S. aureus strain Mu50 lie within the two C terminal-most Eap domains (i.e. Eap34) (Woehl et al. J Immunol 193:6161-6171, 2014). Interestingly, Eap34 binds C4b with an apparent KD that is nearly 100-fold tighter than that of either Eap3 or Eap4 alone (Woehl et al. in Protein Sci 26:1595-1608, 2017). This suggests that linking these two domains into a single molecule is a significant determinant of Eap function. To better understand this property at the structural level, we undertook a solution NMR study of the ~ 23 kDa Eap34 protein. In this communication, we report that greater than 98% of the total non-proline backbone residues have been assigned. These data have been deposited in the BMRB database under the accession number 50210.
Collapse
Affiliation(s)
- Indrani Pal
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, 66506, USA
| | - Nitin Mishra
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, 66506, USA
| | - Alvaro I Herrera
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, 66506, USA
| | - Abhinav Dubey
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Haribabu Arthanari
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Brian V Geisbrecht
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, 66506, USA.
| | - Om Prakash
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, 66506, USA.
| |
Collapse
|
17
|
Comer J, Bassette M, Burghart R, Loyd M, Ishiguro S, Azhagiya Singam ER, Vergara-Jaque A, Nakashima A, Suzuki K, Geisbrecht BV, Tamura M. Beta-1,3 Oligoglucans Specifically Bind to Immune Receptor CD28 and May Enhance T Cell Activation. Int J Mol Sci 2021; 22:ijms22063124. [PMID: 33803858 PMCID: PMC8003162 DOI: 10.3390/ijms22063124] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 03/04/2021] [Accepted: 03/10/2021] [Indexed: 11/16/2022] Open
Abstract
Beta glucans are known to have immunomodulatory effects that mediated by a variety of mechanisms. In this article, we describe experiments and simulations suggesting that beta-1,3 glucans may promote activation of T cells by a previously unknown mechanism. First, we find that treatment of a T lymphoblast cell line with beta-1,3 oligoglucan significantly increases mRNA levels of T cell activation-associated cytokines, especially in the presence of the agonistic anti-CD3 antibody. This immunostimulatory activity was observed in the absence of dectin-1, a known receptor for beta-1,3 glucans. To clarify the molecular mechanism underlying this activity, we performed a series of molecular dynamics simulations and free-energy calculations to explore the interaction of beta-1,3 oligoglucans with potential immune receptors. While the simulations reveal little association between beta-1,3 oligoglucan and the immune receptor CD3, we find that beta-1,3 oligoglucans bind to CD28 near the region identified as the binding site for its natural ligands CD80 and CD86. Using a rigorous absolute binding free-energy technique, we calculate a dissociation constant in the low millimolar range for binding of 8-mer beta-1,3 oligoglucan to this site on CD28. The simulations show this binding to be specific, as no such association is computed for alpha-1,4 oligoglucan. This study suggests that beta-1,3 glucans bind to CD28 and may stimulate T cell activation collaboratively with T cell receptor activation, thereby stimulating immune function.
Collapse
Affiliation(s)
- Jeffrey Comer
- Department of Anatomy and Physiology, Kansas State University, Manhattan, KS 66506, USA; (M.B.); (R.B.); (M.L.); (S.I.); (E.R.A.S.); (A.V.-J.)
- Correspondence: (J.C.); (M.T.)
| | - Molly Bassette
- Department of Anatomy and Physiology, Kansas State University, Manhattan, KS 66506, USA; (M.B.); (R.B.); (M.L.); (S.I.); (E.R.A.S.); (A.V.-J.)
| | - Riley Burghart
- Department of Anatomy and Physiology, Kansas State University, Manhattan, KS 66506, USA; (M.B.); (R.B.); (M.L.); (S.I.); (E.R.A.S.); (A.V.-J.)
| | - Mayme Loyd
- Department of Anatomy and Physiology, Kansas State University, Manhattan, KS 66506, USA; (M.B.); (R.B.); (M.L.); (S.I.); (E.R.A.S.); (A.V.-J.)
| | - Susumu Ishiguro
- Department of Anatomy and Physiology, Kansas State University, Manhattan, KS 66506, USA; (M.B.); (R.B.); (M.L.); (S.I.); (E.R.A.S.); (A.V.-J.)
| | - Ettayapuram Ramaprasad Azhagiya Singam
- Department of Anatomy and Physiology, Kansas State University, Manhattan, KS 66506, USA; (M.B.); (R.B.); (M.L.); (S.I.); (E.R.A.S.); (A.V.-J.)
- Molecular Graphics and Computation Facility, College of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Ariela Vergara-Jaque
- Department of Anatomy and Physiology, Kansas State University, Manhattan, KS 66506, USA; (M.B.); (R.B.); (M.L.); (S.I.); (E.R.A.S.); (A.V.-J.)
- Center for Bioinformatics, Simulation and Modeling (CBSM), Faculty of Engineering, Universidad de Talca, Talca 3460000, Chile
| | | | - Kengo Suzuki
- Euglena Co., Ltd., Tokyo 108-0014, Japan; (A.N.); (K.S.)
| | - Brian V. Geisbrecht
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506, USA;
| | - Masaaki Tamura
- Department of Anatomy and Physiology, Kansas State University, Manhattan, KS 66506, USA; (M.B.); (R.B.); (M.L.); (S.I.); (E.R.A.S.); (A.V.-J.)
- Correspondence: (J.C.); (M.T.)
| |
Collapse
|
18
|
Xu X, Zhang C, Denton DT, O’Connell D, Drolet DW, Geisbrecht BV. Inhibition of the Complement Alternative Pathway by Chemically Modified DNA Aptamers That Bind with Picomolar Affinity to Factor B. J Immunol 2021; 206:861-873. [PMID: 33419768 PMCID: PMC7851746 DOI: 10.4049/jimmunol.2001260] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 12/08/2020] [Indexed: 01/07/2023]
Abstract
The complement system is a conserved component of innate immunity that fulfills diverse roles in defense and homeostasis. Inappropriate activation of complement contributes to many inflammatory diseases, however, which has led to a renewed emphasis on development of therapeutic complement inhibitors. Activation of complement component C3 is required for amplification of complement and is achieved through two multisubunit proteases called C3 convertases. Of these, the alternative pathway (AP) C3 convertase is responsible for a majority of the C3 activation products in vivo, which renders it an attractive target for inhibitor discovery. In this study, we report the identification and characterization of two related slow off-rate modified DNA aptamers (SOMAmer) reagents that inhibit formation of the AP C3 convertase by binding to the proprotease, factor B (FB). These aptamers, known as SL1102 (31 bases) and SL1103 (29 bases), contain uniform substitutions of 5-(N-2-naphthylethylcarboxyamide)-2'-deoxyuridine for deoxythymidine. SL1102 and SL1103 bind FB with K d values of 49 and 88 pM, respectively, and inhibit activation of C3 and lysis of rabbit erythrocytes under AP-specific conditions. Cocrystal structures of SL1102 (3.4 Å) and SL1103 (3.1 Å) bound to human FB revealed that SL1102 and SL1103 recognize a site at the juncture of the CCP1, CCP3, and vWF domains of FB. Consistent with these structures and previously published information, these aptamers inhibited FB binding to C3b and blocked formation of the AP C3 convertase. Together, these results demonstrate potent AP inhibition by modified DNA aptamers and expand the pipeline of FB-binding molecules with favorable pharmacologic properties.
Collapse
Affiliation(s)
- Xin Xu
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506
| | - Chi Zhang
- SomaLogic, Inc., Boulder, CO 80301; and
| | - Dalton T. Denton
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506
| | | | | | - Brian V. Geisbrecht
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506
| |
Collapse
|
19
|
Glaza P, Ranaweera CB, Shiva S, Roy A, Geisbrecht BV, Schoenen FJ, Zolkiewski M. Repurposing p97 inhibitors for chemical modulation of the bacterial ClpB-DnaK bichaperone system. J Biol Chem 2020; 296:100079. [PMID: 33187983 PMCID: PMC7948422 DOI: 10.1074/jbc.ra120.015413] [Citation(s) in RCA: 6] [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: 07/27/2020] [Revised: 10/31/2020] [Accepted: 11/13/2020] [Indexed: 01/18/2023] Open
Abstract
The ClpB–DnaK bichaperone system reactivates aggregated cellular proteins and is essential for survival of bacteria, fungi, protozoa, and plants under stress. AAA+ ATPase ClpB is a promising target for the development of antimicrobials because a loss of its activity is detrimental for survival of many pathogens and no apparent ClpB orthologs are found in metazoans. We investigated ClpB activity in the presence of several compounds that were previously described as inhibitor leads for the human AAA+ ATPase p97, an antitumor target. We discovered that N2,N4-dibenzylquinazoline-2,4-diamine (DBeQ), the least potent among the tested p97 inhibitors, binds to ClpB with a Kd∼60 μM and inhibits the casein-activated, but not the basal, ATPase activity of ClpB with an IC50∼5 μM. The remaining p97 ligands, which displayed a higher affinity toward p97, did not affect the ClpB ATPase. DBeQ also interacted with DnaK with a Kd∼100 μM and did not affect the DnaK ATPase but inhibited the DnaK chaperone activity in vitro. DBeQ inhibited the reactivation of aggregated proteins by the ClpB–DnaK bichaperone system in vitro with an IC50∼5 μM and suppressed the growth of cultured Escherichia coli. The DBeQ-induced loss of E. coli proliferation was exacerbated by heat shock but was nearly eliminated in a ClpB-deficient E. coli strain, which demonstrates a significant selectivity of DBeQ toward ClpB in cells. Our results provide chemical validation of ClpB as a target for developing novel antimicrobials. We identified DBeQ as a promising lead compound for structural optimization aimed at selective targeting of ClpB and/or DnaK.
Collapse
Affiliation(s)
- Przemyslaw Glaza
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, USA
| | - Chathurange B Ranaweera
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, USA
| | - Sunitha Shiva
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, USA
| | - Anuradha Roy
- High Throughput Screening Laboratory, University of Kansas, Lawrence, Kansas, USA; Lead Development and Optimization Shared Resource, University of Kansas Cancer Center, Kansas City, Kansas, USA
| | - Brian V Geisbrecht
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, USA
| | - Frank J Schoenen
- Lead Development and Optimization Shared Resource, University of Kansas Cancer Center, Kansas City, Kansas, USA; Higuchi Biosciences Center, University of Kansas, Lawrence, Kansas, USA
| | - Michal Zolkiewski
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, USA.
| |
Collapse
|
20
|
Velazhahan V, Glaza P, Herrera AI, Prakash O, Zolkiewski M, Geisbrecht BV, Schrick K. Dietary flavonoid fisetin binds human SUMO1 and blocks sumoylation of p53. PLoS One 2020; 15:e0234468. [PMID: 32530958 PMCID: PMC7292393 DOI: 10.1371/journal.pone.0234468] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 01/09/2020] [Accepted: 05/27/2020] [Indexed: 12/21/2022] Open
Abstract
Flavonoids are plant-derived compounds that occur abundantly in fruits and vegetables and have been shown to possess potent anti-cancer, antioxidant, and anti-inflammatory properties. However, their direct targets and molecular mechanism of action are not well characterized, hampering exploitation of the beneficial properties of flavonoids for drug development. Small ubiquitin-related modifier 1 (SUMO1) is attached to target proteins as part of a post-translational modification system implicated in a myriad of cellular processes from nuclear trafficking to transcriptional regulation. Using a combination of surface plasmon resonance, differential scanning fluorimetry and fluorescence quenching studies, we provide evidence for direct binding of the dietary flavonoid fisetin to human SUMO1. Our NMR chemical shift perturbation analyses reveal that binding to fisetin involves four conserved amino acid residues (L65, F66, E67, M82) previously shown to be important for conjugation of SUMO1 to target proteins. In vitro sumoylation experiments indicate that fisetin blocks sumoylation of tumor suppressor p53, consistent with fisetin negatively affecting post-translational modification and thus the biological activity of p53. A series of differential scanning fluorimetry experiments suggest that high concentrations of fisetin result in destabilization and unfolding of SUMO1, presenting a molecular mechanism by which flavonoid binding affects its activity. Overall, our data establish a novel direct interaction between fisetin and SUMO1, providing a mechanistic explanation for the ability of fisetin to modulate multiple key signaling pathways inside cells.
Collapse
Affiliation(s)
- Vaithish Velazhahan
- Division of Biology, Kansas State University, Manhattan, Kansas, United States of America
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, United States of America
| | - Przemyslaw Glaza
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, United States of America
| | - Alvaro I. Herrera
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, United States of America
| | - Om Prakash
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, United States of America
| | - Michal Zolkiewski
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, United States of America
| | - Brian V. Geisbrecht
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, United States of America
| | - Kathrin Schrick
- Division of Biology, Kansas State University, Manhattan, Kansas, United States of America
- Molecular, Cellular and Developmental Biology, Kansas State University, Manhattan, Kansas, United States of America
- * E-mail:
| |
Collapse
|
21
|
Herdendorf TJ, Stapels DAC, Rooijakkers SHM, Geisbrecht BV. Local structural plasticity of the Staphylococcus aureus evasion protein EapH1 enables engagement with multiple neutrophil serine proteases. J Biol Chem 2020; 295:7753-7762. [PMID: 32303641 PMCID: PMC7261791 DOI: 10.1074/jbc.ra120.013601] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 03/26/2020] [Revised: 04/16/2020] [Indexed: 01/07/2023] Open
Abstract
Members of the EAP family of Staphylococcus aureus immune evasion proteins potently inhibit the neutrophil serine proteases (NSPs) neutrophil elastase, cathepsin-G, and proteinase-3. Previously, we determined a 1.8 Å resolution crystal structure of the EAP family member EapH1 bound to neutrophil elastase. This structure revealed that EapH1 blocks access to the enzyme's active site by forming a noncovalent complex with this host protease. To determine how EapH1 inhibits other NSPs, we studied here the effects of EapH1 on cathepsin-G. We found that EapH1 inhibits cathepsin-G with a Ki of 9.8 ± 4.7 nm Although this Ki value is ∼466-fold weaker than the Ki for EapH1 inhibition of neutrophil elastase, the time dependence of inhibition was maintained. To define the physical basis for EapH1's inhibition of cathepsin-G, we crystallized EapH1 bound to this protease, solved the structure at 1.6 Å resolution, and refined the model to Rwork and Rfree values of 17.4% and 20.9%, respectively. This structure revealed a protease-binding mode for EapH1 with cathepsin-G that was globally similar to that seen in the previously determined EapH1-neutrophil elastase structure. The nature of the intermolecular interactions formed by EapH1 with cathepsin-G differed considerably from that with neutrophil elastase, however, with far greater contributions from the inhibitor backbone in the cathepsin-G-bound form. Together, these results reveal that EapH1's ability to form high-affinity interactions with multiple NSP targets is due to its remarkable level of local structural plasticity.
Collapse
Affiliation(s)
- Timothy J. Herdendorf
- Department of Biochemistry & Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506
| | - Daphne A. C. Stapels
- Department of Medical Microbiology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | - Suzan H. M. Rooijakkers
- Department of Medical Microbiology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | - Brian V. Geisbrecht
- Department of Biochemistry & Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506, To whom correspondence should be addressed:
Dept. of Biochemistry and Molecular Biophysics, Kansas State University, 141 Chalmers Hall, 1711 Claflin Rd., Manhattan, KS 66506. Tel.:
785-532-3154; Fax:
785-532-7278; E-mail:
| |
Collapse
|
22
|
Bawa S, Brooks DS, Neville KE, Sagar MAK, Geisbrecht BV, Tennessen JM, Tipping M, Elicieri KW, Geisbrecht ER. Drosophila
TRIM32 cooperates with glycolytic enzymes to promote cell growth. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.07215] [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]
|
23
|
Bawa S, Brooks DS, Neville KE, Tipping M, Sagar MA, Kollhoff JA, Chawla G, Geisbrecht BV, Tennessen JM, Eliceiri KW, Geisbrecht ER. Drosophila TRIM32 cooperates with glycolytic enzymes to promote cell growth. eLife 2020; 9:52358. [PMID: 32223900 PMCID: PMC7105379 DOI: 10.7554/elife.52358] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [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: 10/02/2019] [Accepted: 03/23/2020] [Indexed: 12/13/2022] Open
Abstract
Cell growth and/or proliferation may require the reprogramming of metabolic pathways, whereby a switch from oxidative to glycolytic metabolism diverts glycolytic intermediates towards anabolic pathways. Herein, we identify a novel role for TRIM32 in the maintenance of glycolytic flux mediated by biochemical interactions with the glycolytic enzymes Aldolase and Phosphoglycerate mutase. Loss of Drosophila TRIM32, encoded by thin (tn), shows reduced levels of glycolytic intermediates and amino acids. This altered metabolic profile correlates with a reduction in the size of glycolytic larval muscle and brain tissue. Consistent with a role for metabolic intermediates in glycolysis-driven biomass production, dietary amino acid supplementation in tn mutants improves muscle mass. Remarkably, TRIM32 is also required for ectopic growth - loss of TRIM32 in a wing disc-associated tumor model reduces glycolytic metabolism and restricts growth. Overall, our results reveal a novel role for TRIM32 for controlling glycolysis in the context of both normal development and tumor growth.
Collapse
Affiliation(s)
- Simranjot Bawa
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, United States
| | - David S Brooks
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, United States
| | - Kathryn E Neville
- Department of Biology, Providence College, Providence, United States
| | - Marla Tipping
- Department of Biology, Providence College, Providence, United States
| | - Md Abdul Sagar
- Laboratory for Optical and Computational Instrumentation, Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, United States
| | - Joseph A Kollhoff
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, United States
| | - Geetanjali Chawla
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, India.,Department of Biology, Indiana University, Bloomington, United States
| | - Brian V Geisbrecht
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, United States
| | - Jason M Tennessen
- Department of Biology, Indiana University, Bloomington, United States
| | - Kevin W Eliceiri
- Laboratory for Optical and Computational Instrumentation, Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, United States
| | - Erika R Geisbrecht
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, United States
| |
Collapse
|
24
|
Ghebrehiwet B, Geisbrecht BV, Xu X, Savitt AG, Peerschke EIB. The C1q Receptors: Focus on gC1qR/p33 (C1qBP, p32, HABP-1) 1. Semin Immunol 2019; 45:101338. [PMID: 31744753 DOI: 10.1016/j.smim.2019.101338] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 10/24/2019] [Accepted: 10/24/2019] [Indexed: 10/25/2022]
Abstract
In the past several years, a number of C1q binding surface proteins or receptors have been described. This is not of course surprising considering the complexity of the C1q molecule and its ability to bind to a wide range of cellular and plasma proteins via both its collagen-like [cC1q] region and its heterotrimeric globular heads [gC1q] each of which in turn is capable of binding a specific ligand. However, while each of these "receptor" molecules undoubtedly plays a specific function within its restricted microenvironment, and therefore merits full attention, this review nonetheless, will singularly focus on the structure and function of gC1qR-a multi-functional and multi-compartmental protein, which plays an important role in inflammation, infection, and cancer. Although first identified as a receptor for C1q, gC1qR has been shown to bind to a plethora of proteins found in plasma, on the cell surface and on pathogenic microorganisms. The plasma proteins that bind to gC1qR are mostly blood coagulation proteins and include high molecular weight kininogen [HK], Factor XII [Hageman factor], fibrinogen, thrombin [FII], and multimeric vitronectin. This suggests that gC1qR can play an important role in modulating not only of fibrin formation, particularly at local sites of immune injury and/or inflammation, but by activating the kinin/kallikrein system, it is also able to generate, bradykinin, a powerful vasoactive peptide that is largely responsible for the swelling seen in angioedema. Another important function of gC1qR is in cancer, where it has been shown to play a role in tumor cell survival, growth and metastatic invasion by interacting with critical molecules in the tumor cell microenvironment including those of the complement system and kinin system. Finally, by virtue of its ability to interact with a growing list of pathogen-associated molecules, including bacterial and viral ligands, gC1qR is becoming recognized as an important pathogen recognition receptor [PRR]. Given the numerous roles it plays in a growing list of disease settings, gC1qR has now become a potential target for the development of monoclonal antibody-based and/or small molecule-based therapies.
Collapse
Affiliation(s)
- Berhane Ghebrehiwet
- The Departments of Medicine, Stony Brook University, Stony Brook, NY 11794-8161 USA.
| | - Brian V Geisbrecht
- Kansas State University, Department of Biochemistry and Molecular Biophysics Manhattan, KS 66506 USA
| | - Xin Xu
- Kansas State University, Department of Biochemistry and Molecular Biophysics Manhattan, KS 66506 USA
| | - Anne G Savitt
- The Departments of Medicine, Stony Brook University, Stony Brook, NY 11794-8161 USA
| | - Ellinor I B Peerschke
- The Department of Laboratory Medicine, Memorial Sloan-Kettering Cancer Center, New York, 10065, USA
| |
Collapse
|
25
|
Herdendorf TJ, Geisbrecht BV. Staphylococcus aureus evasion proteins EapH1 and EapH2: Residue-level investigation of an alternative binding motif for human neutrophil elastase. Arch Biochem Biophys 2019; 676:108140. [PMID: 31622584 DOI: 10.1016/j.abb.2019.108140] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 09/20/2019] [Accepted: 10/09/2019] [Indexed: 12/24/2022]
Abstract
The Staphylococcus aureusExtracellular Adherence Protein (Eap) and its homologs, EapH1 and EapH2, are a family of secreted proteins that potently inhibit the neutrophil serine proteases Neutrophil Elastase (hNE), Cathepsin G, and Proteinase 3. Similarly to EapH1, inhibition of hNE by EapH2 is characterized by a rapid association rate (2.9 × 105 M-1s-1) coupled with a very slow dissociation rate (5.9 × 10-4 s-1), yielding an apparent inhibition constant of 2.11 nM. As with EapH1, inhibition of hNE by EapH2 is also time-dependent in character. A phenylalanine in EapH2 replaces the leucine in EapH1 that sits over the hNE catalytic serine and creates a potential steric clash. Indeed, the EapH1 L59F mutant is severely decreased in its ability to inhibit hNE (~9500-fold). When compared to the EapH1:hNE co-crystal structure, a model of the EapH2:hNE complex predicts an alternative binding motif comprised of EapH2 residues 120-127. These putative interfacing residues were individually mutated and kinetically interrogated. The EapH2 N127A mutant resulted in the largest decrease in hNE inhibition (~200-fold) and loss of the time-dependent characteristic. Surprisingly, the time-dependent characteristic was still abolished in the EapH2 T125A mutant, even though it was less perturbed in hNE inhibition (~25-fold). T125 forms an intra-molecular hydrogen bond to the carbonyl oxygen of N127 in the EapH2 crystal structure. Given these observations, we conclude (i) that EapH2 has an altogether distinct hNE binding motif than EapH1, (ii) that N127 is the main functional determinant in EapH2, and (iii) that T125 serves an ancillary role aiding in the optimal orientation of N127.
Collapse
Affiliation(s)
- Timothy J Herdendorf
- Department of Biochemistry & Molecular Biophysics, Kansas State University, Manhattan, KS, 66506, USA
| | - Brian V Geisbrecht
- Department of Biochemistry & Molecular Biophysics, Kansas State University, Manhattan, KS, 66506, USA.
| |
Collapse
|
26
|
Ramyar KX, Xu X, White NM, Keightley A, Geisbrecht BV. Expression, purification, and characterization of a human complement component C3 analog that lacks the C-terminal C345c domain. J Immunol Methods 2019; 473:112633. [PMID: 31319063 DOI: 10.1016/j.jim.2019.07.005] [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: 05/15/2019] [Revised: 06/27/2019] [Accepted: 07/11/2019] [Indexed: 10/26/2022]
Abstract
The complement system consists of a series of soluble and cell-surface proteins that serve numerous roles in innate immunity, development, and homeostasis. Despite its many functions, the central event in the complement system is the proteolytic activation of the 185 kDa complement component 3 (C3) into its opsonin and anaphylatoxin fragments known as C3b (175 kDa) and C3a (10 kDa), respectively. The C3 protein is comprised of thirteen separate structural domains, several of which undergo extensive structural rearrangement upon activation to C3b. In addition to this, the C-terminal C345c domain found in C3, C3b, and the terminal degradation product, C3c (135 kDa), appears to adopt multiple conformations relative to the remainder of the molecule. To facilitate various structure/function studies, we designed two C3 analogs that could be activated to a C345c-less, C3c-like state following treatment with Tobacco Etch Virus (TEV) protease. We generated stably transfected Chinese Hamster Ovary (CHO) cell lines that secrete approximately 1.5 mg of the highest-expressing C3 analog per liter of conditioned culture medium. We purified this C3 analog by sequential immobilized metal ion affinity and size exclusion chromatographies, activated the protein by digestion with TEV protease, and purified the resulting C3c analog by a final size exclusion chromatography. The conformations and activities of our C3 and C3c analogs were assessed by measuring their binding profiles to known C3/b/c ligands by surface plasmon resonance. Together, this work demonstrates the feasibility of producing a C3 analog that can be site-specifically activated by an exogenous proteolytic enzyme.
Collapse
Affiliation(s)
- Kasra X Ramyar
- Department of Biochemistry & Molecular Biophysics, Kansas State University, 141 Chalmers Hall, 1711 Claflin Road, Manhattan, KS 66506, United States of America
| | - Xin Xu
- Department of Biochemistry & Molecular Biophysics, Kansas State University, 141 Chalmers Hall, 1711 Claflin Road, Manhattan, KS 66506, United States of America
| | - Natalie M White
- Department of Biochemistry & Molecular Biophysics, Kansas State University, 141 Chalmers Hall, 1711 Claflin Road, Manhattan, KS 66506, United States of America
| | - Andrew Keightley
- School of Biological Sciences, University of Missouri-Kansas City, 5100 Rockhill Road, Kansas City, MO 64110, United States of America
| | - Brian V Geisbrecht
- Department of Biochemistry & Molecular Biophysics, Kansas State University, 141 Chalmers Hall, 1711 Claflin Road, Manhattan, KS 66506, United States of America.
| |
Collapse
|
27
|
Herrera AI, Dubey A, Geisbrecht BV, Arthanari H, Prakash O. Backbone resonance assignments of innate immune evasion protein EapH2 from the S. aureus. Biomol NMR Assign 2019; 13:219-222. [PMID: 30729401 PMCID: PMC6440808 DOI: 10.1007/s12104-019-09880-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 02/01/2019] [Indexed: 06/05/2023]
Abstract
Staphylococcus aureus is a ubiquitous and persistent pathogen of humans and livestock. The bacterium disrupts the host's innate immune system's ability to recognize and clear bacteria with optimal efficiency by expressing a wide variety of virulence proteins. Two single domain protein homologs (EapH1, EapH2) of the extracellular adherence protein (Eap) have been reported. Eap is a multidomain protein that participates in various protein-protein interactions that inhibit the innate immune response, including both the complement and Neutrophil Serine Proteases (NSPs). EapH1 and EapH2 are also inhibitors of NSPs (Stapels et al., Proc Natl Acad Sci 111:13187-13192, 2014), but lack the ability to inhibit the classical, and lectin pathways of the complement activation system (Woehl et al., J Immunol 193:6161-6171, 2014). We continue the characterization of Eap domains, here with the experiments on EapH2, we acquired a series of 2D and 3D NMR spectra of EapH2 in solution. We completed 99% of expected non-proline backbone 1H, 15N, and 13C resonance assignments of EapH2 and predicted secondary structure via the TALOS-N server. The assignment data have been deposited in the BMRB data bank under Accession Number 27540.
Collapse
Affiliation(s)
- Alvaro I Herrera
- Department of Biochemistry and Molecular Biophysics, Kansas State University, 141 Chalmers Hall, Manhattan, KS, 66506, USA
| | - Abhinav Dubey
- Dana-Farber Cancer Institute, Harvard Medical School, 25 Shattuck Street, Boston, MA, 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Brian V Geisbrecht
- Department of Biochemistry and Molecular Biophysics, Kansas State University, 141 Chalmers Hall, Manhattan, KS, 66506, USA
| | - Haribabu Arthanari
- Dana-Farber Cancer Institute, Harvard Medical School, 25 Shattuck Street, Boston, MA, 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Om Prakash
- Department of Biochemistry and Molecular Biophysics, Kansas State University, 141 Chalmers Hall, Manhattan, KS, 66506, USA.
| |
Collapse
|
28
|
Herdendorf TJ, Geisbrecht BV. Investigation of Human Neutrophil Elastase Inhibition by Staphylococcus aureus EapH1: The Key Role Played by Arginine 89. Biochemistry 2018; 57:6888-6896. [PMID: 30461258 DOI: 10.1021/acs.biochem.8b01134] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Staphylococcus aureus secretes a family of potent, noncovalent inhibitory proteins that selectively target the neutrophil serine proteases neutrophil elastase, cathepsin-G, and proteinase-3. A majority of our understanding of these so-called EAP domain proteins has come from structure/function studies on EapH1 and its effects on human neutrophil elastase (hNE). Inspection of the EapH1/hNE cocrystal structure suggested that EapH1 residues R89, E94, and K95 are positioned near the EapH1/hNE interface and might contribute to the potent inhibition of hNE by EapH1. In this study, we used site directed mutagenesis, kinetic evaluation, and surface plasmon resonance to probe the individual contributions of R89, E94, and K95 to EapH1 function. We found that the wild-type EapH1/hNE complex is characterized by a fast association rate (2.0 × 106 M-1 s-1) and a very slow dissociation rate (4.3 × 10-5 s-1), yielding an apparent inhibition constant of 21 pM. The slow dissociation rate of EapH1 from hNE resulted in a time-dependent inhibition pattern. Although conservative mutants E94Q and K95M, as well as the E94Q/K95M double mutant, had on- and off-rates comparable to wild-type EapH1, mutation of R89 to methionine resulted in a 15,000-fold decrease in inhibition (321 nM) and loss of the time-dependent inhibition characteristic. The double mutants R89M/E94Q and R89M/K95M, as well as the triple mutant R89M/E94Q/K95M were similarly perturbed. Mutation of R89 to lysine restored a portion of the inhibition of hNE (27 nM). Given these observations, we conclude that R89 is a primary contributor to EapH1 function vis-à-vis time-dependent inhibition of hNE.
Collapse
Affiliation(s)
- Timothy J Herdendorf
- Department of Biochemistry & Molecular Biophysics , Kansas State University , Manhattan , Kansas 66506 , United States
| | - Brian V Geisbrecht
- Department of Biochemistry & Molecular Biophysics , Kansas State University , Manhattan , Kansas 66506 , United States
| |
Collapse
|
29
|
Eisenbeis J, Saffarzadeh M, Peisker H, Jung P, Thewes N, Preissner KT, Herrmann M, Molle V, Geisbrecht BV, Jacobs K, Bischoff M. The Staphylococcus aureus Extracellular Adherence Protein Eap Is a DNA Binding Protein Capable of Blocking Neutrophil Extracellular Trap Formation. Front Cell Infect Microbiol 2018; 8:235. [PMID: 30038902 PMCID: PMC6047304 DOI: 10.3389/fcimb.2018.00235] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [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: 03/20/2018] [Accepted: 06/19/2018] [Indexed: 01/07/2023] Open
Abstract
The extracellular adherence protein (Eap) of Staphylococcus aureus is a secreted protein known to exert a number of adhesive and immunomodulatory properties. Here we describe the intrinsic DNA binding activity of this multifunctional secretory factor. By using atomic force microscopy, we provide evidence that Eap can bind and aggregate DNA. While the origin of the DNA substrate (e.g., eukaryotic, bacterial, phage, and artificial DNA) seems to not be of major importance, the DNA structure (e.g., linear or circular) plays a critical role with respect to the ability of Eap to bind and condense DNA. Further functional assays corroborated the nature of Eap as a DNA binding protein, since Eap suppressed the formation of "neutrophil extracellular traps" (NETs), composed of DNA-histone scaffolds, which are thought to function as a neutrophil-mediated extracellular trapping mechanism. The DNA binding and aggregation activity of Eap may thereby protect S. aureus against a specific anti-microbial defense reaction from the host.
Collapse
Affiliation(s)
- Janina Eisenbeis
- Institute of Medical Microbiology and Hygiene, Saarland University, Homburg, Germany
| | - Mona Saffarzadeh
- Department of Biochemistry, Medical Faculty, Justus-Liebig-University, Giessen, Germany
| | - Henrik Peisker
- Institute of Medical Microbiology and Hygiene, Saarland University, Homburg, Germany
| | - Philipp Jung
- Institute of Medical Microbiology and Hygiene, Saarland University, Homburg, Germany
| | - Nicolas Thewes
- Experimental Physics, Saarland University, Saarbrücken, Germany
| | - Klaus T. Preissner
- Department of Biochemistry, Medical Faculty, Justus-Liebig-University, Giessen, Germany
| | - Mathias Herrmann
- Institute of Medical Microbiology and Hygiene, Saarland University, Homburg, Germany
| | - Virginie Molle
- Laboratoire de Dynamique des Interactions Membranaires Normales et Pathologiques, Centre National de la Recherche Scientifique, UMR 5235, Université de Montpellier, Montpellier, France
| | - Brian V. Geisbrecht
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, United States
| | - Karin Jacobs
- Experimental Physics, Saarland University, Saarbrücken, Germany
| | - Markus Bischoff
- Institute of Medical Microbiology and Hygiene, Saarland University, Homburg, Germany
| |
Collapse
|
30
|
Barta ML, Tachiyama S, Muthuramalingam M, Arizmendi O, Villanueva CE, Ramyar KX, Geisbrecht BV, Lovell S, Battaile KP, Picking WL, Picking WD. Using disruptive insertional mutagenesis to identify the in situ structure-function landscape of the Shigella translocator protein IpaB. Protein Sci 2018; 27:1392-1406. [PMID: 29672980 DOI: 10.1002/pro.3428] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [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: 03/05/2018] [Revised: 04/12/2018] [Accepted: 04/16/2018] [Indexed: 11/11/2022]
Abstract
Bacterial type III secretion systems (T3SS) are used to inject proteins into mammalian cells to subvert cellular functions. The Shigella T3SS apparatus (T3SA) is comprised of a basal body, cytoplasmic sorting platform and exposed needle with needle "tip complex" (TC). TC maturation occurs when the translocator protein IpaB is recruited to the needle tip where both IpaD and IpaB control secretion induction. IpaB insertion into the host membrane is the first step of translocon pore formation and secretion induction. We employed disruptive insertional mutagenesis, using bacteriophage T4 lysozyme (T4L), within predicted IpaB loops to show how topological features affect TC functions (secretion control, translocon formation and effector secretion). Insertions within the N-terminal half of IpaB were most likely to result in a loss of steady-state secretion control, however, all but the two that were not recognized by the T3SA retained nearly wild-type hemolysis (translocon formation) and invasiveness levels (effector secretion). In contrast, all but one insertion in the C-terminal half of IpaB maintained secretion control but were impaired for hemolysis and invasion. These nature of the data suggest the latter mutants are defective in a post-secretion event, most likely due to impaired interactions with the second translocator protein IpaC. Intriguingly, only two insertion mutants displayed readily detectable T4L on the bacterial surface. The data create a picture in which the makeup and structure of a functional T3SA TC is highly amenable to physical perturbation, indicating that the tertiary structure of IpaB within the TC is more plastic than previously realized.
Collapse
Affiliation(s)
- Michael L Barta
- Higuchi Biosciences Center, University of Kansas, Lawrence, Kansas, 66047
| | - Shoichi Tachiyama
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, 66045
| | | | - Olivia Arizmendi
- Higuchi Biosciences Center, University of Kansas, Lawrence, Kansas, 66047
| | - Cecilia E Villanueva
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, 66045
| | - Kasra X Ramyar
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, 66506
| | - Brian V Geisbrecht
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, 66506
| | - Scott Lovell
- Protein Structure Laboratory, Del Shankel Structural Biology Center, University of Kansas, Lawrence, KS, 66045
| | - Kevin P Battaile
- IMCA-CAT, Hauptman-Woodward Medical Research Institute, Argonne, Illinois, 60439
| | - Wendy L Picking
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas, 66047
| | - William D Picking
- Higuchi Biosciences Center, University of Kansas, Lawrence, Kansas, 66047.,Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas, 66047
| |
Collapse
|
31
|
Ploscariu NT, de Jong NWM, van Kessel KPM, van Strijp JAG, Geisbrecht BV. Identification and structural characterization of a novel myeloperoxidase inhibitor from Staphylococcus delphini. Arch Biochem Biophys 2018; 645:1-11. [PMID: 29524428 PMCID: PMC5899673 DOI: 10.1016/j.abb.2018.03.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 02/28/2018] [Accepted: 03/06/2018] [Indexed: 01/13/2023]
Abstract
Staphylococcus aureus and related species are highly adapted to their hosts and have evolved numerous strategies to evade the immune system. S. aureus shows resistance to killing following uptake into the phagosome, which suggests that the bacterium evades intracellular killing mechanisms used by neutrophils. We recently discovered an S. aureus protein (SPIN for Staphylococcal Peroxidase INhibitor) that binds to and inhibits myeloperoxidase (MPO), a major player in the oxidative defense of neutrophils. To allow for comparative studies between multiple SPIN sequences, we identified a panel of homologs from species closely related to S. aureus. Characterization of these proteins revealed that SPIN molecules from S. agnetis, S. delphini, S. schleiferi, and S. intermedius all bind human MPO with nanomolar affinities, and that those from S. delphini, S. schleiferi, and S. intermedius inhibit human MPO in a dose-dependent manner. A 2.4 Å resolution co-crystal structure of SPIN-delphini bound to recombinant human MPO allowed us to identify conserved structural features of SPIN proteins, and to propose sequence-dependent physical explanations for why SPIN-aureus binds human MPO with higher affinity than SPIN-delphini. Together, these studies expand our understanding of MPO binding and inhibition by a recently identified component of the staphylococcal innate immune evasion arsenal.
Collapse
Affiliation(s)
- Nicoleta T Ploscariu
- Department of Biochemistry & Molecular Biophysics, Kansas State University, 141 Chalmers Hall, 1711 Claflin Road, Manhattan, KS, 66506, USA
| | - Nienke W M de Jong
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Kok P M van Kessel
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Jos A G van Strijp
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Brian V Geisbrecht
- Department of Biochemistry & Molecular Biophysics, Kansas State University, 141 Chalmers Hall, 1711 Claflin Road, Manhattan, KS, 66506, USA.
| |
Collapse
|
32
|
Herrera AI, Ploscariu NT, Geisbrecht BV, Prakash O. 1H, 15N, and 13C resonance assignments of the third domain from the S. aureus innate immune evasion protein Eap. Biomol NMR Assign 2018; 12:175-178. [PMID: 29372458 PMCID: PMC5871566 DOI: 10.1007/s12104-018-9804-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 01/23/2018] [Indexed: 05/12/2023]
Abstract
Staphylococcus aureus is a widespread and persistent pathogen of humans and livestock. The bacterium expresses a wide variety of virulence proteins, many of which serve to disrupt the host's innate immune system from recognizing and clearing bacteria with optimal efficiency. The extracellular adherence protein (Eap) is a multidomain protein that participates in various protein-protein interactions that inhibit the innate immune response, including both the complement system (Woehl et al in J Immunol 193:6161-6171, 2014) and Neutrophil Serine Proteases (NSPs) (Stapels et al in Proc Natl Acad Sci USA 111:13187-13192, 2014). The third domain of Eap, Eap3, is an ~ 11 kDa protein that was recently shown to bind complement component C4b (Woehl et al in Protein Sci 26:1595-1608, 2017) and therefore play an essential role in inhibiting the classical and lectin pathways of complement (Woehl et al in J Immunol 193:6161-6171, 2014). Since structural characterization of Eap3 is still incomplete, we acquired a series of 2D and 3D NMR spectra of Eap3 in solution. Here we report the backbone and side-chain 1H, 15N, and 13C resonance assignments of Eap3 and its predicted secondary structure via the TALOS-N server. The assignment data have been deposited in the BMRB data bank under accession number 27087.
Collapse
Affiliation(s)
- Alvaro I Herrera
- Department of Biochemistry and Molecular Biophysics, Kansas State University, 141 Chalmers Hall, Manhattan, KS, 66506, USA
| | - Nicoleta T Ploscariu
- Department of Biochemistry and Molecular Biophysics, Kansas State University, 141 Chalmers Hall, Manhattan, KS, 66506, USA
| | - Brian V Geisbrecht
- Department of Biochemistry and Molecular Biophysics, Kansas State University, 141 Chalmers Hall, Manhattan, KS, 66506, USA
| | - Om Prakash
- Department of Biochemistry and Molecular Biophysics, Kansas State University, 141 Chalmers Hall, Manhattan, KS, 66506, USA.
| |
Collapse
|
33
|
Ploscariu NT, Jong N, Strijp J, Geisbrecht BV. Structure/Function Analysis of a Novel Myeloperoxidase Inhibitor from
Staphylococcus delphini. FASEB J 2018. [DOI: 10.1096/fasebj.2018.32.1_supplement.674.21] [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)
| | - Nienke Jong
- Molecular Microbiology and ImmunologyUniversity Medical Center UtrechtUtrechtNetherlands
| | - Jos Strijp
- Molecular Microbiology and ImmunologyUniversity Medical Center UtrechtUtrechtNetherlands
| | | |
Collapse
|
34
|
de Jong NWM, Ploscariu NT, Ramyar KX, Garcia BL, Herrera AI, Prakash O, Katz BB, Leidal KG, Nauseef WM, van Kessel KPM, van Strijp JAG, Geisbrecht BV. A structurally dynamic N-terminal region drives function of the staphylococcal peroxidase inhibitor (SPIN). J Biol Chem 2018; 293:2260-2271. [PMID: 29306874 PMCID: PMC5818189 DOI: 10.1074/jbc.ra117.000134] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [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: 09/28/2017] [Revised: 12/21/2017] [Indexed: 01/07/2023] Open
Abstract
The heme-containing enzyme myeloperoxidase (MPO) is critical for optimal antimicrobial activity of human neutrophils. We recently discovered that the bacterium Staphylococcus aureus expresses a novel immune evasion protein, called SPIN, that binds tightly to MPO, inhibits MPO activity, and contributes to bacterial survival following phagocytosis. A co-crystal structure of SPIN bound to MPO suggested that SPIN blocks substrate access to the catalytic heme by inserting an N-terminal β-hairpin into the MPO active-site channel. Here, we describe a series of experiments that more completely define the structure/function relationships of SPIN. Whereas the SPIN N terminus adopts a β-hairpin confirmation upon binding to MPO, the solution NMR studies presented here are consistent with this region of SPIN being dynamically structured in the unbound state. Curiously, whereas the N-terminal β-hairpin of SPIN accounts for ∼55% of the buried surface area in the SPIN-MPO complex, its deletion did not significantly change the affinity of SPIN for MPO but did eliminate the ability of SPIN to inhibit MPO. The flexible nature of the SPIN N terminus rendered it susceptible to proteolytic degradation by a series of chymotrypsin-like proteases found within neutrophil granules, thereby abrogating SPIN activity. Degradation of SPIN was prevented by the S. aureus immune evasion protein Eap, which acts as a selective inhibitor of neutrophil serine proteases. Together, these studies provide insight into MPO inhibition by SPIN and suggest possible functional synergy between two distinct classes of S. aureus immune evasion proteins.
Collapse
Affiliation(s)
- Nienke W. M. de Jong
- From Medical Microbiology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | - Nicoleta T. Ploscariu
- the Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506
| | - Kasra X. Ramyar
- the Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506
| | - Brandon L. Garcia
- the Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506
| | - Alvaro I. Herrera
- the Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506
| | - Om Prakash
- the Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506
| | - Benjamin B. Katz
- the Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506
| | - Kevin G. Leidal
- the Inflammation Program, Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa 52240, and
| | - William M. Nauseef
- the Inflammation Program, Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa 52240, and ,the Iowa City Veterans Affairs Health Care System, Iowa City, Iowa 52246
| | - Kok P. M. van Kessel
- From Medical Microbiology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | - Jos A. G. van Strijp
- From Medical Microbiology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | - Brian V. Geisbrecht
- the Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506, , To whom correspondence should be addressed:
Dept. of Biochemistry and Molecular Biophysics, Kansas State University, 141 Chalmers Hall, 1711 Claflin Rd., Manhattan, KS 66506. Tel.:
785-532-3154; Fax:
785-532-7278; E-mail:
| |
Collapse
|
35
|
de Jong NWM, Vrieling M, Garcia BL, Koop G, Brettmann M, Aerts PC, Ruyken M, van Strijp JAG, Holmes M, Harrison EM, Geisbrecht BV, Rooijakkers SHM. Identification of a staphylococcal complement inhibitor with broad host specificity in equid Staphylococcus aureus strains. J Biol Chem 2018; 293:4468-4477. [PMID: 29414776 PMCID: PMC5868266 DOI: 10.1074/jbc.ra117.000599] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [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: 10/24/2017] [Revised: 01/25/2018] [Indexed: 01/09/2023] Open
Abstract
Staphylococcus aureus is a versatile pathogen capable of causing a broad range of diseases in many different hosts. S. aureus can adapt to its host through modification of its genome (e.g. by acquisition and exchange of mobile genetic elements that encode host-specific virulence factors). Recently, the prophage φSaeq1 was discovered in S. aureus strains from six different clonal lineages almost exclusively isolated from equids. Within this phage, we discovered a novel variant of staphylococcal complement inhibitor (SCIN), a secreted protein that interferes with activation of the human complement system, an important line of host defense. We here show that this equine variant of SCIN, eqSCIN, is a potent blocker of equine complement system activation and subsequent phagocytosis of bacteria by phagocytes. Mechanistic studies indicate that eqSCIN blocks equine complement activation by specific inhibition of the C3 convertase enzyme (C3bBb). Whereas SCIN-A from human S. aureus isolates exclusively inhibits human complement, eqSCIN represents the first animal-adapted SCIN variant that functions in a broader range of hosts (horses, humans, and pigs). Binding analyses suggest that the human-specific activity of SCIN-A is related to amino acid differences on both sides of the SCIN-C3b interface. These data suggest that modification of this phage-encoded complement inhibitor plays a role in the host adaptation of S. aureus and are important to understand how this pathogen transfers between different hosts.
Collapse
Affiliation(s)
- Nienke W M de Jong
- From the Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, The Netherlands
| | - Manouk Vrieling
- From the Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, The Netherlands.,the Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, United Kingdom
| | - Brandon L Garcia
- the Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506
| | - Gerrit Koop
- the Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands
| | - Matt Brettmann
- the Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506
| | - Piet C Aerts
- From the Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, The Netherlands
| | - Maartje Ruyken
- From the Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, The Netherlands
| | - Jos A G van Strijp
- From the Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, The Netherlands
| | - Mark Holmes
- the Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, United Kingdom, and
| | - Ewan M Harrison
- the Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, United Kingdom
| | - Brian V Geisbrecht
- the Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506
| | - Suzan H M Rooijakkers
- From the Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, The Netherlands,
| |
Collapse
|
36
|
Stapels DAC, Woehl JL, Milder FJ, Tromp AT, van Batenburg AA, de Graaf WC, Broll SC, White NM, Rooijakkers SHM, Geisbrecht BV. Evidence for multiple modes of neutrophil serine protease recognition by the EAP family of Staphylococcal innate immune evasion proteins. Protein Sci 2017; 27:509-522. [PMID: 29114958 DOI: 10.1002/pro.3342] [Citation(s) in RCA: 11] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 11/01/2017] [Accepted: 11/02/2017] [Indexed: 12/18/2022]
Abstract
Neutrophils contain high levels of chymotrypsin-like serine proteases (NSPs) within their azurophilic granules that have a multitude of functions within the immune system. In response, the pathogen Staphylococcus aureus has evolved three potent inhibitors (Eap, EapH1, and EapH2) that protect the bacterium as well as several of its secreted virulence factors from the degradative action of NSPs. We previously showed that these so-called EAP domain proteins represent a novel class of NSP inhibitors characterized by a non-covalent inhibitory mechanism and a distinct target specificity profile. Based upon high levels of structural homology amongst the EAP proteins and the NSPs, as well as supporting biochemical data, we predicted that the inhibited complex would be similar for all EAP/NSP pairs. However, we present here evidence that EapH1 and EapH2 bind the canonical NSP, Neutrophil Elastase (NE), in distinct orientations. We discovered that alteration of EapH1 residues at the EapH1/NE interface caused a dramatic loss of affinity and inhibition of NE, while mutation of equivalent positions in EapH2 had no effect on NE binding or inhibition. Surprisingly, mutation of residues in an altogether different region of EapH2 severely impacted both the NE binding and inhibitory properties of EapH2. Even though EapH1 and EapH2 bind and inhibit NE and a second NSP, Cathepsin G, equally well, neither of these proteins interacts with the structurally related, but non-proteolytic granule protein, azurocidin. These studies expand our understanding of EAP/NSP interactions and suggest that members of this immune evasion protein family are capable of diverse target recognition modes.
Collapse
Affiliation(s)
- Daphne A C Stapels
- Department of Medical Microbiology, University Medical Center Utrecht, 3584, CX Utrecht, The Netherlands
| | - Jordan L Woehl
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, 66506
| | - Fin J Milder
- Department of Medical Microbiology, University Medical Center Utrecht, 3584, CX Utrecht, The Netherlands
| | - Angelino T Tromp
- Department of Medical Microbiology, University Medical Center Utrecht, 3584, CX Utrecht, The Netherlands
| | - Aernoud A van Batenburg
- Department of Medical Microbiology, University Medical Center Utrecht, 3584, CX Utrecht, The Netherlands
| | - Wilco C de Graaf
- Department of Medical Microbiology, University Medical Center Utrecht, 3584, CX Utrecht, The Netherlands
| | - Samuel C Broll
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, 66506
| | - Natalie M White
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, 66506
| | - Suzan H M Rooijakkers
- Department of Medical Microbiology, University Medical Center Utrecht, 3584, CX Utrecht, The Netherlands
| | - Brian V Geisbrecht
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, 66506
| |
Collapse
|
37
|
Ploscariu NT, Herrera AI, Jayanthi S, Suresh Kumar TK, Geisbrecht BV, Prakash O. Backbone and side-chain 1H, 15N, and 13C resonance assignments of a novel Staphylococcal inhibitor of myeloperoxidase. Biomol NMR Assign 2017; 11:285-288. [PMID: 28815423 PMCID: PMC5821262 DOI: 10.1007/s12104-017-9764-5] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 08/09/2017] [Indexed: 06/07/2023]
Abstract
The bacterium Staphylococcus aureus produces an array of anti-inflammatory molecules that prevent the innate immune system from recognizing it as a pathogen and clearing it from the host. In the acute phase of inflammation, our immune system relies on neutrophils to clear invading bacteria. Recently, novel classes of secreted proteins from S. aureus, including the Extracellular Adherence Protein (EAP) family (Stapels et al., Proc Natl Acad Sci USA 111:13187-13192, 2014) and the Staphylococcal Peroxidase Inhibitor (SPIN), (unpublished work) have been identified as highly selective inhibitors acting on Neutrophil Serine Proteases (NSPs) and myeloperoxidase (MPO) respectively. SPIN is a protein found only in Staphylococci, with no sequence homology to any known proteins. Solution NMR structural studies of SPIN are therefore expected to provide a deeper understanding of its interaction with MPO. In this study, we report the backbone and side-chain 1H, 15N, and 13C resonance assignments of SPIN. Furthermore, using the chemical shifts of these resonances, we predicted the secondary structure of SPIN in solution via the TALOS-N server. The assignment data has been deposited in the BMRB data bank under Accession No. 27069.
Collapse
Affiliation(s)
- Nicoleta T Ploscariu
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, 66506, USA
| | - Alvaro I Herrera
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, 66506, USA
| | - Srinivas Jayanthi
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, 72701, USA
| | | | - Brian V Geisbrecht
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, 66506, USA
| | - Om Prakash
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, 66506, USA.
| |
Collapse
|
38
|
Shrestha R, Huang G, Meekins DA, Geisbrecht BV, Li P. Mechanistic Insights into Dye-Decolorizing Peroxidase Revealed by Solvent Isotope and Viscosity Effects. ACS Catal 2017; 7:6352-6364. [PMID: 29308295 PMCID: PMC5751952 DOI: 10.1021/acscatal.7b01861] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [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] [Indexed: 11/29/2022]
Abstract
Dye-decolorizing peroxidases (DyPs) are a family of H2O2-dependent heme peroxidases, which have shown potential applications in lignin degradation and valorization. However, the DyP kinetic mechanism remains underexplored. Using structural biology and solvent isotope (sKIE) and viscosity effects, many mechanistic characteristics have been uncovered for the B-class ElDyP from Enterobacter lignolyticus. Its structure revealed that a water molecule acts as the sixth axial ligand with two channels at diameters of ~3.0 and 8.0 Å leading to the heme center. A conformational change of ERS* to ERS, which have identical spectral characteristics, was proposed as the final step in DyPs' bisubstrate Ping-Pong mechanism. This step is also the rate-determining step in ABTS oxidation. The normal KIE of wild-type ElDyP with D2O2 at pH 3.5 suggested that cmpd 0 deprotonation by the distal aspartate is rate-limiting in the formation of cmpd I, which is more reactive under acidic pH than under neutral or alkaline pH. The viscosity effects and other biochemical methods implied that the reducing substrate binds with cmpd I instead of the free enzyme. The significant inverse sKIEs of kcat/KM and kERS* suggested that the aquo release in DyPs is mechanistically important and may explain the enzyme's adoption of two-electron reduction for cmpd I. The distal aspartate is catalytically more important than the distal arginine and plays key roles in determining DyPs' acidic pH optimum. The kinetic mechanism of D143H-ElDyP was also briefly studied. The results obtained will pave the way for future protein engineering to improve DyPs' lignolytic activity.
Collapse
Affiliation(s)
- Ruben Shrestha
- Department of Chemistry, Kansas State University, Manhattan, KS, 66506, USA
| | - Gaochao Huang
- Department of Chemistry, Kansas State University, Manhattan, KS, 66506, USA
| | - David A. Meekins
- Department of Chemistry, Kansas State University, Manhattan, KS, 66506, USA
| | - Brian V. Geisbrecht
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, 66506, USA
| | - Ping Li
- Department of Chemistry, Kansas State University, Manhattan, KS, 66506, USA
| |
Collapse
|
39
|
de Jong NWM, Ramyar KX, Guerra FE, Nijland R, Fevre C, Voyich JM, McCarthy AJ, Garcia BL, van Kessel KPM, van Strijp JAG, Geisbrecht BV, Haas PJA. Immune evasion by a staphylococcal inhibitor of myeloperoxidase. Proc Natl Acad Sci U S A 2017; 114:9439-9444. [PMID: 28808028 PMCID: PMC5584439 DOI: 10.1073/pnas.1707032114] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Staphylococcus aureus is highly adapted to its host and has evolved many strategies to resist opsonization and phagocytosis. Even after uptake by neutrophils, S. aureus shows resistance to killing, which suggests the presence of phagosomal immune evasion molecules. With the aid of secretome phage display, we identified a highly conserved protein that specifically binds and inhibits human myeloperoxidase (MPO), a major player in the oxidative defense of neutrophils. We have named this protein "staphylococcal peroxidase inhibitor" (SPIN). To gain insight into inhibition of MPO by SPIN, we solved the cocrystal structure of SPIN bound to a recombinant form of human MPO at 2.4-Å resolution. This structure reveals that SPIN acts as a molecular plug that prevents H2O2 substrate access to the MPO active site. In subsequent experiments, we observed that SPIN expression increases inside the neutrophil phagosome, where MPO is located, compared with outside the neutrophil. Moreover, bacteria with a deleted gene encoding SPIN showed decreased survival compared with WT bacteria after phagocytosis by neutrophils. Taken together, our results demonstrate that S. aureus secretes a unique proteinaceous MPO inhibitor to enhance survival by interfering with MPO-mediated killing.
Collapse
Affiliation(s)
- Nienke W M de Jong
- Medical Microbiology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | - Kasra X Ramyar
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506
| | - Fermin E Guerra
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717
| | - Reindert Nijland
- Medical Microbiology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
- Laboratory of Phytopathology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Cindy Fevre
- Medical Microbiology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | - Jovanka M Voyich
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717
| | - Alex J McCarthy
- Medical Microbiology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | - Brandon L Garcia
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506
| | - Kok P M van Kessel
- Medical Microbiology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | - Jos A G van Strijp
- Medical Microbiology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands;
| | - Brian V Geisbrecht
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506
| | - Pieter-Jan A Haas
- Medical Microbiology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| |
Collapse
|
40
|
Garcia BL, Zwarthoff SA, Rooijakkers SHM, Geisbrecht BV. Novel Evasion Mechanisms of the Classical Complement Pathway. J Immunol 2017; 197:2051-60. [PMID: 27591336 DOI: 10.4049/jimmunol.1600863] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 06/23/2016] [Indexed: 12/20/2022]
Abstract
Complement is a network of soluble and cell surface-associated proteins that gives rise to a self-amplifying, yet tightly regulated system with fundamental roles in immune surveillance and clearance. Complement becomes activated on the surface of nonself cells by one of three initiating mechanisms known as the classical, lectin, and alternative pathways. Evasion of complement function is a hallmark of invasive pathogens and hematophagous organisms. Although many complement-inhibition strategies hinge on hijacking activities of endogenous complement regulatory proteins, an increasing number of uniquely evolved evasion molecules have been discovered over the past decade. In this review, we focus on several recent investigations that revealed mechanistically distinct inhibitors of the classical pathway. Because the classical pathway is an important and specific mediator of various autoimmune and inflammatory disorders, in-depth knowledge of novel evasion mechanisms could direct future development of therapeutic anti-inflammatory molecules.
Collapse
Affiliation(s)
- Brandon L Garcia
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506; and
| | - Seline A Zwarthoff
- Medical Microbiology, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Suzan H M Rooijakkers
- Medical Microbiology, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Brian V Geisbrecht
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506; and
| |
Collapse
|
41
|
Woehl JL, Ramyar KX, Katz BB, Walker JK, Geisbrecht BV. The structural basis for inhibition of the classical and lectin complement pathways by S. aureus extracellular adherence protein. Protein Sci 2017; 26:1595-1608. [PMID: 28512867 DOI: 10.1002/pro.3195] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [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: 03/10/2017] [Revised: 05/10/2017] [Accepted: 05/10/2017] [Indexed: 01/07/2023]
Abstract
The extracellular adherence protein (Eap) plays a crucial role in pathogenesis and survival of Staphylococcus aureus by inhibiting the classical and lectin pathways of complement. We have previously shown that Eap binds with nanomolar affinity to complement C4b and disrupts the initial interaction between C4b and C2, thereby inhibiting formation of the classical and lectin pathway C3 pro-convertase. Although an underlying mechanism has been identified, the structural basis for Eap binding to C4b is poorly understood. Here, we show that Eap domains 3 and 4 each contain a low-affinity, but saturable binding site for C4b. Taking advantage of the high lysine content of Eap, we used a zero-length crosslinking approach to map the Eap binding site to both the α'- and γ-chains of C4b. We also probed the C4b/Eap interface through a chemical footprinting approach involving lysine modification, proteolytic digestion, and mass spectrometry. This identified seven lysines in Eap that undergo changes in solvent exposure upon C4b binding. We found that simultaneous mutation of these lysines to either alanine or glutamate diminished C4b binding and complement inhibition by Eap. Together, our results provide insight into Eap recognition of C4b, and suggest that the repeating domains that comprise Eap are capable of multiple ligand-binding modes.
Collapse
Affiliation(s)
- Jordan L Woehl
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, 66506
| | - Kasra X Ramyar
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, 66506
| | - Benjamin B Katz
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, 66506
| | - John K Walker
- Department of Pharmacology and Physiology, St. Louis University School of Medicine, St. Louis, Missouri, 63104
| | - Brian V Geisbrecht
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, 66506
| |
Collapse
|
42
|
Huang G, Shrestha R, Jia K, Geisbrecht BV, Li P. Enantioselective Synthesis of Dilignol Model Compounds and Their Stereodiscrimination Study with a Dye-Decolorizing Peroxidase. Org Lett 2017; 19:1820-1823. [PMID: 28326791 DOI: 10.1021/acs.orglett.7b00587] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A four-step enantioselective approach was developed to synthesize anti (1R,2S)-1a and (1S,2R)-1b containing a β-O-4 linkage in good yields. A significant difference was observed for the apparent binding affinities of four stereospecific lignin model compounds with TcDyP by surface plasmon resonance, which was not translated into a significant difference in enzyme activities. The discrepancy may be attributed to the conformational change involving a loop widely present in DyPs upon H2O2 binding.
Collapse
Affiliation(s)
- Gaochao Huang
- Department of Chemistry and ‡Department of Biochemistry and Molecular Biophysics, Kansas State University , Manhattan, Kansas 66506, United States
| | - Ruben Shrestha
- Department of Chemistry and ‡Department of Biochemistry and Molecular Biophysics, Kansas State University , Manhattan, Kansas 66506, United States
| | - Kaimin Jia
- Department of Chemistry and ‡Department of Biochemistry and Molecular Biophysics, Kansas State University , Manhattan, Kansas 66506, United States
| | - Brian V Geisbrecht
- Department of Chemistry and ‡Department of Biochemistry and Molecular Biophysics, Kansas State University , Manhattan, Kansas 66506, United States
| | - Ping Li
- Department of Chemistry and ‡Department of Biochemistry and Molecular Biophysics, Kansas State University , Manhattan, Kansas 66506, United States
| |
Collapse
|
43
|
Garcia BL, Skaff DA, Chatterjee A, Hanning A, Walker JK, Wyckoff GJ, Geisbrecht BV. Identification of C3b-Binding Small-Molecule Complement Inhibitors Using Cheminformatics. J Immunol 2017; 198:3705-3718. [PMID: 28298523 DOI: 10.4049/jimmunol.1601932] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 02/21/2017] [Indexed: 01/08/2023]
Abstract
The complement system is an elegantly regulated biochemical cascade formed by the collective molecular recognition properties and proteolytic activities of more than two dozen membrane-bound or serum proteins. Complement plays diverse roles in human physiology, such as acting as a sentry against invading microorganisms, priming of the adaptive immune response, and removal of immune complexes. However, dysregulation of complement can serve as a trigger for a wide range of human diseases, which include autoimmune, inflammatory, and degenerative conditions. Despite several potential advantages of modulating complement with small-molecule inhibitors, small-molecule drugs are highly underrepresented in the current complement-directed therapeutics pipeline. In this study, we have employed a cheminformatics drug discovery approach based on the extensive structural and functional knowledge available for the central proteolytic fragment of the cascade, C3b. Using parallel in silico screening methodologies, we identified 45 small molecules that putatively bind C3b near ligand-guided functional hot spots. Surface plasmon resonance experiments resulted in the validation of seven dose-dependent C3b-binding compounds. Competition-based biochemical assays demonstrated the ability of several C3b-binding compounds to interfere with binding of the original C3b ligand that guided their discovery. In vitro assays of complement function identified a single complement inhibitory compound, termed cmp-5, and mechanistic studies of the cmp-5 inhibitory mode revealed it acts at the level of C5 activation. This study has led to the identification of a promising new class of C3b-binding small-molecule complement inhibitors and, to our knowledge, provides the first demonstration of cheminformatics-based, complement-directed drug discovery.
Collapse
Affiliation(s)
- Brandon L Garcia
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506
| | - D Andrew Skaff
- Division of Molecular Biology and Biochemistry, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, MO 64110
| | - Arindam Chatterjee
- Department of Pharmacological and Physiological Science, Saint Louis University School of Medicine, St. Louis, MO 63104; and
| | | | - John K Walker
- Department of Pharmacological and Physiological Science, Saint Louis University School of Medicine, St. Louis, MO 63104; and
| | - Gerald J Wyckoff
- Division of Molecular Biology and Biochemistry, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, MO 64110
| | - Brian V Geisbrecht
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506;
| |
Collapse
|
44
|
Papanastasiou M, Koutsogiannaki S, Sarigiannis Y, Geisbrecht BV, Ricklin D, Lambris JD. Structural Implications for the Formation and Function of the Complement Effector Protein iC3b. J Immunol 2017; 198:3326-3335. [PMID: 28258193 DOI: 10.4049/jimmunol.1601864] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 02/10/2017] [Indexed: 01/17/2023]
Abstract
Complement-mediated opsonization, phagocytosis, and immune stimulation are critical processes in host defense and homeostasis, with the complement activation fragment iC3b playing a key effector role. To date, however, there is no high-resolution structure of iC3b, and some aspects of its structure-activity profile remain controversial. Here, we employed hydrogen-deuterium exchange mass spectrometry to describe the structure and dynamics of iC3b at a peptide resolution level in direct comparison with its parent protein C3b. In our hydrogen-deuterium exchange mass spectrometry study, 264 peptides were analyzed for their deuterium content, providing almost complete sequence coverage for this 173-kDa protein. Several peptides in iC3b showed significantly higher deuterium uptake when compared with C3b, revealing more dynamic, solvent-exposed regions. Most of them resided in the CUB domain, which contains the heptadecapeptide C3f that is liberated during the conversion of C3b to iC3b. Our data suggest a highly disordered CUB, which has acquired a state similar to that of intrinsically disordered proteins, resulting in a predominant form of iC3b that features high structural flexibility. The structure was further validated using an anti-iC3b mAb that was shown to target an epitope in the CUB region. The information obtained in this work allows us to elucidate determinants of iC3b specificity and activity and provide functional insights into the protein's recognition pattern with respect to regulators and receptors of the complement system.
Collapse
Affiliation(s)
- Malvina Papanastasiou
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104; and
| | - Sophia Koutsogiannaki
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104; and
| | - Yiannis Sarigiannis
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104; and
| | - Brian V Geisbrecht
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506
| | - Daniel Ricklin
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104; and
| | - John D Lambris
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104; and
| |
Collapse
|
45
|
Shrestha R, Chen X, Ramyar KX, Hayati Z, Carlson EA, Bossmann SH, Song L, Geisbrecht BV, Li P. Identification of Surface-Exposed Protein Radicals and A Substrate Oxidation Site in A-Class Dye-Decolorizing Peroxidase from Thermomonospora curvata. ACS Catal 2016; 6:8036-8047. [PMID: 29308294 DOI: 10.1021/acscatal.6b01952] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [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: 11/29/2022]
Abstract
Dye-decolorizing peroxidases (DyPs) are a family of heme peroxidases, in which a catalytic distal aspartate is involved in H2O2 activation to catalyze oxidations in acidic conditions. They have received much attention due to their potential applications in lignin compound degradation and biofuel production from biomass. However, the mode of oxidation in bacterial DyPs remains unknown. We have recently reported that the bacterial TcDyP from Thermomonospora curvata is among the most active DyPs and shows activity toward phenolic lignin model compounds (J. Biol. Chem.2015, 290, 23447). Based on the X-ray crystal structure solved at 1.75 Å, sigmoidal steady-state kinetics with Reactive Blue 19 (RB19), and formation of compound II-like product in the absence of reducing substrates observed with stopped-flow spectroscopy and electron paramagnetic resonance (EPR), we hypothesized that the TcDyP catalyzes oxidation of large-size substrates via multiple surface-exposed protein radicals. Among 7 tryptophans and 3 tyrosines in TcDyP consisting of 376 residues for the matured protein, W263, W376, and Y332 were identified as surface-exposed protein radicals. Only the W263 was also characterized as one of surface-exposed oxidation sites. SDS-PAGE and size-exclusion chromatography demonstrated that W376 represents an off-pathway destination for electron transfer, resulting in the crosslinking of proteins in the absence of substrates. Mutation of W376 improved compound I stability and overall catalytic efficiency toward RB19. While Y332 is highly conserved across all four classes of DyPs, its catalytic function in A-class TcDyP is minimal possibly due to its extremely small solvent accessible areas. Identification of surface-exposed protein radicals and substrate oxidation sites is important for understanding DyP mechanism and modulating its catalytic functions for improved activity on phenolic lignin.
Collapse
Affiliation(s)
| | | | | | - Zahra Hayati
- National
High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
| | | | | | - Likai Song
- National
High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
| | | | | |
Collapse
|
46
|
Woehl JL, Takahashi D, Herrera AI, Geisbrecht BV, Prakash O. (1)H, (15)N, and (13)C resonance assignments of Staphylococcus aureus extracellular adherence protein domain 4. Biomol NMR Assign 2016; 10:301-5. [PMID: 27372920 PMCID: PMC5503465 DOI: 10.1007/s12104-016-9688-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 06/22/2016] [Indexed: 05/25/2023]
Abstract
The pathogenic bacterium Staphylococcus aureus has evolved to actively evade many aspects of the human innate immune system by expressing a series of secreted inhibitory proteins. Among these, the extracellular adherence protein (Eap) has been shown to inhibit the classical and lectin pathways of the complement system. By binding to complement component C4b, Eap is able to inhibit formation of the CP/LP C3 pro-convertase. Secreted full-length, mature Eap consists of four ~98 residue domains, all of which adopt a similar beta-grasp fold, and are connected through a short linker region. Through multiple biochemical approaches, it has been determined that the third and fourth domains of Eap are responsible for C4b binding. Here we report the backbone and side-chain resonance assignments of the 11.3 kDa fourth domain of Eap. The assignment data has been deposited in the BMRB database under the accession number 26726.
Collapse
Affiliation(s)
- Jordan L Woehl
- Department of Biochemistry and Molecular Biophysics, Kansas State University, 141 Chalmers Hall, Manhattan, KS, 66506, USA
| | - Daisuke Takahashi
- Department of Biochemistry and Molecular Biophysics, Kansas State University, 141 Chalmers Hall, Manhattan, KS, 66506, USA
| | - Alvaro I Herrera
- Department of Biochemistry and Molecular Biophysics, Kansas State University, 141 Chalmers Hall, Manhattan, KS, 66506, USA
| | - Brian V Geisbrecht
- Department of Biochemistry and Molecular Biophysics, Kansas State University, 141 Chalmers Hall, Manhattan, KS, 66506, USA
| | - Om Prakash
- Department of Biochemistry and Molecular Biophysics, Kansas State University, 141 Chalmers Hall, Manhattan, KS, 66506, USA.
| |
Collapse
|
47
|
Bannantine JP, Lingle CK, Adam PR, Ramyar KX, McWhorter WJ, Stabel JR, Picking WD, Geisbrecht BV. NlpC/P60 domain-containing proteins of Mycobacterium avium subspecies paratuberculosis that differentially bind and hydrolyze peptidoglycan. Protein Sci 2016; 25:840-51. [PMID: 26799947 DOI: 10.1002/pro.2884] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 01/14/2016] [Accepted: 01/19/2016] [Indexed: 01/22/2023]
Abstract
A subset of proteins containing NlpC/P60 domains are bacterial peptidoglycan hydrolases that cleave noncanonical peptide linkages and contribute to cell wall remodeling as well as cell separation during late stages of division. Some of these proteins have been shown to cleave peptidoglycan in Mycobacterium tuberculosis and play a role in Mycobacterium marinum virulence of zebra fish; however, there are still significant knowledge gaps concerning the molecular function of these proteins in Mycobacterium avium subspecies paratuberculosis (MAP). The MAP genome sequence encodes five NlpC/P60 domain-containing proteins. We describe atomic resolution crystal structures of two such MAP proteins, MAP_1272c and MAP_1204. These crystal structures, combined with functional assays to measure peptidoglycan cleavage activity, led to the observation that MAP_1272c does not have a functional catalytic core for peptidoglycan hydrolysis. Furthermore, the structure and sequence of MAP_1272c demonstrate that the catalytic residues normally required for hydrolysis are absent, and the protein does not bind peptidoglycan as efficiently as MAP_1204. While the NlpC/P60 catalytic triad is present in MAP_1204, changing the catalytic cysteine-155 residue to a serine significantly diminished catalytic activity, but did not affect binding to peptidoglycan. Collectively, these findings suggest a broader functional repertoire for NlpC/P60 domain-containing proteins than simply hydrolases.
Collapse
Affiliation(s)
- John P Bannantine
- National Animal Disease Center, USDA-Agricultural Research Service, Ames, Iowa
| | - Cari K Lingle
- School of Biological Sciences, University of Missouri-Kansas City, Kansas City, Missouri
| | - Philip R Adam
- Department of Microbiology & Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma
| | - Kasra X Ramyar
- School of Biological Sciences, University of Missouri-Kansas City, Kansas City, Missouri
| | - William J McWhorter
- School of Biological Sciences, University of Missouri-Kansas City, Kansas City, Missouri
| | - Judith R Stabel
- National Animal Disease Center, USDA-Agricultural Research Service, Ames, Iowa
| | - William D Picking
- Department of Microbiology & Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma
| | - Brian V Geisbrecht
- School of Biological Sciences, University of Missouri-Kansas City, Kansas City, Missouri
| |
Collapse
|
48
|
Georgoutsou-Spyridonos M, Ricklin D, Pratsinis H, Perivolioti E, Pirmettis I, Garcia BL, Geisbrecht BV, Foukas PG, Lambris JD, Mastellos DC, Sfyroera G. Attenuation of Staphylococcus aureus-Induced Bacteremia by Human Mini-Antibodies Targeting the Complement Inhibitory Protein Efb. J Immunol 2015; 195:3946-58. [PMID: 26342032 DOI: 10.4049/jimmunol.1500966] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 08/12/2015] [Indexed: 12/22/2022]
Abstract
Staphylococcus aureus can cause a broad range of potentially fatal inflammatory complications (e.g., sepsis and endocarditis). Its emerging antibiotic resistance and formidable immune evasion arsenal have emphasized the need for more effective antimicrobial approaches. Complement is an innate immune sensor that rapidly responds to bacterial infection eliciting C3-mediated opsonophagocytic and immunomodulatory responses. Extracellular fibrinogen-binding protein (Efb) is a key immune evasion protein of S. aureus that intercepts complement at the level of C3. To date, Efb has not been explored as a target for mAb-based antimicrobial therapeutics. In this study, we have isolated donor-derived anti-Efb IgGs that attenuate S. aureus survival through enhanced neutrophil killing. A phage library screen yielded mini-Abs that selectively inhibit the interaction of Efb with C3 partly by disrupting contacts essential for complex formation. Surface plasmon resonance-based kinetic analysis enabled the selection of mini-Abs with favorable Efb-binding profiles as therapeutic leads. Mini-Ab-mediated blockade of Efb attenuated S. aureus survival in a whole blood model of bacteremia. This neutralizing effect was associated with enhanced neutrophil-mediated killing of S. aureus, increased C5a release, and modulation of IL-6 secretion. Finally, these mini-Abs afforded protection from S. aureus-induced bacteremia in a murine renal abscess model, attenuating bacterial inflammation in kidneys. Overall, these findings are anticipated to pave the way toward novel Ab-based therapeutics for S. aureus-related diseases.
Collapse
Affiliation(s)
- Maria Georgoutsou-Spyridonos
- Department of Biodiagnostic Sciences and Technologies, I/NRASTES, National Center for Scientific Research "Demokritos," 15310 Athens, Greece
| | - Daniel Ricklin
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Haris Pratsinis
- Institute of Biosciences and Applications, National Center for Scientific Research "Demokritos," 15310 Athens, Greece
| | - Eustathia Perivolioti
- Department of Clinical Microbiology, General Hospital "Evangelismos," 10676 Athens, Greece
| | - Ioannis Pirmettis
- Department of Biodiagnostic Sciences and Technologies, I/NRASTES, National Center for Scientific Research "Demokritos," 15310 Athens, Greece
| | - Brandon L Garcia
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506; and
| | - Brian V Geisbrecht
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506; and
| | - Periklis G Foukas
- 2nd Department of Pathology, University of Athens Medical School, Attikon University Hospital, 12462 Chaidari, Greece
| | - John D Lambris
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Dimitrios C Mastellos
- Department of Biodiagnostic Sciences and Technologies, I/NRASTES, National Center for Scientific Research "Demokritos," 15310 Athens, Greece
| | - Georgia Sfyroera
- Department of Biodiagnostic Sciences and Technologies, I/NRASTES, National Center for Scientific Research "Demokritos," 15310 Athens, Greece;
| |
Collapse
|
49
|
Chen C, Shrestha R, Jia K, Gao PF, Geisbrecht BV, Bossmann SH, Shi J, Li P. Characterization of Dye-decolorizing Peroxidase (DyP) from Thermomonospora curvata Reveals Unique Catalytic Properties of A-type DyPs. J Biol Chem 2015. [PMID: 26205819 DOI: 10.1074/jbc.m115.658807] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [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: 11/06/2022] Open
Abstract
Dye-decolorizing peroxidases (DyPs) comprise a new family of heme peroxidases, which has received much attention due to their potential applications in lignin degradation. A new DyP from Thermomonospora curvata (TcDyP) was identified and characterized. Unlike other A-type enzymes, TcDyP is highly active toward a wide range of substrates including model lignin compounds, in which the catalytic efficiency with ABTS (kcat(app)/Km(app) = (1.7 × 10(7)) m(-1) s(-1)) is close to that of fungal DyPs. Stopped-flow spectroscopy was employed to elucidate the transient intermediates as well as the catalytic cycle involving wild-type (wt) and mutant TcDyPs. Although residues Asp(220) and Arg(327) are found necessary for compound I formation, His(312) is proposed to play roles in compound II reduction. Transient kinetics of hydroquinone (HQ) oxidation by wt-TcDyP showed that conversion of the compound II to resting state is a rate-limiting step, which will explain the contradictory observation made with the aspartate mutants of A-type DyPs. Moreover, replacement of His(312) and Arg(327) has significant effects on the oligomerization and redox potential (E°') of the enzyme. Both mutants were found to promote the formation of dimeric state and to shift E°' to a more negative potential. Not only do these results reveal the unique catalytic property of the A-type DyPs, but they will also facilitate the development of these enzymes as lignin degraders.
Collapse
Affiliation(s)
| | | | | | - Philip F Gao
- the Protein Production Group, University of Kansas, Lawrence, Kansas 66045
| | | | | | - Jishu Shi
- Anatomy and Physiology, Kansas State University, Manhattan, Kansas 66506 and
| | - Ping Li
- From the Departments of Chemistry,
| |
Collapse
|
50
|
Skaff DA, McWhorter WJ, Geisbrecht BV, Wyckoff GJ, Miziorko HM. Inhibition of bacterial mevalonate diphosphate decarboxylase by eriochrome compounds. Arch Biochem Biophys 2015; 566:1-6. [PMID: 25499551 PMCID: PMC4456016 DOI: 10.1016/j.abb.2014.12.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 12/01/2014] [Accepted: 12/02/2014] [Indexed: 11/20/2022]
Abstract
Mevalonate diphosphate decarboxylase (MDD; EC 4.1.1.33) catalyzes the irreversible decarboxylation of mevalonate diphosphate in the mevalonate pathway to form isopentenyl diphosphate, which is a precursor in the biosynthesis of many essential polyisoprenoid natural products, including sterols. In low G/C Gram-positive bacteria, which utilize the mevalonate pathway, MDD is required for cell viability and thus is a potential target for development of antibiotic drugs. To identify potential inhibitors of the enzyme, the National Cancer Institute's Mechanistic Diversity Set library of compounds was screened for inhibitors of Staphylococcus epidermidis MDD. From this screen, the compound Eriochrome Black A (EBA), an azo dye, was found to inhibit the enzyme with an IC50 value<5μM. Molecular docking of EBA into a crystal structure of S. epidermidis MDD suggested binding at the active site. EBA, along with the related Eriochrome B and T compounds, was evaluated for its ability to not only inhibit enzymatic activity but to inhibit bacterial growth as well. These compounds exhibited competitive inhibition towards the substrate mevalonate diphosphate, with Ki values ranging from 0.6 to 2.7μM. Non-competitive inhibition was observed versus ATP indicating binding of the inhibitor in the mevalonate diphosphate binding site, consistent with molecular docking predictions. Fluorescence quenching analyses also supported active site binding of EBA. These eriochrome compounds are effective at inhibiting S. epidermidis cell growth on both solid media and in liquid culture (MIC50 from 31 to 350μM) raising the possibility that they could be developed into antibiotic leads targeting pathogenic low-G/C Gram-positive cocci.
Collapse
Affiliation(s)
- D Andrew Skaff
- Division of Molecular Biology and Biochemistry, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, MO 64110, United States
| | - William J McWhorter
- Division of Cell Biology and Biophysics, University of Missouri-Kansas City, Kansas City, MO 64110, United States
| | - Brian V Geisbrecht
- Division of Cell Biology and Biophysics, University of Missouri-Kansas City, Kansas City, MO 64110, United States
| | - Gerald J Wyckoff
- Division of Molecular Biology and Biochemistry, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, MO 64110, United States
| | - Henry M Miziorko
- Division of Molecular Biology and Biochemistry, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, MO 64110, United States.
| |
Collapse
|