An Unusual Two-Domain Thyropin from Tick Saliva: NMR Solution Structure and Highly Selective Inhibition of Cysteine Cathepsins Modulated by Glycosaminoglycans
Jazyk angličtina Země Švýcarsko Médium electronic
Typ dokumentu časopisecké články
Grantová podpora
21-08826S
Czech Science Foundation
RVO 61388963
Institutional project
CZ.02.1.01/0.0/0.0/16_019/0000759
Centre for Research of Pathogenicity and Virulence of Parasites, European Regional Development Fund (ERDF)and the Ministry of Education, Youth and Sports of the Czech Republic (MEYS)
22-30920S
Czech Science Foundation
LUC23037
Ministry of Education, Youth and Sports of the Czech Republic (MEYS)
PubMed
38396918
PubMed Central
PMC10889554
DOI
10.3390/ijms25042240
PII: ijms25042240
Knihovny.cz E-zdroje
- Klíčová slova
- cathepsin, cysteine protease, parasite, protease inhibitor, protein structure, saliva, thyropin, tick,
- MeSH
- cystein MeSH
- glykosaminoglykany MeSH
- kathepsiny metabolismus MeSH
- klíště * metabolismus MeSH
- lidé MeSH
- magnetická rezonanční spektroskopie MeSH
- sliny * metabolismus MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- cystein MeSH
- glykosaminoglykany MeSH
- kathepsiny MeSH
The structure and biochemical properties of protease inhibitors from the thyropin family are poorly understood in parasites and pathogens. Here, we introduce a novel family member, Ir-thyropin (IrThy), which is secreted in the saliva of Ixodes ricinus ticks, vectors of Lyme borreliosis and tick-borne encephalitis. The IrThy molecule consists of two consecutive thyroglobulin type-1 (Tg1) domains with an unusual disulfide pattern. Recombinant IrThy was found to inhibit human host-derived cathepsin proteases with a high specificity for cathepsins V, K, and L among a wide range of screened cathepsins exhibiting diverse endo- and exopeptidase activities. Both Tg1 domains displayed inhibitory activities, but with distinct specificity profiles. We determined the spatial structure of one of the Tg1 domains by solution NMR spectroscopy and described its reactive center to elucidate the unique inhibitory specificity. Furthermore, we found that the inhibitory potency of IrThy was modulated in a complex manner by various glycosaminoglycans from host tissues. IrThy was additionally regulated by pH and proteolytic degradation. This study provides a comprehensive structure-function characterization of IrThy-the first investigated thyropin of parasite origin-and suggests its potential role in host-parasite interactions at the tick bite site.
1st Faculty of Medicine Charles University Katerinska 32 12108 Praha Czech Republic
Biopticka Laborator Mikulasske Namesti 4 32600 Plzen Czech Republic
Institute of Microbiology Czech Academy of Sciences Prumyslova 595 25250 Vestec Czech Republic
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Molina F., Bouanani M., Pau B., Granier C. Characterization of the type-1 repeat from thyroglobulin, a cysteine-rich module found in proteins from different families. Eur. J. Biochem. 1996;240:125–133. doi: 10.1111/j.1432-1033.1996.0125h.x. PubMed DOI
Lenarcic B., Bevec T. Thyropins—New structurally related proteinase inhibitors. Biol. Chem. 1998;379:105–111. PubMed
Rawlings N.D., Barrett A.J., Thomas P.D., Huang X., Bateman A., Finn R.D. The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database. Nucleic Acids Res. 2017;46:D624–D632. doi: 10.1093/nar/gkx1134. PubMed DOI PMC
Mihelic M., Turk D. Two decades of thyroglobulin type-1 domain research. Biol. Chem. 2007;388:1123–1130. doi: 10.1515/BC.2007.155. PubMed DOI
Mihelic M., Dobersek A., Guncar G., Turk D. Inhibitory fragment from the p41 form of invariant chain can regulate activity of cysteine cathepsins in antigen presentation. J. Biol. Chem. 2008;283:14453–14460. doi: 10.1074/jbc.M801283200. PubMed DOI
Guncar G., Pungercic G., Klemencic I., Turk V., Turk D. Crystal structure of MHC class II-associated p41 Ii fragment bound to cathepsin L reveals the structural basis for differentiation between cathepsins L and S. EMBO J. 1999;18:793–803. doi: 10.1093/emboj/18.4.793. PubMed DOI PMC
Lenarcic B., Krishnan G., Borukhovich R., Ruck B., Turk V., Moczydlowski E. Saxiphilin, a saxitoxin-binding protein with two thyroglobulin type 1 domains, is an inhibitor of papain-like cysteine proteinases. J. Biol. Chem. 2000;275:15572–15577. doi: 10.1074/jbc.M001406200. PubMed DOI
Yen T.J., Lolicato M., Thomas-Tran R., Du Bois J., Minor D.L. Structure of the saxiphilin: Saxitoxin (STX) complex reveals a convergent molecular recognition strategy for paralytic toxins. Sci. Adv. 2019;5:eaax2650. doi: 10.1126/sciadv.aax2650. PubMed DOI PMC
Lenarcic B., Turk V. Thyroglobulin type-1 domains in equistatin inhibit both papain-like cysteine proteinases and cathepsin D. J. Biol. Chem. 1999;274:563–566. doi: 10.1074/jbc.274.2.563. PubMed DOI
Galesa K., Pain R., Jongsma M.A., Turk V., Lenarcic B. Structural characterization of thyroglobulin type-1 domains of equistatin. FEBS Lett. 2003;539:120–124. doi: 10.1016/S0014-5793(03)00215-1. PubMed DOI
Bocock J.P., Edgell C.J., Marr H.S., Erickson A.H. Human proteoglycan testican-1 inhibits the lysosomal cysteine protease cathepsin L. Eur. J. Biochem. 2003;270:4008–4015. doi: 10.1046/j.1432-1033.2003.03789.x. PubMed DOI
Meh P., Pavsic M., Turk V., Baici A., Lenarcic B. Dual concentration-dependent activity of thyroglobulin type-1 domain of testican: Specific inhibitor and substrate of cathepsin L. Biol. Chem. 2005;386:75–83. doi: 10.1515/BC.2005.010. PubMed DOI
Sankpal N.V., Brown T.C., Fleming T.P., Herndon J.M., Amaravati A.A., Loynd A.N., Gillanders W.E. Cancer-associated mutations reveal a novel role for EpCAM as an inhibitor of cathepsin-L and tumor cell invasion. BMC Cancer. 2021;21:541. doi: 10.1186/s12885-021-08239-z. PubMed DOI PMC
Yamashita M., Konagaya S. A novel cysteine protease inhibitor of the egg of chum salmon, containing a cysteine-rich thyroglobulin-like motif. J. Biol. Chem. 1996;271:1282–1284. doi: 10.1074/jbc.271.3.1282. PubMed DOI
Fowlkes J.L., Thrailkill K.M., Serra D.M., Nagase H. Insulin-like growth factor binding protein (IGFBP) substrate zymography. A new tool to identify and characterize IGFBP-degrading proteinases. Endocrine. 1997;7:33–36. doi: 10.1007/BF02778059. PubMed DOI
Moreno M.J., Ball M., Rukhlova M., Slinn J., L’Abbe D., Iqbal U., Monette R., Hagedorn M., O’Connor-McCourt M.D., Durocher Y., et al. IGFBP-4 anti-angiogenic and anti-tumorigenic effects are associated with anti-cathepsin B activity. Neoplasia. 2013;15:554–567. doi: 10.1593/neo.13212. PubMed DOI PMC
Fiebiger E., Maehr R., Villadangos J., Weber E., Erickson A., Bikoff E., Ploegh H.L., Lennon-Duménil A.M. Invariant chain controls the activity of extracellular cathepsin L. J. Exp. Med. 2002;196:1263–1269. doi: 10.1084/jem.20020762. PubMed DOI PMC
Porter L.M., Radulović Ž.M., Mulenga A. A repertoire of protease inhibitor families in Amblyomma americanum and other tick species: Inter-species comparative analyses. Parasit. Vectors. 2017;10:152. doi: 10.1186/s13071-017-2080-1. PubMed DOI PMC
Oliveira C.J., Anatriello E., de Miranda-Santos I.K., Francischetti I.M., Sá-Nunes A., Ferreira B.R., Ribeiro J.M. Proteome of Rhipicephalus sanguineus tick saliva induced by the secretagogues pilocarpine and dopamine. Ticks Tick Borne Dis. 2013;4:469–477. doi: 10.1016/j.ttbdis.2013.05.001. PubMed DOI PMC
Bensaoud C., Tenzer S., Poplawski A., Medina J.M., Jmel M.A., Voet H., Mekki I., Aparicio-Puerta E., Cuveele B., Distler U., et al. Quantitative proteomics analysis reveals core and variable tick salivary proteins at the tick-vertebrate host interface. Mol. Ecol. 2022;31:4162–4175. doi: 10.1111/mec.16561. PubMed DOI
Kozelková T., Dyčka F., Lu S., Urbanová V., Frantová H., Sojka D., Šíma R., Horn M., Perner J., Kopáček P. Insight Into the Dynamics of the Ixodes ricinus Nymphal Midgut Proteome. Mol. Cell Proteom. 2023;22:100663. doi: 10.1016/j.mcpro.2023.100663. PubMed DOI PMC
Kotál J., Buša M., Urbanová V., Řezáčová P., Chmelař J., Langhansová H., Sojka D., Mareš M., Kotsyfakis M. Mialostatin, a Novel Midgut Cystatin from Ixodes ricinus Ticks: Crystal Structure and Regulation of Host Blood Digestion. Int. J. Mol. Sci. 2021;22:5371. doi: 10.3390/ijms22105371. PubMed DOI PMC
Kotál J., Stergiou N., Buša M., Chlastáková A., Beránková Z., Řezáčová P., Langhansová H., Schwarz A., Calvo E., Kopecký J., et al. The structure and function of Iristatin, a novel immunosuppressive tick salivary cystatin. Cell Mol. Life Sci. 2019;76:2003–2013. doi: 10.1007/s00018-019-03034-3. PubMed DOI PMC
Martins L.A., Buša M., Chlastáková A., Kotál J., Beránková Z., Stergiou N., Jmel M.A., Schmitt E., Chmelař J., Mareš M., et al. Protease-bound structure of Ricistatin provides insights into the mechanism of action of tick salivary cystatins in the vertebrate host. Cell Mol. Life Sci. 2023;80:339. doi: 10.1007/s00018-023-04993-4. PubMed DOI PMC
Kotsyfakis M., Sá-Nunes A., Francischetti I.M., Mather T.N., Andersen J.F., Ribeiro J.M. Antiinflammatory and immunosuppressive activity of sialostatin L, a salivary cystatin from the tick Ixodes scapularis. J. Biol. Chem. 2006;281:26298–26307. doi: 10.1074/jbc.M513010200. PubMed DOI
Schwarz A., von Reumont B.M., Erhart J., Chagas A.C., Ribeiro J.M., Kotsyfakis M. De novo Ixodes ricinus salivary gland transcriptome analysis using two next-generation sequencing methodologies. FASEB J. 2013;27:4745–4756. doi: 10.1096/fj.13-232140. PubMed DOI PMC
Perner J., Provazník J., Schrenková J., Urbanová V., Ribeiro J.M., Kopáček P. RNA-seq analyses of the midgut from blood- and serum-fed Ixodes ricinus ticks. Sci. Rep. 2016;6:36695. doi: 10.1038/srep36695. PubMed DOI PMC
Paysan-Lafosse T., Blum M., Chuguransky S., Grego T., Pinto B.L., Salazar G.A., Bileschi M.L., Bork P., Bridge A., Colwell L., et al. InterPro in 2022. Nucleic Acids Res. 2022;51:D418–D427. doi: 10.1093/nar/gkac993. PubMed DOI PMC
Pungercic G., Dolenc I., Dolinar M., Bevec T., Jenko S., Kolaric S., Turk V. Individual recombinant thyroglobulin type-1 domains are substrates for lysosomal cysteine proteinases. Biol. Chem. 2002;383:1809–1812. doi: 10.1515/BC.2002.202. PubMed DOI
Denamur S., Chazeirat T., Maszota-Zieleniak M., Vivès R.R., Saidi A., Zhang F., Linhardt R.J., Labarthe F., Samsonov S.A., Lalmanach G., et al. Binding of heparan sulfate to human cystatin C modulates inhibition of cathepsin L: Putative consequences in mucopolysaccharidosis. Carbohydr. Polym. 2022;293:119734. doi: 10.1016/j.carbpol.2022.119734. PubMed DOI
Rein C.M., Desai U.R., Church F.C. Serpin-glycosaminoglycan interactions. Methods Enzymol. 2011;501:105–137. doi: 10.1016/b978-0-12-385950-1.00007-9. PubMed DOI
Li Z., Kienetz M., Cherney M.M., James M.N.G., Brömme D. The Crystal and Molecular Structures of a Cathepsin K: Chondroitin Sulfate Complex. J. Mol. Biol. 2008;383:78–91. doi: 10.1016/j.jmb.2008.07.038. PubMed DOI
David A., Chazeirat T., Saidi A., Lalmanach G., Lecaille F. The Interplay of Glycosaminoglycans and Cysteine Cathepsins in Mucopolysaccharidosis. Biomedicines. 2023;11:810. doi: 10.3390/biomedicines11030810. PubMed DOI PMC
Chazeirat T., Denamur S., Bojarski K.K., Andrault P.M., Sizaret D., Zhang F., Saidi A., Tardieu M., Linhardt R.J., Labarthe F., et al. The abnormal accumulation of heparan sulfate in patients with mucopolysaccharidosis prevents the elastolytic activity of cathepsin V. Carbohydr. Polym. 2021;253:117261. doi: 10.1016/j.carbpol.2020.117261. PubMed DOI
Aguda A.H., Panwar P., Du X., Nguyen N.T., Brayer G.D., Brömme D. Structural basis of collagen fiber degradation by cathepsin K. Proc. Natl. Acad. Sci. USA. 2014;111:17474–17479. doi: 10.1073/pnas.1414126111. PubMed DOI PMC
Sievers F., Wilm A., Dineen D., Gibson T.J., Karplus K., Li W., Lopez R., McWilliam H., Remmert M., Söding J., et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol. Syst. Biol. 2011;7:539. doi: 10.1038/msb.2011.75. PubMed DOI PMC
Bevec T., Stoka V., Pungercic G., Dolenc I., Turk V. Major histocompatibility complex class II-associated p41 invariant chain fragment is a strong inhibitor of lysosomal cathepsin L. J. Exp. Med. 1996;183:1331–1338. doi: 10.1084/jem.183.4.1331. PubMed DOI PMC
Lenarcic B., Ritonja A., Strukelj B., Turk B., Turk V. Equistatin, a new inhibitor of cysteine proteinases from Actinia equina, is structurally related to thyroglobulin type-1 domain. J. Biol. Chem. 1997;272:13899–13903. doi: 10.1074/jbc.272.21.13899. PubMed DOI
Musil D., Zucic D., Turk D., Engh R.A., Mayr I., Huber R., Popovic T., Turk V., Towatari T., Katunuma N., et al. The refined 2.15 A X-ray crystal structure of human liver cathepsin B: The structural basis for its specificity. EMBO J. 1991;10:2321–2330. doi: 10.1002/j.1460-2075.1991.tb07771.x. PubMed DOI PMC
Guncar G., Podobnik M., Pungercar J., Strukelj B., Turk V., Turk D. Crystal structure of porcine cathepsin H determined at 2.1 A resolution: Location of the mini-chain C-terminal carboxyl group defines cathepsin H aminopeptidase function. Structure. 1998;6:51–61. doi: 10.1016/S0969-2126(98)00007-0. PubMed DOI
Horn M., Jílková A., Vondrášek J., Marešová L., Caffrey C.R., Mareš M. Mapping the pro-peptide of the Schistosoma mansoni cathepsin B1 drug target: Modulation of inhibition by heparin and design of mimetic inhibitors. ACS Chem. Biol. 2011;6:609–617. doi: 10.1021/cb100411v. PubMed DOI
Jílková A., Horn M., Řezáčová P., Marešová L., Fajtová P., Brynda J., Vondrášek J., McKerrow J.H., Caffrey C.R., Mareš M. Activation route of the Schistosoma mansoni cathepsin B1 drug target: Structural map with a glycosaminoglycan switch. Structure. 2014;22:1786–1798. doi: 10.1016/j.str.2014.09.015. PubMed DOI
Caglic D., Pungercar J.R., Pejler G., Turk V., Turk B. Glycosaminoglycans facilitate procathepsin B activation through disruption of propeptide-mature enzyme interactions. J. Biol. Chem. 2007;282:33076–33085. doi: 10.1074/jbc.M705761200. PubMed DOI
Almeida P.C., Nantes I.L., Chagas J.R., Rizzi C.C., Faljoni-Alario A., Carmona E., Juliano L., Nader H.B., Tersariol I.L. Cathepsin B activity regulation. Heparin-like glycosaminogylcans protect human cathepsin B from alkaline pH-induced inactivation. J. Biol. Chem. 2001;276:944–951. doi: 10.1074/jbc.M003820200. PubMed DOI
Novinec M., Lenarčič B., Turk B. Cysteine cathepsin activity regulation by glycosaminoglycans. Biomed. Res. Int. 2014;2014:309718. doi: 10.1155/2014/309718. PubMed DOI PMC
Yasuda Y., Li Z., Greenbaum D., Bogyo M., Weber E., Brömme D. Cathepsin V, a Novel and Potent Elastolytic Activity Expressed in Activated Macrophages. J. Biol. Chem. 2004;279:36761–36770. doi: 10.1074/jbc.M403986200. PubMed DOI
Jmel M.A., Aounallah H., Bensaoud C., Mekki I., Chmelař J., Faria F., M’Ghirbi Y., Kotsyfakis M. Insights into the Role of Tick Salivary Protease Inhibitors during Ectoparasite-Host Crosstalk. Int. J. Mol. Sci. 2021;22:892. doi: 10.3390/ijms22020892. PubMed DOI PMC
Panwar P., Hedtke T., Heinz A., Andrault P.M., Hoehenwarter W., Granville D.J., Schmelzer C.E.H., Brömme D. Expression of elastolytic cathepsins in human skin and their involvement in age-dependent elastin degradation. Biochim. Biophys. Acta Gen. Subj. 2020;1864:129544. doi: 10.1016/j.bbagen.2020.129544. PubMed DOI
Dennemärker J., Lohmüller T., Mayerle J., Tacke M., Lerch M.M., Coussens L.M., Peters C., Reinheckel T. Deficiency for the cysteine protease cathepsin L promotes tumor progression in mouse epidermis. Oncogene. 2010;29:1611–1621. doi: 10.1038/onc.2009.466. PubMed DOI PMC
Lecaille F., Chazeirat T., Saidi A., Lalmanach G. Cathepsin V: Molecular characteristics and significance in health and disease. Mol. Aspects Med. 2022;88:101086. doi: 10.1016/j.mam.2022.101086. PubMed DOI
Brömme D., Wilson S. Role of Cysteine Cathepsins in Extracellular Proteolysis. In: Parks W.C., Mecham R.P., editors. Extracellular Matrix Degradation. Springer; Berlin/Heidelberg, Germany: 2011. pp. 23–51.
Vizovišek M., Fonović M., Turk B. Cysteine cathepsins in extracellular matrix remodeling: Extracellular matrix degradation and beyond. Matrix Biol. 2019;75–76:141–159. doi: 10.1016/j.matbio.2018.01.024. PubMed DOI
Senjor E., Kos J., Nanut M.P. Cysteine Cathepsins as Therapeutic Targets in Immune Regulation and Immune Disorders. Biomedicines. 2023;11:476. doi: 10.3390/biomedicines11020476. PubMed DOI PMC
Khamtorn P., Peigneur S., Amorim F.G., Quinton L., Tytgat J., Daduang S. De Novo Transcriptome Analysis of the Venom of Latrodectus geometricus with the Discovery of an Insect-Selective Na Channel Modulator. Molecules. 2021;27:47. doi: 10.3390/molecules27010047. PubMed DOI PMC
Emerich B.L., Ferreira R.C.M., Cordeiro M.N., Borges M.H., Pimenta A.M.C., Figueiredo S.G., Duarte I.D.G., De Lima M.E. δ-Ctenitoxin-Pn1a, a Peptide from Phoneutria nigriventer Spider Venom, Shows Antinociceptive Effect Involving Opioid and Cannabinoid Systems, in Rats. Toxins. 2016;8:106. doi: 10.3390/toxins8040106. PubMed DOI PMC
Benýšek J., Buša M., Rubešová P., Fanfrlík J., Lepšík M., Brynda J., Matoušková Z., Bartz U., Horn M., Gütschow M., et al. Highly potent inhibitors of cathepsin K with a differently positioned cyanohydrazide warhead: Structural analysis of binding mode to mature and zymogen-like enzymes. J. Enzyme Inhib. Med. Chem. 2022;37:515–526. doi: 10.1080/14756366.2021.2024527. PubMed DOI PMC
Brömme D., Li Z., Barnes M., Mehler E. Human cathepsin V functional expression, tissue distribution, electrostatic surface potential, enzymatic characterization, and chromosomal localization. Biochemistry. 1999;38:2377–2385. doi: 10.1021/bi982175f. PubMed DOI
Horn M., Baudyš M., Voburka Z., Kluh I., Vondrášek J., Mareš M. Free-thiol Cys331 exposed during activation process is critical for native tetramer structure of cathepsin C (dipeptidyl peptidase I) Protein Sci. 2002;11:933–943. doi: 10.1110/ps.2910102. PubMed DOI PMC
Horn M., Dolečková-Marešová L., Rulíšek L., Máša M., Vasiljeva O., Turk B., Gan-Erdene T., Baudys M., Mareš M. Activation processing of cathepsin H impairs recognition by its propeptide. Biol. Chem. 2005;386:941–947. doi: 10.1515/BC.2005.109. PubMed DOI
Máša M., Marešová L., Vondrášek J., Horn M., Ježek J., Mareš M. Cathepsin D propeptide: Mechanism and regulation of its interaction with the catalytic core. Biochemistry. 2006;45:15474–15482. doi: 10.1021/bi0614986. PubMed DOI
Perner J., Helm D., Haberkant P., Hatalová T., Kropáčková S., Ribeiro J.M., Kopáček P. The Central Role of Salivary Metalloproteases in Host Acquired Resistance to Tick Feeding. Front. Cell Infect. Microbiol. 2020;10:563349. doi: 10.3389/fcimb.2020.563349. PubMed DOI PMC
Urbanová V., Šíma R., Šauman I., Hajdušek O., Kopáček P. Thioester-containing proteins of the tick Ixodes ricinus: Gene expression, response to microbial challenge and their role in phagocytosis of the yeast Candida albicans. Dev. Comp. Immunol. 2015;48:55–64. doi: 10.1016/j.dci.2014.09.004. PubMed DOI
Perner J., Kropáčková S., Kopáček P., Ribeiro J.M.C. Sialome diversity of ticks revealed by RNAseq of single tick salivary glands. PLoS Negl. Trop. Dis. 2018;12:e0006410. doi: 10.1371/journal.pntd.0006410. PubMed DOI PMC
Jílková A., Řezáčová P., Lepšík M., Horn M., Váchová J., Fanfrlík J., Brynda J., McKerrow J.H., Caffrey C.R., Mareš M. Structural basis for inhibition of cathepsin B drug target from the human blood fluke, Schistosoma mansoni. J. Biol. Chem. 2011;286:35770–35781. doi: 10.1074/jbc.M111.271304. PubMed DOI PMC
Qi D., Scholthof K.B. A one-step PCR-based method for rapid and efficient site-directed fragment deletion, insertion, and substitution mutagenesis. J. Virol. Methods. 2008;149:85–90. doi: 10.1016/j.jviromet.2008.01.002. PubMed DOI
Sojka D., Franta Z., Frantová H., Bartošová P., Horn M., Váchová J., O’Donoghue A.J., Eroy-Reveles A.A., Craik C.S., Knudsen G.M., et al. Characterization of gut-associated cathepsin D hemoglobinase from tick Ixodes ricinus (IrCD1) J. Biol. Chem. 2012;287:21152–21163. doi: 10.1074/jbc.M112.347922. PubMed DOI PMC
Pfaffl M.W. A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res. 2001;29:e45. doi: 10.1093/nar/29.9.e45. PubMed DOI PMC
Fojtík L., Fiala J., Pompach P., Chmelík J., Matoušek V., Beier P., Kukačka Z., Novák P. Fast Fluoroalkylation of Proteins Uncovers the Structure and Dynamics of Biological Macromolecules. J. Am. Chem. Soc. 2021;143:20670–20679. doi: 10.1021/jacs.1c07771. PubMed DOI
Renshaw P.S., Lightbody K.L., Veverka V., Muskett F.W., Kelly G., Frenkiel T.A., Gordon S.V., Hewinson R.G., Burke B., Norman J., et al. Structure and function of the complex formed by the tuberculosis virulence factors CFP-10 and ESAT-6. EMBO J. 2005;24:2491–2498. doi: 10.1038/sj.emboj.7600732. PubMed DOI PMC
Veverka V., Lennie G., Crabbe T., Bird I., Taylor R.J., Carr M.D. NMR assignment of the mTOR domain responsible for rapamycin binding. J. Biomol. NMR. 2006;36((Suppl. 1)):3. doi: 10.1007/s10858-005-4324-1. PubMed DOI
Lee W., Tonelli M., Markley J.L. NMRFAM-SPARKY: Enhanced software for biomolecular NMR spectroscopy. Bioinformatics. 2015;31:1325–1327. doi: 10.1093/bioinformatics/btu830. PubMed DOI PMC
Herrmann T., Güntert P., Wüthrich K. Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA. J. Mol. Biol. 2002;319:209–227. doi: 10.1016/S0022-2836(02)00241-3. PubMed DOI
Shen Y., Delaglio F., Cornilescu G., Bax A. TALOS+: A hybrid method for predicting protein backbone torsion angles from NMR chemical shifts. J. Biomol. NMR. 2009;44:213–223. doi: 10.1007/s10858-009-9333-z. PubMed DOI PMC
Janson G., Zhang C., Prado M.G., Paiardini A. PyMod 2.0: Improvements in protein sequence-structure analysis and homology modeling within PyMOL. Bioinformatics. 2017;33:444–446. doi: 10.1093/bioinformatics/btw638. PubMed DOI
Jumper J., Evans R., Pritzel A., Green T., Figurnov M., Ronneberger O., Tunyasuvunakool K., Bates R., Žídek A., Potapenko A., et al. Highly accurate protein structure prediction with AlphaFold. Nature. 2021;596:583–589. doi: 10.1038/s41586-021-03819-2. PubMed DOI PMC
Jurrus E., Engel D., Star K., Monson K., Brandi J., Felberg L.E., Brookes D.H., Wilson L., Chen J., Liles K., et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci. 2018;27:112–128. doi: 10.1002/pro.3280. PubMed DOI PMC
Meng E.C., Goddard T.D., Pettersen E.F., Couch G.S., Pearson Z.J., Morris J.H., Ferrin T.E. UCSF ChimeraX: Tools for structure building and analysis. Protein Sci. 2023;32:e4792. doi: 10.1002/pro.4792. PubMed DOI PMC
Kukačka Z., Rosůlek M., Jelínek J., Slavata L., Kavan D., Novák P. LinX: A Software Tool for Uncommon Cross-Linking Chemistry. J. Proteome Res. 2021;20:2021–2027. doi: 10.1021/acs.jproteome.0c00858. PubMed DOI
Götze M., Pettelkau J., Fritzsche R., Ihling C.H., Schäfer M., Sinz A. Automated assignment of MS/MS cleavable cross-links in protein 3D-structure analysis. J. Am. Soc. Mass Spectrom. 2015;26:83–97. doi: 10.1007/s13361-014-1001-1. PubMed DOI