Update publications.md

Author: CordeiroLab

content/publications.md

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 > <img src="/assets/images/icons/gscholar_icon.svg" alt="gscholar" width="20" height="20"> **[more on Google Scholar](https://scholar.google.com/citations?user=ZKSPS14AAAAJ&hl=en)**
 ## 2025
-**22.** Santos CC, Schweizer N, Cairrão F, Ramirez J, Osinalde N, Yang M, Gaspar CJ, Rasheva VI, Trigo ML, Hensel Z, Adrain C, Cordeiro TN, Voigt F, Gameiro PA, Mayor U, Domingos PM.* (2025) **Fbxo42 promotes the degradation of Ataxin-2 granules to trigger terminal Xbp1 signaling.** *Nat. Commun.* 16:7523.[link](https://doi.org/10.1038/s41467-025-62417-2)
+**36.** Santos CC, Schweizer N, Cairrão F, Ramirez J, Osinalde N, Yang M, Gaspar CJ, Rasheva VI, Trigo ML, Hensel Z, Adrain C, Cordeiro TN, Voigt F, Gameiro PA, Mayor U, Domingos PM.* (2025) **Fbxo42 promotes the degradation of Ataxin-2 granules to trigger terminal Xbp1 signaling.** *Nat. Commun.* 16:7523.[link](https://doi.org/10.1038/s41467-025-62417-2)
 
-**21.** Hernandez G, Martins ML, Fernandes NP, Veloso T, Lopes J, Gomes, T *, Cordeiro,TN * (2025) **Dynamic ensembles of SARS-CoV-2 N-protein reveal head-to-head coiled-coil-driven oligomerization and phase separation.** *Nucleic Acids Res.* Jun 6;53(11).[link](https://doi.org/10.1093/nar/gkaf502)
+**35.** Hernandez G, Martins ML, Fernandes NP, Veloso T, Lopes J, Gomes, T *, Cordeiro,TN * (2025) **Dynamic ensembles of SARS-CoV-2 N-protein reveal head-to-head coiled-coil-driven oligomerization and phase separation.** *Nucleic Acids Res.* Jun 6;53(11).[link](https://doi.org/10.1093/nar/gkaf502)
 <p align="center">
   <a href="https://doi.org/10.1093/nar/gkaf502" >
   <img src="/assets/images/thumbnail/pub21-thumbnail.png" alt="N-Protein" style="width: 90%; max-width: 100%; height: auto;" />
   </a>  
 </p>
 
-**20.** Gomes T, Ruiz L, Martin-Malpartida P, Bernado P, Baptista AM, Macias MJ, Cordeiro TN* (2025) **KDSAXS: A Tool for Analyzing Binding Equilibria with Saxs Data Using Explicit Models.** *J. Mol. Biol.* *in press* [link](https://doi.org/10.1016/j.jmb.2025.169103)
+**34.** Gomes T, Ruiz L, Martin-Malpartida P, Bernado P, Baptista AM, Macias MJ, Cordeiro TN* (2025) **KDSAXS: A Tool for Analyzing Binding Equilibria with Saxs Data Using Explicit Models.** *J. Mol. Biol.* *in press* [link](https://doi.org/10.1016/j.jmb.2025.169103)
 <p align="center">
   <a href="https://doi.org/10.1016/j.jmb.2025.169103" >
   <img src="/assets/images/thumbnail/pub20-thumbnail.png" alt="KdSAXS" style="width: 90%; max-width: 100%; height: auto;" />
   </a>  
 </p>
 
 ## 2024
-**19.** Vieira MFM, Hernandez G, Zhong Q, Arbesú M, Veloso T, Gomes T, Martins ML, Monteiro H, Frazão C, Frankel G, Zanzoni A,  Cordeiro TN* (2024) **The pathogen-encoded signalling receptor Tir exploits host-like intrinsic disorder for infection.** *Commun. Biol.*, 7, 179. [link](https://doi.org/10.1038/s42003-024-05856-9)
+**33.** Vieira MFM, Hernandez G, Zhong Q, Arbesú M, Veloso T, Gomes T, Martins ML, Monteiro H, Frazão C, Frankel G, Zanzoni A,  Cordeiro TN* (2024) **The pathogen-encoded signalling receptor Tir exploits host-like intrinsic disorder for infection.** *Commun. Biol.*, 7, 179. [link](https://doi.org/10.1038/s42003-024-05856-9)
 <p align="center">
   <a href="https://doi.org/10.1038/s42003-024-05856-9" >
   <img src="/assets/images/thumbnail/pub19-thumbnail.png" alt="Tir" style="width: 90%; max-width: 100%; height: auto;" />
   </a>
 </p>
 
-**18.** Bárria,C., Athayde,D., Hernandez,G., Fonseca,L., Casinhas,J., Cordeiro,T.N., Archer,M., Arraiano,C.M., Brito,J.A., Matos,R.G. (2024) **Structure and function of Campylobacter jejuni polynucleotide phosphorylase (PNPase): Insights into the role of this RNase in pathogenicity.** *Biochimie,* 216, 56–70. [link](https://doi.org/10.1016/j.biochi.2023.10.006)
+**32.** Bárria,C., Athayde,D., Hernandez,G., Fonseca,L., Casinhas,J., Cordeiro,T.N., Archer,M., Arraiano,C.M., Brito,J.A., Matos,R.G. (2024) **Structure and function of Campylobacter jejuni polynucleotide phosphorylase (PNPase): Insights into the role of this RNase in pathogenicity.** *Biochimie,* 216, 56–70. [link](https://doi.org/10.1016/j.biochi.2023.10.006)
 
-**17.** Ghafouri H, Lazar T, Del Conte A, Tenorio Ku LG, PED Consortium, Tompa P, Tosatto SCE, Monzon AM (2024) **PED in 2024: improving the community deposition of structural ensembles for intrinsically disordered proteins.** *Nucleic Acids Res.*, 52, D536–D544. [link](https://doi.org/10.1093/nar/gkad947)
+**31.** Ghafouri H, Lazar T, Del Conte A, Tenorio Ku LG, PED Consortium, Tompa P, Tosatto SCE, Monzon AM (2024) **PED in 2024: improving the community deposition of structural ensembles for intrinsically disordered proteins.** *Nucleic Acids Res.*, 52, D536–D544. [link](https://doi.org/10.1093/nar/gkad947)
 
 ## 2023
-**16.** Marini E, Olivença C, Ramalhete S, Aguirre AM, Ingle P, Melo MN, Antunes W, Minton NP, Hernandez G, Cordeiro TN, et al. (2023) **A sporulation signature protease is required for assembly of the spore surface layers, germination and host colonization in Clostridioides difficile.** *PLoS Pathog.*, 19, e1011741. [link](https://doi.org/10.1371/journal.ppat.1011741)
+**30.** Marini E, Olivença C, Ramalhete S, Aguirre AM, Ingle P, Melo MN, Antunes W, Minton NP, Hernandez G, Cordeiro TN, et al. (2023) **A sporulation signature protease is required for assembly of the spore surface layers, germination and host colonization in Clostridioides difficile.** *PLoS Pathog.*, 19, e1011741. [link](https://doi.org/10.1371/journal.ppat.1011741)
 
-**15.** Gaspar CJ, Gomes T, Martins JC, Melo MN, Adrain C, Cordeiro TN*, Domingos PM*. (2023) **Xport-A functions as a chaperone by stabilizing the first five transmembrane domains of rhodopsin-1.** *iScience*, 26, 108309. [link](https://doi.org/10.1016/j.isci.2023.108309)
+**29.** Gaspar CJ, Gomes T, Martins JC, Melo MN, Adrain C, Cordeiro TN*, Domingos PM*. (2023) **Xport-A functions as a chaperone by stabilizing the first five transmembrane domains of rhodopsin-1.** *iScience*, 26, 108309. [link](https://doi.org/10.1016/j.isci.2023.108309)
 <p align="center">
   <a href="https://doi.org/10.1016/j.isci.2023.108309" >
   <img src="/assets/images/thumbnail/pub15-thumbnail.png" alt="Xport-A" style="width: 70%; height: auto;" />
   </a>
 </p>
 
 ## 2022
-**14.** Pinto D, Gonçalo R, Louro M, Silva MS, Hernandez G, Cordeiro TN, Cordeiro C, São-José C (2022) **On the Occurrence and Multimerization of Two-Polypeptide Phage Endolysins Encoded in Single Genes.** *Microbiol. Spectr.*, 10, e0103722. [link](https://doi.org/10.1128/spectrum.01037-22)
+**28.** Pinto D, Gonçalo R, Louro M, Silva MS, Hernandez G, Cordeiro TN, Cordeiro C, São-José C (2022) **On the Occurrence and Multimerization of Two-Polypeptide Phage Endolysins Encoded in Single Genes.** *Microbiol. Spectr.*, 10, e0103722. [link](https://doi.org/10.1128/spectrum.01037-22)
 
-**13.** Guillien M, Mouhand A, Fournet A, Gontier A, Martí NaviaA, Cordeiro TN, Allemand F, Thureau A, Banères J-L, Bernadó P, et al. (2022) **Structural Insights into the Intrinsically Disordered GPCR C-Terminal Region, Major Actor in Arrestin-GPCR Interaction.** *Biomolecules*, 12. [link](https://doi.org/10.3390/biom12050617)
+**27.** Guillien M, Mouhand A, Fournet A, Gontier A, Martí NaviaA, Cordeiro TN, Allemand F, Thureau A, Banères J-L, Bernadó P, et al. (2022) **Structural Insights into the Intrinsically Disordered GPCR C-Terminal Region, Major Actor in Arrestin-GPCR Interaction.** *Biomolecules*, 12. [link](https://doi.org/10.3390/biom12050617)
 
-**12.** Brissos,V., Borges,P.T., Núñez-Franco,R., Lucas,M.F., Frazão,C., Monza,E., Masgrau,L., Cordeiro,T.N., Martins,L.O. (2022) **Distal Mutations Shape Substrate-Binding Sites during Evolution of a Metallo-Oxidase into a Laccase.** *ACS Catal.*, 12, 9, 5022-5035 [link](https://doi.org/10.1021/acscatal.2c00336)
+**26.** Brissos,V., Borges,P.T., Núñez-Franco,R., Lucas,M.F., Frazão,C., Monza,E., Masgrau,L., Cordeiro,T.N., Martins,L.O. (2022) **Distal Mutations Shape Substrate-Binding Sites during Evolution of a Metallo-Oxidase into a Laccase.** *ACS Catal.*, 12, 9, 5022-5035 [link](https://doi.org/10.1021/acscatal.2c00336)
 
 ## 2021
-**11.** Trindade,I.B., Hernandez,G., Lebègue,E., Barrière,F., Cordeiro,T.N., Piccioli,M., Louro,R.O. (2021) **Conjuring up a ghost: structural and functional characterization of FhuF, a ferric siderophore reductase from *E. coli.*** *J. Biol. Inorg. Chem.*, 26, 313–326. [link](https://doi.org/10.1007/s00775-021-01854-y)
+**25.** Trindade,I.B., Hernandez,G., Lebègue,E., Barrière,F., Cordeiro,T.N., Piccioli,M., Louro,R.O. (2021) **Conjuring up a ghost: structural and functional characterization of FhuF, a ferric siderophore reductase from *E. coli.*** *J. Biol. Inorg. Chem.*, 26, 313–326. [link](https://doi.org/10.1007/s00775-021-01854-y)
 
-**10.** Lazar,T., Martínez-Pérez,E., Quaglia,F., Hatos,A., Chemes,L.B., Iserte,J.A., Méndez,N.A., Garrone,N.A., Saldaño,T.E., Marchetti,J., et al. (2021) **PED in 2021: a major update of the protein ensemble database for intrinsically disordered proteins.** *Nucleic Acids Res.*, 49, D404–D411. [link](https://doi.org/10.1093/nar/gkaa1021)
+**24.** Lazar,T., Martínez-Pérez,E., Quaglia,F., Hatos,A., Chemes,L.B., Iserte,J.A., Méndez,N.A., Garrone,N.A., Saldaño,T.E., Marchetti,J., et al. (2021) **PED in 2021: a major update of the protein ensemble database for intrinsically disordered proteins.** *Nucleic Acids Res.*, 49, D404–D411. [link](https://doi.org/10.1093/nar/gkaa1021)
 
-**9.** Gomes,T., Martin-Malpartida,P., Ruiz,L., Aragón,E., Cordeiro,T.N*. Macias,M.J.* (2021) **Conformational landscape of multidomain SMAD proteins.** *Comput. Struct. Biotechnol. J.*, 19, 5210–5224. [link](https://doi.org/10.1016/j.csbj.2021.09.009)
+**23.** Gomes,T., Martin-Malpartida,P., Ruiz,L., Aragón,E., Cordeiro,T.N*. Macias,M.J.* (2021) **Conformational landscape of multidomain SMAD proteins.** *Comput. Struct. Biotechnol. J.*, 19, 5210–5224. [link](https://doi.org/10.1016/j.csbj.2021.09.009)
 <p align="center">
   <a href="https://doi.org/10.1016/j.csbj.2021.09.009" >
   <img src="/assets/images/thumbnail/pub9-thumbnail.png" alt="Publication 9" style="width: 90%; max-width: 100%; height: auto;" />
   </a>
 </p>
 
-**8.** Ruiz,L., Kaczmarska,Z., Gomes,T., Aragon,E., Torner,C., Freier,R., Baginski,B., Martin-Malpartida,P., de Martin Garrido,N., Marquez,J.A., Cordeiro, T.N., Pluta, R., Macias, M.J. (2021) **Unveiling the dimer/monomer propensities of Smad MH1-DNA complexes.** *Comput. Struct. Biotechnol. J.*, 19, 632–646. [link](https://doi.org/10.1016/j.csbj.2020.12.044)
+**22.** Ruiz,L., Kaczmarska,Z., Gomes,T., Aragon,E., Torner,C., Freier,R., Baginski,B., Martin-Malpartida,P., de Martin Garrido,N., Marquez,J.A., Cordeiro, T.N., Pluta, R., Macias, M.J. (2021) **Unveiling the dimer/monomer propensities of Smad MH1-DNA complexes.** *Comput. Struct. Biotechnol. J.*, 19, 632–646. [link](https://doi.org/10.1016/j.csbj.2020.12.044)
 
 ## 2020
-**7.** Barreto,H.C., Cordeiro,T.N., Henriques,A.O. and Gordo,I. (2020) **Rampant loss of social traits during domestication of a Bacillus subtilis natural isolate.** *Sci. Rep.*, 10, 18886. [link](https://doi.org/10.1038/s41598-020-76017-1)
+**21.** Barreto,H.C., Cordeiro,T.N., Henriques,A.O. and Gordo,I. (2020) **Rampant loss of social traits during domestication of a Bacillus subtilis natural isolate.** *Sci. Rep.*, 10, 18886. [link](https://doi.org/10.1038/s41598-020-76017-1)
 
-**6.** Borges,P.T., Brissos,V., Hernandez,G., Masgrau,L., Lucas,M.F., Monza,E., Frazão,C., Cordeiro,T.N. *, Martins,L.O. * (2020) **Methionine-Rich Loop of Multicopper Oxidase McoA Follows Open-to-Close Transitions with a Role in Enzyme Catalysis.** *ACS Catal.*, 10, 7162–7176. [link](https://doi.org/10.1021/acscatal.0c01623)
+**20.** Borges,P.T., Brissos,V., Hernandez,G., Masgrau,L., Lucas,M.F., Monza,E., Frazão,C., Cordeiro,T.N. *, Martins,L.O. * (2020) **Methionine-Rich Loop of Multicopper Oxidase McoA Follows Open-to-Close Transitions with a Role in Enzyme Catalysis.** *ACS Catal.*, 10, 7162–7176. [link](https://doi.org/10.1021/acscatal.0c01623)
 <p align="center">
   <a href="https://doi.org/10.1021/acscatal.0c01623" >
   <img src="/assets/images/thumbnail/pub6-thumbnail.png" alt="Met-loop" style="width: 70%; max-width: 100%; height: auto;" />
   </a>
 </p>
 
 ## 2019
-**5.** González-Magaña,A., de Opakua,A.I., Merino,N., Monteiro,H., Diercks,T., Murciano-Calles,J., Luque,I., Bernadó,P., Cordeiro,T.N., Biasio,A.D., et al. (2019) **Double Monoubiquitination Modifies the Molecular Recognition Properties of p15PAF Promoting Binding to the Reader Module of Dnmt1.** *ACS Chem. Biol.*, 14, 2315–2326.[link](https://doi.org/10.1021/acschembio.9b00679)
+**19.** González-Magaña,A., de Opakua,A.I., Merino,N., Monteiro,H., Diercks,T., Murciano-Calles,J., Luque,I., Bernadó,P., Cordeiro,T.N., Biasio,A.D., et al. (2019) **Double Monoubiquitination Modifies the Molecular Recognition Properties of p15PAF Promoting Binding to the Reader Module of Dnmt1.** *ACS Chem. Biol.*, 14, 2315–2326.[link](https://doi.org/10.1021/acschembio.9b00679)
 
-**4.** Cordeiro,T.N., Sibille,N., Germain,P., Barthe,P., Boulahtouf,A., Allemand,F., Bailly,R., Vivat,V., Ebel,C., Barducci,A., et al. (2019) **Interplay of protein disorder in retinoic acid receptor heterodimer and its corepressor regulates gene expression.** *Structure*, 27, 1270-1285.e6. [Link](https://doi.org/10.1016/j.str.2019.05.001)
+**18.** Cordeiro,T.N., Sibille,N., Germain,P., Barthe,P., Boulahtouf,A., Allemand,F., Bailly,R., Vivat,V., Ebel,C., Barducci,A., et al. (2019) **Interplay of protein disorder in retinoic acid receptor heterodimer and its corepressor regulates gene expression.** *Structure*, 27, 1270-1285.e6. [Link](https://doi.org/10.1016/j.str.2019.05.001)
 
-**3.** Orellana,L., Thorne,A.H., Lema,R., Gustavsson,J., Parisian,A.D., Hospital,A., Cordeiro,T.N., Bernadó,P., Scott,A.M., Brun-Heath,I., et al. (2019) **Oncogenic mutations at the EGFR ectodomain structurally converge to remove a steric hindrance on a kinase-coupled cryptic epitope.** *Proc Natl Acad Sci USA*, 116, 10009–10018. [link](https://doi.org/10.1073/pnas.1821442116)
+**17.** Orellana,L., Thorne,A.H., Lema,R., Gustavsson,J., Parisian,A.D., Hospital,A., Cordeiro,T.N., Bernadó,P., Scott,A.M., Brun-Heath,I., et al. (2019) **Oncogenic mutations at the EGFR ectodomain structurally converge to remove a steric hindrance on a kinase-coupled cryptic epitope.** *Proc Natl Acad Sci USA*, 116, 10009–10018. [link](https://doi.org/10.1073/pnas.1821442116)
 
-**2.** Fernandes,C.G., Martins,D., Hernandez,G., Sousa,A.L., Freitas,C., Tranfield,E.M., Cordeiro,T.N., Serrano,M., Moran,C.P. and Henriques,A.O. (2019) **Temporal and spatial regulation of protein cross-linking by the pre-assembled substrates of a Bacillus subtilis spore coat transglutaminase.** *PLoS Genet.*, 15, e1007912. [link](https://doi.org/10.1371/journal.pgen.1007912)
+**16.** Fernandes,C.G., Martins,D., Hernandez,G., Sousa,A.L., Freitas,C., Tranfield,E.M., Cordeiro,T.N., Serrano,M., Moran,C.P. and Henriques,A.O. (2019) **Temporal and spatial regulation of protein cross-linking by the pre-assembled substrates of a Bacillus subtilis spore coat transglutaminase.** *PLoS Genet.*, 15, e1007912. [link](https://doi.org/10.1371/journal.pgen.1007912)
 
-**1.** Arbesú,M., Maffei,M., Cordeiro,T.N., Teixeira,J.M.C., Pérez,Y., Bernadó,P., Roche,S. and Pons,M. (2017) **The unique domain forms a fuzzy intramolecular complex in src family kinases.** *Structure*, 25, 630-640.e4. [link](https://doi.org/10.1016/j.str.2017.02.011)
+**15.** Arbesú,M., Maffei,M., Cordeiro,T.N., Teixeira,J.M.C., Pérez,Y., Bernadó,P., Roche,S. and Pons,M. (2017) **The unique domain forms a fuzzy intramolecular complex in src family kinases.** *Structure*, 25, 630-640.e4. [link](https://doi.org/10.1016/j.str.2017.02.011)
 
 > 
 > Before ITQB NOVA, Publications arising from **Post Doctoral**, **PhD**, **MSc & BSc** work