Twinning for excellence in biophysics of protein interactions and self-assembly

Deliverables

Report on dissemination, exploitation, and communication activities
Final report on staff exchanges outcomes
Final report on training schools

Data management plan
Updated Data management plan

Publications

Constant-pH MD simulations of the protonation-triggered conformational switching in diphtheria toxin translocation domain

Author(s): Nuno F.B. Oliveira, Alexey S. Ladokhin, Miguel Machuqueiro
Published in: Biophysical Journal, Issue 123, 2024, ISSN 0006-3495
Publisher: Elsevier BV
DOI: 10.1016/J.BPJ.2024.08.023

The Dimensionality of Hydrogen Bond Networks Induces Diverse Physical Properties of Peptide Crystals

Author(s): Hui Yuan, Pierre-Andre Cazade, Chengqian Yuan, Bin Xue, Vijay Bhooshan Kumar, Rusen Yang, Gal Finkelstein-Zuta, Lihi Gershon, Maoz Lahav, Sigal Rencus-Lazar, Yi Cao, Davide Levy, Damien Thompson, Ehud Gazit
Published in: ACS Materials Letters, Issue 6, 2024, ISSN 2639-4979
Publisher: American Chemical Society (ACS)
DOI: 10.34961/RESEARCHREPOSITORY-UL.26561434

Biophysical Studies of Amyloid-Binding Fluorophores to Tau AD Core Fibrils Formed without Cofactors

Author(s): Daniela P. Freitas, Joana Saavedra, Isabel Cardoso, Cláudio M. Gomes
Published in: International Journal of Molecular Sciences, Issue 25, 2024, ISSN 1422-0067
Publisher: MDPI AG
DOI: 10.3390/IJMS25189946

Recent advances on molecular dynamics-based techniques to address drug membrane permeability with atomistic detail

Author(s): André M.M. Gomes, Paulo J. Costa, Miguel Machuqueiro
Published in: BBA Advances, Issue 4, 2023, ISSN 2667-1603
Publisher: Elsevier BV
DOI: 10.1016/J.BBADVA.2023.100099

A human microglial cell model of autosomal recessive spastic ataxia of Charlevoix-Saguenay

Author(s): Fernanda Murtinheira, Elisa Farsetti, Luana Macedo, Ana Sofia Boasinha, Mario S. Rodrigues, Adelaide Fernandes, Federico Herrera
Published in: Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease, Issue 1870, 2024, ISSN 0925-4439
Publisher: Elsevier BV
DOI: 10.1016/J.BBADIS.2024.167452

S100B chaperone multimers suppress the formation of oligomers during Aβ42 aggregation

Author(s): António J. Figueira, Joana Saavedra, Isabel Cardoso, Cláudio M. Gomes
Published in: Frontiers in Neuroscience, Issue 17, 2023, ISSN 1662-453X
Publisher: Frontiers Media SA
DOI: 10.3389/FNINS.2023.1162741

Probing the Interactions of Thiazole Abietane Inhibitors with the Human Serine Hydrolases ABHD16A and ABHD12

Author(s): Tiina J. Ahonen, Choa P. Ng, Beatriz Farinha, Bárbara Almeida, Bruno L. Victor, Christopher Reynolds, Eija Kalso, Jari Yli-Kauhaluoma, Jennifer Greaves, Vânia M. Moreira
Published in: ACS Medicinal Chemistry Letters, Issue 14, 2023, ISSN 1948-5875
Publisher: American Chemical Society (ACS)
DOI: 10.1021/ACSMEDCHEMLETT.3C00313

Functional modulation of RAGE activation by multimeric S100B using single-domain antibodies

Author(s): Margarida C. Simões, Joana S. Cristóvão, Els Pardon, Jan Steyaert, Günter Fritz, Cláudio M. Gomes
Published in: Journal of Biological Chemistry, Issue 300, 2024, ISSN 0021-9258
Publisher: Elsevier BV
DOI: 10.1016/J.JBC.2024.107983

Molecular Engineering of Ordered Piezoelectric Sulfonic Acid‐Containing Assemblies

Author(s): Hui Yuan, Pierre‐Andre Cazade, Shuaikang Zhou, Linda J. W. Shimon, Chengqian Yuan, Dan Tan, Cunshun Liu, Wei Fan, Vijayakanth Thangavel, Yi Cao, Damien Thompson, Xuehai Yan, Rusen Yang, Bin Xue, Ehud Gazit
Published in: Small, Issue 20, 2023, ISSN 1613-6810
Publisher: Wiley
DOI: 10.1002/SMLL.202309493

Neuronal expression of S100B triggered by oligomeric Aβ peptide contributes to protection against cytoskeletal damage and synaptic loss

Author(s): Joana Saavedra, Mariana Nascimento, António J. Figueira, Marina I. Oliveira da Silva, Tiago Gião, João Oliveira, Márcia A. Liz, Cláudio M. Gomes, Isabel Cardoso
Published in: Frontiers in Molecular Neuroscience, Issue 18, 2025, ISSN 1662-5099
Publisher: Frontiers Media SA
DOI: 10.3389/FNMOL.2025.1636365

Is There a Functional Role for the Knotted Topology in Protein UCH-L1?

Author(s): Sara G. F. Ferreira, Manoj K. Sriramoju, Shang-Te Danny Hsu, Patrícia F. N. Faísca, Miguel Machuqueiro
Published in: Journal of Chemical Information and Modeling, Issue 64, 2024, ISSN 1549-9596
Publisher: American Chemical Society (ACS)
DOI: 10.1021/ACS.JCIM.4C00880

A selection and optimization strategy for single-domain antibodies targeting the PHF6 linear peptide within the tau intrinsically disordered protein

Author(s): Justine Mortelecque, Orgeta Zejneli, Séverine Bégard, Margarida C. Simões, Lea ElHajjar, Marine Nguyen, François-Xavier Cantrelle, Xavier Hanoulle, Jean-Christophe Rain, Morvane Colin, Cláudio M. Gomes, Luc Buée, Isabelle Landrieu, Clément Danis, Elian Dupré
Published in: Journal of Biological Chemistry, Issue 300, 2024, ISSN 0021-9258
Publisher: Elsevier BV
DOI: 10.1016/J.JBC.2024.107163EXTERNALLINK

Morphological and Biophysical Study of S100A9 Protein Fibrils by Atomic Force Microscopy Imaging and Nanomechanical Analysis

Author(s): Ana P. Carapeto, Carlos Marcuello, Patrícia F. N. Faísca, Mário S. Rodrigues
Published in: Biomolecules, Issue 14, 2024, ISSN 2218-273X
Publisher: MDPI AG
DOI: 10.3390/BIOM14091091

Role of topology in protein thermal stability

Author(s): João N. C. Especial, Beatriz P. Teixeira, Ana Nunes, Miguel Machuqueiro, Patrícia F. N. Faísca
Published in: Physical Review Research, Issue 8, 2026, ISSN 2643-1564
Publisher: American Physical Society (APS)
DOI: 10.1103/9KZY-W2TZ

Sacsin deletion decreases cell viscoelasticity and motility in a glial cell model of autosomal recessive spastic ataxia of Charlevoix Saguenay

Author(s): Fernanda Murtinheira, João Belo, Ana Sofia Boasinha, Tiago T. Robalo, Vukosava M. Torres, Francisco R. Pinto, Constança Pimenta, Patricia Nascimento, Mario S. Rodrigues, Federico Herrera
Published in: Archives of Biochemistry and Biophysics, Issue 772, 2025, ISSN 0003-9861
Publisher: Elsevier BV
DOI: 10.1016/J.ABB.2025.110569

Synthesis, Activity, Toxicity, and In Silico Studies of New Antimycobacterial N-Alkyl Nitrobenzamides

Author(s): João P. Pais, Olha Antoniuk, David Pires, Tiago Delgado, Andreia Fortuna, Paulo J. Costa, Elsa Anes, Luis Constantino
Published in: Pharmaceuticals, Issue 17, 2024, ISSN 1424-8247
Publisher: MDPI AG
DOI: 10.3390/PH17050608

Amyloid-like Structures in Marine Adhesive Proteins

Author(s): Mariana Rodrigues Santos, Bárbara Joana Henriques, Romana Santos
Published in: Marine Drugs, Issue 23, 2025, ISSN 1660-3397
Publisher: MDPI AG
DOI: 10.3390/MD23090363

Secondary Modification of S100B Influences Anti Amyloid-β Aggregation Activity and Alzheimer’s Disease Pathology

Author(s): Romina Coelho, Chiara A. De Benedictis, Ann Katrin Sauer, António J. Figueira, Hélio Faustino, Andreas M. Grabrucker, Cláudio M. Gomes
Published in: International Journal of Molecular Sciences, Issue 25, 2024, ISSN 1422-0067
Publisher: MDPI AG
DOI: 10.3390/IJMS25031787

S100B Mitigates Cytoskeletal and Mitochondrial Alterations in a Glial Cell Model of Autosomal Recessive Spastic Ataxia of Charlevoix-Saguenay

Author(s): Ana Sofia Boasinha, Fernanda Murtinheira, Susana Solá, Cláudio M. Gomes, Federico Herrera
Published in: Molecular Neurobiology, Issue 62, 2025, ISSN 0893-7648
Publisher: Springer Science and Business Media LLC
DOI: 10.1007/S12035-025-05057-3

Adding the AMBER 14SB Force Field to the Stochastic Titration CpHMD Method

Author(s): João G. N. Sequeira, Adrian E. Roitberg, Miguel Machuqueiro
Published in: Journal of Chemical Theory and Computation, Issue 21, 2025, ISSN 1549-9618
Publisher: American Chemical Society (ACS)
DOI: 10.26434/CHEMRXIV-2025-38NFP

Discrete Actuation of Water‐Responsive Crystalline Metal–Peptide Frameworks

Author(s): Hui Yuan, Yiming Tang, Elma Naranjo, Pierre‐Andre Cazade, Yifei Yao, Vijayakanth Thangavel, Rusen Yang, Sigal Rencus‐Lazar, Damien Thompson, Linda J. W. Shimon, Guanghong Wei, Xi Chen, Ehud Gazit
Published in: Angewandte Chemie International Edition, Issue 64, 2025, ISSN 1433-7851
Publisher: Wiley
DOI: 10.1002/ANIE.202513629

Decoding the secrets: how conformational and structural regulators inhibit the human 20S proteasome

Author(s): Pedro M. P. Fernandes, Romina A. Guedes, Bruno L. Victor, Jorge A. R. Salvador, Rita C. Guedes
Published in: Frontiers in Chemistry, Issue 11, 2024, ISSN 2296-2646
Publisher: Frontiers Media SA
DOI: 10.3389/FCHEM.2023.1322628

Is spastic ataxia 8 a protein misfolding disorder?

Author(s): Pedro Ferreira-Peralta, Brenda França, Fernanda Murtinheira, Mario S. Rodrigues, Federico Herrera
Published in: Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease, Issue 1870, 2024, ISSN 0925-4439
Publisher: Elsevier BV
DOI: 10.1016/J.BBADIS.2023.166882

Asymmetric post-translational modifications regulate the nuclear translocation of STAT3 homodimers in response to leukemia inhibitory factor

Author(s): Mickael Diallo, Constança Pimenta, Fernanda Murtinheira, Daniela Martins-Alves, Francisco R. Pinto, André Abrantes da Costa, Ricardo Letra-Vilela, Vanesa Martin, Carmen Rodriguez, Mário S. Rodrigues, Federico Herrera
Published in: Cellular Oncology, Issue 47, 2023, ISSN 2211-3428
Publisher: Springer Science and Business Media LLC
DOI: 10.21203/RS.3.RS-3188959/V1

Unraveling the Aquaporin-3 Inhibitory Effect of Rottlerin by Experimental and Computational Approaches

Author(s): Inês Paccetti-Alves, Marta S. P. Batista, Catarina Pimpão, Bruno L. Victor, Graça Soveral
Published in: International Journal of Molecular Sciences, Issue 24, 2023, ISSN 1422-0067
Publisher: MDPI AG
DOI: 10.3390/IJMS24066004

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