Integrative Conformational Ensembles of Sic1 Using Different Initial Pools and Optimization Methods

Autor: Gregory-Neal W. Gomes, Ashley Namini, Claudiu C. Gradinaru

Publikováno v: Frontiers in Molecular Biosciences, Vol 9 (2022)

Intrinsically disordered proteins play key roles in regulatory protein interactions, but their detailed structural characterization remains challenging. Here we calculate and compare conformational ensembles for the disordered protein Sic1 from yeast

Externí odkaz: https://doaj.org/article/d0b02bef31d5493c950fd75b93ab2a8d

Ligand modulation of the conformational dynamics of the A2A adenosine receptor revealed by single-molecule fluorescence

Autor: Claudiu C. Gradinaru, Gregory-Neal W. Gomes, Aimen Malik, Alexander P. Orazietti, Aditya Pandey, Dennis D. Fernandes, Chris Neale, Libin Ye, Xudong Wang, Yuchong Li, R. Scott Prosser

Publikováno v: Scientific Reports, Vol 11, Iss 1, Pp 1-16 (2021)

G protein-coupled receptors (GPCRs) are the largest class of transmembrane proteins, making them an important target for therapeutics. Activation of these receptors is modulated by orthosteric ligands, which stabilize one or several states within a c

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::229f39b61615c1d868bea3ff9c6ae4f5
https://doaj.org/article/1d5a6aaa4ef3450b9bd0c50f9ac512ec

PED in 2021: a major update of the protein ensemble database for intrinsically disordered proteins

Autor: Kiersten M. Ruff, Tamas Lazar, Claudiu C. Gradinaru, María Silvina Fornasari, Silvio C. E. Tosatto, Javier Iserte, Marie Skepö, Julia Marchetti, Sonia Longhi, Teresa Head-Gordon, Toby J. Gibson, Nicolás A. Méndez, Gregory-Neal W. Gomes, Malene Ringkjøbing Jensen, Nicolás A. Garrone, Pau Bernadó, Martin Blackledge, Alexander Miguel Monzon, Dmitri I. Svergun, András Hatos, Julie D. Forman-Kay, Cristina Marino-Buslje, Edward A. Lemke, Eric Fagerberg, Ana Julia Velez Rueda, Sylvain D. Vallet, Elizabeth Martínez-Pérez, Sylvie Ricard-Blum, Tiago N. Cordeiro, Federica Quaglia, Tadeo E. Saldaño, Damiano Piovesan, Peter Tompa, Tanja Mittag, Gustavo Parisi, Mihaly Varadi, Rohit V. Pappu, Lucía B. Chemes, Giovanni Minervini, Edoardo Salladini

Publikováno v: Nucleic Acids Research
Nucleic Acids Research, Oxford University Press, 2021, 49 (D1), pp.D404-D411. ⟨10.1093/nar/gkaa1021⟩
Nucleic acids research, vol 49, iss D1
Nucleic Acids Research, 2021, 49 (D1), pp.D404-D411. ⟨10.1093/nar/gkaa1021⟩
Nucleic Acids Research, Oxford University Press, In press, ⟨10.1093/nar/gkaa1021⟩
Nucleic Acids Research, In press, ⟨10.1093/nar/gkaa1021⟩

The Protein Ensemble Database (PED) (https://proteinensemble.org), which holds structural ensembles of intrinsically disordered proteins (IDPs), has been significantly updated and upgraded since its last release in 2016. The new version, PED 4.0, has

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d62579a66daeda9d1cb3ef52f41885bf
https://hal.univ-grenoble-alpes.fr/hal-03433964/document

Ligand Modulation of the Conformational Dynamics of the A2A Adenosine Receptor Revealed by Single-Molecule Fluorescence

Autor: Aimen Malik, Alexander P. Orazietti, Xudong Wang, Aditya Pandey, Dennis D. Fernandes, Claudiu C. Gradinaru, Scott Prosser, Yuchong Li, Chris Neale, Libin Ye, Gregory-Neal W. Gomes

G protein-coupled receptors (GPCRs) are the largest class of transmembrane proteins, making them an important target for therapeutics. Activation of these receptors is modulated by orthosteric ligands, which stabilize one or several states within a c

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::ff1903f8fd605263e1f6d3f85a98cc01
https://doi.org/10.1101/2020.09.20.305425

Integrating multiple experimental data to determine conformational ensembles of an intrinsically disordered protein

Autor: Gregory-Neal W. Gomes, Julie D. Forman-Kay, Mickael Krzeminski, Ashley Namini, Claudiu C. Gradinaru, Teresa Head-Gordon, Tanja Mittag, Erik W. Martin

Intrinsically disordered proteins (IDPs) have fluctuating heterogeneous conformations, which makes structural characterization challenging. Although challenging, characterizing the conformational ensembles of IDPs is of great interest, since their co

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d4e31c0e7c8e17ebc098ff74c4e431f7