Pau Bernado
Structure et fonction de protéines hautement flexibles
04 67 41 77 15
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Liste des publications
2024
Site-Specific Incorporation of Fluorinated Prolines into Proteins and their Impact on Neighbouring Residues
Elena-Real CA, Urbanek A, Sagar A, Mohanty P, Levy G, Morato A, Fournet A, Allemand F, Sibille N, Mittal J, Sinnaeve D, Bernado P, Chemistry, 2024
Structure of the aminoterminal domain of the birnaviral multifunctional VP3 protein and its unexplored critical role
Ferrero DS, Gimenez MC, Sagar A, Rodriguez JM, Caston JR, Terebiznik MR, Bernado P, Verdaguer N, PNAS Nexus, 2024
Weighted families of contact maps to characterize conformational ensembles of (highly-)flexible proteins
Gonzalez-Delgado J, Bernado P, Neuvial P, Cortes J, Bioinformatics, 2024
A molten globule ensemble primes Arf1-GDP for the nucleotide switch
Koduru T, Hantman N, Peters EV, Jaworek MW, Wang J, Zhang S, McCallum SA, Gillilan RE, Fossat MJ, Roumestand C, Sagar A, Winter R, Bernado P, Cherfils J, Royer CA, Proc Natl Acad Sci U S A, 2024
PED in 2024: improving the community deposition of structural ensembles for intrinsically disordered proteins
Ghafouri H, Lazar T, Del Conte A, Tenorio Ku LG, Tompa P, Tosatto SCE, Monzon AM, Aspromonte MC, Bernado P, Chaves-Arquero B, Chemes LB, Clementel D, Cordeiro TN, Elena-Real CA, Feig M, Felli IC, Ferrari C, Forman-Kay JD, Gomes T, Gondelaud F, Gradinaru CC, Ha-Duong T, Head-Gordon T, Heidarsson PO, Janson G, Jeschke G, Leonardi E, Liu ZH, Longhi S, Lund XL, Macias MJ, Martin-Malpartida P, Mercadante D, Mouhand A, Nagy G, Nugnes MV, Perez-Canadillas JM, Pesce G, Pierattelli R, Piovesan D, Quaglia F, Ricard-Blum S, Robustelli P, Sagar A, Salladini E, Senicourt L, Sibille N, Teixeira JMC, Tsangaris TE, Varadi M, Nucleic Acids Res, 2024
2023
Structure-function relationships in protein homorepeats
Elena-Real CA, Mier P, Sibille N, Andrade-Navarro MA, Bernado P, Curr Opin Struct Biol, 2023
A cyclin-dependent kinase-mediated phosphorylation switch of disordered protein condensation
Valverde JM, Dubra G, Phillips M, Haider A, Elena-Real C, Fournet A, Alghoul E, Chahar D, Andres-Sanchez N, Paloni M, Bernado P, van Mierlo G, Vermeulen M, van den Toorn H, Heck AJR, Constantinou A, Barducci A, Ghosh K, Sibille N, Knipscheer P, Krasinska L, Fisher D, Altelaar M, Nat Commun, 2023
Phosphorylation motif dictates GPCR C-terminal domain conformation and arrestin interaction
Guillien M, Mouhand A, Sagar A, Fournet A, Allemand F, Pereira GAN, Thureau A, Bernado P, Baneres JL, Sibille N, Structure, 2023
Site-Specific Introduction of Alanines for the Nuclear Magnetic Resonance Investigation of Low-Complexity Regions and Large Biomolecular Assemblies
Elena-Real CA, Urbanek A, Imbert L, Morato A, Fournet A, Allemand F, Sibille N, Boisbouvier J, Bernado P, ACS Chem Biol, 2023
Structural analysis of the Candida albicans mitochondrial DNA maintenance factor Gcf1p reveals a dynamic DNA-bridging mechanism
Tarres-Sole A, Battistini F, Gerhold JM, Pietrement O, Martinez-Garcia B, Ruiz-Lopez E, Lyonnais S, Bernado P, Roca J, Orozco M, Le Cam E, Sedman J, Sola M, Nucleic Acids Res, 2023
Multi-site-specific isotopic labeling accelerates high-resolution structural investigations of pathogenic huntingtin exon-1
Elena-Real CA, Urbanek A, Lund XL, Morato A, Sagar A, Fournet A, Estana A, Bellande T, Allemand F, Cortes J, Sibille N, Melki R, Bernado P, Structure, 2023
WASCO: A Wasserstein-based statistical tool to compare conformational ensembles of intrinsically disordered proteins
Gonzalez-Delgado J, Sagar A, Zanon C, Lindorff-Larsen K, Bernado P, Neuvial P, Cortes J, J Mol Biol, 2023
The structure of pathogenic huntingtin exon 1 defines the bases of its aggregation propensity
Elena-Real CA, Sagar A, Urbanek A, Popovic M, Morato A, Estana A, Fournet A, Doucet C, Lund XL, Shi ZD, Costa L, Thureau A, Allemand F, Swenson RE, Milhiet PE, Crehuet R, Barducci A, Cortes J, Sinnaeve D, Sibille N, Bernado P, Nat Struct Mol Biol, 2023
2022
The sequence context in poly-alanine regions: structure, function and conservation
Mier P, Elena-Real CA, Cortes J, Bernado P, Andrade-Navarro MA, Bioinformatics, 2022
Disentangling polydisperse biomolecular systems by Chemometrics decomposition of SAS data
Sagar A, Bernado P, Methods Enzymol, 2022
Statistical proofs of the interdependence between nearest neighbor effects on polypeptide backbone conformations
Gonzalez-Delgado J, Bernado P, Neuvial P, Cortes J, J Struct Biol, 2022
eIF4G1 N-terminal intrinsically disordered domain is a multi-docking station for RNA, Pab1, Pub1, and self-assembly
Chaves-Arquero B, Martinez-Lumbreras S, Sibille N, Camero S, Bernado P, Jimenez M, Zorrilla S, Perez-Canadillas JM, Front Mol Biosci, 2022
Low Complexity Induces Structure in Protein Regions Predicted as Intrinsically Disordered
Goncalves-Kulik M, Mier P, Kastano K, Cortes J, Bernado P, Schmid F, Andrade-Navarro MA, Biomolecules, 2022
Conformational buffering underlies functional selection in intrinsically disordered protein regions
Gonzalez-Foutel NS, Glavina J, Borcherds WM, Safranchik M, Barrera-Vilarmau S, Sagar A, Estana A, Barozet A, Garrone NA, Fernandez-Ballester G, Blanes-Mira C, Sanchez IE, de Prat-Gay G, Cortes J, Bernado P, Pappu RV, Holehouse AS, Daughdrill GW, Chemes LB, Nat Struct Mol Biol, 2022
Tailoring the NIR-II Photoluminescence of Single Thiolated Au25Nanoclusters by Selective Binding to Proteins
Bertorelle F, Wegner KD, Peri Bakuli M, Fakhouri H, Comby-Zerbino C, Sagar A, Bernado P, Resch-Genger U, Bonaci-Kouteck V, Le Guevel X, Antoine R, Chemistry, 2022
Structural Insights into the Intrinsically Disordered GPCR C-Terminal Region, Major Actor in Arrestin-GPCR Interaction
Guillien M, Mouhand A, Fournet A, Gontier A, Marti Navia A, Cordeiro TN, Allemand F, Thureau A, Baneres JL, Bernado P, Sibille N, Biomolecules, 2022
Molecular and cellular insight into Escherichia coli SslE and its role during biofilm maturation
Corsini PM, Wang S, Rehman S, Fenn K, Sagar A, Sirovica S, Cleaver L, Edwards-Gayle CJC, Mastroianni G, Dorgan B, Sewell LM, Lynham S, Iuga D, Franks WT, Jarvis J, Carpenter GH, Curtis MA, Bernado P, Darbari VC, Garnett JA, NPJ Biofilms Microbiomes, 2022
A FRET-Based Biosensor for the Src N-Terminal Regulatory Element
Iruela G, Fernandez A, Sagar A, Carvajal FJ, Bernado P, Pons M, Biosensors (Basel), 2022
2021
delta133p53beta isoform pro-invasive activity is regulated through an aggregation-dependent mechanism in cancer cells
Arsic N, Slatter T, Gadea G, Villain E, Fournet A, Kazantseva M, Allemand F, Sibille N, Seveno M, de Rossi S, Mehta S, Urbach S, Bourdon JC, Bernado P, Kajava AV, Braithwaite A, Roux P, Nat Commun, 2021
The diversity of molecular interactions involving intrinsically disordered proteins: A molecular modeling perspective
Clerc I, Sagar A, Barducci A, Sibille N, Bernado P, Cortes J, Comput Struct Biotechnol J, 2021
Structure and thermodynamics of transient protein-protein complexes by chemometric decomposition of SAXS datasets
Sagar A, Herranz-Trillo F, Langkilde AE, Vestergaard B, Bernado P, Structure, 2021
An integrative structural biology analysis of von Willebrand factor binding and processing by ADAMTS-13 in solution
Del Amo-Maestro L, Sagar A, Pompach P, Goulas T, Scavenius C, Ferrero DS, Castrillo-Briceno M, Taules M, Enghild JJ, Bernado P, Xavier Gomis-Ruth F, J Mol Biol, 2021
Comment on the Optimal Parameters to Derive Intrinsically Disordered Protein Conformational Ensembles from Small-Angle X-ray Scattering Data Using the Ensemble Optimization Method
Sagar A, Jeffries CM, Petoukhov MV, Svergun DI, Bernado P, J Chem Theory Comput, 2021
Interdomain linkers tailor the stability of immunoglobulin repeats in polyproteins
Joshi T, Garg S, Estana A, Cortes J, Bernado P, Das S, Kammath AR, Sagar A, Rakshit S, Biochem Biophys Res Commun, 2021
Structural Insights into the Interaction of the Intrinsically Disordered Co-activator TIF2 with Retinoic Acid Receptor Heterodimer (RXR/RAR)
Senicourt L, le Maire A, Allemand F, Carvalho JE, Guee L, Germain P, Schubert M, Bernado P, Bourguet W, Sibille N, J Mol Biol, 2021
PED in 2021: a major update of the protein ensemble database for intrinsically disordered proteins
Lazar T, Martinez-Perez E, Quaglia F, Hatos A, Chemes LB, Iserte JA, Mendez NA, Garrone NA, Saldano TE, Marchetti J, Rueda AJV, Bernado P, Blackledge M, Cordeiro TN, Fagerberg E, Forman-Kay JD, Fornasari MS, Gibson TJ, Gomes GW, Gradinaru CC, Head-Gordon T, Jensen MR, Lemke EA, Longhi S, Marino-Buslje C, Minervini G, Mittag T, Monzon AM, Pappu RV, Parisi G, Ricard-Blum S, Ruff KM, Salladini E, Skepo M, Svergun D, Vallet SD, Varadi M, Tompa P, Tosatto SCE, Piovesan D, Nucleic Acids Res, 2021
2020
Robust Cell-Free Expression of Sub-Pathological and Pathological Huntingtin Exon-1 for NMR Studies. General Approaches for the Isotopic Labeling of Low-Complexity Proteins
Morato A, Elena-Real CA, Popovic M, Fournet A, Zhang K, Allemand F, Sibille N, Urbanek A, Bernado P, Biomolecules, 2020
Predicting Secondary Structure Propensities in IDPs Using Simple Statistics from Three-Residue Fragments
Estana A, Barozet A, Mouhand A, Vaisset M, Zanon C, Fauret P, Sibille N, Bernado P, Cortes J, J Mol Biol, 2020
Flanking Regions Determine the Structure of the Poly-Glutamine in Huntingtin through Mechanisms Common among Glutamine-Rich Human Proteins
Urbanek A, Popovic M, Morato A, Estana A, Elena-Real CA, Mier P, Fournet A, Allemand F, Delbecq S, Andrade-Navarro MA, Cortes J, Sibille N, Bernado P, Structure, 2020
Evidence of the Reduced Abundance of Proline cis Conformation in Protein Poly Proline Tracts
Urbanek A, Popovic M, Elena-Real CA, Morato A, Estana A, Fournet A, Allemand F, Gil AM, Cativiela C, Cortes J, Jimenez AI, Sibille N, Bernado P, J Am Chem Soc, 2020
Integrative Biophysics: Protein Interaction and Disorder
Yang S, Bernado P, J Mol Biol, 2020
Disentangling the complexity of low complexity proteins
Mier P, Paladin L, Tamana S, Petrosian S, Hajdu-Soltesz B, Urbanek A, Gruca A, Plewczynski D, Grynberg M, Bernado P, Gaspari Z, Ouzounis CA, Promponas VJ, Kajava AV, Hancock JM, Tosatto SCE, Dosztanyi Z, Andrade-Navarro MA, Brief Bioinformatics, 2020
Site-Specific Isotopic Labeling (SSIL) - Access to High-Resolution Structural and Dynamic Information in Low Complexity Proteins
Urbanek A, Elena-Real CA, Popovic M, Morato A, Fournet A, Allemand F, Delbecq S, Sibille N, Bernado P, Chembiochem, 2020
Molecular basis for fibroblast growth factor 23 O-glycosylation by GalNAc-T3
de Las Rivas M, Paul Daniel EJ, Narimatsu Y, Companon I, Kato K, Hermosilla P, Thureau A, Ceballos-Laita L, Coelho H, Bernado P, Marcelo F, Hansen L, Maeda R, Lostao A, Corzana F, Clausen H, Gerken TA, Hurtado-Guerrero R, Nat Chem Biol, 2020
Structural Characterization of Protein-Protein Interactions with pyDockSAXS
Jimenez-Garcia B, Bernado P, Fernandez-Recio J, Methods Mol Biol, 2020
The importance of definitions in the study of polyQ regions: A tale of thresholds, impurities and sequence context
Mier P, Elena-Real C, Urbanek A, Bernado P, Andrade-Navarro MA, Comput Struct Biotechnol J, 2020
IDPs and their complexes in GPCR and nuclear receptor signaling
Guillien M, le Maire A, Mouhand A, Bernado P, Bourguet W, Baneres JL, Sibille N, Prog Mol Biol Transl Sci, 2020
Structural Analyses of Intrinsically Disordered Proteins by Small-Angle X-Ray Scattering
Sagar A, Svergun D, Bernado P, Methods Mol Biol, 2020
2019
Double Monoubiquitination Modifies the Molecular Recognition Properties of p15
Gonzalez-Magana A, de Opakua AI, Merino N, Monteiro H, Diercks T, Murciano-Calles J, Luque I, Bernado P, Cordeiro TN, Biasio A, Blanco FJ, ACS Chem Biol, 2019
Interplay of Protein Disorder in Retinoic Acid Receptor Heterodimer and Its Corepressor Regulates Gene Expression
Cordeiro TN, Sibille N, Germain P, Barthe P, Boulahtouf A, Allemand F, Bailly R, Vivat V, Ebel C, Barducci A, Bourguet W, le Maire A, Bernado P, Structure, 2019
Oncogenic mutations at the EGFR ectodomain structurally converge to remove a steric hindrance on a kinase-coupled cryptic epitope
Orellana L, Thorne AH, Lema R, Gustavsson J, Parisian AD, Hospital A, Cordeiro TN, Bernado P, Scott AM, Brun-Heath I, Lindahl E, Cavenee WK, Furnari FB, Orozco M, Proc Natl Acad Sci USA, 2019
Investigating the Formation of Structural Elements in Proteins Using Local Sequence-Dependent Information and a Heuristic Search Algorithm
Estana A, Ghallab M, Bernado P, Cortes J, Molecules, 2019
Realistic Ensemble Models of Intrinsically Disordered Proteins Using a Structure-Encoding Coil Database
Estana A, Sibille N, Delaforge E, Vaisset M, Cortes J, Bernado P, Structure, 2019
2018
Hybrid parallelization of a multi-tree path search algorithm: Application to highly-flexible biomolecules
Estana A, Molloy K, Vaisset M, Sibille S, Simeon T, Bernado P, Cortes J, Parallel computing, 2018
Protein Flexibility and Synergy of HMG Domains Underlie U-Turn Bending of DNA by TFAM in Solution
Rubio-Cosials A, Battistini F, Gansen A, Cuppari A, Bernado P, Orozco M, Langowski J, Toth K, Sola M, Biophys J, 2018
A General Strategy to Access Structural Information at Atomic Resolution in Polyglutamine Homorepeats
Urbanek A, Morato A, Allemand F, Delaforge E, Fournet A, Popovic M, Delbecq S, Sibille N, Bernado P, Angew Chem Int Ed Engl, 2018
Solution scattering approaches to dynamical ordering in biomolecular systems
Bernado P, Shimizu N, Zaccai G, Kamikubo H, Sugiyama M, Biochim Biophys Acta, 2018
A General Strategy to Access Atomic Resolution Structural Information in Poly-Glutamine Homo-Repeats
Bernado P, Urbanek A, Morato A, Allemand F, Delaforge E, Fournet A, Popovic M, Delbecq S, Sibille N, Angew Chem Int Ed Engl, 2018
Noninvasive Structural Analysis of Intermediate Species During Fibrillation: An Application of Small-Angle X-Ray Scattering
Langkilde AE, Herranz-Trillo F, Bernado P, Vestergaard B, Methods Mol Biol, 2018
2017
Disulfide driven folding for a conditionally disordered protein
Fraga H, Pujols J, Gil-Garcia M, Roque A, Bernardo-Seisdedos G, Santambrogio C, Bech-Serra JJ, Canals F, Bernado P, Grandori R, Millet O, Ventura S, Sci Rep, 2017
The Unique Domain Forms a Fuzzy Intramolecular Complex in Src Family Kinases
Arbesu M, Maffei M, Cordeiro TN, Teixeira JM, Perez Y, Bernado P, Roche S, Pons M, Structure, 2017
Disentangling polydispersity in the PCNA-p15PAF complex, a disordered, transient and multivalent macromolecular assembly
Cordeiro TN, Chen PC, De Biasio A, Sibille N, Blanco FJ, Hub JS, Crehuet R, Bernado P, Nucleic Acids Res, 2017
Small-angle scattering studies of intrinsically disordered proteins and their complexes
Cordeiro TN, Herranz-Trillo F, Urbanek A, Estana A, Cortes J, Sibille N, Bernado P, Curr Opin Struct Biol, 2017
Structural Analysis of Multi-component Amyloid Systems by Chemometric SAXS Data Decomposition
Herranz-Trillo F, Groenning M, van Maarschalkerweerd A, Tauler R, Vestergaard B, Bernado P, Structure, 2017
Conformational Characterization of Intrinsically Disordered Proteins and Its Biological Significance
Delaforge E, Cordeiro TN, Bernado P, Sibille N, Modern Magnetic Resonance, 2017
Structural Characterization of Highly Flexible Proteins by Small-Angle Scattering
Cordeiro TN, Herranz-Trillo F, Urbanek A, Estana A, Cortes J, Sibille N, Bernado P, Adv Exp Med Biol, 2017
The metastasis suppressor KISS1 is an intrinsically disordered protein slightly more extended than a random coil
Ibanez de Opakua A, Merino N, Villate M, Cordeiro TN, Ormaza G, Sanchez-Carbayo M, Diercks T, Bernado P, Blanco FJ, PLoS ONE, 2017
2016
Ensemble Structure of the Highly Flexible Complex Formed between Vesicular Stomatitis Virus Unassembled Nucleoprotein and its Phosphoprotein Chaperone
Yabukarksi F, Leyrat C, Martinez N, Communie G, Ivanov I, Ribeiro EA, Buisson M, Gerard FC, Bourhis JM, Jensen MR, Bernado P, Blackledge M, Jamin M, J Mol Biol, 2016
Ensemble Structure of the Highly Flexible Complex Formed between Vesicular Stomatitis Virus Unassembled Nucleoprotein and its Phosphoprotein Chaperone
Yabukarski F, Leyrat C, Martinez N, Communie G, Ivanov I, Ribeiro EA, Buisson M, Gerard FC, Bourhis JM, Jensen MR, Bernado P, Blackledge M, Jamin M, J Mol Biol, 2016
Active Site-Directed Inhibitors of Prolyl Oligopeptidase Abolishes its Conformational Dynamics
Lopez A, Herranz-Trillo F, Kotev M, Gairi M, Guallar V, Bernado P, Millet O, Tarrago T, Giralt E, Chembiochem, 2016
2015
Dynamic interplay between catalytic and lectin domains of GalNAc-transferases modulates protein O-glycosylation
Lira-Navarrete E, de Las Rivas M, Companon I, Pallares MC, Kong Y, Iglesias-Fernandez J, Bernardes GJ, Peregrina JM, Rovira C, Bernado P, Bruscolini P, Clausen H, Lostao A, Corzana F, Hurtado-Guerrero R, Nat Commun, 2015
Structure of p15(PAF)-PCNA complex and implications for clamp sliding during DNA replication and repair
De Biasio A, de Opakua AI, Mortuza GB, Molina R, Cordeiro TN, Castillo F, Villate M, Merino N, Delgado S, Gil-Carton D, Luque I, Diercks T, Bernado P, Montoya G, Blanco FJ, Nat Commun, 2015
pyDockSAXS: protein-protein complex structure by SAXS and computational docking
Jimenez-Garcia B, Pons C, Svergun DI, Bernado P, Fernandez-Recio J, Nucleic Acids Res, 2015
A Three-protein Charge Zipper Stabilizes a Complex Modulating Bacterial Gene Silencing
Cordeiro TN, Garcia J, Bernado P, Millet O, Pons M, J Biol Chem, 2015
The hexameric structure of the human mitochondrial replicative helicase Twinkle
Fernandez-Millan P, Lazaro M, Cans1z-Arda S, Gerhold JM, Rajala N, Schmitz CA, Silva-Espina C, Gil D, Bernado P, Valle M, Spelbrink JN, Sola M, Nucleic Acids Res, 2015
2014
Multiple Stable Conformations Account for Reversible Concentration-Dependent Oligomerization and Autoinhibition of a Metamorphic Metallopeptidase
Lopez-Pelegrin M, Cerda-Costa N, Cintas-Pedrola A, Herranz-Trillo F, Bernado P, Peinado JR, Arolas JL, Gomis-Ruth FX, Angew Chem Int Ed Engl, 2014
p15(PAF) Is an Intrinsically Disordered Protein with Nonrandom Structural Preferences at Sites of Interaction with Other Proteins
De Biasio A, Ibanez de Opakua A, Cordeiro TN, Villate M, Merino N, Sibille N, Lelli M, Diercks T, Bernado P, Blanco FJ, Biophys J, 2014
2013
Hinged plakin domains provide specialized degrees of articulation in envoplakin, periplakin and desmoplakin
Al-Jassar C, Bernado P, Chidgey M, Overduin M, PLoS One, 2013
Lipid binding by the Unique and SH3 domains of c-Src suggests a new regulatory mechanism
Perez Y, Maffei M, Igea A, Amata I, Gairi M, Nebreda AR, Bernado P, Pons M, Sci Rep, 2013
Conformational transitions in human translin enable nucleic acid binding
Perez-Cano L, Eliahoo E, Lasker K, Wolfson HJ, Glaser F, Manor H, Bernado P, Fernandez-Recio J, Nucleic Acids Res, 2013
2012
Analysis of intrinsically disordered proteins by small-angle X-ray scattering
Bernado P, Svergun DI, Methods Mol Biol, 2012
Structural analysis of intrinsically disordered proteins by small-angle X-ray scattering.
Bernado P, Svergun DI, Mol Biosyst, 2012
Defining the nature of thermal intermediate in 3 state folding proteins: apoflavodoxin, a study case
Garcia-Fandino R, Bernado P, Ayuso-Tejedor S, Sancho J, Orozco M, PLoS Comput Biol, 2012
Flexible-meccano: a tool for the generation of explicit ensemble descriptions of intrinsically disordered proteins and their associated experimental observables.
Ozenne V, Bauer F, Salmon L, Huang JR, Jensen MR, Segard S, Bernado P, Charavay C, Blackledge M, Bioinformatics, 2012
Measurement and analysis of NMR residual dipolar couplings for the study of intrinsically disordered proteins
Salmon L, Jensen MR, Bernado P, Blackledge M, Methods Mol Biol, 2012
Structural characterization of intrinsically disordered proteins by the combined use of NMR and SAXS.
Sibille N, Bernado P, Biochem. Soc. Trans., 2012
2011
Studying partially folded and intrinsically disordered proteins using NMR residual dipolar couplings.
Jensen MR, Ozenne V, Nodet G, Markwick P, Bernado P, Blackledge M, Handbook on protein NMR, 2011
Human mitochondrial transcription factor A induces a U-turn structure in the light strand promoter
Rubio-Cosials A, Sidow JF, Jimenez-Menendez N, Fernandez-Millan P, Montoya J, Jacobs HT, Coll M, Bernado P, Sola M, Nat Struct Mol Biol, 2011
Indirect DNA Readout by an H-NS Related Protein: Structure of the DNA Complex of the C-Terminal Domain of Ler
Cordeiro TN, Schmidt H, Madrid C, Juarez A, Bernado P, Griesinger C, Garcia J, Pons M, PLoS pathogens, 2011
Protein loop compaction and the origin of the effect of arginine and glutamic acid mixtures on solubility, stability and transient oligomerization of proteins
Blobel J, Brath U, Bernado P, Diehl C, Ballester L, Sornosa A, Akke M, Pons M, Eur Biophys J, 2011
Structural analysis of an equilibrium folding intermediate in the apoflavodoxin native ensemble by small-angle X-ray scattering
Ayuso-Tejedor S, Garcia-Fandino R, Orozco M, Sancho J, Bernado P, J Mol Biol, 2011
Indirect DNA readout by an H-NS related protein: structure of the DNA complex of the C-terminal domain of Ler
Cordeiro TN, Schmidt H, Madrid C, Juarez A, Bernado P, Griesinger C, Garcia J, Pons M, PLoS Pathog, 2011
2010
Structural disorder within sendai virus nucleoprotein and phosphoprotein: insight into the structural basis of molecular recognition
Jensen MR, Bernado P, Houben K, Blanchard L, Marion D, Ruigrok RW, Blackledge M, Protein Pept Lett, 2010
Structural characterization of protein-protein complexes by integrating computational docking with small-angle scattering data
Pons C, D'Abramo M, Svergun DI, Orozco M, Bernado P, Fernandez-Recio J, J Mol Biol, 2010
The dimeric structure and the bivalent recognition of H3K4me3 by the tumor suppressor ING4 suggests a mechanism for enhanced targeting of the HBO1 complex to chromatin
Palacios A, Moreno A, Oliveira BL, Rivera T, Prieto J, Garcia P, Fernandez-Fernandez MR, Bernado P, Palmero I, Blanco FJ, J Mol Biol, 2010
Human mitochondrial mTERF wraps around DNA through a left-handed superhelical tandem repeat
Jimenez-Menendez N, Fernandez-Millan P, Rubio-Cosials A, Arnan C, Montoya J, Jacobs HT, Bernado P, Coll M, Uson I, Sola M, Nat Struct Mol Biol, 2010
Structure and Dynamics of Ribosomal Protein L12: An Ensemble Model Based on SAXS and NMR Relaxation
Bernado P, Modig K, Grela P, Svergun DI, Tchorzewski M, Pons M, Akke M, Biophys J, 2010
Structural biology: Proteins in dynamic equilibrium
Bernado P, Blackledge M, Nature, 2010
Low resolution structural approaches to multi-protein assemblies
Bernado P, Wiley Interdisciplinary Reviews: Computational Molecular Science (WIREs:CMS), 2010
Effect of interdomain dynamics on the structure determination of modular proteins by small-angle scattering
Bernado P, Eur Biophys J, 2010
Design and structure of an equilibrium protein folding intermediate: a hint into dynamical regions of proteins
Ayuso-Tejedor S, Angarica VE, Bueno M, Campos LA, Abian O, Bernado P, Sancho J, Jimenez MA, J Mol Biol, 2010
2009
Dynamic interactions of proteins in complex networks: a more structured view
Stein A, Pache RA, Bernado P, Pons M, Aloy P, Febs J, 2009
Structural characterization of the natively unfolded N-terminal domain of human c-Src kinase: insights into the role of phosphorylation of the unique domain
Perez Y, Gairi M, Pons M, Bernado P, J Mol Biol, 2009
Quantitative determination of the conformational properties of partially folded and intrinsically disordered proteins using NMR dipolar couplings
Jensen MR, Markwick PR, Meier S, Griesinger C, Zweckstetter M, Grzesiek S, Bernado P, Blackledge M, Structure, 2009
ProtSA: a web application for calculating sequence specific protein solvent accessibilities in the unfolded ensemble
Estrada J, Bernado P, Blackledge M, Sancho J, BMC Bioinformatics, 2009
Structural characterization of alpha-synuclein in an aggregation prone state
Cho MK, Nodet G, Kim HY, Jensen MR, Bernado P, Fernandez CO, Becker S, Blackledge M, Zweckstetter M, Protein Sci, 2009
Weak oligomerization of low-molecular-weight protein tyrosine phosphatase is conserved from mammals to bacteria
Blobel J, Bernado P, Xu H, Jin C, Pons M, Febs J, 2009
Low-resolution structures of transient protein-protein complexes using small-angle X-ray scattering
Blobel J, Bernado P, Svergun DI, Tauler R, Pons M, J Am Chem Soc, 2009
Structural characterization of unphosphorylated STAT5a oligomerization equilibrium in solution by small-angle X-ray scattering
Bernado P, Perez Y, Blobel J, Fernandez-Recio J, Svergun DI, Pons M, Protein Sci, 2009
A self-consistent description of the conformational behavior of chemically denatured proteins from NMR and small angle scattering
Bernado P, Blackledge M, Biophys J, 2009
On the use of low resolution data to improve structure prediction of proteins and protein complexes
DaAbramo M, Meyer T, Bernado P, Pons C, Fernandez-Recio J, Orozco M, J Chem Theo Comput, 2009
2008
Structural characterization of the active and inactive states of Src kinase in solution by small-angle X-ray scattering
Bernado P, Perez Y, Svergun DI, Pons M, J Mol Biol, 2008
Interaction of human complement with Sbi, a staphylococcal immunoglobulin-binding protein: indications of a novel mechanism of complement evasion by Staphylococcus aureus
Burman JD, Leung E, Atkins KL, O'Seaghdha MN, Lango L, Bernado P, Bagby S, Svergun DI, Foster TJ, Isenman DE, van den Elsen JM, J Biol Chem, 2008
Structural relationships among the ribosomal stalk proteins from the three domains of life
Grela P, Bernado P, Svergun D, Kwiatowski J, Abramczyk D, Grankowski N, Tchorzewski M, J Mol Evol, 2008
Domain conformation of tau protein studied by solution small-angle X-ray scattering
Mylonas E, Hascher A, Bernado P, Blackledge M, Mandelkow E, Svergun DI, Biochemistry, 2008
2007
Structural characterization of flexible proteins using small-angle X-ray scattering
Bernado P, Mylonas E, Petoukhov MV, Blackledge M, Svergun DI, J Am Chem Soc, 2007
Protein tyrosine phosphatase oligomerization studied by a combination of 15N NMR relaxation and 129Xe NMR. Effect of buffer containing arginine and glutamic acid
Blobel J, Schmidl S, Vidal D, Nisius L, Bernado P, Millet O, Brunner E, Pons M, J Am Chem Soc, 2007
Amino acid bulkiness defines the local conformations and dynamics of natively unfolded alpha-synuclein and tau
Cho MK, Kim HY, Bernado P, Fernandez CO, Blackledge M, Zweckstetter M, J Am Chem Soc, 2007
Structural characterization of the ribosomal P1A-P2B protein dimer by small-angle X-ray scattering and NMR spectroscopy
Grela P, Helgstrand M, Krokowski D, Boguszewska A, Svergun D, Liljas A, Bernado P, Grankowski N, Akke M, Tchorzewski M, Biochemistry, 2007
Highly populated turn conformations in natively unfolded tau protein identified from residual dipolar couplings and molecular simulation
Mukrasch MD, Markwick P, Biernat J, Bergen M, Bernado P, Griesinger C, Mandelkow E, Zweckstetter M, Blackledge M, J Am Chem Soc, 2007
2006
Residual dipolar couplings in short peptides reveal systematic conformational preferences of individual amino acids
Dames SA, Aregger R, Vajpai N, Bernado P, Blackledge M, Grzesiek S, J Am Chem Soc, 2006
Sequence-specific solvent accessibilities of protein residues in unfolded protein ensembles
Bernado P, Blackledge M, Sancho J, Biophys J, 2006
2005
Defining long-range order and local disorder in native alpha-synuclein using residual dipolar couplings
Bernado P, Bertoncini CW, Griesinger C, Zweckstetter M, Blackledge M, J Am Chem Soc, 2005
A structural model for unfolded proteins from residual dipolar couplings and small-angle x-ray scattering
Bernado P, Blanchard L, Timmins P, Marion D, Ruigrok RW, Blackledge M, Proc Natl Acad Sci U S A, 2005
Protein backbone dynamics from N-HN dipolar couplings in partially aligned systems: a comparison of motional models in the presence of structural noise
Bouvignies G, Bernado P, Blackledge M, J Magn Reson, 2005
Identification of slow correlated motions in proteins using residual dipolar and hydrogen-bond scalar couplings
Bouvignies G, Bernado P, Meier S, Cho K, Grzesiek S, Bruschweiler R, Blackledge M, Proc Natl Acad Sci U S A, 2005
Hydrodynamic models and computational methods for NMR relaxation
Garcia de la Torre J, Bernado P, Pons M, Methods Enzymol, 2005
2004
Anisotropic small amplitude Peptide plane dynamics in proteins from residual dipolar couplings
Bernado P, Blackledge M, J Am Chem Soc, 2004
Local dynamic amplitudes on the protein backbone from dipolar couplings: toward the elucidation of slower motions in biomolecules
Bernado P, Blackledge M, J Am Chem Soc, 2004
Interpretation of NMR relaxation properties of Pin1, a two-domain protein, based on Brownian dynamic simulations
Bernado P, Fernandes MX, Jacobs DM, Fiebig K, Garcia de la Torre J, Pons M, J Biomol NMR, 2004
Macromolecular crowding in biological systems: hydrodynamics and NMR methods
Bernado P, Garcia de la Torre J, Pons M, J Mol Recognit, 2004
2003
Combined use of NMR relaxation measurements and hydrodynamic calculations to study protein association. Evidence for tetramers of low molecular weight protein tyrosine phosphatase in solution
Bernado P, Akerud T, Garcia de la Torre J, Akke M, Pons M, J Am Chem Soc, 2003
Peptide binding induces large scale changes in inter-domain mobility in human Pin1
Jacobs DM, Saxena K, Vogtherr M, Bernado P, Pons M, Fiebig KM, J Biol Chem, 2003
2002
Lanthanide modulation of the orientation of macromolecules induced by purple membrane
Bernado P, Barbieri R, Padros E, Luchinat C, Pons M, J Am Chem Soc, 2002
Interpretation of 15N NMR relaxation data of globular proteins using hydrodynamic calculations with HYDRONMR
Bernado P, Garcia de la Torre J, Pons M, J Biomol NMR, 2002
NMR measurement of the off rate from the first calcium-binding site of the synaptotagmin I C2A domain
Millet O, Bernado P, Garcia J, Rizo J, Pons M, FEBS Lett, 2002