EnsembleFlex: Protein structure ensemble analysis made easy.

Schneider M, Marquez JA, Leach AR

Structure (London, England : 1993), 2025

doi:10.1016/j.str.2025.07.001.

The future of integrated structural biology.

Schwalbe H, Audergon P, Haley N, Amaro CA, Agirre J, Baldus M, Banci L, Baumeister W, Blackledge M, Carazo JM, Carugo KD, Celie P, Felli I, Hart DJ, Hauß T, Lehtiö L, Lindorff-Larsen K, Márquez J, Matagne A, Pierattelli R, Rosato A, Sobott F, Sreeramulu S, Steyaert J, Sussman JL, Trantirek L, Weiss MS, Wilmanns M

Structure (London, England : 1993), 2024

doi:10.1016/j.str.2024.08.014.

X-ray structure and enzymatic study of a bacterial NADPH oxidase highlight the activation mechanism of eukaryotic NOX.

Petit-Hartlein I, Vermot A, Thepaut M, Humm AS, Dupeux F, Dupuy J, Chaptal V, Marquez JA, Smith SME, Fieschi F

eLife, 2024

doi:10.7554/eLife.93759.

Plasticity of the binding pocket in peptide transporters underpins promiscuous substrate recognition.

Kotov V, Killer M, Jungnickel KEJ, Lei J, Finocchio G, Steinke J, Bartels K, Strauss J, Dupeux F, Humm AS, Cornaciu I, Márquez JA, Pardon E, Steyaert J, Löw C

Cell reports, 2023

doi:10.1016/j.celrep.2023.112831.

Rational design of the zonulin inhibitor AT1001 derivatives as potential anti SARS-CoV-2.

Di Micco S, Rahimova R, Sala M, Scala MC, Vivenzio G, Musella S, Andrei G, Remans K, Mammri L, Snoeck R, Bifulco G, Di Matteo F, Vestuto V, Campiglia P, Márquez JA, Fasano A

European journal of medicinal chemistry, 2022

doi:10.1016/j.ejmech.2022.114857.

Crystal structure of the Phospholipase A and acyltransferase 4 (PLAAT4) catalytic domain.

Wehlin A, Cornaciu I, Antonio Marquez J, Perrakis A, von Castelmur E

Journal of structural biology, 2022

doi:10.1016/j.jsb.2022.107903.

Inhibition of acyl-ACP thioesterase as site of action of the commercial herbicides cumyluron, oxaziclomefone, bromobutide, methyldymron and tebutam.

Johnen P, Zimmermann S, Betz M, Hendriks J, Zimmermann A, Marnet M, De I, Zimmermann G, Kibat C, Cornaciu I, Mariaule V, Pica A, Clavel D, Márquez JA, Witschel M

Pest management science, 2022

doi:10.1002/ps.7004.

Unveiling the dimer/monomer propensities of Smad MH1-DNA complexes.

Ruiz L, Kaczmarska Z, Gomes T, Aragon E, Torner C, Freier R, Baginski B, Martin-Malpartida P, de Martin Garrido N, Márquez JA, Cordeiro TN, Pluta R, Macias MJ

Computational and structural biotechnology journal, 2021

doi:10.1016/j.csbj.2020.12.044.

An automated platform for structural analysis of membrane proteins through serial crystallography.

Healey RD, Basu S, Humm AS, Leyrat C, Cong X, Golebiowski J, Dupeux F, Pica A, Granier S, Márquez JA

Cell reports methods, 2021

doi:10.1016/j.crmeth.2021.100102.

The automated crystallography pipelines at the EMBL HTX facility in Grenoble.

Cornaciu I, Bourgeas R, Hoffmann G, Dupeux F, Humm AS, Mariaule V, Pica A, Clavel D, Seroul G, Murphy P, Márquez JA

Journal of visualized experiments : JoVE, 2021

doi:10.3791/62491.

Di-phosphorylated BAF shows altered structural dynamics and binding to DNA, but interacts with its nuclear envelope partners.

Marcelot A, Petitalot A, Ropars V, Le Du MH, Samson C, Dubois S, Hoffmann G, Miron S, Cuniasse P, Marquez JA, Thai R, Theillet FX, Zinn-Justin S

Nucleic acids research, 2021

doi:10.1093/nar/gkab184.

Structural bases for the allergenicity of Fra a 1.02 in strawberry fruits.

Orozco-Navarrete B, Kaczmarska Z, Dupeux F, Garrido-Arandia M, Pott D, Perales AD, Casañal A, Márquez JA, Valpuesta V, Merchante C

Journal of agricultural and food chemistry, 2020

doi:10.1021/acs.jafc.9b05714.

Fragment-based discovery of non-bisphosphonate binders of Trypanosoma brucei farnesyl pyrophosphate synthase.

Münzker L, Petrick J, Schleberger C, Clavel D, Cornaciu I, Wilcken R, Márquez JA, Klebe G, Marzinzik A, Jahnke W

Chembiochem : a European journal of chemical biology, 2020

doi:10.1002/cbic.202000246.

Structural basis for distinct roles of SMAD2 and SMAD3 in FOXH1 pioneer-directed TGF-β signaling.

Aragón E, Wang Q, Zou Y, Morgani SM, Ruiz L, Kaczmarska Z, Su J, Torner C, Tian L, Hu J, Shu W, Agrawal S, Gomes T, Márquez JA, Hadjantonakis AK, Massagué J, Macias MJ

Genes & development, 2019

doi:10.1101/gad.330837.119.

Structural basis for genome wide recognition of 5-bp GC motifs by SMAD transcription factors.

Martin-Malpartida P, Batet M, Kaczmarska Z, Freier R, Gomes T, Aragón E, Zou Y, Wang Q, Xi Q, Ruiz L, Vea A, Márquez JA, Massagué J, Macias MJ

Nature communications, 2017

doi:10.1038/s41467-017-02054-6.

Principles and methods used to grow and optimize crystals of protein-metallodrug adducts, to determine metal binding sites and to assign metal ligands.

Russo Krauss I, Ferraro G, Pica A, Márquez JA, Helliwell JR, Merlino A

Metallomics : integrated biometal science, 2017

doi:10.1039/c7mt00219j.

Bacterial protease uses distinct thermodynamic signatures for substrate recognition.

Bezerra GA, Ohara-Nemoto Y, Cornaciu I, Fedosyuk S, Hoffmann G, Round A, Márquez JA, Nemoto TK, Djinović-Carugo K

Scientific reports, 2017

doi:10.1038/s41598-017-03220-y.

Three-dimensional structure of full-length NtrX, an unusual member of the NtrC family of response regulators.

Fernández I, Cornaciu I, Del Carmen Carrica M, Uchikawa E, Hoffmann G, Sieira R, Márquez JA, Goldbaum FA

Journal of molecular biology, 2017

doi:10.1016/j.jmb.2016.12.022.

Structure of p300 in complex with acyl-CoA variants.

Kaczmarska Z, Ortega E, Goudarzi A, Huang H, Kim S, Márquez JA, Zhao Y, Khochbin S, Panne D

Nature Chemical Biology, 2017

doi:10.1038/nchembio.2217.

Siropins, novel serine protease inhibitors from gut microbiota acting on human proteases involved in inflammatory bowel diseases.

Mkaouar H, Akermi N, Mariaule V, Boudebbouze S, Gaci N, Szukala F, Pons N, Marquez J, Gargouri A, Maguin E, Rhimi M

Microbial cell factories, 2016

doi:10.1186/s12934-016-0596-2.

Automated harvesting and processing of protein crystals through laser photoablation.

Zander U, Hoffmann G, Cornaciu I, Marquette JP, Papp G, Landret C, Seroul G, Sinoir J, Röwer M, Felisaz F, Rodriguez-Puente S, Mariaule V, Murphy P, Mathieu M, Cipriani F, Márquez JA

Acta crystallographica. Section D, Structural biology, 2016

doi:10.1107/s2059798316000954.

Calcium-dependent oligomerization of CAR proteins at cell membrane modulates ABA signaling

Diaz M, Sanchez-Barrena MJ, Gonzalez-Rubio JM, Rodriguez L, Fernandez D, Antoni R, Yunta C, Belda-Palazon B, Gonzalez-Guzman M, Peirats-Llobet M, Menendez M, Boskovic J, Marquez JA, Rodriguez PL, Albert A

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2016

doi:10.1073/pnas.1512779113.

Arc is a flexible modular protein capable of reversible self-oligomerization

Myrum C, Baumann A, Bustad HJ, Flydal MI, Mariaule V, Alvira S, Cuellar J, Haavik J, Soule J, Valpuesta JM, Marquez JA, Martinez A, Bramham CR

BIOCHEMICAL JOURNAL, 2015

doi:10.1042/BJ20141446.

C2-Domain Abscisic Acid-Related Proteins Mediate the Interaction of PYR/PYL/RCAR Abscisic Acid Receptors with the Plasma Membrane and Regulate Abscisic Acid Sensitivity in Arabidopsis.

Rodriguez L, Gonzalez-Guzman M, Diaz M, Rodrigues A, Izquierdo-Garcia AC, Peirats-Llobet M, Fernandez MA, Antoni R, Fernandez D, Marquez JA, Mulet JM, Albert A, Rodriguez PL

The Plant cell, 2014

doi:10.1105/tpc.114.129973.

A gatekeeper helix determines the substrate specificity of Sjogren-Larsson Syndrome enzyme fatty aldehyde dehydrogenase

Keller MA, Zander U, Fuchs JE, Kreutz C, Watschinger K, Mueller T, Golderer G, Liedl KR, Ralser M, Kräutler B, Werner ER, Marquez JA

Nature communications, 2014

doi:10.1038/ncomms5439.

Estimation of crystallization likelihood through a fluorimetric thermal stability assay

Mariaule V, Dupeux F, Márquez JA

Methods in molecular biology (Clifton, N.J.), 2014

doi:10.1007/978-1-62703-691-7_13.

CrystalDirect™: a novel approach for automated crystal harvesting based on photoablation of thin films

Márquez JA, Cipriani F

Methods in molecular biology (Clifton, N.J.), 2014

doi:10.1007/978-1-62703-691-7_14.

The strawberry pathogenesis-related 10 (PR-10) Fra a proteins control flavonoid biosynthesis by binding to metabolic intermediates

Casañal A, Zander U, Muñoz C, Dupeux F, Luque I, Botella MA, Schwab W, Valpuesta V, Marquez JA

The Journal of biological chemistry, 2013

doi:10.1074/jbc.m113.501528.

Purification, crystallization and preliminary X-ray analysis of the strawberry allergens Fra a 1E and Fra a 3 in the presence of catechin

Casañal A, Zander U, Dupeux F, Valpuesta V, Marquez JA

Acta crystallographica. Section F, Structural biology and crystallization communications, 2013

doi:10.1107/s1744309113006945.

Structure of the MutLα C-terminal domain reveals how Mlh1 contributes to Pms1 endonuclease site

Gueneau E, Dherin C, Legrand P, Tellier-Lebegue C, Gilquin B, Bonnesoeur P, Londino F, Quemener C, Le Du MH, Márquez JA, Moutiez M, Gondry M, Boiteux S, Charbonnier JB

Nature structural & molecular biology, 2013

doi:10.1038/nsmb.2511.

CrystalDirect: a new method for automated crystal harvesting based on laser-induced photoablation of thin films

Cipriani F, Röwer M, Landret C, Zander U, Felisaz F, Márquez JA

Acta crystallographica. Section D, Biological crystallography, 2012

doi:10.1107/s0907444912031459.

Structural insights into PYR/PYL/RCAR ABA receptors and PP2Cs

Santiago J, Dupeux F, Betz K, Antoni R, Gonzalez-Guzman M, Rodriguez L, Márquez JA, Rodriguez PL

Plant science : an international journal of experimental plant biology, 2012

doi:10.1016/j.plantsci.2010.11.014.

A thermal stability assay can help to estimate the crystallization likelihood of biological samples

Dupeux F, Röwer M, Seroul G, Blot D, Márquez JA

Acta crystallographica. Section D, Biological crystallography, 2011

doi:10.1107/s0907444911036225.

A thermodynamic switch modulates abscisic acid receptor sensitivity

Dupeux F, Santiago J, Betz K, Twycross J, Park SY, Rodriguez L, Gonzalez-Guzman M, Jensen MR, Krasnogor N, Blackledge M, Holdsworth M, Cutler SR, Rodriguez PL, Márquez JA

The EMBO journal, 2011

doi:10.1038/emboj.2011.294.

Structural characterization of filaments formed by human Xrcc4-Cernunnos/XLF complex involved in nonhomologous DNA end-joining

Ropars V, Drevet P, Legrand P, Baconnais S, Amram J, Faure G, Márquez JA, Piétrement O, Guerois R, Callebaut I, Le Cam E, Revy P, de Villartay JP, Charbonnier JB

Proceedings of the National Academy of Sciences of the United States of America, 2011

doi:10.1073/pnas.1100758108.

Modulation of abscisic acid signaling in vivo by an engineered receptor-insensitive protein phosphatase type 2C allele

Dupeux F, Antoni R, Betz K, Santiago J, Gonzalez-Guzman M, Rodriguez L, Rubio S, Park SY, Cutler SR, Rodriguez PL, Márquez JA

Plant physiology, 2011

doi:10.1104/pp.110.170894.

Atomic structure of a nanobody-trapped domain-swapped dimer of an amyloidogenic beta2-microglobulin variant

Domanska K, Vanderhaegen S, Srinivasan V, Pardon E, Dupeux F, Marquez JA, Giorgetti S, Stoppini M, Wyns L, Bellotti V, Steyaert J

Proceedings of the National Academy of Sciences of the United States of America, 2011

doi:10.1073/pnas.1008560108.

The abscisic acid receptor PYR1 in complex with abscisic acid

Santiago J, Dupeux F, Round A, Antoni R, Park SY, Jamin M, Cutler SR, Rodriguez PL, Márquez JA

Nature, 2009

doi:10.1038/nature08591.

Modulation of drought resistance by the abscisic acid receptor PYL5 through inhibition of clade A PP2Cs

Santiago J, Rodrigues A, Saez A, Rubio S, Antoni R, Dupeux F, Park SY, Márquez JA, Cutler SR, Rodriguez PL

The Plant journal : for cell and molecular biology, 2009

doi:10.1111/j.1365-313x.2009.03981.x.

Expression, crystallization and X-ray data collection from microcrystals of the extracellular domain of the human inhibitory receptor expressed on myeloid cells IREM-1

Dimasi N, Flot D, Dupeux F, Márquez JA

Acta crystallographica. Section F, Structural biology and crystallization communications, 2007

doi:10.1107/s1744309107004903.

The crystal structure of the extracellular domain of the inhibitor receptor expressed on myeloid cells IREM-1

Márquez JA, Galfré E, Dupeux F, Flot D, Moran O, Dimasi N

Journal of molecular biology, 2007

doi:10.1016/j.jmb.2007.01.011.

Plastic-embedded protein crystals

Ravelli RB, Haselmann-Weiss U, McGeehan JE, McCarthy AA, Marquez JA, Antony C, Frangakis AS, Stranzl G

Journal of synchrotron radiation, 2007

doi:10.1107/s0909049506043111.

Structure of the full-length enzyme I of the phosphoenolpyruvate-dependent sugar phosphotransferase system

Márquez J, Reinelt S, Koch B, Engelmann R, Hengstenberg W, Scheffzek K

The Journal of biological chemistry, 2006

doi:10.1074/jbc.m513721200.

The invertase inhibitor Nt-CIF from tobacco: a highly thermostable four-helix bundle with an unusual N-terminal extension

Hothorn M, D'Angelo I, Márquez JA, Greiner S, Scheffzek K

Journal of molecular biology, 2004

doi:10.1016/j.jmb.2003.10.066.

Conformation of full-length Bruton tyrosine kinase (Btk) from synchrotron X-ray solution scattering

Márquez JA, Smith CI, Petoukhov MV, Lo Surdo P, Mattsson PT, Knekt M, Westlund A, Scheffzek K, Saraste M, Svergun DI

The EMBO journal, 2003

doi:10.1093/emboj/cdg448.

Pyrophosphate-producing protein dephosphorylation by HPr kinase/phosphorylase: a relic of early life?

Mijakovic I, Poncet S, Galinier A, Monedero V, Fieulaine S, Janin J, Nessler S, Marquez JA, Scheffzek K, Hasenbein S, Hengstenberg W, Deutscher J

Proceedings of the National Academy of Sciences of the United States of America, 2002

doi:10.1073/pnas.212410399.

Evolutionary relationship between the bacterial HPr kinase and the ubiquitous PEP-carboxykinase: expanding the P-loop nucleotidyl transferase superfamily

Russell RB, Márquez JA, Hengstenberg W, Scheffzek K

FEBS letters, 2002

doi:10.1016/s0014-5793(02)02518-8.

Structure of the full-length HPr kinase/phosphatase from Staphylococcus xylosus at 1.95 A resolution: Mimicking the product/substrate of the phospho transfer reactions

Márquez JA, Hasenbein S, Koch B, Fieulaine S, Nessler S, Russell RB, Hengstenberg W, Scheffzek K

Proceedings of the National Academy of Sciences of the United States of America, 2002

doi:10.1073/pnas.052461499.

Pleckstrin homology (PH) domains

Márquez JA, Saraste M

2002

doi:10.1002/0471203076.emm0744.

Identification of Candida tropicalis HSR1, a gene of the heat-shock factor-related family, which confers salt tolerance in Saccharomyces cerevisiae.

Ali R, Pascual-Ahuir A, Marquez JA, Malik KA, Serrano R

Yeast (Chichester, England), 2001

doi:10.1002/yea.710.

A pea nuclear protein that is induced by dehydration belongs to the vicilin superfamily.

Castillo J, Rodrigo MI, Márquez JA, Zúñiga A, Franco L

European journal of biochemistry / FEBS, 2000

doi:10.1046/j.1432-1327.2000.01229.x.

The Ssn6-Tup1 repressor complex of Saccharomyces cerevisiae is involved in the osmotic induction of HOG-dependent and -independent genes

Márquez JA, Pascual-Ahuir A, Proft M, Serrano R

The EMBO journal, 1998

doi:10.1093/emboj/17.9.2543.

Multiple transduction pathways regulate the sodium-extrusion gene PMR2/ENA1 during salt stress in yeast.

Márquez JA, Serrano R

FEBS letters, 1996

doi:10.1016/0014-5793(96)00157-3.