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Design, synthesis and structural analysis of mixed α/β-peptides that adopt stable cyclic hairpin-like conformations
Tetrahedron van der Knaap M, Otero JM, Llamas-Saiz A, van Raaij MJ , Lageveen LI, Busscher HJ, Grotenbreg GM, van der Marel GA, Overkleeft HS, Overhand. The strategic replacement of four α-amino acid residues of a cyclo-(ααααα)2 peptide by β-, β2- or...
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Phytochrome-imposed oscillations in PIF3-protein abundance regulate hypocotyl growth under diurnal light-dark conditions in Arabidopsis
Plant Journal Soy J, Leivar P, González-Schain N, Sentandreu M, Prat S , Quail PH, Monte E. Arabidopsis seedlings display rhythmic growth when grown under diurnal conditions, with maximal elongation rates occurring at the end of the night in short day...
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Structural characterization of microcin E492 amyloid formation: Identification of the precursors
Journal of Structural Biology Arranz R, Mercado G, Martín-Benito J, Giraldo R, Monasterio O, Lagos R, Valpuesta JM . Microcin E492 is a low-molecular weight, channel-forming bacteriotoxin that generates amyloid structures. Using electron microscopy and...
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Architecture and nucleic acids recognition mechanism of the THO complex, an mRNP assembly factor
EMBO Journal Peña A, Gewartowski K, Mroczek S, Cuéllar J, Szykowska A, Prokop A, Czarnocki-Cieciura M, Piwowarski J, Tous C, Aguilera A, Carrascosa JL , Valpuesta JM , Dziembowski A. The THO complex is a key factor in co-transcriptional formation of...
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AUXIN BINDING PROTEIN1: the outsider
Plant Cell Sauer M , Kleine-Vehn J. AUXIN BINDING PROTEIN1 (ABP1) is one of the first characterized proteins that bind auxin and has been implied as a receptor for a number of auxin responses. Early studies characterized its auxin binding properties...
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Mitochondrial variability as a source of extrinsic cellular noise
PLoS Computational Biology Johnston IG, Gaal1 B, das Neves RP, Enver T, Iborra FJ , Jones NS. We present a study investigating the role of mitochondrial variability in generating noise in eukaryotic cells. Noise in cellular physiology plays an...
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Using DNA as a fiducial marker to study SMC complex interactions with the atomic force microscope
Biophysical Journal Fuentes-Perez ME, Gwynn EJ, Dillingham MS, Moreno-Herrero F . Atomic force microscopy can potentially provide information on protein volumes, shapes, and interactions but is susceptible to variable tip-induced artifacts. In this...
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Key role of two FtsA terminal domains in its bidirectional polymerization
Journal of Biological Chemistry Krupka M, Rivas G, Rico AI, Vicente M . The effect of two different truncations involving either the 1C domain or the simultaneous absence of the S12–13 β-strands of the FtsA protein from Streptococcus pneumoniae ,...
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Minimizing tip-sample forces in jumping mode atomic force microscopy in liquid
Ultramicroscopy Ortega-Esteban A, Horcas I, Hernando-Pérez M, Ares P, Pérez-Berná AJ, San Martín C , Carrascosa JL , de Pablo PJ, Gómez-Herrero J. Control and minimization of tip–sample interaction forces are imperative tasks to maximize the...
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Transmissible gastroenteritis coronavirus RNA-dependent RNA polymerase and nonstructural proteins 2, 3, and 8 are incorporated into viral particles
Journal of Virology Nogales A, Márquez-Jurado S, Galán C, Enjuanes L , Almazán F. Coronavirus replication and transcription are processes mediated by a protein complex, with the RNA-dependent RNA polymerase (RdRp) as a main component. Proteomic...
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Structural basis for DNA recognition and loading into a viral packaging motor
PNAS Büttner CR, Chechik M, Ortiz-Lombardía M, Smits C, Ebong IO, Chechik V, Jeschke G, Dykeman E, Benini S, Robinson CV, Alonso JC , Antson AA. Genome packaging into preformed viral procapsids is driven by powerful molecular motors. The small...
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A novel two-component system involved in the transition to secondary metabolism in Streptomyces coelicolor
PLoS ONE Rozas D, Gullón S, Mellado RP . Bacterial two-component signal transduction regulatory systems are the major set of signalling proteins frequently mediating responses to changes in the environment. They typically consist of a sensor, a...
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Insights into minor group rhinovirus uncoating: the X-ray structure of the HRV2 empty capsid
PLoS PATHOGENS Garriga D, Pickl-Herk A, Luque D, Wruss J, Castón JR , Blaas D, Verdaguer N. Upon attachment to their respective receptor, human rhinoviruses (HRVs) are internalized into the host cell via different pathways but undergo similar...
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Crystallization of the C-terminal domain of the bacteriophage T7 fibre protein gp17
Acta Crystallogr Sect F Struct Biol Cryst Commun Garcia-Doval C, van Raaij MJ . Bacteriophage T7 attaches to its host using the C-terminal domains of its six fibres, which are trimers of the gp17 protein. A C-terminal fragment of gp17 consisting of...
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The ζ Toxin Induces a Set of Protective Responses and Dormancy
PLoS ONE Lioy VS, Machon C, Tabone M, Gonzalez-Pastor JE, Daugelavicius R, Ayora S , Alonso JC . The ζε module consists of a labile antitoxin protein, ε, which in dimer form (ε(2)) interferes with the action of the long-living monomeric ζ...
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Estimation of bacterial diversity using next generation sequencing of 16S rDNA: a comparison of different workflows
BMC Bioinformatics Barriuso J, Valverde JR, Mellado RP . Next generation sequencing (NGS) enables a more comprehensive analysis of bacterial diversity from complex environmental samples. NGS data can be analysed using a variety of workflows. We test...
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Host-Range Restriction of Vaccinia Virus E3L Deletion Mutant Can Be Overcome In Vitro, but Not In Vivo, by Expression of the Influenza Virus NS1 Protein
PLoS ONE Guerra S, Abaitua F, Martínez-Sobrido L, Esteban M , García-Sastre A, Rodríguez D . During the last decades, research focused on vaccinia virus (VACV) pathogenesis has been intensified prompted by its potential beneficial application as a...
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Aberrant epigenetic regulation of bromodomain Brd4 in human colon cancer
Journal of Molecular Medicine Rodriguez RM, Huidobro C, Urdinguio RG, Mangas C, Soldevilla B, Domínguez G, Bonilla F, Fernandez AF, Fraga MF . The bromodomain protein BRD4 is involved in cell proliferation and cell cycle progression, primarily through...
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A promoter DNA demethylation landscape of human hematopoietic differentiation
Nucleic Acids Research Calvanese V, Fernández AF, Urdinguio RG, Suárez-Alvarez B, Mangas C, Pérez-García V, Bueno C, Montes R, Ramos-Mejía V, Martínez-Camblor P, Ferrero C, Assenov Y, Bock C, Menendez P, Carrera AC , Lopez-Larrea C, Fraga MF . Global...
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Epigenetics and the environment: emerging patterns and implications
Nature Reviews Genetics Feil R, Fraga MF . Epigenetic phenomena in animals and plants are mediated by DNA methylation and stable chromatin modifications. There has been considerable interest in whether environmental factors modulate the establishment...