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Showing 1–14 of 14 results
Advanced filters: Author: Raul Perez-Jimenez Clear advanced filters

  • The CRISPR–Cas9 system is widely studied for its role as a phage defence system and for gene editing applications, but its evolutionary origins are poorly understood. Here the authors use ancestral sequence reconstruction to determine the evolutionary history and ancient protein sequences of Streptococcus pyogenes Cas9 ancestors.

    • Borja Alonso-Lerma
    • Ylenia Jabalera
    • Raul Perez-Jimenez
    Research
    Nature Microbiology
    Volume: 8, P: 77-90

  • Exhibiting low-energy (un)folding barriers and fast kinetics, ultrafast folding proteins are enticing models to study protein dynamics. The authors use single molecule force spectroscopy AFM to capture the compliant behaviour hallmarking the dynamics of ultrafast folding proteins under force.

    • Antonio Reifs
    • Irene Ruiz Ortiz
    • Raul Perez-Jimenez
    ResearchOpen Access
    Communications Physics
    Volume: 6, P: 1-7

  • Previous investigations have indicated that the model protein CspB folds in a simple two-state fashion. Here, the authors provide direct experimental evidence for that the energy landscape of two-state folding proteins is highly heterogeneous and that unfolding can occur via multiple pathways.

    • Jörg Schönfelder
    • Raul Perez-Jimenez
    • Victor Muñoz
    ResearchOpen Access
    Nature Communications
    Volume: 7, P: 1-8

  • Using phylogenetic analysis, ancestral forms of thioredoxin reflecting the sequences likely to have existed at key evolutionary points have now been synthesized and analyzed. Single-molecule analysis indicates that all of the reconstructed enzymes use the extant reaction mechanism but that the most ancient are optimally active at low pH and resistant to higher temperatures, conditions that would have existed on early earth.

    • Raul Perez-Jimenez
    • Alvaro Inglés-Prieto
    • Julio M Fernandez
    Research
    Nature Structural & Molecular Biology
    Volume: 18, P: 592-596

  • Thioredoxins (Trxs) reduce disulfide bonds via a Michaelis-Menten mechanism. Upon substrate stretching at high forces, an SN2 reaction can be used by bacterial Trxs. A third mechanism, single-electron transfer, is now revealed in Trxs of either bacterial or eukaryotic origin, and is correlated with the depth of the Trx substrate-binding groove.

    • Raul Perez-Jimenez
    • Jingyuan Li
    • Julio M Fernandez
    Research
    Nature Structural & Molecular Biology
    Volume: 16, P: 890-896

  • The pilus type 1 of uropathogenic E. coli must resist mechanical forces to remain attached to the epithelium. Here the authors use single-molecule force spectroscopy to demonstrate a hierarchy of mechanical stability among the pilus domains and show that the oxidoreductase DsbA also acts as a folding chaperone on the domains.

    • Alvaro Alonso-Caballero
    • Jörg Schönfelder
    • Raul Perez-Jimenez
    ResearchOpen Access
    Nature Communications
    Volume: 9, P: 1-11

  • Single-molecule spectroscopy analyses of titin fragments from modern animals and reconstructed from the last common ancestors to mammals, sauropsids and tetrapods shed light on the evolution of the mechanical properties of muscle titin from the Paleozoic to our days.

    • Aitor Manteca
    • Jörg Schönfelder
    • Raul Perez-Jimenez
    Research
    Nature Structural & Molecular Biology
    Volume: 24, P: 652-657

  • Thioredoxins catalyze disulphide bond reduction in all living organisms. Single-molecule force-clamp spectroscopy has revealed that there are two alternative forms of the catalytic reaction: the first requires a reorientation of the disulphide bond in the substrate and the second involves an elongation of the disulphide bond in the substrate.

    • Arun P. Wiita
    • Raul Perez-Jimenez
    • Julio M. Fernandez
    Research
    Nature
    Volume: 450, P: 124-127

  • Enzymes are effective at chemically converting low-value biomass to technological materials. Here, an ancestral lytic polysaccharide monooxygenase enzyme is used to synthesize chitin nanocrystals, which are used as a matrix for cell growth and to create conducting graphene oxide bioinks.

    • Leire Barandiaran
    • Borja Alonso-Lerma
    • Raul Perez-Jimenez
    ResearchOpen Access
    Communications Materials
    Volume: 3, P: 1-10

  • The efficient biocatalytic processing of cellulose is a longstanding goal. Here, an ancient endogluconase is recreated using ancestral sequence reconstruction and the basis for its thermal stability and favourable catalytic properties are probed computationally.

    • Nerea Barruetabeña
    • Borja Alonso-Lerma
    • Raul Perez-Jimenez
    ResearchOpen Access
    Communications Chemistry
    Volume: 2, P: 1-13

  • Enzymes are effective at upgrading natural materials to high-performance biomaterials. Here, an ancestral endoglucanase is used to obtain highly crystalline cellulose nanocrystals, which can act as a matrix for cell growth and be combined with graphene for conducting inks.

    • Borja Alonso-Lerma
    • Leire Barandiaran
    • Raul Perez-Jimenez
    ResearchOpen Access
    Communications Materials
    Volume: 1, P: 1-10

  • Single-molecule studies of fast-folding proteins can reveal key mechanisms of folding. Here atomic force microscopy studies of single gpW proteins reveals an energetic barrier to folding induced by the low external force of 3–10 pN applied by the microscope.

    • Jörg Schönfelder
    • David De Sancho
    • Raul Perez-Jimenez
    ResearchOpen Access
    Communications Chemistry
    Volume: 1, P: 1-9