Browsing by Author "De Sancho, David"
Now showing items 1-11 of 11
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Atomistic molecular simulations of Aβ-Zn conformational ensembles
Aduriz Arrizabalaga, Julen; López de Pariza Sanz, Xabier; De Sancho Sánchez, David (Wiley, 2024-01)The amyloid-forming Aβ peptide is able to interact with metal cations to form very stable complexes that influence fibril formation and contribute to the onset of Alzheimer's disease. Multiple structures of peptides derived ... -
Competitive binding of HIF-1α and CITED2 to the TAZ1 domain of CBP from molecular simulations
Ruiz Ortiz, Irene; De Sancho Sánchez, David (RSC, 2020-04-03)Many intrinsically disordered proteins (IDPs) are involved in complex signalling networks inside the cell. Their particular binding modes elicit different types of responses that can be subtly regulated. Here we study the ... -
Compliant mechanical response of the ultrafast folding protein EnHD under force
Reifs, Antonio; Ruiz Ortiz, Irene; Ochandorena Saa, Amaia; Schönfelder, Jörg; De Sancho Sánchez, David; Muñoz, Víctor; Pérez Jiménez, Raúl (Nature, 2023-02)Ultrafast folding proteins have become an important paradigm in the study of protein folding dynamics. Due to their low energetic barriers and fast kinetics, they are amenable for study by both experiment and simulation. ... -
Design of ancestral enzymes for engineering nanobiomaterials.
Barandiaran Larrea, Leyre (2019-12-16)La mejora de las enzimas para su uso industrial, donde las condiciones no son las naturales de las enzimas, es fundamental si queremos que operen de una forma eficiente. En esta tesis utilizamos una técnica llamada ... -
High-throughput virtual search of small molecules for controlling the mechanical stability of human CD4
Reifs, Antonio; Fernández Calvo, Alba; Alonso Lerma, Borja; Schönfelder, Jörg; Franco, David; Ortega Muñoz, Mariano; Casares, Salvador; Jiménez López, Concepción; Saa, Laura; López Cortajarena, Aitziber ; De Sancho Sánchez, David; San Sebastián Larzabal, Eider ; Pérez Jiménez, Raul (Elsevier, 2024-04)Protein mechanical stability determines the function of a myriad of proteins, especially proteins from the extracellular matrix. Failure to maintain protein mechanical stability may result in diseases and disorders such ... -
Mechanochemical evolution of the giant muscle protein tititn as inferred from resurrecter proteins
Manteca González, Aitor (2017-07-07)The sarcomere-based structure of muscles is conserved among vertebrates; however, vertebrate muscle physiology is extremely diverse. A molecular explanation for this muscle diversity and its evolution has not been proposed. ... -
Phase separation in amino acid mixtures is governed by composition
De Sancho Sánchez, David (Cell Press, 2022-11)Macromolecular phase separation has recently come to immense prominence as it is central to the formation of membraneless organelles, leading to a new paradigm of cellular organization. This type of phase transition, often ... -
Protein nanomechanics: from fast-folding proteins to microbial infections
Reifs Carmona, Antonio (2023-09-21)Esta tesis explora los límites de la técnica de SMFS (Single-molecule force spectroscopy) AFM (atomicforce microscopy), estudiando la estabilidad mecánica de proteínas en todo su espectro, desde las lábiles proteínas de ... -
Rules governing metal coordination in Aβ–Zn(ii) complex models from quantum mechanical calculations
Aduriz Arrizabalaga, Julen; Mercero Larraza, José María ; De Sancho Sánchez, David; López de Pariza Sanz, Xabier (RSC, 2023-10)Transition metals directly contribute to the neurotoxicity of the aggregates of the amyloid-forming Aβ peptide. The understanding and rationalization of the coordination modes of metals to Aβ amyloid is, therefore, of ... -
Slow Folding of a Helical Protein: Large Barriers, Strong Internal Friction, or a Shallow, Bumpy Landscape?
Subramanian, Sandhyaa; Golla, Hemashree; Divakar, Kalivarathan; Kannan, Adithi; De Sancho Sánchez, David; Naganathan, Athi N. (American Chemical Society, 2020-10-15)The rate at which a protein molecule folds is determined by opposing energetic and entropic contributions to the free energy that shape the folding landscape. Delineating the extent to which they impact the diffusional ... -
The interaction landscape of amyloid beta-Zn(II) from molecular dynamics simulations
Aduriz Arrizabalaga, Julen (2021-02-26)Abstract (English) Amyloid fibrils are stable forms of misfolded proteins associated with numerous neurode-generative diseases. Among these, Alzheimer’s disease may be the most prevalent, with over 50 million dementia ...