Publications

2024

The strongest protein binder is surprisingly labile. A. Fernandez-Calvo, A. Reifs, L. Saa, A. L. Cortajarena, D. De Sancho, R. Perez-Jimenez. Protein Sci. 33, e5030 (2024).
Biallelic variants in SNUPN cause a limb girdle muscular dystrophy with myofibrillar-like features. P. Iruzubieta, A. Damborenea, M. Ioghen, S. Bajew, R. Fernandez-Torrón, A. Töpf, A. Herrero-Reiriz, D. Epure, K. Vill, A. Hernández-Laín, M. Manterola, M. Azkargorta, O. Pikatza-Menoio, L. Pérez-Fernandez, M. García-Puga, G. Gaina, A. Bastian, I. Streata, M. C. Walter, W. Müller-Felber, S. Thiele, S. Moragón, N. Bastida-Lertxundi, A. López-Cortajarena, F. Elortza, G. Gereñu, S. Alonso-Martin, V. Straub, D. de Sancho, R. Teleanu, A. López de Munain & L. Blázquez. Brain (2024). In press.
High-throughput virtual search of small molecules for controlling the mechanical stability of human CD4. A. Reifs, A. Fernandez-Calvo, B. Alonso-Lerma, J. Schönfelder, D. Franco, M. Ortega-Muñoz, S. Casares, C. Jimenez-Lopez, L. Saa, A. L. Cortajarena, D. De Sancho, E. San Sebastian, R. Perez-Jimenez. J. Biol. Chem. 300, 107133 (2024).
Atomistic molecular simulations of Aβ-Zn conformational ensembles. Julen Aduriz-Arrizabalaga, Xabier Lopez & David De Sancho*. Proteins, 92, 134-144 (2024). BioRxiv Preprint.

2023

Amino acid substitutions hydrophilizing the core of titin domains cause dilated cardiomyopathy. I. Martinez-Martin, A. Crousilles, J. Pablo Ochoa, D. Velazquez-Carreras, S. A. Mortensen, E. Herrero-Galan, F. Dominguez, P. Garcia-Pavia, D. de Sancho, M. Wilmanns, J. Alegre-Cebollada. Cell Reports 42, 113490 (2023). BioRxiv preprint.
Rules governing metal coordination in clusters from Aβ-Zn (II) complexes from quantum mechanical calculations. J. Aduriz-Arrizabalaga, J. M Mercero, D. De Sancho & X. López. Phys. Chem. Chem. Phys. 25, 27618-27627 (2023). ChemRxiv preprint.
Influence of metal binding on the conformational landscape of neurofilament peptides. D. Silva-Brea, D. De Sancho* & X. López*. Phys. Chem. Chem. Phys., 25 (39), 26429-26442 (2023). Inside Cover.
Compliant mechanical response of the ultrafast folding protein EnHD under force. Reifs, A., Ruiz Ortiz, I., Saa, A.O., Schönfelder, J., De Sancho, D., Muñoz, V. & Perez-Jimenez, R. Commun. Phys. 6, 7 (2023).

2022

Phase separation in amino acid mixtures is governed by composition. D. De Sancho. Biophys. J. 121, 4119-4127 (2022). Preprint available from BioRxiv.
Influence of non-protein amino-acid mimosine in peptide conformational propensities from novel Amber force field parameters. A. Urriolabeitia, D. De Sancho & X. López. J. Phys. Chem. B 126, 2959–2967 (2022). Preprint available from ChemRxiv.
Prediction of Folding and Unfolding Rates of Proteins with Simple Models. D. De Sancho and V. Muñoz. In Protein Folding: Methods and Protocols , Methods in Molecular Biology, 2376 (2022).

2021

Mechanism of hydrogen sulfide dependent inhibition of FeFe hydrogenase. C. Felbek, F. Arrigoni, D. De Sancho, A. Bailly, RB. Best, V. Fourmond, L. Bertini, C. Leger. ACS Catal. 11, 15162-15176 (2021).
Markov state models from hierarchical density-based assignment. I. Mitxelena, X. López & D. De Sancho*. J. Chem. Phys. 155, 054102 (2021). Preprint available from BioRxiv.
Nanomechanical Phenotypes in Cardiac Myosin-Binding Protein C Mutants That Cause Hypertrophic Cardiomyopathy. C. Suay-Corredera, M. Rosaria Pricolo, D. Velázquez-Carreras, D. Pathak, N. Nandwani, C. Pimenta-Lopes, D. Sánchez-Ortiz, I. Urrutia-Irazabal, S. Vilches, F. Dominguez, G. Frisso, L. Monserrat, P. García-Pavía, D. De Sancho, J. A. Spudich, K. M. Ruppel, E. Herrero-Galán & J. Alegre-Cebollada. ACS Nano. 15, 10203–10216 (2021).

2020

Coarse-grained molecular simulations of the binding of the SARS-CoV 2 spike protein RBD to the ACE2 cell receptor. D. De Sancho*, R. Perez-Jimenez & J. A. Gavira. Preprint available from BioRxiv. Simulation data available at OSF.
Slow Folding of a Helical Protein: Large Barriers, Strong Internal Friction, or a Shallow, Bumpy Landscape? S. Subramanian, H. Golla, K. Divakar, A. Kannan, D. De Sancho* & A. N. Naganathan*. J. Phys. Chem. B. 124, 8973-8983 (2020).
Theoretical characterization of Al(III) binding to KSPVPKSPVEEKG: Insights into the propensity of aluminum to interact with key sequences for neurofilament formation. R. Grande-Aztatzi, E. Formoso, J. Mujika, D. De Sancho & X. Lopez. J. Bioinorg. Chem. 210, 111169 (2020).
Competitive binding of HIF-1α and CITED2 to the TAZ1 domain of CBP from molecular simulations, I. Ruiz-Ortiz & D. De Sancho*. Phys. Chem. Chem. Phys. 22, 8118-8127 (2020). Preprint available from ChemRxiv.

2019

An Abl-FBP17 mechanosensing system couples local plasma membrane curvature and stress fiber remodeling during mechanoadaptation. A. Echarri, D. Pavón, S. Sánchez, M. García-García, E. Calvo, C. Huerta-López, D. Velázquez-Carreras, C. Viaris de Lesegno, N. Ariotti, A. Lázaro-Carrillo, R. Strippoli, D. De Sancho, J. Alegre-Cebollada, C. Lamaze, R. Parton & M. Del Pozo Barriuso. Nat. Commun. 10, 5828 (2019).
MasterMSM: A Package for Constructing Master Equation Models of Molecular Dynamics. D. De Sancho* & A. Aguirre. J. Chem. Inf. Model. 59, 3625-3629 (2019). Preprint available from ChemRxiv.
Resurrection of efficient Precambrian endoglucanases for biomass hydrolysis. N. Barruetabeña, B. Alonso-Lerma, A. Galera-Prat, N. Joudeh, L. Barandiaran, L. Aldazabal, M. Arbulu, M. Alcalde, D. De Sancho, J. A. Gavira, M. Carrion-Vazquez, R. Perez-Jimenez. Commun. Chem. 2, 75 (2019). Featured in Chemistry World.

2018

Reversible two-state folding of the ultrafast protein gpW under mechanical force. J. Schönfelder†, D. De Sancho†, R. Berkovich, R. B. Best, V. Munoz, R. Perez-Jimenez, Commun. Chem. 1, 59 (2018).
Instrumental Effects in the Dynamics of an Ultrafast Folding Protein Under Mechanical Force, D. De Sancho*, J. Schönfelder, R. B. Best, R. Perez-Jimenez, V. Munoz. J. Phys. Chem. B, 122, 11147-11154 (2018).
Mechanical architecture and folding of bacterial pilus domains resolved with single-molecule force spectroscopy. A. Alonso-Caballero, J. Schönfelder , S. Poly, F. Corsetti, D. De Sancho, E. Artacho & R. Pérez-Jiménez. Nat. Commun. 9, 2758 (2018).
MSM/RD: Coupling Markov state models of molecular kinetics with reaction-diffusion simulations. M. Dibak, M. J. del Razo, D. De Sancho, C. Schütte, and F. Noé. J Chem. Phys. 148, 214107 (2018).
The life of proteins under mechanical force, J. Schönfelder, A. Alonso-Caballero, D. De Sancho & R. Pérez Jiménez. Chem. Soc. Rev. 47, 3558-3573 (2018).

2017

Interplay between Folding Mechanism and Binding Modes in Folding Coupled to Binding Processes. R. Sharma, D. De Sancho* & V. Muñoz*. Phys. Chem. Chem. Phys. 19, 28512-28516 (2017).
The Influence of Disulfide Bonds in the Mechanical Stability of Proteins is Context Dependent. A. Manteca, A. Alonso-Caballero, M. Fertin, S. Poly, D. De Sancho* & R. Pérez-Jiménez*, J. Biol. Chem. 292, 13374-13380 (2017).
Mechanochemical Evolution of the Giant Muscle Protein Titin as Inferred from Resurrected Proteins, A. Manteca, J. Schönfelder, A. Alonso-Caballero, M. J. Fertín, N. Barruetabeña, B. F. Faria, E. Herrero-Galán, J. Alegre-Cebollada, D. De Sancho & R. Pérez-Jiménez. Nat. Struct. Mol. Biol. 24, 652-657 (2017). Cover article.

2016

The Power of Force: Insights into the Protein Folding Process Using Single-Molecule Force Spectroscopy. J Schöenfelder, D De Sancho & R Pérez-Jiménez, J. Mol. Biol. 428, 4245-4257 (2016).
Reconciling intermediates in mechanical unfolding experiments with two-state protein folding in bulk. D De Sancho* and RB Best*, J. Phys. Chem. Lett. 7, 3798-3803 (2016).
Multifrequency force microscopy of helical protein assembly on a virus. A. Callo, A. Eleta-López, P. Stoliar, D De Sancho, S. Santos, A. Verdaguer and A. Bittner, Sci. Rep. 6, 21899 (2016).

2015

Bridging experiments and native-centric simulations of a downhill folding protein. A. N. Naganathan* & D De Sancho*, J. Phys. Chem. B 119, 14295-14933 (2015).
The response of Greek key proteins to changes in connectivity depends on the nature of their secondary structure. KR Kemplen, D De Sancho & J Clarke, J. Mol. Biol. 427, 2159-2165 (2015).

postdoc - r. Best Group

Mechanism of O2 diffusion and reduction in Fe-Fe hydrogenase. A. Kubas†, C. Orain†, D De Sancho†, L. Saujet, M. Sensi, C. Gauquelin, I. Meynial-Salles, P. Soucaille, H. Bottin, C. Baffert, V. Fourmond, R.B. Best, J. Blumberger and C. Leger, Nat. Chem. 9, 88-95 (2016). See press release from nanoGUNE. Commentary on Phys.org.
Computation of rate constants for diffusion of small ligands to and from buried protein active sites. PH Wang, D De Sancho, RB Best & J Blumberger, Methods Enzymol. 578, 299-326 (2016).
Modulation of Protein Folding Internal Friction by Local and Global Barrier Heights. W. Zheng, D De Sancho & R.B. Best, J. Phys. Chem. Lett. 7, 1028-1034 (2016).
Markov state models of protein misfolding. A. Sirur, D De Sancho and R. B. Best, J. Chem. Phys. 144, 075101 (2016).
Dependence of internal friction on folding mechanism. W Zheng, D De Sancho, T Hoppe & RB Best, J. Am. Chem. Soc. 137, 3283-3290 (2015).
Identification of mutational hot spots for substrate diffusion: Application to myoglobin. D De Sancho, A Kubas, PH Wang, J Blumberger & RB Best, J. Chem. Theory Comput. 11, 1919-1927 (2015).
Coarse grained simulation of intrinsically disordered proteins. C.M. Baker, R.B. Best & D De Sancho, In Computational Approaches to Protein Dynamics , M. Fuxreiter, p. 283-304. CRC Press, Taylor & Francis, ISBN 9781466561571, (2015).
Interplay between partner and ligand facilitates the folding and binding of an intrinsically disordered protein. J M Rogers, V Oleinikovas, C T Wong, D De Sancho, C M Baker & J Clarke, Proc. Natl. Acad. Sci. USA 111, 15420-15425 (2014).
Molecular origin of 'internal friction' effects in protein folding rates. D De Sancho*, A Sirur & R B Best*, Nat. Commun. 5, 4307 (2014).
Aerobic damage of [FeFe] hydrogenases: activation barriers for O2 chemical attachment. A Kubas, D De Sancho, R B Best & J. Blumberger, Angew. Chem. Int. Ed. 53, 4081-4084 (2014).
Engineering Folding Dynamics from Two-State to Downhill: Application to λ-Repressor. J W Carter, C M Baker, R B Best & D De Sancho*, J. Phys. Chem. B 117, 13435-13443 (2013).
Folding kinetics and unfolded state dynamics of the GB1 hairpin from molecular simulations. D De Sancho, J Mittal & R B Best, J. Chem. Theory Comput. 9, 1743-1753 (2013).
Residue specific alpha-helix propensities from molecular simulation. R B Best, D De Sancho & J Mittal, Biophys. J. 102, 1462-1467 (2012).
Modulation of IDP binding mechanism and rates by helix propensity and non-native interactions: association of HIF1alpha with CBP. D De Sancho & R B Best, Mol. Biosys. 8, 256-267 (2012).
What is the time scale for α-helix nucleation? D De Sancho & R B Best, J. Am. Chem. Soc. 133, 6809-6816 (2011).

Postdoc - V. Muñoz group

Integrated prediction of protein folding and unfolding rates from only size and structural class. D De Sancho & V Muñoz, Phys. Chem. Chem. Phys. 13, 17030-17043 (2011).
Exploiting the downhill folding regime via experiment. V Muñoz, M Sadqi, A N Naganathan & D De Sancho, HFSP Journal 2, 342-353 (2008).
Protein folding rates and stability: How much is there beyond size? D De Sancho, U Doshi & V Muñoz, J. Am. Chem. Soc. 131, 2074-2075 (2009).

PhD thesis - A. Rey group

Energy minimizations with a combination of two knowledge based potentials for protein folding. D De Sancho & A Rey, J. Comput. Chem. 29 1684-1692 (2008).
Evaluation of coarse grained models for hydrogen bonds in proteins. D De Sancho & A Rey, J. Comput. Chem. 28 1187-1199 (2007).
Evaluation of a mean field potential with different interaction centers. M Larriva, D De Sancho & A Rey, Physica A 371 449-462 (2006).
Assessment of protein folding potentials with an evolutionary method. D De Sancho & A Rey, J. Chem. Phys. 125 014904 (2006).
Thermodynamics of Go type models for protein folding. L Prieto, D De Sancho & A Rey, J. Chem. Phys. 123 154903 (2005).
Evolutionary method for the assembly of rigid fragments. D De Sancho, L Prieto, A M Rubio & A Rey, J. Comput. Chem. 26 131-141 (2005).

* : corresponding author, † : equally contributed