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Biochemistry and soft matter

Using the battery of available computational methods, from electronic structure based methods to classical simulations, we focus on systems of biological interest. In particular we investigate the structure and reactivity of proteins and enzymes, drug design, processes in cellular membranes, enzymatic reactions in crowded media and soft nanoparticles in solution.


Some relevant publications in this topic are:


1,6-Cyclophellitol cyclosulfates: a new class of irreversible glycosidase inhibitor.
M. Artola, L. Wu, M. J. Ferraz, C.-L. Kuo, L. Raich, I. Z. Breen, W. A. Offen, J. D. C.
Codée, G. A. van der Marel, C. Rovira, J. M. F. G. Aerts, G. J. Davies, H. S. Overkleeft.
ACS Centr. Sci., 3 (2017) 784–793.


Precise probing of residue roles by post-translational β,γ-C,N aza-Michael mutagenesis in enzyme active sites.
J. Dadová, K.-J. Wu, P. G. Isenegger, J. C. Errey, G. J. L. Bernardes, J. M. Chalker, L. Raich, C. Rovira, B. G. Davis.
ACS Centr. Sci., 3 (2017) 1168–1173.


Iron oxide nanoparticles - in vivo/in vitro biomedical applications and in silico studies.
M. Nedyalkova, B. Donkova, J. Romanova, G. Tzvetkov, S. Madurga, V. Simeonov.
Adv. Colloid Interface Sci., 249 (2017) 192-212.


Bioengineering a single-protein junction.
M. P. Ruiz, A. C. Aragonès, N. Camarero, J. G. Vilhena, M. Ortega, L. A. Zotti, R. Pérez, J. C. Cuevas, P. Gorostiza, I. Díez-Pérez.
J. Am. Chem. Soc., 139 (2017) 15337-15346.


Computational study of ibuprofen removal from water by adsorption in realistic activated carbons.
D. Bahamon, L. Carro, S. Guri, L. F. Vega.
J. Colloid Interface Sci., 498 (2017) 323.


Operative mechanism of hole-assisted negative charge motion in ground states of radical-anion molecular wires.
C. Franco, P. Mayorga Burrezo, V. Lloveras, R. Caballero, I. Alcon, S. T. Bromley, M.
Mas-Torrent, F. Langa, J. T. Lopez Navarrete, C. Rovira, J. Casado, J. Veciana.
J. Am. Chem. Soc., 139 (2017) 1027-1039.


Computational design of experiment unveils the conformational reaction coordinate of GH125 α-mannosidases.
S. Alonso-Gil, A. Males, P. Z. Fernandes, S. J. Williams, G. J. Davies, C. Rovira.
J. Am. Chem. Soc., 139 (2017) 1085–1088.


Contribution of shape and charge to the inhibition of a family GH99 endo-alpha-1,2-mannanase.
M. Petricevic, L. F. Sobala, P. Z. Fernandes, L. Raich, A. J. Thompson, G. Bernardo-Seisdedos, O. Millet, S. Zhu, M. Sollogoub, J. Jiménez-Barbero, C. Rovira, G. J. Davies, S. J. Williams.
J. Am. Chem. Soc., 139 (2017) 1089–1097.


Carba-cyclophellitols are neutral retaining glucosidase inhibitors.
T. J. M. Beenakker, D. P. A. Wander, W. A. Offen, M. Artola, L. Raich, M. J. Ferraz, K.-Y. Li, J. H. P. M. Houben, E. R. van Rijssel, T. Hansen, G. A. van der Marel, J. D. C. Codée, J. M. F. G. Aerts, C. Rovira, G. J. Davies, H. S. Overkleeft.
J. Am. Chem. Soc., 139 (2017) 6534–6537.


A front-face ‘SNi synthase’ engineered from a retaining ‘double-SN2’ hydrolase.
J. Iglesias-Fernández, S. M. Hancock, S. S. Lee, M. Khan, J. Kirkpatrick, N. J. Oldham, K. McAuley, A. Fordham-Skelton, C. Rovira, B. G. Davis.
Nat. Chem. Biol., 139 (2017) 874–881.



A β-mannannase with a lysozyme fold and a novel molecular catalytic mechanism.
Y. Jin, M. Petricevic, A. John, L. Raich, H. Jenkins, L. Portela De Souza, F. Cuskin, H. J. Gilbert, C. Rovira, E. D. Goddard-Borger, S. J. Williams, G. J. Davies.
ACS Cent. Sci. 2 (2016) 896.


Violation of DNA neighbor exclusion principle in RNA recognition.
M. Yousuf, I. S. Youn, J. Yun, L. Rasheed, R. Valero, G. Shi, K. S. Kim.
Chem. Sci. 7 (2016) 3581.


A trapped covalent intermediate of a glycoside hydrolase on the pathway to transglycosylation. Insights from experiments and quantum mechanics/molecular mechanics simulations.
L. Raich, V. Borodkin, W. Fang, J. Castro-López, D. van Aalten, R. Hurtado-Guerrero, C. Rovira.

J. Am. Chem. Soc. 138 (2016) 3325.


Structure of the reduced copper active site in pre-processed galactose oxidase: ligand tuning for one-electron O2 activation in cofactor biogenesis.
R. E. Cowley, J. Cirera, M. F. Qayyum, D. Rokhsana, B. Hedman, K. O. Hodgson, D. M. Dooley, E. I. Solomon.

J. Am. Chem. Soc. 138 (2016) 13219.


Assessment of the sampling performance of multiple-copy dynamics versus a unique trajectory.

J. J. Pérez, M. S. Tomas, J. Rubio-Martinez.
J. Chem. Inf. Model. 56 (2016) 1950.


Enzymatic cleavage of glycosidic bonds: strategies on how to setup and control a QM/MM metadynamics simulation.
L. Raich, A. Nin-Hill, A. Ardèvol, C. Rovira.
Methods Enzymol. 577 (2016) 159.



Theoretical study of the free energy surface and kinetics of the hepatitis C virus NS3/NS4A serine protease reaction with the NS5A/5B substrate. Does the generally accepted tetrahedral intermediate exist?

J. A. Martínez-González, M. González, L. Masgrau, R. Martínez

ACS Catal. 5 (2015) 246.


A single glycosidase harnesses different pyranoside ring transition state conformations for hydrolysis of mannosides and glucosides.

A. Tankrathok, J. Iglesias-Fernández, R. J. Williams, S. Pengthaisong, S. Baiya, Z. Hakki, R. C. Robinson, M. Hrmova, C. Rovira, S. J. Williams, J. R. Ketudat Cairns.
ACS Catal. 5 (2015) 6041.


Evidence for a boat conformation at the transition state of GH76 α-1,6-mannanases; key enzymes in bacterial and fungal mannoprotein metabolism.

A. J. Thompson, G. Speciale, J. Iglesias-Fernández, Z. Hakki, T. Belz, A. Cartmell, R. J. Spears, E. Chandler, J. Stepper, H. J. Gilbert, C. Rovira, S. J. Williams, G. J. Davies.

Angew. Chem. Int. Ed. 54 (2015) 5378.


The complete conformational free energy landscape of β-xylose reveals a two-fold catalytic itinerary for β-xylanases.

J. Iglesias-Fernández, L. Raich, A. Ardèvol, C. Rovira.

Chem. Sci. 6 (2015) 1167.


Reaction mechanisms in carbohydrate-active enzymes: glycosyl hydrolases and glycosyltransferases. Insights from ab initio QM/MM molecular dynamics simulations.

A. Ardèvol, C. Rovira.

J. Am. Chem. Soc. 137 (2015) 7528. Editor’s choice & JACS Spotlight.


The molecular mechanism of the catalase-like activity of horseradish peroxidase.

P. Campomanes, U. Rothlisberger, M- Alfonso-Prieto, C. Rovira.

J. Am. Chem. Soc. 137 (2015) 11170.


The role of hydrogen bonds in the stabilization of silver-mediated cytosine tetramers.

L. A. Espinosa Leal, A. Karpenko, S. Swasey, E. G. Gwinn, V. Rojas-Cervellera, C. Rovira, O. Lopez-Acevedo.
J. Phys. Chem. Lett. 6 (2015) 4061.


Dynamic interplay between catalytic and lectin domains of GalNAc- transferases modulates protein O-glycosylation.

E. Lira-Navarrete, M. de las Rivas, I. Compañón, M. C. Pallarés, Y. Kong, J. Iglesias- Fernández, G. J. L. Bernardes, J. M. Peregrina, C. Rovira, P. Bernadó, P. Bruscolini, H. Clausen, A. Lostao, F. Corzana, R. Hurtado-Guerrero.
Nat. Commun. 6 (2015) 6937.


Privateer: a software for conformational validation of cyclic carbohydrate structures.

J. Agirre, J. Iglesias-Fernández, C. Rovira, G. J. Davies, K. Wilson, K. Cowtan.

Nat. Struct. Mol. Biol. 22 (2015) 833.


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