• 1 SOUTH 0.11

Accepting Doctoral Students

19962020

Research output per year

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Research Output

2020

Affinity for the Interface Underpins Potency of Antibodies Operating In Membrane Environments

Rujas, E., Insausti, S., Leaman, D. P., Carravilla, P., González-Resines, S., Monceaux, V., Sánchez-Eugenia, R., García-Porras, M., Iloro, I., Zhang, L., Elortza, F., Julien, J-P., Saéz-Cirión, A., Zwick, M. B., Eggeling, C., Ojida, A., Domene, C., Caaveiro, J. M. M. & Nieva, J. L., 18 Aug 2020, In : Cell Reports. 32, 7, 108037.

Research output: Contribution to journalArticle

Open Access

Differential Stability of Aurein 1.2 Pores in Model Membranes of Two Probiotic Strains

Balatti, G. E. E., Domene, C., Martini, M. F. F. & Pickholz, M., 20 Aug 2020, In : Journal of Chemical Information and Modeling.

Research output: Contribution to journalArticle

Effect of anionic lipids on ion permeation through the KcsA K+-channel

Oakes, V., Furini, S. & Domene, C., 13 Jul 2020, In : Biochimica Et Biophysica Acta-Biomembranes. 1862, 11, 183406.

Research output: Contribution to journalArticle

Insights into the mechanisms of K+ permeation in K+-channels from computer simulations

Oakes, V., Furini, S. & Domene, C., 14 Jan 2020, In : Journal of Chemical Theory and Computation. 16, 1, p. 794-799

Research output: Contribution to journalArticle

Mechanism of molecular oxygen diffusion in a hypoxia sensing prolyl hydroxylase using multiscale simulation

Domene, C., Jorgensen, C. & Schofield, C. J., 5 Feb 2020, In : Journal of the American Chemical Society. 142, 5, p. 2253-2263 11 p.

Research output: Contribution to journalArticle

The Bilayer Collective Properties Govern the Interaction of an HIV-1 Antibody with the Viral Membrane

Carravilla, P., Darré, L., Oar-Arteta, I. R., Vesga, A. G., Rujas, E., de Las Heras-Martínez, G., Domene, C., Nieva, J. L. & Requejo-Isidro, J., 7 Jan 2020, In : Biophysical Journal. 118, 1, p. 44-56

Research output: Contribution to journalArticle

1 Citation (Scopus)
2019

Antibiotic resistance and host immune evasion in Staphylococcus aureus mediated by a metabolic adaptation

Jiang, J-H., Bhuiyan, M. S., Shen, H-H., Cameron, D. R., Rupasinghe, T. W. T., Wu, C-M., Le Brun, A. P., Kostoulias, X., Domene, C., Fulcher, A. J., McConville, M. J., Howden, B. P., Lieschke, G. J. & Peleg, A. Y., 26 Feb 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 9, p. 3722-3727 6 p.

Research output: Contribution to journalArticle

Open Access
File
8 Citations (Scopus)
24 Downloads (Pure)

Capturing the Molecular Mechanism of Anesthetic Action by Simulation Methods

Oakes, V. & Domene, C., 8 May 2019, In : Chemical Reviews. 119, 9, p. 5998-6014 17 p.

Research output: Contribution to journalReview article

Open Access
File
2 Citations (Scopus)
50 Downloads (Pure)
1 Citation (Scopus)

Influence of Cholesterol and its Stereoisomers on Members of the Serotonin Receptor Family

Oakes, V. & Domene, C., 5 Apr 2019, In : Journal of Molecular Biology. 431, 8, p. 1633-1649 17 p.

Research output: Contribution to journalArticle

Open Access
File
1 Citation (Scopus)
12 Downloads (Pure)

Modulation of the potassium channel KcsA by anionic phospholipids: Role of arginines at the non-annular lipid binding sites

Poveda, J. A., Giudici, A. M., Renart, M. L., Millet, O., Morales, A., González-Ros, J. M., Oakes, V., Furini, S. & Domene, C., 1 Oct 2019, In : Biochimica Et Biophysica Acta-Biomembranes. 1861, 10, 183029.

Research output: Contribution to journalArticle

Open Access
File
5 Citations (Scopus)
2 Downloads (Pure)
2018

2-oxoglutarate regulates binding of hydroxylated hypoxia-inducible factor to prolyl hydroxylase domain 2

Domene, C., Abboud, M. I., McAllister, T. E., Leung, I. K. H., Chowdhury, R., Jorgensen, C., Mecinović, J., Lippl, K., Hancock, R. L., Hopkinson, R. J., Kawamura, A., Claridge, T. D. W. & Schofield, C. J., 28 Mar 2018, In : Chemical Communications. 54, 25, p. 3130-3133 4 p.

Research output: Contribution to journalArticle

Open Access
13 Citations (Scopus)

Exposure of the HIV-1 broadly neutralizing antibody 10E8 MPER epitope on the membrane surface by gp41 transmembrane domain scaffolds

Oakes, V., Torralba, J., Rujas, E., Nieva, J. L., Domene, C. & Apellaniz, B., 1 Jun 2018, In : Biochimica et Biophysica Acta. 1860, 6, p. 1259-1271 13 p.

Research output: Contribution to journalArticle

Open Access
File
2 Citations (Scopus)
34 Downloads (Pure)

Ion-triggered selectivity in bacterial sodium channels

Furini, S. & Domene, C., 22 May 2018, In : Proceedings of the National Academy of Sciences of the United States of America. 115, 21, p. 5450-5455 6 p.

Research output: Contribution to journalArticle

Open Access
File
6 Citations (Scopus)
51 Downloads (Pure)

Location and character of volatile general anesthetics binding sites in the transmembrane domain of TRPV1

Jorgensen, C. & Domene, C., 4 Sep 2018, In : Molecular Pharmaceutics. 15, 9, p. 3920-3930 11 p.

Research output: Contribution to journalArticle

Open Access
File
4 Citations (Scopus)
25 Downloads (Pure)

Role of zinc and magnesium ions in the modulation of phosphoryl transfer in protein tyrosine phosphatase 1B

Bellomo, E., Abro, A., Hogstrand, C., Maret, W. & Domene, C., 28 Mar 2018, In : Journal of the American Chemical Society. 140, 12, p. 4446-4454 9 p.

Research output: Contribution to journalArticle

Open Access
File
9 Citations (Scopus)
38 Downloads (Pure)

Stereospecific Interactions of Cholesterol in a Model Cell Membrane: Implications for the Membrane Dipole Potential

Oakes, V. & Domene, C., 1 Jun 2018, In : Journal of Membrane Biology. 251, 3, p. 507-519 13 p.

Research output: Contribution to journalArticle

Open Access
File
6 Citations (Scopus)
32 Downloads (Pure)

Understanding Conformational Dynamics of Complex Lipid Mixtures Relevant to Biology

Friedman, R., Khalid, S., Aponte-Santamaría, C., Arutyunova, E., Becker, M., Boyd, K. J., Christensen, M., Coimbra, J. T. S., Concilio, S., Daday, C., van Eerden, F. J., Fernandes, P. A., Gräter, F., Hakobyan, D., Heuer, A., Karathanou, K., Keller, F., Lemieux, M. J., Marrink, S. J., May, E. R. & 15 others, Mazumdar, A., Naftalin, R., Pickholz, M., Piotto, S., Pohl, P., Quinn, P., Ramos, M. J., Schiøtt, B., Sengupta, D., Sessa, L., Vanni, S., Zeppelin, T., Zoni, V., Bondar, A-N. & Domene, C., 1 Dec 2018, In : Journal of Membrane Biology. 251, 5-6, p. 609-631 23 p.

Research output: Contribution to journalReview article

Open Access
14 Citations (Scopus)
2017

13C-Carbamylation as a mechanistic probe for the inhibition of class D β-lactamases by avibactam and halide ions

Lohans, C. T., Wang, D. Y., Jorgensen, C., Cahill, S. T., Clifton, I. J., McDonough, M. A., Oswin, H. P., Spencer, J., Domene Nunez, C., Claridge, T. D. W., Brem, J. & Schofield, C. J., 28 Jul 2017, In : Organic and Biomolecular Chemistry. 15, 28, p. 6024-6032 9 p.

Research output: Contribution to journalArticle

9 Citations (Scopus)

Functional Mapping of the N-terminal Arginine Cluster and C-terminal Acidic Residues of Kir6.2 channel Fused to a G Protein-Coupled Receptor

Principalli, M. A., Lemel, L., Rongier, A., Godet, A-C., Langer, K., Revilloud, J., Darré, L., Domene Nunez, C., Vivaudou, M. & Moreau, C. J., Oct 2017, In : Biochimica Et Biophysica Acta-Biomembranes. 1859, 10, p. 2144-2153 10 p.

Research output: Contribution to journalArticle

Membrane Phase-Dependent Occlusion of Intramolecular GLUT1 Cavities Demonstrated by Simulations

Iglesias-Fernandez, J., Quinn, P. J., Naftalin, R. J. & Domene Nunez, C., 28 Mar 2017, In : Biophysical Journal. 112, 6, p. 1176-1184 9 p.

Research output: Contribution to journalArticle

7 Citations (Scopus)

Oxytocin Modulates Nociception as an Agonist of Pain-Sensing TRPV1

Nersesyan, Y., Demirkhanyan, L., Cabezas-Bratesco, D., Oakes, V., Kusuda, R., Dawson, T., Sun, X., Cao, C., Cohen, A. M., Chelluboina, B., Veeravalli, K. K., Zimmermann, K., Domene Nunez, C., Brauchi, S. & Zakharian, E., 7 Nov 2017, In : Cell Reports. 21, 6, p. 1681-1691 11 p.

Research output: Contribution to journalArticle

Open Access
35 Citations (Scopus)

Ribonucleotide Reductase Requires Subunit Switching in Hypoxia to Maintain DNA Replication

Foskolou, I. P., Jorgensen, C., Leszczynska, K. B., Olcina, M. M., Tarhonskaya, H., Haisma, B., D’Angiolella, V., Myers, W. K., Domene Nunez, C., Flashman, E. & Hammond, E. M., 1 Apr 2017, In : Molecular Cell. 66, 2, p. 206-220 e9.

Research output: Contribution to journalArticle

Open Access
20 Citations (Scopus)
2016

A perspective on structural and computational work on collagen

Domene Nunez, C., Jorgensen, C. & Abbasi, S. W., 28 Sep 2016, In : Physical Chemistry Chemical Physics. 18, 36, p. 24802-24811 10 p.

Research output: Contribution to journalArticle

13 Citations (Scopus)

Chapter 2: Molecular Dynamics Simulations: Principles and Applications for the Study of Membrane Proteins

Oakes, V. & Domene Nunez, C., 1 Dec 2016, Computational Biophysics of Membrane Proteins. Domene, C. (ed.). Royal Society of Chemistry, p. 19-58 40 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Computational Biophysics of Membrane Proteins

Domene Nunez, M. C., 1 Dec 2016, Royal Society of Chemistry. (Theoretical and Computational Chemistry Series)

Research output: Book/ReportBook

Computational studies of transport in ion channels using metadynamics

Furini, S. & Domene Nunez, C., 1 Jul 2016, In : Biochimica Et Biophysica Acta-Biomembranes. 1858, 7 Pt B, p. 1733-1740 8 p.

Research output: Contribution to journalArticle

Open Access
18 Citations (Scopus)

Energetics of Ion Permeation in an Open-Activated TRPV1 Channel

Jorgensen, C., Furini, S. & Domene Nunez, C., 20 Sep 2016, In : Biophysical Journal. 111, 6, p. 1214-1222 9 p.

Research output: Contribution to journalArticle

Open Access
11 Citations (Scopus)

Exploring the Dynamics of the TWIK-1 Channel

Oakes, V., Furini, S., Pryde, D. & Domene Nunez, C., 1 Aug 2016, In : Biophysical Journal. 111, 4, p. 775-784 10 p.

Research output: Contribution to journalArticle

Open Access
3 Citations (Scopus)

Lateral fenestrations in K+-channels explored using MD simulations

Jorgensen, C., Darre Castell, L., Oakes, V., Torella, R., Pryde, D. & Domene Nunez, C., 1 Jul 2016, In : Molecular Pharmaceutics. 13, 7, p. 2263-2273 11 p.

Research output: Contribution to journalArticle

Open Access
13 Citations (Scopus)

Structural basis for oxygen degradation domain selectivity of the HIF prolyl hydroxylases

Chowdhury, R., Leung, I. K. H., Tian, Y-M., Abboud, M. I., Ge, W., Domene Nunez, C., Cantrelle, F-X., Landrieu, I., Hardy, A. P., Pugh, C. W., Ratcliffe, P. J., Claridge, T. D. W. & Schofield, C. J., 26 Aug 2016, In : Nature Communications. 7, p. 1-10 10 p., 12673.

Research output: Contribution to journalArticle

Open Access
42 Citations (Scopus)

Voltage-Gated Sodium Channels: Mechanistic Insights From Atomistic Molecular Dynamics Simulations

Oakes, V., Furini, S. & Domene Nunez, C., 1 Mar 2016, In : Current Topics in Membranes. 78, p. 183-214

Research output: Contribution to journalArticle

5 Citations (Scopus)
2015

Antimicrobial peptide dendrimer interacts with phosphocholine membranes in a fluidity dependent manner: A neutron reflection study combined with molecular dynamics simulations

Lind, T. K., Darré, L., Domene Nunez, C., Urbanczyk-Lipkowska, Z., Cardenas, M. & Wacklin, H. P., 1 Oct 2015, In : Biochimica Et Biophysica Acta-Biomembranes. 1848, 10, Part A, p. 2075-2084 10 p.

Research output: Contribution to journalArticle

Open Access
15 Citations (Scopus)

Bias-Exchange Metadynamics Simulations: An Efficient Strategy for the Analysis of Conduction and Selectivity in Ion Channels

Domene Nunez, C., Barbini, P. & Furini, S., 1 Apr 2015, In : Journal of Chemical Theory and Computation. 11, 4, p. 1896-1906 11 p.

Research output: Contribution to journalArticle

25 Citations (Scopus)

Binding of Capsaicin to the TRPV1 Ion Channel

Darre Castell, L. & Domene Nunez, C., 1 Dec 2015, In : Molecular Pharmaceutics. 12, 12, p. 4454-4465 12 p.

Research output: Contribution to journalArticle

47 Citations (Scopus)

Blocking the Passage: C60 Geometrically Clogs K+ Channels

Calvaresi, M., Furini, S., Domene Nunez, C., Bottoni, A. & Zerbetto, F., 1 May 2015, In : ACS Nano. 9, 5, p. 4827-4834 8 p.

Research output: Contribution to journalArticle

Open Access
22 Citations (Scopus)

In Silico Identification of PAP-1 Binding Sites in the Kv1.2 Potassium Channel

Jorgensen, C., Darre Castell, L., Vanommeslaeghe, K., Omoto, K., Pryde, D. & Domene Nunez, C., 1 Apr 2015, In : Molecular Pharmaceutics. 12, 4, p. 1299-1307 9 p.

Research output: Contribution to journalArticle

10 Citations (Scopus)

Molecular Dynamics Simulations and Neutron Reflectivity as an Effective Approach To Characterize Biological Membranes and Related Macromolecular Assemblies

Darre Castell, L., Iglesias-Fernandez, J., Kohlmeyer, A., Wacklin, H. & Domene Nunez, C., 1 Oct 2015, In : Journal of Chemical Theory and Computation. 11, 10, p. 4875-4884 10 p.

Research output: Contribution to journalArticle

14 Citations (Scopus)

Permeation and Dynamics of an Open-Activated TRPV1 Channel

Darré, L., Furini, S. & Domene Nunez, C., 30 Jan 2015, In : Journal of Molecular Biology. 427, 2, p. 537-549 13 p.

Research output: Contribution to journalArticle

31 Citations (Scopus)

Quantifying the Binding Interaction between the Hypoxia-Inducible Transcription Factor and the von Hippel-Lindau Suppressor

Domene Nunez, C., Jorgensen, C., Vanommeslaeghe, K., Schofield, C. J. & MacKerell, A., 1 Aug 2015, In : Journal of Chemical Theory and Computation. 11, 8, p. 3946-3954 9 p.

Research output: Contribution to journalArticle

1 Citation (Scopus)

Surfactin at the Water/Air Interface and in Solution

Iglesias-Fernández, J., Darre, L., Kohlmeyer, A., Thomas, R. K., Shen, H. H. & Domene Nunez, C., 1 Oct 2015, In : Langmuir . 31, 40, p. 11097-11104 8 p.

Research output: Contribution to journalArticle

12 Citations (Scopus)
2014

Cholesterol-Dependent Membrane Fusion Induced by the gp41 Membrane-Proximal External Region-Transmembrane Domain Connection Suggests a Mechanism for Broad HIV-1 Neutralization

Apellániz, B., Rujas, E., Carravilla, P., Requejo-Isidro, J., Huarte, N., Domene Nunez, C. & Nieva, J. L., 1 Nov 2014, In : Journal of Virology. 88, 22, p. 13367-13377 11 p.

Research output: Contribution to journalArticle

26 Citations (Scopus)

Development of GoSlo-SR-5-69, a potent activator of large conductance Ca2+-activated K+ (BK) channels

Roy, S., Large, R. J., Akande, A. M., Kshatri, A., Webb, T. I., Domene Nunez, C., Sergeant, G. P., McHale, N. G., Thornbury, K. D. & Hollywood, M. A., 21 Mar 2014, In : European Journal of Medicinal Chemistry. 75, p. 426-437 12 p.

Research output: Contribution to journalArticle

17 Citations (Scopus)

DNA Recognition Process of the Lactose Repressor Protein Studied via Metadynamics and Umbrella Sampling Simulations

Furini, S. & Domene Nunez, C., 1 Nov 2014, In : Journal of Physical Chemistry B. 118, 46, p. 13059-13065 7 p.

Research output: Contribution to journalArticle

4 Citations (Scopus)

Effects of the Protonation State of the EEEE Motif of a Bacterial Na+-channel on Conduction and Pore Structure

Furini, S., Barbini, P. & Domene Nunez, C., 21 May 2014, In : Biophysical Journal. 106, 10, p. 2175-2183 9 p.

Research output: Contribution to journalArticle

Open Access
18 Citations (Scopus)

Structure and Immunogenicity of a Peptide Vaccine, Including the Complete HIV-1 gp41 2F5 Epitope: IMPLICATIONS FOR ANTIBODY RECOGNITION MECHANISM AND IMMUNOGEN DESIGN

Serrano, S., Araujo, A., Apellaniz, B., Bryson, S., Carravilla, P., de la Arada, I., Huarte, N., Rujas, E., Pai, E. F., Arrondo, J. L. R., Domene Nunez, C., Angeles Jimenez, M. & Nieva, J. L., 1 Mar 2014, In : Journal of Biological Chemistry. 289, 10, p. 6565-6580 16 p.

Research output: Contribution to journalArticle

19 Citations (Scopus)
2013

DNA-recognition process described by MD simulations of the lactose repressor protein on a specific and a non-specific DNA sequence

Furini, S., Barbini, P. & Domene Nunez, C., Apr 2013, In : Nucleic Acids Research. 41, 7, p. 3963-3972

Research output: Contribution to journalArticle

Open Access
36 Citations (Scopus)

K+ and Na+ Conduction in Selective and Nonselective Ion Channels Via Molecular Dynamics Simulations

Furini, S. & Domene Nunez, C., 15 Oct 2013, In : Biophysical Journal. 105, 8, p. 1737-1745 9 p.

Research output: Contribution to journalArticle

Open Access
27 Citations (Scopus)