Carmen Domene Nunez

2021

Multiple Interactions of Glucose with the Extra-Membranous Loops of GLUT1 Aid Transport

Gonzalez-Resines, S., Quinn, P. J., Naftalin, R. J. & Domene, C., 26 Jul 2021, In: JOURNAL OF CHEMICAL INFORMATION AND MODELING. 61, 7, p. 3559-3570 12 p.

Research output: Contribution to journal › Article › peer-review

4 Citations (Scopus)

2018

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 journal › Article › peer-review

Open Access

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22 Citations (Scopus)

303 Downloads (Pure)

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., 26 Jun 2017, (E-pub ahead of print) In: ORGANIC AND BIOMOLECULAR CHEMISTRY. 15, 28, p. 6024-6032 9 p.

Research output: Contribution to journal › Article › peer-review

Open Access

19 Citations (Scopus)

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

Lohans, C. T., Wang, D., Jorgensen, C., Cahill, S., Clifton, I. J., McDonough, M. A., Oswin, H. P., Spencer, J., Domene, C., Claridge, T. D. W., Brem, J. & Schofield, C. J., 26 Jun 2017, In: ORGANIC AND BIOMOLECULAR CHEMISTRY. 28

Research output: Contribution to journal › Article › peer-review

Open Access

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, C., Vivaudou, M. & Moreau, C. J., Oct 2017, In: Biochimica et Biophysica Acta (BBA)-Biomembranes. 1859, 10, p. 2144-2153

Research output: Contribution to journal › Article › peer-review

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2 Citations (Scopus)

174 Downloads (Pure)

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

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

Research output: Contribution to journal › Article › peer-review

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9 Citations (Scopus)

179 Downloads (Pure)

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, C., Brauchi, S. & Zakharian, E., 7 Nov 2017, (E-pub ahead of print) In: Cell Reports. 21, 6, p. 1681-1691 11 p.

Research output: Contribution to journal › Article › peer-review

Open Access

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99 Citations (Scopus)

236 Downloads (Pure)

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, C., Flashman, E. & Hammond, E. M., 13 Apr 2017, In: MOLECULAR CELL. 66, 2, p. 206-220

Research output: Contribution to journal › Article › peer-review

Open Access

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61 Citations (Scopus)

237 Downloads (Pure)

2016

A perspective on structural and computational work on collagen

Domene, C., Jorgensen, C. & Abbasi, S. W., 17 Aug 2016, In: Physical Chemistry Chemical Physics. 18, 36, p. 24802-24811 10 p.

Research output: Contribution to journal › Literature review › peer-review

Open Access

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27 Citations (Scopus)

442 Downloads (Pure)

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

Oakes, V. & Domene, C., 5 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 proceeding › Other chapter contribution › peer-review

1 Citation (Scopus)

Computational Biophysics of Membrane Proteins

Domene Nunez, M. C., 5 Dec 2016, Royal Society of Chemistry.

Research output: Book/Report › Book › peer-review

Computational studies of transport in ion channels using metadynamics

Furini, S. & Domene, C., Jul 2016, In: Biochimica et Biophysica Acta (BBA)-Biomembranes. 1858, 7 Pt B, p. 1733-40 8 p.

Research output: Contribution to journal › Article › peer-review

Open Access

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33 Citations (Scopus)

191 Downloads (Pure)

Energetics of Ion Permeation in an Open-Activated TRPV1 Channel

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

Research output: Contribution to journal › Article › peer-review

Open Access

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17 Citations (Scopus)

151 Downloads (Pure)

Exploring the Dynamics of the TWIK-1 Channel

Oakes, V., Furini, S., Pryde, D. & Domene, C., 23 Aug 2016, In: Biophysical Journal. 111, 4, p. 775-784 10 p.

Research output: Contribution to journal › Article › peer-review

Open Access

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7 Citations (Scopus)

163 Downloads (Pure)

Lateral fenestrations in K+-channels explored using MD simulations

Jorgensen, C., Darre Castell, L., Oakes, V., Torella, R., Pryde, D. & Domene, C., 5 Jul 2016, In: Molecular Pharmaceutics. 13, 7, p. 2263-2273 11 p.

Research output: Contribution to journal › Article › peer-review

Open Access

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21 Citations (Scopus)

491 Downloads (Pure)

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, 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, 1, 10 p., 12673.

Research output: Contribution to journal › Article › peer-review

Open Access

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101 Citations (Scopus)

185 Downloads (Pure)

The use of multiscale molecular simulations in understanding a relationship between the structure and function of biological systems of the brain: The application to monoamine oxidase enzymes

Vianello, R., Domene, C. & Mavri, J., 15 Jul 2016, In: Frontiers in Neuroscience. 10, JUL, 327.

Research output: Contribution to journal › Article › peer-review

Open Access

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35 Citations (Scopus)

215 Downloads (Pure)

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

Oakes, V. J., Furini, S. & Domene, C., 14 Mar 2016, (E-pub ahead of print) In: CURRENT TOPICS IN MEMBRANES.

Research output: Contribution to journal › Article › peer-review

Open Access

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8 Citations (Scopus)

328 Downloads (Pure)

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, C., Urbanczyk-Lipkowska, Z., Cardenas, M. & Wacklin, H. P., Oct 2015, In: BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES. 1848, 10, p. 2075-2084 10 p.

Research output: Contribution to journal › Article › peer-review

26 Citations (Scopus)

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

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

Research output: Contribution to journal › Article › peer-review

Open Access

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37 Citations (Scopus)

157 Downloads (Pure)

Binding of Capsaicin to the TRPV1 Ion Channel

Darre Castell, L. & Domene, C., 7 Dec 2015, In: Molecular Pharmaceutics. 12, 12, p. 4454-4465 12 p.

Research output: Contribution to journal › Article › peer-review

70 Citations (Scopus)

Blocking the Passage: C-60 Geometrically Clogs K+ Channels

Calvaresi, M., Furini, S., Domene, C., Bottoni, A. & Zerbetto, F., 26 May 2015, In: ACS Nano. 9, 5, p. 4827-4834 8 p.

Research output: Contribution to journal › Article › peer-review

Open Access

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43 Citations (Scopus)

175 Downloads (Pure)

Conduction and Selectivity in Na+ Channels Analyzed by Bias-Exchange Metadynamics Simulations

Furini, S., Barbini, P. & Domene, C., 27 Jan 2015, In: Biophysical Journal. 108, 2, p. 490A-490A 1 p., 2476.

Research output: Contribution to journal › Conference paper › peer-review

Open Access

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186 Downloads (Pure)

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

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

Research output: Contribution to journal › Article › peer-review

14 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, C., 13 Oct 2015, In: Journal of Chemical Theory and Computation. 11, 10, p. 4875-4884 10 p.

Research output: Contribution to journal › Article › peer-review

20 Citations (Scopus)

Permeation and Dynamics of an Open-Activated TRPV1 Channel

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

Research output: Contribution to journal › Article › peer-review

36 Citations (Scopus)

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

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

Research output: Contribution to journal › Article › peer-review

Open Access

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1 Citation (Scopus)

185 Downloads (Pure)

Surfactin at the Water/Air Interface and in Solution

Iglesias-Fernández, J., Darre Castell, L., Kohlmeyer, A., Thomas, R. K., Shen, H. H. & Domene, C., 13 Oct 2015, In: Langmuir : the ACS journal of surfaces and colloids. 31, 40, p. 11097-11104 8 p.

Research output: Contribution to journal › Article › peer-review

17 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, C. & Nieva, J. L., Nov 2014, In: Journal of virology. 88, 22, p. 13367-13377 11 p.

Research output: Contribution to journal › Article › peer-review

36 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, 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 journal › Article › peer-review

23 Citations (Scopus)

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

Furini, S. & Domene, C., 20 Nov 2014, In: JOURNAL OF PHYSICAL CHEMISTRY B. 118, 46, p. 13059-13065 7 p.

Research output: Contribution to journal › Article › peer-review

8 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, C., 20 May 2014, In: Biophysical Journal. 106, 10, p. 2175-2183 9 p.

Research output: Contribution to journal › Article › peer-review

26 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, C., Angeles Jimenez, M. & Nieva, J. L., 7 Mar 2014, In: Journal of Biological Chemistry. 289, 10, p. 6565-6580 16 p.

Research output: Contribution to journal › Article › peer-review

Open Access

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25 Citations (Scopus)

176 Downloads (Pure)

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, C., 2013, (E-pub ahead of print) In: Nucleic Acids Research.

Research output: Contribution to journal › Article › peer-review

47 Citations (Scopus)

Fusogenic Activity of the HIV-1 Gp41 MPER-TMD Region: Mechanism and Targeting by Immunogens and Inhibitors

Nieva, J. L., Apellaniz, B., Domene, C., Huarte, N. & Largo, E., 29 Jan 2013, In: Biophysical Journal. 104, 2, p. 90A-90A 1 p., 472.

Research output: Contribution to journal › Conference paper › peer-review

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

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

Research output: Contribution to journal › Literature review › peer-review

35 Citations (Scopus)

On Conduction and Permeation in a Bacterial Sodium Channel

Domene, C. & Furini, S., 29 Jan 2013, In: Biophysical Journal. 104, 2, p. 135A-135A 1 p., 692.

Research output: Contribution to journal › Conference paper › peer-review

Simulating the Pyrolysis of Polyazides: a Mechanistic Case Study of the [P(N-3)(6)](-) Anion

Domene, C., Portius, P., Fowler, P. W. & Bernasconi, L., 18 Feb 2013, In: INORGANIC CHEMISTRY. 52, 4, p. 1747-1754 8 p.

Research output: Contribution to journal › Article › peer-review

3 Citations (Scopus)

Strong and weak zinc binding sites in human zinc-alpha 2-glycoprotein

Kumar, A., Hati, D., Mohajer Thaker, T., Miah, L., Cunningham, P., Domene, C., Bui, T., Drake, A. & McDermott, L., 11 Dec 2013, In: FEBS Letters. 587, 24, p. 3949-3954 6 p.

Research output: Contribution to journal › Article › peer-review

19 Citations (Scopus)

2012

Dynamics of a bacterial multidrug ABC transporter in the inward- and outward-facing conformations

Mehmood, S., Domene, C., Forest, E. & Jault, J-M., 3 Jul 2012, In: Proceedings of the National Academy of Sciences of the United States of America. 109, 27, p. 10832-10836 5 p.

Research output: Contribution to journal › Article › peer-review

88 Citations (Scopus)

Effects of point mutations in pVHL on the binding of HIF-1 alpha

Domene, C. & Illingworth, C. J. R., Mar 2012, In: Proteins. 80, 3, p. 733-746 14 p.

Research output: Contribution to journal › Article › peer-review

18 Citations (Scopus)

Molecular Dynamics Simulations of the TrkH Membrane Protein

Domene, C. & Furini, S., 28 Feb 2012, In: Biochemistry. 51, 8, p. 1559-1565 7 p.

Research output: Contribution to journal › Article › peer-review

22 Citations (Scopus)

Nonselective Conduction in a Mutated NaK Channel with Three Cation-Binding Sites

Furini, S. & Domene, C., 21 Nov 2012, In: Biophysical Journal. 103, 10, p. 2106-2114 9 p.

Research output: Contribution to journal › Article › peer-review

15 Citations (Scopus)

On Conduction in a Bacterial Sodium Channel

Furini, S. & Domene, C., 5 Apr 2012, In: PL o S Computational Biology. 8, 4, 7 p., 1002476.

Research output: Contribution to journal › Article › peer-review

Open Access

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79 Citations (Scopus)

145 Downloads (Pure)

Voltage-sensor cycle fully described

Domene, C., 29 May 2012, In: Proceedings of the National Academy of Sciences of the United States of America. 109, 22, p. 8362-8363 2 p.

Research output: Contribution to journal › Comment/debate

1 Citation (Scopus)

2011

Gating at the Selectivity Filter of Ion Channels that Conduct Na+ and K+ Ions

Furini, S. & Domene, C., 5 Oct 2011, In: Biophysical Journal. 101, 7, p. 1623-1631 9 p.

Research output: Contribution to journal › Article › peer-review

18 Citations (Scopus)

On Conduction and Gating in K+-Channels

Domene, C. & Furini, S., 2 Feb 2011, Biophysical Journal. 3 ed. CELL PRESS, Vol. 100. p. 579a-579a 1 p.

Research output: Chapter in Book/Report/Conference proceeding › Conference paper › peer-review

Selectivity and Permeation of Alkali Metal Ions in K+-channels

Furini, S. & Domene, C., 24 Jun 2011, In: Journal of Molecular Biology. 409, 5, p. 867-878 12 p.

Research output: Contribution to journal › Article › peer-review

28 Citations (Scopus)

Structural and biochemical analyses reveal how ornithine acetyl transferase binds acidic and basic amino acid substrates

Iqbal, A., Clifton, I. J., Chowdhury, R., Ivison, D., Domene, C. & Schofield, C. J., 21 Sept 2011, In: Organic & biomolecular chemistry. 9, 18, p. 6219-6225 7 p.

Research output: Contribution to journal › Article › peer-review

4 Citations (Scopus)

2010

Chemical Basis for the Selectivity of the von Hippel Lindau Tumor Suppressor pVHL for Prolyl-Hydroxylated HIF-1 alpha

Illingworth, C. J. R., Loenarz, C., Schofield, C. J. & Domene, C., 17 Aug 2010, In: Biochemistry. 49, 32, p. 6936-6944 9 p.

Research output: Contribution to journal › Article › peer-review

15 Citations (Scopus)

Carmen Domene Nunez

Research output

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