Support for the UKCP consortium
Lead Research Organisation:
King's College London
Department Name: Physics
Abstract
Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.
Organisations
People |
ORCID iD |
| Carla Molteni (Principal Investigator) |
Publications
Botten D
(2015)
Structural Properties of Green Tea Catechins
in The Journal of Physical Chemistry B
Comitani F
(2017)
Mapping the conformational free energy of aspartic acid in the gas phase and in aqueous solution.
in The Journal of chemical physics
Comitani F
(2014)
Insights into the binding of GABA to the insect RDL receptor from atomistic simulations: a comparison of models.
in Journal of computer-aided molecular design
Comitani F
(2015)
Elucidating ligand binding and channel gating mechanisms in pentameric ligand-gated ion channels by atomistic simulations.
in Biochemical Society transactions
Comitani F
(2016)
The Free Energy Landscape of GABA Binding to a Pentameric Ligand-Gated Ion Channel and Its Disruption by Mutations.
in Journal of chemical theory and computation
Corsini NR
(2017)
Unravelling the Roles of Size, Ligands, and Pressure in the Piezochromic Properties of CdS Nanocrystals.
in Nano letters
Crnjar A
(2019)
Mutagenesis computer experiments in pentameric ligand-gated ion channels: the role of simulation tools with different resolution.
in Interface focus
Crnjar A
(2019)
Trans- Cis Proline Switches in a Pentameric Ligand-Gated Ion Channel: How They Are Affected by and How They Affect the Biomolecular Environment.
in The journal of physical chemistry letters
Fulford M
(2019)
DeepIce: A Deep Neural Network Approach To Identify Ice and Water Molecules.
in Journal of chemical information and modeling
| Description | We studied the binding of the neurotransmitter GABA to models of the insect RDL receptors, a ligand gated ion channel involved in insecticide resistance. This was done first with conventional ligand-protein docking and molecular dynamics simulations and then with the innovative enhanced sampling funnel-metadynamics method. Results for the wild-type and mutants are consistent with experiments and provide the neurotransmitter-binding free energy landscape and its disruption by mutations. We also investigated the serotonin-activated 5-HT3 receptor with a model including a mimic of the cell membrane. We investigated the binding of the green tea polyphenol EGCg to the cardiac protein troponin C, involved in heart contractions, to elucidate the potential role of EGCg as calcium regulator. We explored the conformational free energy landscape of aspartic acid and green tea polyphenols in the gas phase and aqueous solution. We evaluated the free energy of melting and re-crystallization at surfaces of hexagonal ice as part of a study to understand the mechanism of growth of ice crystals at different temperature. We estimated the rate of recrystallization and the structure and properties of the quasi-liquid layer at ice surfaces as a function of temperature. We investigated the piezochromic properties of CdS nanocrystals by calculating the absorption spectra under pressure with time-dependent density functional theory. |
| Exploitation Route | Ligand gated ion channels are involved in neuronal disorders and target sites for drugs and insecticides so understanding their activation mechanisms may be relevant for the chemical and pharmaceutical industries. Green tea is becoming popular for its alleged health benefits so the study of its active components may also be relevant for the pharmaceutical, cosmetic and healthcare sectors. Ice is important for the environment and understanding how its growth is affected by temperature is interesting for climate change. The piezochromic properties of semiconductor nanocrystals may be exploited for pressure sensors. |
| Sectors | Agriculture, Food and Drink,Chemicals,Electronics,Environment,Healthcare,Pharmaceuticals and Medical Biotechnology |
| URL | http://ukcp.ac.uk |
| Description | This grant was part of a large consortium containing 19 different nodes (university departments) led by Prof. Matt Probert at the University of York. Please see the overview and impact summary of EPSRC Grant EP/K013564/1. The resources help train PhD students in biological and nanomaterials simulations which went on to a variety of career in academia, finance and data science. |
| First Year Of Impact | 2016 |
| Sector | Chemicals,Education,Environment,Pharmaceuticals and Medical Biotechnology |
| Impact Types | Societal,Economic |
| Description | Support for the UKCP consortium |
| Amount | £9,987 (GBP) |
| Funding ID | EP/P022472/1 |
| Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 04/2017 |
| End | 03/2022 |
| Title | Data Files for Mapping the Conformational Free Energy of Aspartic Acid in the Gas Phase and in Aqueous Solution |
| Description | Supporting data for "Mapping the conformational free energy of aspartic acid in the gas phase and in aqueous solution" , Federico Comitani, Kevin Rossi, Michele Ceriotti, M. Eugenia Sanz and Carla Molteni, The Journal of Chemical Physics 146, 145102 (2017); https://doi.org/10.1063/1.4979519 |
| Type Of Material | Database/Collection of data |
| Year Produced | 2017 |
| Provided To Others? | Yes |
| Impact | Development of a simulation protocol combining force-field based metadynamics, sketch-map analysis, and quantum chemical calculations able to produce an exhaustive conformational exploration that can be applied to amino acid and peptides with complex conformational landscapes. |
| Title | DeepIce |
| Description | Deep Neural Network for identifying the phase of water and ice molecules |
| Type Of Material | Computer model/algorithm |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | This is useful as an example of applying deep neural networks to distinguish structurally different molecular environments. |
| URL | https://github.com/mfulford/DeepIce |
| Title | Simulation data I (molecular dynamics) for 'Trans-Cis Proline Switches in a Pentameric Ligand-Gated Ion Channel - How They Are Affected by and How They Affect the Biomolecular Environment' |
| Description | Pentameric ligand-gated ion channels (pLGICs) are important neuroreceptors, embedded in neuronal membranes, that mediate fast synaptic transmission. The molecular details of their working mechanisms have still to be fully unravelled due to their complexity and limited structural information available. Here we focus on a potential molecular switch in a prototypical pLGIC, the serotonin-activated 5-HT3 receptor, consisting of the trans-cis isomerization of a proline at the interface between the extracellular and transmembrane domain. We investigate this switch within the receptor with molecular dynamics (data reported here) and metadynamics simulations. The molecular dynamics simulations were performed for four different models, named 5Trans (with Pro281 in the trans conformation for all the five subunits), 3Cis (with Pro281 in the cis conformation in subunits 1, 3 and 4), 5Cis (with the five Pro281 in cis), and 5Trans5Cis (with the five Pro281 in trans and the five Pro274 in cis). |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| Impact | These data show molecular dynamics simulations of a pentameric ligand gated ion channel embedded in a lipid bilayer and provide useful information for setting up simulations of similar systems within the research group and outside. |
| Title | Simulation data II (metadynamics) for 'Trans-Cis Proline Switches in a Pentameric Ligand-Gated Ion Channel - How They Are Affected by and How They Affect the Biomolecular Environment' |
| Description | Pentameric ligand-gated ion channels (pLGICs) are important neuroreceptors, embedded in neuronal membranes, that mediate fast synaptic transmission. The molecular details of their working mechanisms have still to be fully unravelled due to their complexity and limited structural information available. Here we focus on a potential molecular switch in a prototypical pLGIC, the serotonin-activated 5-HT3 receptor, consisting of the trans-cis isomerization of a proline at the interface between the extracellular and transmembrane domain. We investigate this switch within the receptor with metadynamics simulations (data reported here) and molecular dynamics. The metadynamics simulations concern the isomerisation process of Pro281 in subunit 3. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| Impact | These data show how to carry out an enhanced sampling study with metadynamics of proline isomerization in a complex biomolecular environment, useful for computational scientists interested in similar systems. |
| Title | Simulation data for The Free Energy Landscape of GABA Binding to a Pentameric Ligand-gated Ion Channel and its Disruption by Mutations |
| Description | Supporting data for the paper Federico Comitani, Vittorio Limongelli and Carla Molteni, "The Free Energy Landscape of GABA Binding to a Pentameric Ligand-gated Ion Channel and its Disruption by Mutations", J. Chem. Theory Comput. 12, 3398-3406 (2016). DOI: 10.1021/acs.jctc.6b00303 |
| Type Of Material | Database/Collection of data |
| Year Produced | 2016 |
| Provided To Others? | Yes |
| Impact | Simulation protocol for the free energy landscape of a neurotransmitter binding to a pentameric ligand gated ion channel using the funnel metadynamics method. |
| Title | Simulation data for: Piezochromic effects in CdS nanocrystals: the roles of size, ligands and pressure |
| Description | Simulation data supporting the publication Unravelling the Roles of Size, Ligands, and Pressure in the Piezochromic Properties of CdS Nanocrystals, N.R.C. Corsini, N.D.M. Hine, P.D. Haynes and C. Molteni, Nano Lett., 2017, 17 (2), pp 1042-1048, DOI: 10.1021/acs.nanolett.6b04461 |
| Type Of Material | Database/Collection of data |
| Year Produced | 2016 |
| Provided To Others? | Yes |
| Impact | Simulation protocol for large time-dependent DFT calculations of CdS nanocrystals |
| URL | https://zenodo.org/record/58269#.WpQqK0x2u88 |