Publications
171 results found
Gould I, 2016, Molecular dynamics studies targeting the DNA-binding process of ERG focusing on autoinhibition and sequence recognition, Publisher: AMER CHEMICAL SOC, ISSN: 0065-7727
Zamora JE, Sheehan A, Papadaki M, et al., 2016, Troponin structure and effects of phosphorylation and mutations studied by molecular dynamics simulations, 60th Annual Meeting of the Biophysical-Society, Publisher: Biophysical Society, Pages: 208A-208A, ISSN: 1542-0086
Madej BD, Gould IR, Walker RC, 2015, A parameterization of cholesterol for mixed lipid bilayer simulation within the amber lipid14 force field, Journal of Physical Chemistry B, Vol: 119, Pages: 12424-12435, ISSN: 1520-6106
The Amber Lipid14 force field is expanded to include cholesterol parameters for all-atom cholesterol and lipid bilayer molecular dynamics simulations. The General Amber and Lipid14 force fields are used as a basis for assigning atom types and basic parameters. A new RESP charge derivation for cholesterol is presented, and tail parameters are adapted from Lipid14 alkane tails. 1,2-Dimyristoyl-sn-glycero-3-phosphocholine (DMPC), 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayers are simulated at a range of cholesterol contents. Experimental bilayer structural properties are compared with bilayer simulations and are found to be in good agreement. With this parameterization, another component of complex membranes is available for molecular dynamics with the Amber Lipid14 force field.
Buyandelger B, Mansfield C, Kostin S, et al., 2015, ZBTB17 (MIZ1) Is Important for the Cardiac Stress Response and a Novel Candidate Gene for Cardiomyopathy and Heart Failure., Circulation. Cardiovascular Genetics, Vol: 8, Pages: 643-652, ISSN: 1942-3268
BACKGROUND: -Mutations in sarcomeric and cytoskeletal proteins are a major cause of hereditary cardiomyopathies, but our knowledge remains incomplete as to how the genetic defects execute their effects. METHODS AND RESULTS: -We used cysteine and glycine-rich protein 3 (CSRP3), a known cardiomyopathy gene, in a yeast two-hybrid screen and identified zinc finger and BTB domain containing protein 17 (ZBTB17) as a novel interacting partner. ZBTB17 is a transcription factor that contains the peak association signal (rs10927875) at the replicated 1p36 cardiomyopathy locus. ZBTB17 expression protected cardiac myocytes from apoptosis in vitro and in a mouse model with cardiac myocyte-specific deletion of Zbtb17, which develops cardiomyopathy and fibrosis after biomechanical stress. ZBTB17 also regulated cardiac myocyte hypertrophy in vitro and in vivo in a calcineurin-dependent manner. CONCLUSIONS: -We revealed new functions for ZBTB17 in the heart, a transcription factor which may play a role as a novel cardiomyopathy gene.
Messer AE, Papadaki M, Marston SB, et al., 2015, Molecular Dynamics Studies on Phosphorylated and Unphosphorylated Cardiac Troponin, 59th Annual Meeting of the Biophysical-Society, Publisher: CELL PRESS, Pages: 447A-447A, ISSN: 0006-3495
Skjevik AA, Madej BD, Dickson CJ, et al., 2015, All-atom lipid bilayer self-assembly with the AMBER and CHARMM lipid force fields, CHEMICAL COMMUNICATIONS, Vol: 51, Pages: 4402-4405, ISSN: 1359-7345
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- Citations: 53
Dent MR, Lopez-Duarte I, Dickson CJ, et al., 2015, Imaging phase separation in model lipid membranes through the use of BODIPY based molecular rotors, PHYSICAL CHEMISTRY CHEMICAL PHYSICS, Vol: 17, Pages: 18393-18402, ISSN: 1463-9076
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- Citations: 73
Gould IR, 2014, Time dependent DFT calculations of the reaction center of photosystem II, 248th National Meeting of the American-Chemical-Society (ACS), Publisher: AMER CHEMICAL SOC, ISSN: 0065-7727
Aronica PGA, Gould IR, Leatherbarrow RJ, 2014, Development of a new protocol for computational site-directed mutagenesis, 248th National Meeting of the American-Chemical-Society (ACS), Publisher: AMER CHEMICAL SOC, ISSN: 0065-7727
Gould IR, 2014, Structure of the interaction between troponin I N-terminal peptide and the N-terminal lobe of troponin C studied by molecular dynamics, 248th National Meeting of the American-Chemical-Society (ACS), Publisher: AMER CHEMICAL SOC, ISSN: 0065-7727
Walker RC, Dickson CJ, Madej BD, et al., 2014, Amber lipid force field: Lipid14 and beyond, 248th National Meeting of the American-Chemical-Society (ACS), Publisher: AMER CHEMICAL SOC, ISSN: 0065-7727
Papadaki M, Gould I, Messer A, et al., 2014, Investigation of the effect of troponin I phosphorylation on troponin C by molecular dynamics simulations, CARDIOVASCULAR RESEARCH, Vol: 103, ISSN: 0008-6363
Dufton N, Almagro LO, Birdsey G, et al., 2014, THE ENDOTHELIAL TRANSCRIPTION FACTOR ERG INHIBITS VASCULAR INFLAMMATION, HEART, Vol: 100, Pages: A115-A116, ISSN: 1355-6037
Dickson CJ, Madej BD, Skjevik AA, et al., 2014, Lipid14: The Amber Lipid Force Field, JOURNAL OF CHEMICAL THEORY AND COMPUTATION, Vol: 10, Pages: 865-879, ISSN: 1549-9618
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- Citations: 868
Gould I, Messer AE, Papadaki M, et al., 2014, Modulation of the Interaction between Troponin I N-Terminal Peptide and Troponin C by Phosphorylation Studied by Molecular Dynamics, 58th Annual Meeting of the Biophysical-Society, Publisher: CELL PRESS, Pages: 349A-349A, ISSN: 0006-3495
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- Citations: 2
Madej BD, Dickson CJ, Walker RC, et al., 2013, Modular amber lipid force field for the simulation of complex membranes and membrane bound proteins, 245th National Meeting of the American-Chemical-Society (ACS), Publisher: AMER CHEMICAL SOC, ISSN: 0065-7727
Walker RC, Madej B, Gould IR, et al., 2013, Lipid 12: Accurate membrane simulations with a redesigned modular phospholipid force field for AMBER, 245th National Meeting of the American-Chemical-Society (ACS), Publisher: AMER CHEMICAL SOC, ISSN: 0065-7727
Gould IR, 2012, Molecular dynamics investigations into the mechanism of action of fructose 1,6-bisphosphate aldolase, in mycobacterium tuberculosis, 11th International Biorelated Polymer Symposium / 243rd National Spring Meeting of the American-Chemical-Society (ACS), Publisher: AMER CHEMICAL SOC, ISSN: 0065-7727
Gould IR, 2012, MULES (Mutational Locally Enhanced Sampling) a new method for quantitative prediction of relative binding free energies, 11th International Biorelated Polymer Symposium / 243rd National Spring Meeting of the American-Chemical-Society (ACS), Publisher: AMER CHEMICAL SOC, ISSN: 0065-7727
Gould IR, 2012, Evaluation of quantum chemical methods for the prediction of non-specific binding of positron emission tomography tracers, 11th International Biorelated Polymer Symposium / 243rd National Spring Meeting of the American-Chemical-Society (ACS), Publisher: AMER CHEMICAL SOC, ISSN: 0065-7727
Bradshaw RT, Aronica PGA, Tate EW, et al., 2012, Developing mutational locally enhanced sampling (MULES) for predicting relative binding free energies at protein-protein interfaces, 11th International Biorelated Polymer Symposium / 243rd National Spring Meeting of the American-Chemical-Society (ACS), Publisher: AMER CHEMICAL SOC, ISSN: 0065-7727
Rosen SAJ, Gaffney PRJ, Gould IR, 2012, Understanding the interactions of inositol phosphates with protein kinase B using long time-scale simulations, 11th International Biorelated Polymer Symposium / 243rd National Spring Meeting of the American-Chemical-Society (ACS), Publisher: AMER CHEMICAL SOC, ISSN: 0065-7727
Dickson CJ, Rosso L, Walker RC, et al., 2012, Lipid bilayer simulations: Expanding time and space with the General Amber Force Field, 11th International Biorelated Polymer Symposium / 243rd National Spring Meeting of the American-Chemical-Society (ACS), Publisher: AMER CHEMICAL SOC, ISSN: 0065-7727
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- Citations: 2
Rosen SAJ, Gaffney PRJ, Gould I, 2012, Flipping inositol phosphates: A molecular dynamics approach to understanding the selectivity of protein kinase B, 11th International Biorelated Polymer Symposium / 243rd National Spring Meeting of the American-Chemical-Society (ACS), Publisher: AMER CHEMICAL SOC, ISSN: 0065-7727
Dickson CJ, Rosso L, Betz RM, et al., 2012, GAFFlipid: a General Amber Force Field for the accurate molecular dynamics simulation of phospholipid, Soft Matter, Vol: 8, Pages: 9617-9627-9617-9627
Previous attempts to simulate phospholipid bilayers using the General Amber Force Field (GAFF) yielded many bilayer characteristics in agreement with experiment, however when using a tensionless NPT ensemble the bilayer is seen to compress to an undesirable extent resulting in low areas per lipid and high order parameters in comparison to experiment. In this work, the GAFF Lennard-Jones parameters for the simulation of acyl chains are corrected to allow the accurate and stable simulation of pure lipid bilayers. Lipid bilayers comprised of six phospholipid types were simulated for timescales approaching a quarter of a microsecond under tensionless constant pressure conditions using Graphics Processing Units. Structural properties including area per lipid, volume per lipid, bilayer thickness, order parameter and headgroup hydration show favourable agreement with available experimental values. Expanding the system size from 72 to 288 lipids and a more experimentally realistic 2 [times] 288 lipid bilayer stack induces little change in the observed properties. This preliminary work is intended for combination with the new AMBER Lipid11 modular force field as part of on-going attempts to create a modular phospholipid AMBER force field allowing tensionless NPT simulations of complex lipid bilayers.
Bradshaw RT, Aronica PGA, Tate EW, et al., 2012, Mutational Locally Enhanced Sampling (MULES) for quantitative prediction of the effects of mutations at protein-protein interfaces, CHEMICAL SCIENCE, Vol: 3, Pages: 1503-1511, ISSN: 2041-6520
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- Citations: 2
Rosen SAJ, Gaffney PRJ, Spiess B, et al., 2012, Understanding the relative affinity and specificity of the pleckstrin homology domain of protein kinase B for inositol phosphates, PHYSICAL CHEMISTRY CHEMICAL PHYSICS, Vol: 14, Pages: 929-936, ISSN: 1463-9076
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- Citations: 13
Rosen SAJ, Gaffney PRJ, Gould IR, 2011, A theoretical investigation of inositol 1,3,4,5-tetrakisphosphate, PHYSICAL CHEMISTRY CHEMICAL PHYSICS, Vol: 13, Pages: 1070-1081, ISSN: 1463-9076
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- Citations: 7
Dickson C, Gould I, Rosso L, et al., 2011, The Relationship between Drug-Lipid Interaction Energy and Non-Specific Binding, JOURNAL OF LABELLED COMPOUNDS & RADIOPHARMACEUTICALS, Vol: 54, Pages: S135-S135, ISSN: 0362-4803
Dickson CJ, Gee AD, Bennacef I, et al., 2011, Further evaluation of quantum chemical methods for the prediction of non-specific binding of positron emission tomography tracers, Phys. Chem. Chem. Phys., Vol: 13, Pages: 21552-21557-21552-21557
The non-specific binding of candidate positron emission tomography (PET) radiotracers causes resulting PET images to have poor contrast and is a key determinant for the success or failure of imaging drugs. Non-specific binding is thought to arise when radiotracers bind to cell membranes and moieties other than their intended target. Our previous preliminary work has proposed the use of the drug-lipid interaction energy descriptor to predict the level of non-specific binding in vivo using a limited set of ten well known PET radiotracers with kinetic modelling data taken from the literature. This work validates and extends the use of the drug-lipid interaction energy descriptor using a new set of twenty-two candidate PET radiotracers with non-specific binding data recently collected at the same imaging centre with consistent methodology. As with the previous set of radiotracers, a significant correlation is found between the quantum chemical drug-lipid interaction energy and in vivo non-specific binding experimental values. In an effort to speed up the calculation process, several semi-empirical quantum chemical methods were assessed for their ability to reproduce the ab initio results. However no single semi-empirical method was found to consistently reproduce the level of correlation achieved with ab initio quantum chemical methods.
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