169 results found
Abdel-Aty H, Gould IR, 2022, Large-Scale Distributed Training of Transformers for Chemical Fingerprinting, JOURNAL OF CHEMICAL INFORMATION AND MODELING, Vol: 62, Pages: 4852-4862, ISSN: 1549-9596
Pavadai E, Rynkiewicz MJ, Yang Z, et al., 2022, Modulation of cardiac thin filament structure by phosphorylated troponin-I analyzed by protein-protein docking and molecular dynamics simulation., Archives of Biochemistry and Biophysics, Vol: 725, Pages: 109282-109282, ISSN: 0003-9861
Tropomyosin, controlled by troponin-linked Ca2+-binding, regulates muscle contraction by a macromolecular scale steric-mechanism that governs myosin-crossbridge-actin interactions. At low-Ca2+, C-terminal domains of troponin-I (TnI) trap tropomyosin in a position on thin filaments that interferes with myosin-binding, thus causing muscle relaxation. Steric inhibition is reversed at high-Ca2+ when TnI releases from F-actin-tropomyosin as Ca2+ and the TnI switch-peptide bind to the N-lobe of troponin-C (TnC). The opposite end of cardiac TnI contains a phosphorylation-sensitive ∼30 residue-long N-terminal peptide that is absent in skeletal muscle, and likely modifies these interactions in hearts. Here, PKA-dependent phosphorylation of serine 23 and 24 modulates Ca2+ and possibly switch-peptide binding to TnC, causing faster relaxation during the cardiac-cycle (lusitropy). The cardiac-specific N-terminal TnI domain is not captured in crystal structures of troponin or in cryo-EM reconstructions of thin filaments; thus, its global impact on thin filament structure and function is uncertain. Here, we used protein-protein docking and molecular dynamics simulation-based protocols to build a troponin model that was guided by and hence consistent with the recent seminal Yamada structure of Ca2+-activated thin filaments. We find that when present on thin filaments, phosphorylated Ser23/24 along with adjacent polar TnI residues interact closely with both tropomyosin and the N-lobe of TnC during our simulations. These interactions would likely bias tropomyosin to an off-state positioning on actin. In situ, such enhanced relaxation kinetics would promote cardiac lusitropy.
Pavadai E, Rynkiewicz MJ, Yang Z, et al., 2022, N-Terminal domains of cardiac troponin-I modulate thin filament structure, Publisher: CELL PRESS, Pages: 37-37, ISSN: 0006-3495
Abdel Aty H, Strutt R, Mcintyre N, et al., 2022, Machine learning platform for determining experimental lipid phase behaviour from small angle X-ray scattering patterns by pre-training on synthetic data, Digital Discovery, Vol: 1, Pages: 98-107
Lipid membranes are vital in a wide range of biological and biotechnical systems; they undepin functions from modulation of protein activity to drug uptake and delivery. Understanding the structure, interactions, self-assembly and phase behaviour of lipids is critical to developing a molecular undertanding of biological membrane mediated processes, establishing engineering approaches to biotechnical membrane application development. Small Angle X-ray Scattering (SAXS) is the de facto method used to analyse the structure of self-assembled lipid systems. The resultant diffraction patterns are however extremely difficult to assign automatically with researchers spending considerable time often analysing patterns ex situ from a beamline facility, reducing experimental capacity and optimisation. Furthermore, research projects will often focus on particular lipid compositions and thus would benefit significantly from a method which can be rapidly optimised for a range of samples of interest. We present a generalisable machine learning pipeline that is able to classify lipid phases based on their raw, experimental SAXS spectra, with >99% accuracy and an inference time of <60 ms, enabling high throughput on-site analysis. We achieved this through application of a synthetic data generation system, capable of building synthetic SAXS patterns from the underlying physics which dictate phase behaviour, and we also propose an extension of our system to synthetically generate co-existence phase spectra with known composition ratios. Pre-training our machine learning model on this synthetic data, and fine-tuning on experimental samples empowers the model in achieving state-of-the-art, rapid lipid phase classification, allowing researchers to be able to adapt their experiments on site if needed and hence massively accelerate high throughput lipid research.
Dickson CJ, Walker RC, Gould IR, 2022, Lipid21: complex lipid membrane simulations with AMBER., Journal of Chemical Theory and Computation, Vol: 18, ISSN: 1549-9618
We extend the modular AMBER lipid force field to include anionic lipids, polyunsaturated fatty acid (PUFA) lipids, and sphingomyelin, allowing the simulation of realistic cell membrane lipid compositions, including raft-like domains. Head group torsion parameters are revised, resulting in improved agreement with NMR order parameters, and hydrocarbon chain parameters are updated, providing a better match with phase transition temperature. Extensive validation runs (0.9 μs per lipid type) show good agreement with experimental measurements. Furthermore, the simulation of raft-like bilayers demonstrates the perturbing effect of increasing PUFA concentrations on cholesterol molecules. The force field derivation is consistent with the AMBER philosophy, meaning it can be easily mixed with protein, small molecule, nucleic acid, and carbohydrate force fields.
Vilar Compte R, Reeh K, Summers P, et al., 2020, Design, synthesis and evaluation of a tripodal receptor for phosphatidylinositol phosphates, Scientific Reports, Vol: 10, ISSN: 2045-2322
Phosphatidylinositol phosphates (PIPs) are membrane phospholipids that play crucial roles in a wide range of cellular processes. Their function is dictated by the number and positions of the phosphate groups in the inositol ring (with seven different PIPs being active in the cell). Therefore, there is significant interest in developing small-molecule receptors that can bind selectively to these species and in doing so affect their cellular function or be the basis for molecular probes. However, to date there are very few examples of such molecular receptors. Towards this aim, herein we report a novel tripodal molecule that acts as receptor for mono- and bis-phosphorylated PIPs in a cell free environment. To assess their affinity to PIPs we have developed a new cell free assay based on the ability of the receptor to prevent alkaline phosphatase from hydrolysing these substrates. The new receptor displays selectivity towards two out of the seven PIPs, namely PI(3)P and PI(3,4)P2. To rationalise these results, a DFT computational study was performed which corroborated the experimental results and provided insight into the host–guest binding mode.
Kavanagh MA, Karlsson JK, Colburn JD, et al., 2020, A TDDFT investigation of the Photosystem II reaction center: Insights into the precursors to charge separation, Proceedings of the National Academy of Sciences of USA, Vol: 117, Pages: 19705-19712, ISSN: 0027-8424
Photosystem II (PS II) captures solar energy and directs charge separation (CS) across the thylakoid membrane during photosynthesis. The highly oxidizing, charge-separated state generated within its reaction center (RC) drives water oxidation. Spectroscopic studies on PS II RCs are difficult to interpret due to large spectral congestion, necessitating modeling to elucidate key spectral features. Herein, we present results from time-dependent density functional theory (TDDFT) calculations on the largest PS II RC model reported to date. This model explicitly includes six RC chromophores and both the chlorin phytol chains and the amino acid residues <6 Å from the pigments’ porphyrin ring centers. Comparing our wild-type model results with calculations on mutant D1-His-198-Ala and D2-His-197-Ala RCs, our simulated absorption-difference spectra reproduce experimentally observed shifts in known chlorophyll absorption bands, demonstrating the predictive capabilities of this model. We find that inclusion of both nearby residues and phytol chains is necessary to reproduce this behavior. Our calculations provide a unique opportunity to observe the molecular orbitals that contribute to the excited states that are precursors to CS. Strikingly, we observe two high oscillator strength, low-lying states, in which molecular orbitals are delocalized over ChlD1 and PheD1 as well as one weaker oscillator strength state with molecular orbitals delocalized over the P chlorophylls. Both these configurations are a match for previously identified exciton–charge transfer states (ChlD1+PheD1−)* and (PD2+PD1−)*. Our results demonstrate the power of TDDFT as a tool, for studies of natural photosynthesis, or indeed future studies of artificial photosynthetic complexes.
Kavanagh M, Gould I, Barter L, 2019, Excited states of the photosystem II reaction center, ACS Fall National Meeting and Exposition, Publisher: AMER CHEMICAL SOC, ISSN: 0065-7727
Toroz D, Khanna T, Gould I, 2019, Modelling the effect of BSEP inhibitors in lipid bilayers by means of all atom Molecular Dynamics (MD) simulation, ACS Omega, Vol: 4, Pages: 3341-3350, ISSN: 2470-1343
The human bile salt export pump (BSEP) is a membrane protein expressed on the canalicular plasma membrane domain of hepatocytes, which mediates active transport of unconjugated and conjugated bile salts from liver cells into bile. Genetically inherited defects in BSEP expression or activity causes cholestatic liver injury, and many drugs that cause cholestatic drug-induced liver injury (DILI) in humans have been shown to inhibit BSEP activity in vitro and in vivo, suggesting this could be one of the mechanisms that initiates human DILI. The relationship between BSEP inhibition and molecular physicochemical properties has been previously investigated identifying calculated lipophilicity and molecular weight to be significantly correlated with BSEP inhibition. Predictive BSEP classification models, constructed through multiple quantitative structure-activity relationship modeling approaches, exhibit significant anomalies with differences in experimental IC50 values of three orders of magnitude for molecules of the same calculated lipophilicity and molecular weight. The interaction of these molecules with the lipid bilayer membrane has been identified as a major contributory factor to BSEP inhibition. In this study we apply unbiased molecular dynamics (MD) simulations to study the permeation times as well as orientation preferences of BSEP inhibitors in two different lipids (saturated DMPC and unsaturated POPC). The simulations reveal that strong BSEP inhibitors have the slowest permeation times, in both POPC and DMPC, with a secondary conclusion that the time of permeation is more rapid in POPC than DMPC. The orientation of the molecules in the membrane reveals strong correlation with chemical structure, molecules containing only hydroxyl and carboxylic groups orient themselves perpendicular to the membrane whereas molecules containing nitrogen atoms exhibit no orientational preference in respect of the membrane. Finally, H-bonding interactions computed between the mo
Gould I, Toroz D, 2019, A computational study of Anthracyclines interacting with lipid bilayers: Correlation of membrane insertion rates, orientation effects and localisation with cytotoxicity, Scientific Reports, Vol: 9, ISSN: 2045-2322
Anthracyclines interact with DNA and topoisomerase II as well as with cell membranes, and it is these latter interactions that can cause an increase in their cytotoxic activity. In the present study a detailed computational analysis of the initial insertion, orientation and nature of the interaction occurring between Anthracyclines and two different lipid bilayers (unsaturated POPC and saturated DMPC) is explored through molecular dynamics (MD) simulations; four Anthracyclines: Doxorubicin (DOX), Epirubicin (EPI), Idarubicin (IDA) and Daunorubicin (DAU) were examined. The results indicate that the increased cytotoxicity of DOX, in comparison to the other three analogues, is correlated with its ability to diffuse at a faster rate into the bilayers. Additionally, DOX exhibited considerably different orientational behaviour once incorporated into the bilayer and exhibited a higher propensity to interact with the hydrocarbon tails in both lipids indicating a higher probability of transport to the other leaflet of the bilayer.
Yuan Q, Toroz D, Kidley N, et al., 2018, Mechanism of photoinduced triplet intermolecular hydrogen transfer between cycloxydim and chlorothalonil, The Journal of Physical Chemistry Part A: Molecules, Spectroscopy, Kinetics, Environment and General Theory, Vol: 122, Pages: 4285-4293, ISSN: 1089-5639
The possible reaction mechanisms for the experimentally observed hydrogen transfer between the herbicide cycloxydim (CD) and the triplet fungicide chlorothalonil (CT) were identified with density functional theory (DFT) and time-dependent density function theory (TDDFT) computations. Excited energy transfer (EET) calculations indicate that reactants for intermolecular hydrogen transfer were formed via energy transfer from triplet CT to ground state CD. Three possible reaction pathways after EET were identified, and hydrogen transfer from the hydroxyl group on the cyclohexane ring of CD to CT exhibited the lowest energy barrier. Natural population analysis (NPA) along the reaction pathways has confirmed that the pathways involved either electron transfer induced proton transfer or coupled electron–proton transfer, leading to different potential energy profiles. Electrostatic potential (ESP) study substantiated the reaction mechanisms in different pathways. This study suggests an explanation for the accelerated photodegradation of CD by CT and provides a pipeline for future studies of photoinduced intermolecular hydrogen transfer.
Wang S, Gould I, 2018, All-atom molecular dynamics of an ion-channel formed by viral protein U in lipid bilayers, 255th National Meeting and Exposition of the American-Chemical-Society (ACS) - Nexus of Food, Energy, and Water, Publisher: AMER CHEMICAL SOC, ISSN: 0065-7727
Marston SB, Messer AE, Eiros-Zamora J, et al., 2018, The Molecular Defects in Ca2+ Regulation due to Mutations that Cause Hypertrophic Cardiomyopathy can be Reversed by Small Molecules that Bind to Troponin, 62nd Annual Meeting of the Biophysical-Society, Publisher: CELL PRESS, Pages: 37A-37A, ISSN: 0006-3495
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Marston SSB, Choudry A, Kren V, et al., 2017, The molecular defect in hypertrophic cardiomyopathy and drugs that correct the defect, EUROPEAN JOURNAL OF HEART FAILURE, Vol: 19, Pages: 252-252, ISSN: 1388-9842
Yuan Q, Gould I, Kidley N, 2017, Density functional theory study on triplet intermolecular hydrogen transfer between cycloxydim and chlorothalonil, 253rd National Meeting of the American-Chemical-Society (ACS) on Advanced Materials, Technologies, Systems, and Processes, Publisher: AMER CHEMICAL SOC, ISSN: 0065-7727
Khanna T, Barter L, Gould I, 2017, Development and application of the AMBER molecular mechanics force field to investigate herbicide interaction in plants, 253rd National Meeting of the American-Chemical-Society (ACS) on Advanced Materials, Technologies, Systems, and Processes, Publisher: AMER CHEMICAL SOC, ISSN: 0065-7727
Zamora JE, Hoben G, Sheehan A, et al., 2017, EGCG and Sylibins as treatment for inherited cardiomyopathies: Binding simulations to cardiac troponin, 253rd National Meeting of the American-Chemical-Society (ACS) on Advanced Materials, Technologies, Systems, and Processes, Publisher: AMER CHEMICAL SOC, ISSN: 0065-7727
Barlow NE, Smpokou E, Friddin MS, et al., 2017, Engineering plant membranes using droplet interface bilayers, Biomicrofluidics, Vol: 11, ISSN: 1932-1058
Droplet interface bilayers (DIBs) have become widely recognised as a robust platform for constructing model membranes and are emerging as a key technology for the bottom-up assembly of synthetic cell-like and tissue-like structures. DIBs are formed when lipid-monolayer coated water droplets are brought together inside a well of oil, which is excluded from the interface as the DIB forms. The unique features of the system, compared to traditional approaches (e.g., supported lipid bilayers, black lipid membranes, and liposomes), is the ability to engineer multi-layered bilayer networks by connecting multiple droplets together in 3D, and the capability to impart bilayer asymmetry freely within these droplet architectures by supplying droplets with different lipids. Yet despite these achievements, one potential limitation of the technology is that DIBs formed from biologically relevant components have not been well studied. This could limit the reach of the platform to biological systems where bilayer composition and asymmetry are understood to play a key role. Herein, we address this issue by reporting the assembly of asymmetric DIBs designed to replicate the plasma membrane compositions of three different plant species; Arabidopsis thaliana, tobacco, and oats, by engineering vesicles with different amounts of plant phospholipids, sterols and cerebrosides for the first time. We show that vesicles made from our plant lipid formulations are stable and can be used to assemble asymmetric plant DIBs. We verify this using a bilayer permeation assay, from which we extract values for absolute effective bilayer permeation and bilayer stability. Our results confirm that stable DIBs can be assembled from our plant membrane mimics and could lead to new approaches for assembling model systems to study membrane translocation and to screen new agrochemicals in plants.
Beuerle MG, Dufton NP, Randi AM, et al., 2016, Molecular dynamics studies on the DNA-binding process of ERG, Molecular BioSystems, Vol: 12, Pages: 3600-3610, ISSN: 1742-206X
The ETS family of transcription factors regulate gene targets by binding to a core GGAA DNA-sequence. The ETS factor ERG is required for homeostasis and lineage-specific functions in endothelial cells, some subset of haemopoietic cells and chondrocytes; its ectopic expression is linked to oncogenesis in multiple tissues. To date details of the DNA-binding process of ERG including DNA-sequence recognition outside the core GGAA-sequence are largely unknown. We combined available structural and experimental data to perform molecular dynamics simulations to study the DNA-binding process of ERG. In particular we were able to reproduce the ERG DNA-complex with a DNA-binding simulation starting in an unbound configuration with a final root-mean-square-deviation (RMSD) of 2.1 Å to the core ETS domain DNA-complex crystal structure. This allowed us to elucidate the relevance of amino acids involved in the formation of the ERG DNA-complex and to identify Arg385 as a novel key residue in the DNA-binding process. Moreover we were able to show that water-mediated hydrogen bonds are present between ERG and DNA in our simulations and that those interactions have the potential to achieve sequence recognition outside the GGAA core DNA-sequence. The methodology employed in this study shows the promising capabilities of modern molecular dynamics simulations in the field of protein DNA-interactions.
Dent MR, López-Duarte I, Dickson CJ, et al., 2016, Imaging plasma membrane phase behaviour in live cells using a thiophene-based molecular rotor, Chemical Communications, Vol: 52, Pages: 13269-13272, ISSN: 1364-548X
Molecular rotors have emerged as versatile probes of microscopic viscosity in lipid bilayers, although it has proved difficult to find probes that stain both phases equally in phase-separated bilayers. Here, we investigate the use of a membrane-targeting viscosity-sensitive fluorophore based on a thiophene moiety with equal affinity for ordered and disordered lipid domains to probe ordering and viscosity within artificial lipid bilayers and live cell plasma membranes.
Walker R, Madej B, Lin C, et al., 2016, Adventures in the world of lipids: Towards the routine simulation of complex membranes and membrane bound proteins, Publisher: AMER CHEMICAL SOC, ISSN: 0065-7727
Zamora JE, Papadaki M, Messer AE, et al., 2016, Troponin structure: its modulation by Ca(2+) and phosphorylation studied by molecular dynamics simulations., Physical Chemistry Chemical Physics, Vol: 18, Pages: 20691-20707, ISSN: 1463-9084
The only available crystal structure of the human cardiac troponin molecule (cTn) in the Ca(2+) activated state does not include crucial segments, including the N-terminus of the cTn inhibitory subunit (cTnI). We have applied all-atom molecular dynamics (MD) simulations to study the structure and dynamics of cTn, both in the unphosphorylated and bis-phosphorylated states at Ser23/Ser24 of cTnI. We performed multiple microsecond MD simulations of wild type (WT) cTn (6, 5 μs) and bisphosphorylated (SP23/SP24) cTn (9 μs) on a 419 amino acid cTn model containing human sequence cTnC (1-161), cTnI (1-171) and cTnT (212-298), including residues not present in the crystal structure. We have compared our results to previous computational studies, and proven that longer simulations and a water box of at least 25 Å are needed to sample the interesting conformational shifts both in the native and bis-phosphorylated states. As a consequence of the introduction into the model of the C-terminus of cTnT that was missing in previous studies, cTnC-cTnI interactions that are responsible for the cTn dynamics are altered. We have also shown that phosphorylation does not increase cTn fluctuations, and its effects on the protein-protein interaction profiles cannot be assessed in a significant way. Finally, we propose that phosphorylation could provoke a loss of Ca(2+) by stabilizing out-of-coordination distances of the cTnC's EF hand II residues, and in particular Ser 69.
Sheehan A, Zamora JE, Papadaki M, et al., 2016, Structural investigation of the cardiac troponin complex by molecular dynamics, Cardiovascular Research, Vol: 111, Pages: S32-S32, ISSN: 1755-3245
Aronica PG, Verma C, Popovic B, et al., 2016, The Parasol Protocol for computational mutagenesis, Protein Engineering Design & Selection, Vol: 29, Pages: 253-261, ISSN: 1741-0134
To aid in the discovery and development of peptides and proteins as therapeutic agents, a virtual screen can be used to predict trends and direct workflow. We have developed the Parasol Protocol, a dynamic method implemented using the AMBER MD package, for computational site-directed mutagenesis. This tool can mutate between any pair of amino acids in a computationally expedient, automated manner. To demonstrate the potential of this methodology, we have employed the protocol to investigate a test case involving stapled peptides, and have demonstrated good agreement with experiment.
Skjevik AA, Madej BD, Dickson CJ, et al., 2016, Simulation of lipid bilayer self-assembly using all-atom lipid force fields, Physical Chemistry Chemical Physics, Vol: 18, Pages: 10573-10584, ISSN: 1463-9084
In this manuscript we expand significantly on our earlier communication by investigating the bilayer self-assembly of eight different types of phospholipids in unbiased molecular dynamics (MD) simulations using three widely used all-atom lipid force fields. Irrespective of the underlying force field, the lipids are shown to spontaneously form stable lamellar bilayer structures within 1 microsecond, the majority of which display properties in satisfactory agreement with the experimental data. The lipids self-assemble via the same general mechanism, though at formation rates that differ both between lipid types, force fields and even repeats on the same lipid/force field combination. In addition to zwitterionic phosphatidylcholine (PC) and phosphatidylethanolamine (PE) lipids, anionic phosphatidylserine (PS) and phosphatidylglycerol (PG) lipids are represented. To our knowledge this is the first time bilayer self-assembly of phospholipids with negatively charged head groups is demonstrated in all-atom MD simulations.
Yang L, Madej B, Skjevik A, et al., 2016, Extension of the Amber Lipid14 force field to glycolipids: Parameterization and validation, Publisher: AMER CHEMICAL SOC, ISSN: 0065-7727
Walker R, Madej B, Lin C, et al., 2016, Adventures in the world of lipids: Towards the routine simulation of membranes, Publisher: AMER CHEMICAL SOC, ISSN: 0065-7727
Gould I, 2016, Mapping charge transfer pathways in wild-type and mutant photosystem II using time dependent density functional theory, Publisher: AMER CHEMICAL SOC, ISSN: 0065-7727
Madej B, Dickson C, Skjevik A, et al., 2016, Expansion of the Amber Lipid14 force field: Enabling complex membrane molecular dynamics, Publisher: AMER CHEMICAL SOC, ISSN: 0065-7727
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
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