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Lisgarten DR, Palmer RA, Cooper JB, Naylor CE, Talbert RC, Howlin BJ, Lisgarten JN, Konc J, Najmudin S, Lobley CMC. Ultra-high resolution X-ray structure of orthorhombic bovine pancreatic Ribonuclease A at 100K. BMC Chem 2023; 17:91. [PMID: 37501200 PMCID: PMC10375658 DOI: 10.1186/s13065-023-00959-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 05/09/2023] [Indexed: 07/29/2023] Open
Abstract
The crystal structure of orthorhombic Bovine Pancreatic Ribonuclease A has been determined to 0.85 Å resolution using low temperature, 100 K, synchrotron X-ray data collected at 16000 keV (λ = 0.77 Å). This is the first ultra-high-resolution structure of a native form of Ribonuclease A to be reported. Refinement carried out with anisotropic displacement parameters, stereochemical restraints, inclusion of H atoms in calculated positions, five [Formula: see text] moieties, eleven ethanol molecules and 293 water molecules, converged with final R values of R1(Free) = 0.129 (4279 reflections) and R1 = 0.112 (85,346 reflections). The refined structure was deposited in the Protein Data Bank as structure 7p4r. Conserved waters, using four high resolution structures, have been investigated. Cluster analysis identified clusters of water molecules that are associated with the active site of Bovine Ribonuclease A. Particular attention has been paid to making detailed comparisons between the present structure and other high quality Bovine Pancreatic Ribonuclease A X-ray crystal structures with special reference to the deposited classic monoclinic structure 3RN3 Howlin et al. (Acta Crystallogr A 45:851-861, 1989). Detailed studies of various aspects of hydrogen bonding and conformation have been carried out with particular reference to active site residues Lys-1, Lys-7, Gln-11, His-12, Lys-41, Asn-44, Thr-45, Lys-66, His-119 and Ser-123. For the two histidine residues in the active site the initial electron density map gives a clear confirmation that the position of His-12 is very similar in the orthorhombic structure to that in 3RN3. In 3RN3 His-119 exhibited poor electron density which was modelled and refined as two distinct sites, A (65%) and B (35%) but with respect to His-119 in the present ultra-high resolution orthorhombic structure there is clear electron density which was modelled and refined as a single conformation distinct from either conformation A or B in 3RN3. Other points of interest include Serine-32 which is disordered at the end of the sidechain in the present orthorhombic form but has been modelled as a single form in 3RN3. Lysine-66: there is density indicating a possible conformation for this residue. However, the density is relatively weak, and the conformation is unclear. Three types of amino acid representation in the ultra-high resolution electron density are examined: (i) sharp with very clearly resolved features, for example Lys-37; (ii) well resolved but clearly divided into two conformations which are well behaved in the refinement, both having high quality geometry, for example Tyr-76; (iii) poor density and difficult or impossible to model, an example is Lys-31 for which density is missing except for Cβ. The side chains of Gln-11, His-12, Lys-41, Thr-45 and His-119 are generally recognised as being closely involved in the enzyme activity. It has also been suggested that Lys-7, Asp-44, Lys-66, Phe-120, Asp-121 and Ser-123 may also have possible roles in this mechanism. A molecular dynamics study on both structures has investigated the conformations of His-119 which was modelled as two conformations in 3RN3 but is observed to have a single clearly defined conformation in the present orthorhombic structure. MD has also been used to investigate Lys-31, Lys-41 and Ser32. The form of the Ribonuclease A enzyme used in both the present study and in 3RN3 (Howlin et al. in Acta Crystallogr A 45:851-861, 1989) includes a sulphate anion which occupies approximately the same location as the [Formula: see text] phosphate group in protein nucleotide complexes (Borkakoti et al. in J Mol Biol 169:743-755, 1983). The present structure contains 5 [Formula: see text] groups SO41151-SO41155 two of which, SO41152 and SO41153 are disordered, SO41152 being in the active site, and 11 EtOH molecules, EOH A 201-EOH A 211 all of which have good geometry. H atoms were built into the EtOH molecules geometrically. Illustrations of these features in the present structure are included here. The sulphates are presumably present in the material purchased for use in the present study. 293 water molecules are included in the present structure compared to 134 in 3RN3 (Howlin et al. in Acta Crystallogr A 45:851-861, 1989).
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Affiliation(s)
- David R Lisgarten
- Biomolecular Research Group, School of Psychology and Life Sciences, Canterbury Christ Church University, North Holmes Road, Canterbury Kent, CT1 1QU, UK
| | - Rex A Palmer
- Department of Crystallography, Biochemical Sciences, Birkbeck College, Malet St., London, WC1E7HX, UK.
| | - Jon B Cooper
- Division of Medicine, UCL, Gower Street, London, WC1E 6BT, UK
- Kisaco Research, 41a Maltby Street, London, SE1 3PA, UK
| | - Claire E Naylor
- Biomolecular Research Group, School of Psychology and Life Sciences, Canterbury Christ Church University, North Holmes Road, Canterbury, Kent, CT1 1QU, UK
| | - Rosemary C Talbert
- Biomolecular Research Group, School of Psychology and Life Sciences, Canterbury Christ Church University, North Holmes Road, Canterbury Kent, CT1 1QU, UK
| | - Brendan J Howlin
- Chemical Sciences Division, Faculty of Health and Medical Sciences, University of Surrey, Surrey, Guildford, GU2 7HX, UK
| | - John N Lisgarten
- School of Science, University of Greenwich (Medway Campus), Kent, Chatham Maritime, ME4 4TB, UK
| | - Janez Konc
- National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia
| | - Shabir Najmudin
- Randall Centre for Cell and Molecular Biophysics, Faculty of Life Sciences and Medicine, King's College, 3rd Floor New Hunt's House, London, SE1 1UL, UK
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Huang Z, Calicchia E, Jurewicz I, Muñoz E, Garriga R, Portale G, Howlin BJ, Keddie JL. Two-Dimensional Triblock Peptide Assemblies for the Stabilization of Pickering Emulsions with pH Responsiveness. ACS Appl Mater Interfaces 2022; 14:53228-53240. [PMID: 36378993 PMCID: PMC9716523 DOI: 10.1021/acsami.2c17558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 11/02/2022] [Indexed: 06/16/2023]
Abstract
A variety of two-dimensional (2D) nanomaterials, including graphene oxide and clays, are known to stabilize Pickering emulsions to fabricate structures for functions in sensors, catalysts, and encapsulation. We introduce here a novel Pickering emulsion using self-assembled amphiphilic triblock oligoglycine as the emulsifier. Peptide amphiphiles are more responsive to environmental changes (e.g., pH, temperature, and ionic strength) than inorganic 2D materials, which have a chemically rigid, in-plane structure. Noncovalent forces between the peptide molecules change with the environment, thereby imparting responsiveness. We provide new evidence that the biantennary oligoglycine, Gly4-NH-C10H20-NH-Gly4, self-assembles into 2D platelet structures, denoted as tectomers, in solution at a neutral buffered pH using small-angle X-ray scattering and molecular dynamics simulations. The molecules are stacked in the platelets with a linear conformation, rather than in a U-shape. We discovered that the lamellar oligoglycine platelets adsorbed at an oil/water interface and stabilized oil-in-water emulsions. This is the first report of 2D oligoglycine platelets being used as a Pickering stabilizer. The emulsions showed a strong pH response in an acidic environment. Thus, upon reducing the pH, the protonation of the terminal amino groups of the oligoglycine induced disassembly of the lamellar structure due to repulsive electrostatic forces, leading to emulsion destabilization. To demonstrate the application of the material, we show that a model active ingredient, β-carotene, in the oil is released upon decreasing the pH. Interestingly, in pH 9 buffer, the morphology of the oil droplets evolved over time, as the oligoglycine stabilizer created progressively a thicker interfacial layer. This demonstration opens a new route to use self-assembled synthetic peptide amphiphiles to stabilize Pickering emulsions, which can be significant for biomedical and pharmaceutical applications.
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Affiliation(s)
- Zhiwei Huang
- Department
of Physics, Faculty of Engineering and Physical Sciences, University of Surrey, GuildfordGU2 7XH, U.K.
| | - Eleonora Calicchia
- Groningen
Research Institute of Pharmacy, University
of Groningen, A. Deusinglaan 1, Groningen9713 AV, The Netherlands
- Zernike
Institute for Advanced Materials, Faculty of Mathematics and Natural
Sciences, University of Groningen, Nijenborgh 4, Groningen9747AG, The
Netherlands
| | - Izabela Jurewicz
- Department
of Physics, Faculty of Engineering and Physical Sciences, University of Surrey, GuildfordGU2 7XH, U.K.
| | - Edgar Muñoz
- Instituto
de Carboquímica ICB-CSIC, Miguel Luesma Castán 4, 50018Zaragoza, Spain
| | - Rosa Garriga
- Departamento
de Química Física, Universidad
de Zaragoza, 50009Zaragoza, Spain
| | - Giuseppe Portale
- Zernike
Institute for Advanced Materials, Faculty of Mathematics and Natural
Sciences, University of Groningen, Nijenborgh 4, Groningen9747AG, The
Netherlands
| | - Brendan J. Howlin
- Department
of Chemistry, Faculty of Engineering and Physical Sciences, University of Surrey, Guildford, Surrey GU2 7XH, U.K.
| | - Joseph L. Keddie
- Department
of Physics, Faculty of Engineering and Physical Sciences, University of Surrey, GuildfordGU2 7XH, U.K.
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Vallée C, Howlin BJ, Lewis R. Single ion free energy calculation in ASIC1: the importance of the HG loop. Phys Chem Chem Phys 2022; 24:13824-13830. [PMID: 35616206 DOI: 10.1039/d2cp01563c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Acid Sensing Ion Channels (ASICs) are one of the most studied channels of the Epithelial Sodium Channel/Degenerin (ENaC/DEG) superfamily. They are responsible for excitatory responses following acidification of the extracellular medium and are involved in several important physiological roles. The ASIC1 subunit can form a functional homotrimeric channel and its structure is currently the most characterised of the whole ENaC/DEG family. Here we computed the free energy profiles for single ion permeation in two different structures of ASIC1 using both Na+ and Cl- as permeating ions. The first structure is the open structure of the channel from the PDB entry 4NTW, and the second structure is the closed structure with the re-entrant loop which contains the highly conserved 'HG' motif form PDB entry 6VTK. Both structures show cation selective free energy profiles, however the profiles of the permeating Na+ differ significantly between the two structures. Indeed, whereas there is only a small energetically favorable (-0.5 kcal mol-1) location for Na+ in the open channel (4NTW) near the end of the pore, we observed a clear ion binding site (-7.8 kcal mol-1) located in between the 'GAS' belt and the 'HG' loop for the channel containing the re-entrant loop (6VTK). Knowing that the 'GAS' motif was determined as the selectivity filter, our results support previous observations while addressing the importance of the 'HG' motif for the interactions between the pore and the permeating cations.
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Affiliation(s)
- Cédric Vallée
- Leverhulme Quantum Biology Doctoral Training Centre, University of Surrey, Guildford GU2 5XH, UK. .,Department of Chemistry, Faculty of Engineering and Physical Sciences, University of Surrey, Guildford GU2 7XH, UK.,School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7AL, UK
| | - Brendan J Howlin
- Leverhulme Quantum Biology Doctoral Training Centre, University of Surrey, Guildford GU2 5XH, UK. .,Department of Chemistry, Faculty of Engineering and Physical Sciences, University of Surrey, Guildford GU2 7XH, UK
| | - Rebecca Lewis
- Leverhulme Quantum Biology Doctoral Training Centre, University of Surrey, Guildford GU2 5XH, UK. .,School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7AL, UK
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Abstract
Ageing is a major risk factor for many conditions including cancer, cardiovascular and neurodegenerative diseases. Pharmaceutical interventions that slow down ageing and delay the onset of age-related diseases are a growing research area. The aim of this study was to build a machine learning model based on the data of the DrugAge database to predict whether a chemical compound will extend the lifespan of Caenorhabditis elegans. Five predictive models were built using the random forest algorithm with molecular fingerprints and/or molecular descriptors as features. The best performing classifier, built using molecular descriptors, achieved an area under the curve score (AUC) of 0.815 for classifying the compounds in the test set. The features of the model were ranked using the Gini importance measure of the random forest algorithm. The top 30 features included descriptors related to atom and bond counts, topological and partial charge properties. The model was applied to predict the class of compounds in an external database, consisting of 1738 small-molecules. The chemical compounds of the screening database with a predictive probability of ≥ 0.80 for increasing the lifespan of Caenorhabditis elegans were broadly separated into (1) flavonoids, (2) fatty acids and conjugates, and (3) organooxygen compounds.
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Affiliation(s)
- Sofia Kapsiani
- Department of Chemistry, FEPS, University of Surrey, Guildford, Surrey, GU2 7XH, UK
| | - Brendan J Howlin
- Department of Chemistry, FEPS, University of Surrey, Guildford, Surrey, GU2 7XH, UK.
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Bone MA, Macquart T, Hamerton I, Howlin BJ. A Novel Approach to Atomistic Molecular Dynamics Simulation of Phenolic Resins Using Symthons. Polymers (Basel) 2020; 12:polym12040926. [PMID: 32316377 PMCID: PMC7240706 DOI: 10.3390/polym12040926] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 04/08/2020] [Accepted: 04/15/2020] [Indexed: 11/26/2022] Open
Abstract
Materials science is beginning to adopt computational simulation to eliminate laboratory trial and error campaigns—much like the pharmaceutical industry of 40 years ago. To further computational materials discovery, new methodology must be developed that enables rapid and accurate testing on accessible computational hardware. To this end, the authors utilise a novel methodology concept of intermediate molecules as a starting point, for which they propose the term ‘symthon’ (The term ‘Symthon’ is being used as a simulation equivalent of the synthon, popularised by Dr Stuart Warren in ‘Organic Synthesis: The Disconnection Approach’, OUP: Oxford, 1983.) rather than conventional monomers. The use of symthons eliminates the initial monomer bonding phase, reducing the number of iterations required in the simulation, thereby reducing the runtime. A novel approach to molecular dynamics, with an NVT (Canonical) ensemble and variable unit cell geometry, was used to generate structures with differing physical and thermal properties. Additional script methods were designed and tested, which enabled a high degree of cure in all sampled structures. This simulation has been trialled on large-scale atomistic models of phenolic resins, based on a range of stoichiometric ratios of formaldehyde and phenol. Density and glass transition temperature values were produced, and found to be in good agreement with empirical data and other simulated values in the literature. The runtime of the simulation was a key consideration in script design; cured models can be produced in under 24 h on modest hardware. The use of symthons has been shown as a viable methodology to reduce simulation runtime whilst generating accurate models.
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Affiliation(s)
- Matthew A. Bone
- Department of Chemistry & Faculty of Engineering and Physical Sciences, University of Surrey, Guildford, Surrey GU2 7XH, UK;
- Bristol Composites Institute (ACCIS), Department of Aerospace Engineering, School of Civil, Aerospace, and Mechanical Engineering, University of Bristol, Queen’s Building, University Walk, Bristol BS8 1TR, UK; (T.M.); (I.H.)
- Correspondence:
| | - Terence Macquart
- Bristol Composites Institute (ACCIS), Department of Aerospace Engineering, School of Civil, Aerospace, and Mechanical Engineering, University of Bristol, Queen’s Building, University Walk, Bristol BS8 1TR, UK; (T.M.); (I.H.)
| | - Ian Hamerton
- Bristol Composites Institute (ACCIS), Department of Aerospace Engineering, School of Civil, Aerospace, and Mechanical Engineering, University of Bristol, Queen’s Building, University Walk, Bristol BS8 1TR, UK; (T.M.); (I.H.)
| | - Brendan J. Howlin
- Department of Chemistry & Faculty of Engineering and Physical Sciences, University of Surrey, Guildford, Surrey GU2 7XH, UK;
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Malkhasian AY, Howlin BJ. Automated drug design of kinase inhibitors to treat Chronic Myeloid Leukemia. J Mol Graph Model 2019; 91:52-60. [DOI: 10.1016/j.jmgm.2019.05.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 05/17/2019] [Accepted: 05/17/2019] [Indexed: 11/25/2022]
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Binks FC, Cavalli G, Henningsen M, Howlin BJ, Hamerton I. On the use of benzaldehyde to improve the storage stability of one-pot, epoxy ionic liquid formulations. Eur Polym J 2019. [DOI: 10.1016/j.eurpolymj.2018.12.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Binks FC, Cavalli G, Henningsen M, Howlin BJ, Hamerton I. Investigating the mechanism through which ionic liquids initiate the polymerisation of epoxy resins. POLYMER 2018. [DOI: 10.1016/j.polymer.2018.01.087] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Mooring L, Thompson S, Hall SA, Pani S, Zioupos P, Swan M, Stone C, Howlin BJ, Hamerton I. ‘Phoenix polymers’: fire induced nanohardness in fibril-forming aromatic cyanate esters. RSC Adv 2018; 8:36264-36271. [PMID: 35558471 PMCID: PMC9088260 DOI: 10.1039/c8ra07449f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 10/11/2018] [Indexed: 11/28/2022] Open
Abstract
For the first time we present nanoindentation analysis of charred, cured aromatic cyanate esters, which exhibit outstanding mechanical properties when analysed under applied loads of 0.1–300 mN. Following charring (900 °C for 10 minutes to achieve graphitised structures), the samples display a remarkable combination of a modulus of elasticity of around 25 GPa and nanohardness of 300 kgf mm−2, making them some 30–40% stiffer than bone and practically as hard as tooth enamel. At the same time we find that under the same conditions the chars are highly resilient, displaying complete elastic recovery with very little plastic deformation. When cured in the presence of copper(ii) acetylacetonate (200 ppm) in dodecylphenol (1% w/v active copper suspension) to form a polycyanurate, compound (2) forms a dense, consolidated structure compared with compound (1) under the same conditions. At high magnification, the presence of a nanoscale, fibrillar structure is observed, accounting for the high resilience. For the first time we present nanoindentation analysis of charred, cured aromatic cyanate esters, which exhibit outstanding mechanical properties when analysed under applied loads of 0.1–300 mN.![]()
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Affiliation(s)
| | | | | | - Silvia Pani
- Department of Physics
- Faculty of Engineering and Physical Sciences
- University of Surrey
- Surrey
- UK
| | - Peter Zioupos
- Cranfield Forensic Institute
- CDS
- Cranfield University
- UK
| | | | | | | | - Ian Hamerton
- Bristol Composites Institute (ACCIS)
- Department of Aerospace Engineering
- School of Civil, Aerospace, and Mechanical Engineering
- Queen's Building
- University of Bristol
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Lisgarten DR, Palmer RA, Lobley CMC, Naylor CE, Chowdhry BZ, Al-Kurdi ZI, Badwan AA, Howlin BJ, Gibbons NCJ, Saldanha JW, Lisgarten JN, Basak AK. Ultra-high resolution X-ray structures of two forms of human recombinant insulin at 100 K. Chem Cent J 2017; 11:73. [PMID: 29086855 PMCID: PMC5539060 DOI: 10.1186/s13065-017-0296-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Accepted: 07/12/2017] [Indexed: 11/30/2022] Open
Abstract
The crystal structure of a commercially available form of human recombinant (HR) insulin, Insugen (I), used in the treatment of diabetes has been determined to 0.92 Å resolution using low temperature, 100 K, synchrotron X-ray data collected at 16,000 keV (λ = 0.77 Å). Refinement carried out with anisotropic displacement parameters, removal of main-chain stereochemical restraints, inclusion of H atoms in calculated positions, and 220 water molecules, converged to a final value of R = 0.1112 and Rfree = 0.1466. The structure includes what is thought to be an ordered propanol molecule (POL) only in chain D(4) and a solvated acetate molecule (ACT) coordinated to the Zn atom only in chain B(2). Possible origins and consequences of the propanol and acetate molecules are discussed. Three types of amino acid representation in the electron density are examined in detail: (i) sharp with very clearly resolved features; (ii) well resolved but clearly divided into two conformations which are well behaved in the refinement, both having high quality geometry; (iii) poor density and difficult or impossible to model. An example of type (ii) is observed for the intra-chain disulphide bridge in chain C(3) between Sγ6–Sγ11 which has two clear conformations with relative refined occupancies of 0.8 and 0.2, respectively. In contrast the corresponding S–S bridge in chain A(1) shows one clearly defined conformation. A molecular dynamics study has provided a rational explanation of this difference between chains A and C. More generally, differences in the electron density features between corresponding residues in chains A and C and chains B and D is a common observation in the Insugen (I) structure and these effects are discussed in detail. The crystal structure, also at 0.92 Å and 100 K, of a second commercially available form of human recombinant insulin, Intergen (II), deposited in the Protein Data Bank as 3W7Y which remains otherwise unpublished is compared here with the Insugen (I) structure. In the Intergen (II) structure there is no solvated propanol or acetate molecule. The electron density of Intergen (II), however, does also exhibit the three types of amino acid representations as in Insugen (I). These effects do not necessarily correspond between chains A and C or chains B and D in Intergen (II), or between corresponding residues in Insugen (I). The results of this comparison are reported.Conformations of PheB25 and PheD25 in three insulin structures: implications for biological activity? Insulin residues PheB25 and PheD25 are considered to be important for insulin receptor binding and changes in biological activity occur when these residues are modified. In porcine insulin and Intergen (II) PheB25 adopts conformation B and PheD25 conformation D. However, unexpectedly PheB25 in Insugen (I) human recombinant insulin adopts two distinct conformations corresponding to B and D, Figure 1 and PheD25 adopts a single conformation corresponding to B not D, Figure 2. Conformations of this residue in the ultra-high resolution structure of Insugen (I) are therefore unique within this set. Figures were produced with Biovia, Discovery Studio 2016. ![]()
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Affiliation(s)
- David R Lisgarten
- Biomolecular Research Group, School of Human and Life Sciences, Canterbury Christ Church University, North Holmes Road, Canterbury, Kent, CT1 1QU, UK
| | - Rex A Palmer
- Department of Crystallography, Biochemical Sciences, Birkbeck College, Malet St, London, WC1E7HX, UK.
| | - Carina M C Lobley
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, UK
| | - Claire E Naylor
- Molecular Dimensions Ltd, Unit 6, Goodwin Business Park, Willie Snaith Road, Newmarket, Suffolk, CB8 7SQ, UK
| | - Babur Z Chowdhry
- Faculty of Engineering & Science, University of Greenwich (Medway Campus), Chatham Maritime, Kent, ME4 4TB, UK
| | - Zakieh I Al-Kurdi
- The Jordanian Pharmaceutical Manufacturing Company (PLC), Suwagh Subsidiary for Drug Delivery Systems, P.O. Box 94, Naor, 11710, Jordan
| | - Adnan A Badwan
- The Jordanian Pharmaceutical Manufacturing Company (PLC), Suwagh Subsidiary for Drug Delivery Systems, P.O. Box 94, Naor, 11710, Jordan
| | - Brendan J Howlin
- Chemical Sciences Division, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, GU2 7HX, UK
| | - Nicholas C J Gibbons
- Department of Natural Sciences, School of Science and Technology, University of Middlesex, Hendon Campus, The Burroughs, London, NW4 4BT, UK
| | - José W Saldanha
- MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London, NW71AA, UK
| | - John N Lisgarten
- Faculty of Engineering & Science, University of Greenwich (Medway Campus), Chatham Maritime, Kent, ME4 4TB, UK
| | - Ajit K Basak
- Department of Crystallography, Biochemical Sciences, Birkbeck College, Malet St, London, WC1E7HX, UK
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Crawford AO, Cavalli G, Howlin BJ, Hamerton I. Improving the hydrolytic stability of aryl cyanate esters by examining the effects of extreme environments on polycyanurate copolymers. REACT FUNCT POLYM 2016. [DOI: 10.1016/j.reactfunctpolym.2016.10.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Hamerton I, Hay JN, Howlin BJ, Jones JR, Lu SY, Webb GA, Bader MG. A Tritium–Hydrogen Exchange Procedure for Determining the Concentration of Exchangeable Sites on PAN Based Carbon Fibres. HIGH PERFORM POLYM 2016. [DOI: 10.1088/0954-0083/9/3/007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A non-destructive tritium–hydrogen exchange procedure has been developed in order to determine the concentration of exchangeable hydrogens on surfaces, and in this particular instance it has been used on carbon fibres. The results show that the concentrations of ‘active sites’ on the surfaces of Courtaulds Grafil XAS and XAU carbon fibres are 2.61 and 0.08 μmol g−1 respectively. When the XAS fibres are subjected to a standard methylation procedure the concentration of exchangeable hydrogens is reduced to 0.79 μmol g−1.On the other hand, when XAU fibres are subjected to oxidation in concentrated nitric acid, the concentration of exchangeable hydrogens is increased to 10.27 μmol g−1.
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Affiliation(s)
| | | | | | | | | | - Graham A Webb
- Department of Chemistry, University of Surrey, Guildford GU2 5XH, UK
| | - Michael G Bader
- Department of Materials Science and Engineering, University of Surrey, Guildford GU2 5XH, UK
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Allington RD, Hamerton I, Hay JN, Howlin BJ, Attwood D. Inverse Gas Chromatography Characterization of Carbon Fiber Surfaces - Effects of Applied Surface Treatment. HIGH PERFORM POLYM 2016. [DOI: 10.1177/0954008305051919] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Inverse gas chromatography (IGC) is used to characterize the surfaces of carbon fibers subjected to electrolytic surface treatment at a range of treatment levels. Surface area analysis via BET shows only small differences in specific surface area as a function of treatment level. IGC data yield dispersive surface energies and the acid-base character of the fiber surfaces and show that surface treatment up to the standard level causes a reduction in the dispersive surface energy, consistent with surface oxidation and the corresponding X-ray photoelectron spectroscopy (XPS) results. Surface treatment also has a major effect on the acid-base characteristics of the fiber, its initially basic nature being replaced by acidic character and then amphoteric behavior at higher treatment levels.
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Affiliation(s)
- Richard D. Allington
- Chemistry Division, School of Biomedical and Molecular Sciences, University of Surrey, Guildford, Surrey, GU2 7XH, UK
| | - Ian Hamerton
- Chemistry Division, School of Biomedical and Molecular Sciences, University of Surrey, Guildford, Surrey, GU2 7XH, UK,
| | - John N. Hay
- Chemistry Division, School of Biomedical and Molecular Sciences, University of Surrey, Guildford, Surrey, GU2 7XH, UK
| | - Brendan J. Howlin
- Chemistry Division, School of Biomedical and Molecular Sciences, University of Surrey, Guildford, Surrey, GU2 7XH, UK
| | - David Attwood
- British Aerospace (Operations) Ltd., Sowerby Research Centre, Filton, Bristol, BS12 7QW, UK
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14
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Abstract
The synthesis of a novel phenylethynyl-terminated siloxane polymer is described, by reaction of the amine-terminated siloxane with 4-phenylethynylphthalic anhydride. The oligomer (PET-PDMS) is electron beam (EB) curable, in contrast to the commercial phenylethynyl-terminated imide, PETI-5, probably as a result of increased polymer chain mobility arising from siloxane incorporation. Raman spectroscopy indicates that the cure mechanisms for electron beam and thermal cure of PET-PDMS are different. PET-PDMS appears to undergo chain scission under the influence of an electron beam. Differential scanning calorimetry of the EB cured polymer is also consistent with a mechanism involving cleavage of siloxane linkages.
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Affiliation(s)
- Ian Hamerton
- Chemistry, SBLS, University of Surrey, Guildford, Surrey, GU2 7XH, UK
| | - John N. Hay'
- Chemistry, SBLS, University of Surrey, Guildford, Surrey, GU2 7XH, UK Tel. 00 44 (0)1483 689586 Fax. 00 44 (0)1483 686851
| | | | | | - Paula O'Gara
- Chemistry, SBLS, University of Surrey, Guildford, Surrey, GU2 7XH, UK
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15
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Crawford AO, Cavalli G, Howlin BJ, Hamerton I. Investigation of structure property relationships in liquid processible, solvent free, thermally stable bismaleimide-triazine (BT) resins. REACT FUNCT POLYM 2016. [DOI: 10.1016/j.reactfunctpolym.2016.03.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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16
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Wan Hassan WA, Liu J, Howlin BJ, Ishida H, Hamerton I. Examining the influence of bisphenol A on the polymerisation and network properties of an aromatic benzoxazine. POLYMER 2016. [DOI: 10.1016/j.polymer.2016.01.041] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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17
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Affiliation(s)
- Aramice Y.S. Malkhasian
- Faculty of Science, Department of Chemistry, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Brendan J. Howlin
- FEPS, Department of Chemistry, University of Surrey, Guildford, Surrey GU2 7XH, UK
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18
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Dobreva MA, Green RJ, Mueller-Harvey I, Salminen JP, Howlin BJ, Frazier RA. Size and molecular flexibility affect the binding of ellagitannins to bovine serum albumin. J Agric Food Chem 2014; 62:9186-94. [PMID: 25162485 DOI: 10.1021/jf502174r] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Binding to bovine serum albumin of monomeric (vescalagin and pedunculagin) and dimeric ellagitannins (roburin A, oenothein B, and gemin A) was investigated by isothermal titration calorimetry and fluorescence spectroscopy, which indicated two types of binding sites. Stronger and more specific sites exhibited affinity constants, K1, of 10(4)-10(6) M(-1) and stoichiometries, n1, of 2-13 and dominated at low tannin concentrations. Weaker and less-specific binding sites had K2 constants of 10(3)-10(5) M(-1) and stoichiometries, n2, of 16-30 and dominated at higher tannin concentrations. Binding to stronger sites appeared to be dependent on tannin flexibility and the presence of free galloyl groups. Positive entropies for all but gemin A indicated that hydrophobic interactions dominated during complexation. This was supported by an exponential relationship between the affinity, K1, and the modeled hydrophobic accessible surface area and by a linear relationship between K1 and the Stern-Volmer quenching constant, K(SV).
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Affiliation(s)
- Marina A Dobreva
- School of Agriculture, Policy and Development, University of Reading , Earley Gate, P.O. Box 236, Reading RG6 6AT, United Kingdom
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19
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Hamerton I, Howlin BJ, Yeung SYC. Studying structure–property relationships in oligomeric engineering thermoplastics by controlled preparation of low molecular weight polymers. REACT FUNCT POLYM 2014. [DOI: 10.1016/j.reactfunctpolym.2014.04.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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20
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Meijles DN, Fan LM, Howlin BJ, Li JM. Molecular insights of p47phox phosphorylation dynamics in the regulation of NADPH oxidase activation and superoxide production. J Biol Chem 2014; 289:22759-22770. [PMID: 24970888 PMCID: PMC4132782 DOI: 10.1074/jbc.m114.561159] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Phagocyte superoxide production by a multicomponent NADPH oxidase is important in host defense against microbial invasion. However inappropriate NADPH oxidase activation causes inflammation. Endothelial cells express NADPH oxidase and endothelial oxidative stress due to prolonged NADPH oxidase activation predisposes many diseases. Discovering the mechanism of NADPH oxidase activation is essential for developing novel treatment of these diseases. The p47phox is a key regulatory subunit of NADPH oxidase; however, due to the lack of full protein structural information, the mechanistic insight of p47phox phosphorylation in NADPH oxidase activation remains incomplete. Based on crystal structures of three functional domains, we generated a computational structural model of the full p47phox protein. Using a combination of in silico phosphorylation, molecular dynamics simulation and protein/protein docking, we discovered that the C-terminal tail of p47phox is critical for stabilizing its autoinhibited structure. Ser-379 phosphorylation disrupts H-bonds that link the C-terminal tail to the autoinhibitory region (AIR) and the tandem Src homology 3 (SH3) domains, allowing the AIR to undergo phosphorylation to expose the SH3 pocket for p22phox binding. These findings were confirmed by site-directed mutagenesis and gene transfection of p47phox−/− coronary microvascular cells. Compared with wild-type p47phox cDNA transfected cells, the single mutation of S379A completely blocked p47phox membrane translocation, binding to p22phox and endothelial O2⨪ production in response to acute stimulation of PKC. p47phox C-terminal tail plays a key role in stabilizing intramolecular interactions at rest. Ser-379 phosphorylation is a molecular switch which initiates p47phox conformational changes and NADPH oxidase-dependent superoxide production by cells.
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Affiliation(s)
- Daniel N Meijles
- Faculty of Health and Medical Science, University of Surrey, Surrey GU2 7XH, United Kingdom,; Faculty of Engineering and Physical Sciences, University of Surrey, Surrey GU2 7XH, United Kingdom
| | - Lampson M Fan
- John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, United Kingdom, and
| | - Brendan J Howlin
- Faculty of Engineering and Physical Sciences, University of Surrey, Surrey GU2 7XH, United Kingdom
| | - Jian-Mei Li
- Faculty of Health and Medical Science, University of Surrey, Surrey GU2 7XH, United Kingdom,.
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21
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Baggott A, Bass JR, Hall SA, Hamerton I, Howlin BJ, Mooring L, Sparks D. At the Limits of Simulation: A New Method to Predict Thermal Degradation Behavior in Cyanate Esters and Nanocomposites Using Molecular Dynamics Simulation. MACROMOL THEOR SIMUL 2014. [DOI: 10.1002/mats.201300141] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Alex Baggott
- Faculty of Engineering and Physical Sciences, Chemistry Department; University of Surrey; Guildford Surrey GU2 7XH UK
| | - Joanne R. Bass
- Faculty of Engineering and Physical Sciences, Chemistry Department; University of Surrey; Guildford Surrey GU2 7XH UK
| | - Stephen A. Hall
- Faculty of Engineering and Physical Sciences, Chemistry Department; University of Surrey; Guildford Surrey GU2 7XH UK
| | - Ian Hamerton
- Faculty of Engineering and Physical Sciences, Chemistry Department; University of Surrey; Guildford Surrey GU2 7XH UK
| | - Brendan J. Howlin
- Faculty of Engineering and Physical Sciences, Chemistry Department; University of Surrey; Guildford Surrey GU2 7XH UK
| | - Lyndsey Mooring
- Faculty of Engineering and Physical Sciences, Chemistry Department; University of Surrey; Guildford Surrey GU2 7XH UK
| | - David Sparks
- Faculty of Engineering and Physical Sciences, Chemistry Department; University of Surrey; Guildford Surrey GU2 7XH UK
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22
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Hamerton I, McNamara LT, Howlin BJ, Smith PA, Cross P, Ward S. Developing toughened aromatic polybenzoxazines using thermoplastic oligomers and telechelics, part 1: Preparation and characterization of the functionalized oligomers. J Appl Polym Sci 2014. [DOI: 10.1002/app.40875] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Ian Hamerton
- Faculty of Engineering and Physical Sciences, Department of Chemistry; University of Surrey; Guildford Surrey GU2 7XH United Kingdom
| | - Lisa T. McNamara
- Faculty of Engineering and Physical Sciences, Department of Chemistry; University of Surrey; Guildford Surrey GU2 7XH United Kingdom
| | - Brendan J. Howlin
- Faculty of Engineering and Physical Sciences, Department of Chemistry; University of Surrey; Guildford Surrey GU2 7XH United Kingdom
| | - Paul A. Smith
- Faculty of Engineering and Physical Sciences, Department of Mechanical Engineering Sciences; University of Surrey; Guildford Surrey GU2 7XH United Kingdom
| | - Paul Cross
- Cytec, R414, Wilton Centre; Redcar TS10 4RF United Kingdom
| | - Steven Ward
- Cytec, R414, Wilton Centre; Redcar TS10 4RF United Kingdom
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23
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Hamerton I, McNamara LT, Howlin BJ, Smith PA, Cross P, Ward S. Kinetics and Cure Mechanism in Aromatic Polybenzoxazines Modified Using Thermoplastic Oligomers and Telechelics. Macromolecules 2014. [DOI: 10.1021/ma500242w] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | | | | | - Paul Cross
- Cytec, R414 Wilton Centre, Redcar, TS10 4RF, U.K
| | - Steven Ward
- Cytec, R414 Wilton Centre, Redcar, TS10 4RF, U.K
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24
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Hamerton I, McNamara LT, Howlin BJ, Smith PA, Cross P, Ward S. Toughening Mechanisms in Aromatic Polybenzoxazines Using Thermoplastic Oligomers and Telechelics. Macromolecules 2014. [DOI: 10.1021/ma5002436] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | | | | | - Paul Cross
- Cytec, R414 Wilton Centre, Redcar, TS10 4RF, U.K
| | - Steven Ward
- Cytec, R414 Wilton Centre, Redcar, TS10 4RF, U.K
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25
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Hamerton I, Howlin BJ, Tilbrook DA. Examining the preparation and characterization of coatings based on linear aromatic terpoly(methoxy-cyanurate-thiocyanurate)s. POLYM INT 2014. [DOI: 10.1002/pi.4604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Ian Hamerton
- Department of Chemistry, Faculty of Engineering and Physical Sciences; University of Surrey; Guildford Surrey GU2 7XH UK
| | - Brendan J. Howlin
- Department of Chemistry, Faculty of Engineering and Physical Sciences; University of Surrey; Guildford Surrey GU2 7XH UK
| | - David A. Tilbrook
- Department of Chemistry, Faculty of Engineering and Physical Sciences; University of Surrey; Guildford Surrey GU2 7XH UK
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26
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Hamerton I, Howlin BJ, Tilbrook DA. Examining thermal stability and structure property relationships in coatings based on linear aromatic poly(methoxy-thiocyanurate)s. Polym Degrad Stab 2013. [DOI: 10.1016/j.polymdegradstab.2013.08.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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27
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Hamerton I, Thompson S, Howlin BJ, Stone CA. New Method To Predict the Thermal Degradation Behavior of Polybenzoxazines from Empirical Data Using Structure Property Relationships. Macromolecules 2013. [DOI: 10.1021/ma401444z] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ian Hamerton
- Department of Chemistry, Faculty of Engineering and Physical
Sciences, University of Surrey, Guildford, Surrey, GU2 7XH, U.K
| | - Scott Thompson
- Department of Chemistry, Faculty of Engineering and Physical
Sciences, University of Surrey, Guildford, Surrey, GU2 7XH, U.K
| | - Brendan J. Howlin
- Department of Chemistry, Faculty of Engineering and Physical
Sciences, University of Surrey, Guildford, Surrey, GU2 7XH, U.K
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28
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Hamerton I, McNamara LT, Howlin BJ, Smith PA, Cross P, Ward S. Examining the Initiation of the Polymerization Mechanism and Network Development in Aromatic Polybenzoxazines. Macromolecules 2013; 46:5117-5132. [PMID: 23853391 PMCID: PMC3707310 DOI: 10.1021/ma401014h] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 06/10/2013] [Indexed: 11/28/2022]
Abstract
Three bis-benzoxazine monomers based on the aniline derivatives of bisphenol A (BA-a), bisphenol F (BF-a), and 3,3'-thiodiphenol (BT-a) are examined using a variety of spectroscopic, chromatographic, and thermomechanical techniques. The effect on the polymerization of the monomers is compared using two common compounds, 3,3'-thiodiphenol (TDP) and 3,3'-thiodipropionic acid (TDA), at a variety of loadings. It is found that the diacid has a greater effect on reducing the onset of polymerization and increasing cross-link density and Tg for a given benzoxazine. However, the addition of >5 wt % of the diacid had a detrimental effect on the cross-link density, Tg, and thermal stability of the polymer. The kinetics of the polymerization of BA-a were found to be well described using an autocatalytic model for which values of n = 1.64 and m = 2.31 were obtained for the early and later stages of reaction (activation energy = 81 kJ/mol). Following recrystallization the same monomer yielded values n = 1.89, m = 0.89, and Ea = 94 kJ/mol (confirming the influence of higher oligomers on reactivity). The choice of additive (in particular the magnitude of its pKa) appears to influence the nature of the network formation from a linear toward a more clusterlike growth mechanism.
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Affiliation(s)
- Ian Hamerton
- Department of Chemistry and Department of Mechanical Engineering Sciences, Faculty of Engineering and Physical Sciences, University of Surrey , Guildford, Surrey GU2 7XH, U.K
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29
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Abstract
Updated models of the Rat Cytochrome P450 2D enzymes are produced based on the recent x-ray structures of the Human P450 2D6 enzyme both with and without a ligand bound. The differences in species selectivity between the epimers quinine and quinidine are rationalised using these models and the results are discussed with regard to previous studies. A close approach to the heme is not observed in this study. The x-ray structure of the enzyme with a ligand bound is shown to be a better model for explaining the observed experimental binding of quinine and quinidine. Hence models with larger closed binding sites are recommended for comparative docking studies. This is consistent with molecular recognition in Cytochrome P450 enzymes being the result of a number of non-specific interactions in a large binding site.
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Affiliation(s)
- Grace H. C. Edmund
- Department of Chemistry, Faculty of Engineering and Physical Sciences, University of Surrey, Guildford, Surrey, United Kingdom
| | - David F. V. Lewis
- Department of Chemistry, Faculty of Engineering and Physical Sciences, University of Surrey, Guildford, Surrey, United Kingdom
| | - Brendan J. Howlin
- Department of Chemistry, Faculty of Engineering and Physical Sciences, University of Surrey, Guildford, Surrey, United Kingdom
- * E-mail:
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30
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Wan Hassan WA, Hamerton I, Howlin BJ. Prediction of selected physical and mechanical properties of a telechelic polybenzoxazine by molecular simulation. PLoS One 2013; 8:e61179. [PMID: 23577206 PMCID: PMC3620114 DOI: 10.1371/journal.pone.0061179] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Accepted: 03/07/2013] [Indexed: 11/19/2022] Open
Abstract
Molecular simulation is becoming an important tool for both understanding polymeric structures and predicting their physical and mechanical properties. In this study, temperature ramped molecular dynamics simulations are used to predict two physical properties (i.e., glass transition temperature and thermal degradation temperature) of a previously synthesised and published telechelic benzoxazine. Plots of simulated density versus temperature show decreases in density within the same temperature range as experimental values for the thermal degradation. The predicted value for the thermal degradation temperature for the cured polybenzoxazine based on the telechelic polyetherketone (PEK) monomer was ca. 400°C, in line with the experimental thermal degradation temperature range of 450°C to 500°C. Mechanical Properties of both the unmodified PEK and the telechelic benzoxazines are simulated and compared to experimental values (where available). The introduction of the benoxazine moieties are predicted to increase the elastic moduli in line with the increase of crosslinking in the system.
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Affiliation(s)
| | | | - Brendan J. Howlin
- Department of Chemistry, University of Surrey, Guildford, Surrey, United Kingdom
- * E-mail:
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31
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Mhlanga P, Wan Hassan WA, Hamerton I, Howlin BJ. Using combined computational techniques to predict the glass transition temperatures of aromatic polybenzoxazines. PLoS One 2013; 8:e53367. [PMID: 23326419 PMCID: PMC3542367 DOI: 10.1371/journal.pone.0053367] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Accepted: 11/30/2012] [Indexed: 11/19/2022] Open
Abstract
The Molecular Operating Environment software (MOE) is used to construct a series of benzoxazine monomers for which a variety of parameters relating to the structures (e.g. water accessible surface area, negative van der Waals surface area, hydrophobic volume and the sum of atomic polarizabilities, etc.) are obtained and quantitative structure property relationships (QSPR) models are formulated. Three QSPR models (formulated using up to 5 descriptors) are first used to make predictions for the initiator data set (n = 9) and compared to published thermal data; in all of the QSPR models there is a high level of agreement between the actual data and the predicted data (within 0.63–1.86 K of the entire dataset). The water accessible surface area is found to be the most important descriptor in the prediction of Tg. Molecular modelling simulations of the benzoxazine polymer (minus initiator) carried out at the same time using the Materials Studio software suite provide an independent prediction of Tg. Predicted Tg values from molecular modelling fall in the middle of the range of the experimentally determined Tg values, indicating that the structure of the network is influenced by the nature of the initiator used. Hence both techniques can provide predictions of glass transition temperatures and provide complementary data for polymer design.
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Affiliation(s)
- Phumzile Mhlanga
- Department of Chemistry, University of Surrey, Guildford, Surrey, United Kingdom
| | | | - Ian Hamerton
- Department of Chemistry, University of Surrey, Guildford, Surrey, United Kingdom
| | - Brendan J. Howlin
- Department of Chemistry, University of Surrey, Guildford, Surrey, United Kingdom
- * E-mail:
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32
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Hamerton I, Howlin BJ, Mitchell AL, McNamara LT, Takeda S. Systematic examination of thermal, mechanical and dielectrical properties of aromatic polybenzoxazines. REACT FUNCT POLYM 2012. [DOI: 10.1016/j.reactfunctpolym.2012.07.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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33
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Crawford AO, Hamerton I, Cavalli G, Howlin BJ. Quantifying the effect of polymer blending through molecular modelling of cyanurate polymers. PLoS One 2012; 7:e44487. [PMID: 22970230 PMCID: PMC3435312 DOI: 10.1371/journal.pone.0044487] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Accepted: 08/03/2012] [Indexed: 11/18/2022] Open
Abstract
Modification of polymer properties by blending is a common practice in the polymer industry. We report here a study of blends of cyanurate polymers by molecular modelling that shows that the final experimentally determined properties can be predicted from first principles modelling to a good degree of accuracy. There is always a compromise between simulation length, accuracy and speed of prediction. A comparison of simulation times shows that 125ps of molecular dynamics simulation at each temperature provides the optimum compromise for models of this size with current technology. This study opens up the possibility of computer aided design of polymer blends with desired physical and mechanical properties.
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Affiliation(s)
- Alasdair O. Crawford
- Department of Chemistry, University of Surrey, Guildford, Surrey, United Kingdom
| | - Ian Hamerton
- Department of Chemistry, University of Surrey, Guildford, Surrey, United Kingdom
| | - Gabriel Cavalli
- Department of Chemistry, University of Surrey, Guildford, Surrey, United Kingdom
| | - Brendan J. Howlin
- Department of Chemistry, University of Surrey, Guildford, Surrey, United Kingdom
- * E-mail:
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34
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Crawford AO, Howlin BJ, Cavalli G, Hamerton I. Examining the thermo-mechanical properties of novel cyanate ester blends through empirical measurement and simulation. REACT FUNCT POLYM 2012. [DOI: 10.1016/j.reactfunctpolym.2012.05.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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35
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Hall SA, Howlin BJ, Hamerton I, Baidak A, Billaud C, Ward S. Solving the problem of building models of crosslinked polymers: an example focussing on validation of the properties of crosslinked epoxy resins. PLoS One 2012; 7:e42928. [PMID: 22916182 PMCID: PMC3423435 DOI: 10.1371/journal.pone.0042928] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Accepted: 07/15/2012] [Indexed: 11/18/2022] Open
Abstract
The construction of molecular models of crosslinked polymers is an area of some difficulty and considerable interest. We report here a new method of constructing these models and validate the method by modelling three epoxy systems based on the epoxy monomers bisphenol F diglycidyl ether (BFDGE) and triglycidyl-p-amino phenol (TGAP) with the curing agent diamino diphenyl sulphone (DDS). The main emphasis of the work concerns the improvement of the techniques for the molecular simulation of these epoxies and specific attention is paid towards model construction techniques, including automated model building and prediction of glass transition temperatures (T(g)). Typical models comprise some 4200-4600 atoms (ca. 120-130 monomers). In a parallel empirical study, these systems have been cast, cured and analysed by dynamic mechanical thermal analysis (DMTA) to measure T(g). Results for the three epoxy systems yield good agreement with experimental T(g) ranges of 200-220°C, 270-285°C and 285-290°C with corresponding simulated ranges of 210-230°C, 250-300°C, and 250-300°C respectively.
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Affiliation(s)
- Stephen A. Hall
- Chemical Sciences Division, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Brendan J Howlin
- Chemical Sciences Division, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
- * E-mail:
| | - Ian Hamerton
- Chemical Sciences Division, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | | | - Claude Billaud
- Cytec Engineered Materials, R422 The Wilton Centre, Cleveland, Ohio, United States of America
| | - Steven Ward
- Cytec Engineered Materials, R422 The Wilton Centre, Cleveland, Ohio, United States of America
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36
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Meijles DN, Howlin BJ, Li JM. Consensus in silico computational modelling of the p22phox subunit of the NADPH oxidase. Comput Biol Chem 2012; 39:6-13. [DOI: 10.1016/j.compbiolchem.2012.05.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Revised: 05/02/2012] [Accepted: 05/02/2012] [Indexed: 11/24/2022]
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37
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Meijles DN, Howlin BJ, Li JM. 121 Bioinformatic imaging and molecular investigation for a role of p22 phoxC242T polymorphism in inhibiting endothelial ROS production. Heart 2012. [DOI: 10.1136/heartjnl-2012-301877b.121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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38
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39
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Barakzai KND, Howlin BJ, Lockley WJS, Sfyrakis K. Analysis of labelled compounds by mass spectroscopy in the presence of heavy isotopes at natural abundance: the NAIC program. J Labelled Comp Radiopharm 2009. [DOI: 10.1002/jlcr.1675] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Hamerton I, Howlin BJ, Klewpatinond P, Takeda S. Examination of the Thermal and Thermomechanical Behavior of Novel Cyanate Ester Homopolymers and Blends with Low Coefficients of Thermal Expansion. Macromolecules 2009. [DOI: 10.1021/ma901657n] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ian Hamerton
- Chemical Sciences Division, Faculty of Health and Molecular Sciences, University of Surrey, Guildford, Surrey GU2 7XH, United Kingdom
| | - Brendan J. Howlin
- Chemical Sciences Division, Faculty of Health and Molecular Sciences, University of Surrey, Guildford, Surrey GU2 7XH, United Kingdom
| | - Paul Klewpatinond
- Chemical Sciences Division, Faculty of Health and Molecular Sciences, University of Surrey, Guildford, Surrey GU2 7XH, United Kingdom
| | - Shinji Takeda
- Advanced Materials Research & Development Centre, Hitachi Chemical Co. Ltd., 1500 Ogawa, Chikusei, Ibaraki 317-8555, Japan
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Green RCE, Thumser AE, Povey D, Saldanha JW, Potter BS, Palmer RA, Howlin BJ. A comparative study of the single crystal X-ray determination and molecular modelling of the binding of oligomycin to ATP synthase. Comput Biol Chem 2009; 33:189-95. [PMID: 19217349 DOI: 10.1016/j.compbiolchem.2009.01.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2008] [Revised: 01/08/2009] [Accepted: 01/09/2009] [Indexed: 11/26/2022]
Abstract
Recently published X-ray structures of three common forms, A, B and C, of oligomycin, including absolute configurations, are investigated to examine their binding to ATP Synthase. The X-ray studies reveal regions with differences in three-dimensional structure and hydrogen bonding propensity between the oligomycins, which may be associated with their potential to bind to sites on ATP Synthase. Computational docking studies carried out using MOE with the X-ray structures and an homology model of the F(O) domain of ATP Synthase from Escherichia coli, are used to derive an induced fit pocket. Docking of all oligomycins to this pocket indicate that the B and C forms bind more tightly than the A form. Consideration of the single crystal X-ray data alone indicate the B form may be the best inhibitor and that O(24) is the most important ligating group for binding, this is supported by the docking data. The latter reveals Asn214 and other key proton translocating residues to be the main residues contacted by the inhibitor. These data allow the binding modes of different forms of oligomycin to be deduced from X-ray single crystal data supported by molecular modelling and computational docking studies.
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Affiliation(s)
- Roderic C E Green
- Chemical Sciences Division, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey GU2 7HX, UK
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Lockley WJS, Sfyrakis K, Howlin BJ, Jones JR, Wilkinson DJ. Some IT and data processing applications for2H,3H,11C,13C and14C-labelling. J Labelled Comp Radiopharm 2007. [DOI: 10.1002/jlcr.1247] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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43
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Hamerton I, Emsley AM, Hay JN, Herman H, Howlin BJ, Jepson P. The development of controllable complex curing agents for epoxy resins : Part 3. An investigation of the shelf life and thermal dissociation behaviour of bis(acetanilido)-tris(acetato)dicuprate(ii). ACTA ACUST UNITED AC 2006. [DOI: 10.1039/b510393b] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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44
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Tanczos AC, Palmer RA, Potter BS, Saldanha JW, Howlin BJ. Antagonist binding in the rat muscarinic receptor A study by docking and X-ray crystallography. Comput Biol Chem 2005; 28:375-85. [PMID: 15556478 DOI: 10.1016/j.compbiolchem.2004.09.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2004] [Revised: 09/29/2004] [Accepted: 09/29/2004] [Indexed: 11/15/2022]
Abstract
A series of agonists to the rat muscarinic receptor have been docked computationally to the active site of a homology model of rat M1 muscarinic receptor. The agonists were modelled on the X-ray crystal structure of atropine, which is reported here and the docking studies are shown to reproduce correctly the order of experimental binding affinities for the agonists as well as indicate where there appear to be inconsistencies in the experimental data. The crystal and molecular structure of atropine (tropine tropate; alpha-[hydroxymethyl]benzeneacetic acid 8-methyl[3.2.1]oct-3-yl ester C17H23NO3) has been determined by X-ray crystallography using an automated Patterson search method, and refined by full-matrix least-squares to a final R of 0.0452 for 2701 independent observed reflections and 192 parameters using Mo Kalpha radiation, lambda=0.71073A at 150K. The compound crystallises in space group Fdd2 with Z=16 molecules per unit cell.
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Affiliation(s)
- Anna C Tanczos
- Department of Chemistry, School of Biomedical and Molecular Sciences, University of Surrey, Guildford, Surrey GU2 7XH, UK
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45
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Sfyrakis K, Provata A, Povey DC, Howlin BJ. Local sequential minimization of double stranded B-DNA using Monte Carlo annealing. J Mol Model 2004; 10:185-97. [PMID: 15042433 DOI: 10.1007/s00894-004-0182-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2003] [Accepted: 12/15/2003] [Indexed: 11/28/2022]
Abstract
A software algorithm has been developed to investigate the folding process in B-DNA structures in vacuum under a simple and accurate force field. This algorithm models linear double stranded B-DNA sequences based on a local, sequential minimization procedure. The original B-DNA structures were modeled using initial nucleotide structures taken from the Brookhaven database. The models contain information at the atomic level allowing one to investigate as accurately as possible the structure and characteristics of the resulting DNA structures. A variety of DNA sequences and sizes were investigated containing coding and non-coding, random and real, homogeneous or heterogeneous sequences in the range of 2 to 40 base pairs. The force field contains terms such as angle bend, Lennard-Jones, electrostatic interactions and hydrogen bonding which are set up using the Dreiding II force field and defined to account for the helical parameters such as twist, tilt and rise. A close comparison was made between this local minimization algorithm and a global one (previously published) in order to find out advantages and disadvantages of the different methods. From the comparison, this algorithm gives better and faster results than the previous method, allowing one to minimize larger DNA segments. DNA segments with a length of 40 bases need approximately 4 h, while 2.5 weeks are needed with the previous method. After each minimization the angles between phosphate-oxygen-carbon A1, the oxygen-phosphate-oxygen A2 and the average helical twists were calculated. From the generated fragments it was found that the bond angles are A1=150 degrees +/-2 degrees and A2=130 degrees +/-10 degrees, while the helical twist is 36.6 degrees +/-2 degrees in the A strand and A1=150 degrees +/-6 degrees and A2=130+/-6 degrees with helical twist 39.6 degrees +/-2 degrees in the B strand for the DNA segment with the same sequence as the Dickerson dodecamer.
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Affiliation(s)
- Konstantinos Sfyrakis
- School of Biomedical and Life Sciences, Chemistry, University of Surrey, GU2 7XH, Guildford, UK
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Hamerton I, Emsley AM, Howlin BJ, Klewpatinond P, Takeda S. Studies on a dicyanate containing four phenylene rings and polycyanurate copolymers. 3. Application of mathematical models to determine the kinetics of the thermal degradation processes. POLYMER 2004. [DOI: 10.1016/j.polymer.2004.01.071] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Sfyrakis K, Provata A, Povey DC, Howlin BJ. Full-strand Minimization of Single and Double Stranded B-DNA Using Monte-Carlo Annealing. Molecular Simulation 2003. [DOI: 10.1080/0892702021000008858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Hamerton I, Emsley AM, Howlin BJ, Klewpatinond P, Takeda S. Studies on a dicyanate containing four phenylene rings and polycyanurate blends. 2. Application of mathematical models to the catalysed polymerization process. POLYMER 2003. [DOI: 10.1016/s0032-3861(03)00495-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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49
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Hamerton I, Howlin BJ, Klewpatinond P, Takeda S. Conformational studies of polycyanurates: a study of internal stress versus molecular structure. POLYMER 2002. [DOI: 10.1016/s0032-3861(02)00297-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Chaplin A, Hamerton I, Howlin BJ, Barton JM. Development of Novel Functionalized Aryl Cyanate Ester Oligomers. 1. Synthesis and Thermal Characterization of the Monomers. Macromolecules 2002. [DOI: 10.1021/ma00096a013] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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