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Cousins A, Olivares O, Markert E, Manoharan A, Bubnova X, Bresolin S, Degn M, Li Z, Silvestri D, McGregor G, Tumanov S, Sumpton D, Kamphorst JJ, Michie AM, Herzyk P, Valsecchi MG, Yeoh AE, Schmiegelow K, Te Kronnie G, Gottlieb E, Halsey C. Central nervous system involvement in childhood acute lymphoblastic leukemia is linked to upregulation of cholesterol biosynthetic pathways. Leukemia 2022; 36:2903-2907. [PMID: 36289348 PMCID: PMC9712090 DOI: 10.1038/s41375-022-01722-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 09/28/2022] [Accepted: 10/04/2022] [Indexed: 11/09/2022]
Affiliation(s)
- A Cousins
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - O Olivares
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - E Markert
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
- Cancer Research UK Beatson Institute, Glasgow, UK
| | - A Manoharan
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - X Bubnova
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - S Bresolin
- Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - M Degn
- Department of Pediatrics and Adolescent Medicine, The Juliane Marie Centre, The University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Z Li
- VIVA-NUS Centre for Translational Research in Acute Leukaemia, Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore
| | - D Silvestri
- Center of Biostatistics for Clinical Epidemiology, Department of Health Science, University of Milano-Bicocca, Milano, Italy
| | - G McGregor
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
- Cancer Research UK Beatson Institute, Glasgow, UK
| | - S Tumanov
- Cancer Research UK Beatson Institute, Glasgow, UK
| | - D Sumpton
- Cancer Research UK Beatson Institute, Glasgow, UK
| | - J J Kamphorst
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
- Cancer Research UK Beatson Institute, Glasgow, UK
| | - A M Michie
- Paul O'Gorman Leukaemia Research Centre, School of Cancer Sciences, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - P Herzyk
- Glasgow Polyomics, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
- Institute of Molecular, Cell and Systems Biology, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - M G Valsecchi
- Center of Biostatistics for Clinical Epidemiology, Department of Health Science, University of Milano-Bicocca, Milano, Italy
| | - A E Yeoh
- VIVA-NUS Centre for Translational Research in Acute Leukaemia, Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore
- VIVA-University Children's Cancer Centre, Khoo Teck Puat-National University Children's Medical Institute, National University Hospital, National University Health System, Singapore, 119228, Singapore
| | - K Schmiegelow
- Department of Pediatrics and Adolescent Medicine, The Juliane Marie Centre, The University Hospital Rigshospitalet, Copenhagen, Denmark
- Institute of Clinical Medicine, Faculty of Medicine, University of Copenhagen and Juliane Marie Centre, the University Hospital Rigshospitalet, Copenhagen, Denmark
| | - G Te Kronnie
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - E Gottlieb
- The Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
| | - C Halsey
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.
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Rodie ME, Mudaliar MAV, Herzyk P, McMillan M, Boroujerdi M, Chudleigh S, Tobias ES, Ahmed SF. Androgen-responsive non-coding small RNAs extend the potential of HCG stimulation to act as a bioassay of androgen sufficiency. Eur J Endocrinol 2017; 177:339-346. [PMID: 28733293 DOI: 10.1530/eje-17-0404] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 06/27/2017] [Accepted: 07/21/2017] [Indexed: 02/02/2023]
Abstract
BACKGROUND It is unclear whether a short-term change in circulating androgens is associated with changes in the transcriptome of the peripheral blood mononuclear cells (PBMC). AIMS AND METHODS To explore the effect of hCG stimulation on the PBMC transcriptome, 12 boys with a median age (range) of 0.7 years (0.3, 11.2) who received intramuscular hCG 1500u on 3 consecutive days as part of their investigations underwent transcriptomic array analysis on RNA extracted from peripheral blood mononuclear cells before and after hCG stimulation. RESULTS Median pre- and post-hCG testosterone for the overall group was 0.7 nmol/L (<0.5, 6) and 7.9 nmol/L (<0.5, 31.5), respectively. Of the 12 boys, 3 (25%) did not respond to hCG stimulation with a pre and post median serum testosterone of <0.5 nmol/L and <0.5 nmol/L, respectively. When corrected for gene expression changes in the non-responders to exclude hCG effects, all 9 of the hCG responders consistently demonstrated a 20% or greater increase in the expression of piR-37153 and piR-39248, non-coding PIWI-interacting RNAs (piRNAs). In addition, of the 9 responders, 8, 6 and 4 demonstrated a 30, 40 and 50% rise, respectively, in a total of 2 further piRNAs. In addition, 3 of the responders showed a 50% or greater rise in the expression of another small RNA, SNORD5. On comparing fold-change in serum testosterone with fold-change in the above transcripts, a positive correlation was detected for SNORD5 (P = 0.01). CONCLUSIONS The identification of a dynamic and androgen-responsive PBMC transcriptome extends the potential value of the hCG test for the assessment of androgen sufficiency.
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Affiliation(s)
- M E Rodie
- Developmental Endocrinology Research Group, University of Glasgow, Glasgow, UK
| | | | - P Herzyk
- Glasgow Polyomics
- Institute of Molecular Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - M McMillan
- Developmental Endocrinology Research Group, University of Glasgow, Glasgow, UK
| | - M Boroujerdi
- Developmental Endocrinology Research Group, University of Glasgow, Glasgow, UK
| | | | - E S Tobias
- Developmental Endocrinology Research Group, University of Glasgow, Glasgow, UK
- Glasgow Molecular Pathology Node
- Academic Medical Genetics and Pathology, Laboratory Medicine Building, Queen Elizabeth University Hospital, University of Glasgow, Glasgow, UK
| | - S F Ahmed
- Developmental Endocrinology Research Group, University of Glasgow, Glasgow, UK
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3
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Marasco V, Herzyk P, Robinson J, Spencer KA. Pre- and Post-Natal Stress Programming: Developmental Exposure to Glucocorticoids Causes Long-Term Brain-Region Specific Changes to Transcriptome in the Precocial Japanese Quail. J Neuroendocrinol 2016; 28:10.1111/jne.12387. [PMID: 26999292 PMCID: PMC5103168 DOI: 10.1111/jne.12387] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 03/04/2016] [Accepted: 03/15/2016] [Indexed: 01/16/2023]
Abstract
Exposure to stress during early development can permanently influence an individual's physiology and behaviour, and affect its subsequent health. The extent to which elevated glucocorticoids cause such long-term 'programming' remains largely untested. In the present study, using the Japanese quail as our study species, we independently manipulated exposure to corticosterone during pre- and/or post-natal development and investigated the subsequent effects on global gene expression profiles within the hippocampus and hypothalamus upon achieving adulthood. Our results showed that the changes in transcriptome profiles in response to corticosterone exposure clearly differed between the hippocampus and the hypothalamus. We also showed that these effects depended on the developmental timing of exposure and identified brain-region specific gene expression patterns that were either: (i) similarly altered by corticosterone regardless of the developmental stage in which hormonal exposure occurred or (ii) specifically and uniquely altered by either pre-natal or post-natal exposure to corticosterone. Corticosterone-treated birds showed alterations in networks of genes that included known markers of the programming actions of early-life adversity (e.g. brain-derived neurotrophic factor and mineralocorticoid receptor within the hippocampus; corticotrophin-releasing hormone and serotonin receptors in the hypothalamus). Altogether, for the first time, these findings provide experimental support for the hypothesis that exposure to elevated glucocorticoids during development may be a key hormonal signalling pathway through which the long-term phenotypic effects associated with early-life adversity emerge and potentially persist throughout the lifespan. These data also highlight that stressors might have different long-lasting impacts on the brain transcriptome depending on the developmental stage in which they are experienced; more work is now required to relate these mechanisms to organismal phenotypic differences.
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Affiliation(s)
- V. Marasco
- Institute of Biodiversity, Animal Health and Comparative MedicineUniversity of GlasgowGlasgowUK
| | - P. Herzyk
- Institute of Molecular Cell and Systems BiologyUniversity of GlasgowGlasgowUK
- Glasgow PolyomicsWolfson Wohl Cancer Research CentreUniversity of GlasgowGlasgowUK
| | - J. Robinson
- Institute of Biodiversity, Animal Health and Comparative MedicineUniversity of GlasgowGlasgowUK
| | - K. A. Spencer
- School of Psychology and NeuroscienceUniversity of St AndrewsSt AndrewsUK
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4
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Wotton S, Terry A, Kilbey A, Jenkins A, Herzyk P, Cameron E, Neil JC. Gene array analysis reveals a common Runx transcriptional programme controlling cell adhesion and survival. Oncogene 2008; 27:5856-66. [PMID: 18560354 DOI: 10.1038/onc.2008.195] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The Runx genes are important in development and cancer, where they can act either as oncogenes or tumour suppressors. We compared the effects of ectopic Runx expression in established fibroblasts, where all three genes produce an indistinguishable phenotype entailing epithelioid morphology and increased cell survival under stress conditions. Gene array analysis revealed a strongly overlapping transcriptional signature, with no examples of opposing regulation of the same target gene. A common set of 50 highly regulated genes was identified after further filtering on regulation by inducible RUNX1-ER. This set revealed a strong bias toward genes with annotated roles in cancer and development, and a preponderance of targets encoding extracellular or surface proteins, reflecting the marked effects of Runx on cell adhesion. Furthermore, in silico prediction of resistance to glucocorticoid growth inhibition was confirmed in fibroblasts and lymphoid cells expressing ectopic Runx. The effects of fibroblast expression of common RUNX1 fusion oncoproteins (RUNX1-ETO, TEL-RUNX1 and CBFB-MYH11) were also tested. Although two direct Runx activation target genes were repressed (Ncam1 and Rgc32), the fusion proteins appeared to disrupt the regulation of downregulated targets (Cebpd, Id2 and Rgs2) rather than impose constitutive repression. These results elucidate the oncogenic potential of the Runx family and reveal novel targets for therapeutic inhibition.
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Affiliation(s)
- S Wotton
- Faculty of Veterinary Medicine, Molecular Oncology Laboratory,Institute of Comparative Medicine, University of Glasgow, Glasgow, Scotland.
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5
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Wright RHG, Dornan ES, Donaldson MM, MacFarlane M, Herzyk P, Morgan IM. TopBP1 contains transcriptional regulatory domains and regulates gene pathways involved in breast cancer. Breast Cancer Res 2008. [PMCID: PMC3300724 DOI: 10.1186/bcr1905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Tarabykina S, Scott DJ, Herzyk P, Hill TJ, Tame JR, Kriajevska M, Lafitte D, Derrick PJ, Dodson GG, Maitland NJ, Lukanidin EM, Bronstein IB. The dimerization interface of the metastasis-associated protein S100A4 (Mts1): in vivo and in vitro studies. J Biol Chem 2001; 276:24212-22. [PMID: 11278510 DOI: 10.1074/jbc.m009477200] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The S100 calcium-binding proteins are implicated in signal transduction, motility, and cytoskeletal dynamics. The three-dimensional structure of several S100 proteins revealed that the proteins form non-covalent dimers. However, the mechanism of the S100 dimerization is still obscure. In this study we characterized the dimerization of S100A4 (also named Mts1) in vitro and in vivo. Analytical ultracentrifugation revealed that apoS100A4 was present in solution as a mixture of monomers and dimers in a rapidly reversible equilibrium (K(d) = 4 +/- 2 microm). The binding of calcium promoted dimerization. Replacement of Tyr-75 by Phe resulted in the stabilization of the dimer. Helix IV is known to form the major part of the dimerization interface in homologous S100 proteins. By using the yeast two-hybrid system we showed that only a few residues of helix IV, namely Phe-72, Tyr-75, Phe-78, and Leu-79, are essential for dimerization in vivo. A homology model demonstrated that these residues form a hydrophobic cluster on helix IV. Their role is to stabilize the structure of individual subunits rather than provide specific interactions across the dimerization surface. Our mutation data showed that the specificity at the dimerization surface is not particularly stringent, which is consistent with recent data indicating that S100 proteins can form heterodimers.
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Affiliation(s)
- S Tarabykina
- Department of Molecular Cancer Biology, Danish Cancer Society, Copenhagen DK-2100, Denmark
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7
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Herzyk P, Hubbard RE. Combined biophysical and biochemical information confirms arrangement of transmembrane helices visible from the three-dimensional map of frog rhodopsin. J Mol Biol 1998; 281:741-54. [PMID: 9710543 DOI: 10.1006/jmbi.1998.1981] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The electron density projection map of frog rhodopsin at 6 A resolution had been until recently the most direct evidence for the three-dimensional structure of a transmembrane domain of any G-protein-coupled receptor. Only three out of seven transmembrane helices are clearly defined, whilst the other four are hidden in a patch of unresolved electron density. A model of the seven-helix bundle has been created by generating positions and orientations for the four unresolved helices through performing a conformational search directed by structural restraints derived from other experimental data. These four helices are significantly tilted with respect to the membrane normal, and the cytosolic end of helix C is inserted between helices D and E. These calculations produce positions and orientations for these additional helices that are consistent with the recently published low-resolution three-dimensional map, and provide a template for more detailed modelling of rhodopsin structure and function.
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Affiliation(s)
- P Herzyk
- Chemistry Department, University of York, York, YO10 5DD, UK
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8
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Abstract
Molecular models of the transmembrane domain of the phospholamban pentamer have been generated by a computational method that uses the experimentally measured effects of systematic single-site mutations as a guiding force in the modeling procedure. This method makes the assumptions that 1) the phospholamban transmembrane domain is a parallel five-helix bundle, and 2) nondisruptive mutation positions are lipid exposed, whereas 3) disruptive or partially disruptive mutations are not. Our procedure requires substantially less computer time than systematic search methods, allowing rapid assessment of the effects of different experimental results on the helix arrangement. The effectiveness of the approach is investigated in test calculations on two helix-dimer systems of known structure. Two independently derived sets of mutagenesis data were used to define the restraints for generating models of phospholamban. Both resulting models are left-handed, highly symmetrical pentamers. Although the overall bundle geometry is very similar in the two models, the orientation of individual helices differs by approximately 50 degrees, resulting in different sets of residues facing the pore. This demonstrates how differences in restraints can have an effect on the model structures generated, and how the violation of these restraints can identify inconsistent experimental data.
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Affiliation(s)
- P Herzyk
- Department of Chemistry, University of York, Heslington, England.
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9
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Prusis P, Schiöth HB, Muceniece R, Herzyk P, Afshar M, Hubbard RE, Wikberg JE. Modeling of the three-dimensional structure of the human melanocortin 1 receptor, using an automated method and docking of a rigid cyclic melanocyte-stimulating hormone core peptide. J Mol Graph Model 1997; 15:307-17, 334. [PMID: 9640562 DOI: 10.1016/s1093-3263(98)00004-7] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A model is presented of the melanocortin 1 receptor (MC1R), constructed by use of an unbiased, objective method. The model is created directly from data derived from multiple sequence analysis, a low-resolution EM-projection map of rhodopsin, and the approximate membrane thickness. The model agrees well with available data concerning natural mutations of MC1Rs occurring in different species. A model is also presented of the most rigid ligand for this receptor, the cyclic pentapeptide cHFRWG, shown docked in the receptor model. The receptor-ligand complex model agrees well with available experimental data. The ligand is located between transmembrane region 1 (TM1), TM2, TM3, TM6, and TM7 of the receptor. Multiple interactions occur between ligand and receptor, including interactions with Leu-48 (TM1), Ser-52 (TM1), Glu-55 (TM1), Asn-91 (TM2), Glu-94 (TM2), Thr-95 (TM2) Ile-98 (TM2), Asp-121 (TM3), Thr-124 (TM3), Phe-257 (TM6), Phe-283 (TM7), Asn-290 (TM7), and Asp-294 (TM7) of the receptor.
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10
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Peitsch MC, Herzyk P, Wells TN, Hubbard RE. Automated modelling of the transmembrane region of G-protein coupled receptor by Swiss-model. Recept Channels 1996; 4:161-4. [PMID: 9014239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Molecular modelling of the transmembrane helices of G-protein coupled receptors is an increasingly used method to identify the possible three-dimensional environment of key residues. Thereby site-directed mutagenesis experiments, aimed at the understanding of the receptor-ligand interactions, can be designed in a rational way. The modelling methods are however not generally available to experimentalists, and often require expensive software and hardware. To overcome these limitations, we have constructed a World Wide Web server for the automated protein modelling of user-defined transmembrane helices. The service is freely available at this address: http:/(/)expasy.hcuge.ch/swissmod/SWISS-MODEL.++ +html.
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Affiliation(s)
- M C Peitsch
- BioInformatics, Glaxo Institute for Molecular Biology, Geneva, Switzerland
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11
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Abstract
A rule-based automated method is presented for modeling the structures of the seven transmembrane helices of G-protein-coupled receptors. The structures are generated by using a simulated annealing Monte Carlo procedure that positions and orients rigid helices to satisfy structural restraints. The restraints are derived from analysis of experimental information from biophysical studies on native and mutant proteins, from analysis of the sequences of related proteins, and from theoretical considerations of protein structure. Calculations are presented for two systems. The method was validated through calculations using appropriate experimental information for bacteriorhodopsin, which produced a model structure with a root mean square (rms) deviation of 1.87 A from the structure determined by electron microscopy. Calculations are also presented using experimental and theoretical information available for bovine rhodopsin to assign the helices to a projection density map and to produce a model of bovine rhodopsin that can be used as a template for modeling other G-protein-coupled receptors.
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Affiliation(s)
- P Herzyk
- Department of Chemistry, University of York, Heslington, United Kingdom.
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12
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13
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Abstract
A reduced representation of proteins has been developed for use in restraint satisfaction calculations with dynamic simulated annealing. Each amino acid residue is represented by up to four spherical virtual atoms. The virtual bonds and excluded volume of these atoms has been parameterized by analysis of 83 protein structures determined at high resolution by X-ray crystallography. The use of the new representation in NOE distance restraint satisfaction has been compared with the standard all-atom representation for the determination of the structures of crambin, echistatin, and protein G. Using the reduced representation, there is a 30-fold decrease in the computer time needed for generating a single structure, and up to a 20-fold decrease in the time taken to produce an acceptable structure compared to using the all-atom representation. The root mean square deviation between the mean structure obtained with all-atom and reduced representations is between 1.5 and 1.7 A for C alpha atoms. The new representation is adequate for describing the "low-resolution" features of protein structure such as the general fold and the positions of secondary structure elements. It can also provide an initial structure for more detailed refinement with the full all-atom representation.
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Affiliation(s)
- P Herzyk
- Department of Chemistry, University of York, Heslington, England
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14
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Cooke RM, Carter BG, Murray-Rust P, Hartshorn MJ, Herzyk P, Hubbard RE. The solution structure of echistatin: evidence for disulphide bond rearrangement in homologous snake toxins. Protein Eng 1992; 5:473-7. [PMID: 1438157 DOI: 10.1093/protein/5.6.473] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The solution structure of the fibrinogen antagonist, echistatin, has been determined by a combination of NMR and simulated annealing methods. While the structure of the disulphide-linked core is well-defined by the NMR data, the N- and C-termini and the loop bearing the RGD sequence (which is responsible for the fibrinogen antagonist properties) are poorly defined. The pattern of disulphide bridges, which could not be determined by classical methods, was predicted by a statistical analysis of the simulated annealing structures. This pattern is distinct from that for the homologous protein kistrin, leading to the novel suggestion that homologous proteins possess non-conserved patterns of disulphide bridges.
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Affiliation(s)
- R M Cooke
- Glaxo Group Research, Greenford, Middlesex, UK
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15
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Abstract
Molecular dynamics simulations have been undertaken for a B-form dodecanucleotide duplex in solution with and without an intercalated proflavine molecule between the central C.G base pairs. The introduction of this simple intercalator affects both the conformational features and dynamic properties of the oligonucleotide double helix. Changes are seen in the rms atomic fluctuations and anisotropy of phosphate, sugar and base atoms. The backbone conformation is slightly changed on average and more sugars adopt the C3' endo conformation in the simulation of the complex compared with the simulation of the oligonucleotide alone. Both major and minor grooves becomes wider on average with the addition of the intercalating drug. Flanking A.T base pairs on both sides of the intercalation site have undergone an increase in flexibility, with the base pairs, especially at the 5' side, having the N1...N3 hydrogen bonds being broken.
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Affiliation(s)
- P Herzyk
- Cancer Research Campaign Biomolecular Structure Unit, Institute of Cancer Research, Sutton, Surrey, UK
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16
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Abstract
Molecular dynamics simulations have been performed on the dinucleoside monophosphates rGpC and dCpG, the latter in its intercalation complex with the acridine drug proflavine. The simulations were performed on the crystal structures, with crystallographically-located solvent molecules. It was found that satisfactory results were best obtained with restraints placed on the movements of the water molecules. Motions of individual atoms have been examined in terms of rms fluctuations and anisotropy and correlation functions. Relative motions of groups (phosphates, sugars, bases and proflavine molecules) have been analysed.
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Affiliation(s)
- P Herzyk
- Department of Crystallography, Birkbeck College, London, U.K
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17
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Orozco M, Laughton CA, Herzyk P, Neidle S. Molecular-mechanics modelling of drug-DNA structures; the effects of differing dielectric treatment on helix parameters and comparison with a fully solvated structural model. J Biomol Struct Dyn 1990; 8:359-73. [PMID: 2176506 DOI: 10.1080/07391102.1990.10507810] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
This study analyses the influence that the nature of the dielectric constant has on the final structures obtained from in vacuo molecular mechanics calculations on a drug-DNA complex and compares these structures with the energy minimised complex including explicit solvent molecules. Minimisations have been performed on a proflavine-decanucleotide structure, where the drug was intercalated at the d(CpG) site of the d(GpApTpApCpGpApTpApC) decamer duplex, using two expressions for the dielectric constant: a distance-independent, epsilon ij = EPS, and a distance-dependent, epsilon ij = EPS*Rij, form and for values of EPS from 1 to 8. Significantly different structures are obtained for the distance-independent and the distance-dependent expressions of the dielectric constant. The use of a distance-independent dielectric constant leads to distorted structures, which are very sensitive to slight changes in the value of EPS. The use of a distance-dependent dielectric constant leads to less distorted and more stable structures. The effects on helical parameters are analysed in detail. The structures obtained for different values of EPS (within the distance-dependent formalism) seem to converge for values of EPS equal to 4 or greater. Based on these results a distance-dependent form of the dielectric with an EPS value of 4 is recommended in order to produce reliable refined nucleic acid structures by molecular mechanics. These conclusions have been supported by molecular-mechanics minimisation of the same structure with the inclusion of explicit water molecules and counter-ions.
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Affiliation(s)
- M Orozco
- Cancer Research Campaign Biomolecular Structure Unit, Institute of Cancer Research Sutton, Surrey, United Kingdom
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18
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Abstract
A molecular model has been derived for the intercalation of proflavine into the CpG site of the decamer duplex of d(GATACGATAC). The starting geometry of the intercalation site was taken from previous crystallographic studies on the d(CpG)-proflavine complex, and molecular mechanics used to obtain a stereochemically acceptable structure. This has widened grooves compared to standard A- or B- double helices, as well as distinct conformational, roll, twist and tilt features.
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Affiliation(s)
- S Neidle
- Cancer Research Campaign Biomolecular Structure Unit, Institute of Cancer Research, Sutton, Surrey, UK
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Herzyk P, Beveridge A, Neidle S. Conformational properties of 3'-azido-3'deoxy-thymidine (AZT), an inhibitor of HIV reverse transcriptase. Biochem Biophys Res Commun 1987; 145:1356-61. [PMID: 2440430 DOI: 10.1016/0006-291x(87)91587-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The low-energy conformations of 3'-azido-3'-deoxy-thymidine, (AZT), an inhibitor of retroviral reverse transcriptase, have been studied by molecular mechanics techniques. A force-field has been developed for the azido group by quantum-mechanical methods, and used in the analysis. The global low-energy structure of AZT has C3'-endo sugar pucker, an anti glycosidic angle, and a g+ C4'-C5' conformation. It is concluded that the AZT molecule has conformational properties that are very similar to those of standard deoxypyrimidines.
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