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[해외논문] Considering both small and large scale motions of vascular endothelial growth factor (VEGF) is crucial for reliably predicting its binding affinities to DNA aptamers 원문보기

RSC advances, v.11 no.16, 2021년, pp.9315 - 9326  

Lee, Wook (Department of Chemistry, Pohang University of Science and Technology (POSTECH) Pohang 37673 Korea) ,  Park, Jae Whee (Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Korea ymrhee@kaist.ac.kr) ,  Go, Yeon Ju (Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Korea ymrhee@kaist.ac.kr) ,  Kim, Won Jong (Department of Chemistry, Pohang University of Science and Technology (POSTECH) Pohang 37673 Korea) ,  Rhee, Young Min (Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Korea ymrhee@kaist.ac.kr)

Abstract AI-Helper 아이콘AI-Helper

Vascular endothelial growth factor 165 (VEGF165), a predominant isoform of VEGF signal proteins, is an ideal target for developing drugs against various diseases. It is composed of a heparin binding domain (HBD) and a receptor binding domain (RBD), which are connected by a flexible linker. Among the...

참고문헌 (72)

  1. Risau W. Mechanisms of angiogenesis Nature 1997 386 671 674 10.1038/386671a0 9109485 

  2. Carmeliet P. Angiogenesis in life, disease and medicine Nature 2005 438 932 936 10.1038/nature04478 16355210 

  3. Hanahan D. Weinberg R. A. Hallmarks of cancer: the next generation Cell 2011 144 646 674 10.1016/j.cell.2011.02.013 21376230 

  4. Azizi G. Boghozian R. Mirshafiey A. The potential role of angiogenic factors in rheumatoid arthritis Int. J. Rheum. Dis. 2014 17 369 383 10.1111/1756-185X.12280 24467605 

  5. Miller J. W. Le Couter J. Strauss E. C. Ferrara N. Vascular endothelial growth factor a in intraocular vascular disease Ophthalmology 2013 120 106 114 10.1016/j.ophtha.2012.07.038 23031671 

  6. Pousa I. D. Maté J. Gisbert J. P. Angiogenesis in inflammatory bowel disease Eur. J. Clin. Invest. 2008 38 73 81 10.1111/j.1365-2362.2007.01914.x 18226040 

  7. Ved N. Hulse R. P. Bestall S. M. Donaldson L. F. Bainbridge J. W. Bates D. O. Vascular endothelial growth factor-A165b ameliorates outer-retinal barrier and vascular dysfunction in the diabetic retina Clin. Sci. 1979 131 1225 1243 10.1042/CS20170102 

  8. Ferrara N. Gerber H.-P. LeCouter J. The biology of VEGF and its receptors Nat. Med. 2003 9 669 676 10.1038/nm0603-669 12778165 

  9. Witmer A. N. Vrensen G. F. J. M. Van Noorden C. J. F. Schlingemann R. O. Vascular endothelial growth factors and angiogenesis in eye disease Prog. Retinal Eye Res. 2003 22 1 29 10.1016/S1350-9462(02)00043-5 

  10. Ishida S. Usui T. Yamashiro K. Kaji Y. Amano S. Ogura Y. Hida T. Oguchi Y. Ambati J. Miller J. W. Gragoudas E. S. Ng Y.-S. D'Amore P. A. Shima D. T. Adamis A. P. VEGF164-mediated inflammation is required for pathological, but not physiological, ischemia-induced retinal neovascularization J. Exp. Med. 2003 198 483 489 10.1084/jem.20022027 12900522 

  11. Ng E. W. M. Adamis A. P. Targeting angiogenesis, the underlying disorder in neovascular age-related macular degeneration Can. J. Ophthalmol. 2005 40 352 368 10.1016/S0008-4182(05)80078-X 15947805 

  12. Uciechowska-Kaczmarzyk U. Babik S. Zsila F. Bojarski K. K. Beke-Somfai T. Samsonov S. A. Molecular dynamics-based model of VEGF-A and its heparin interactions J. Mol. Graphics Modell. 2018 82 157 166 10.1016/j.jmgm.2018.04.015 

  13. Tuerk C. Gold L. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase Science 1990 249 505 510 10.1126/science.2200121 2200121 

  14. Nimjee S. M. Rusconi C. P. Sullenger B. A. Aptamers: an emerging class of therapeutics Annu. Rev. Med. 2005 56 555 583 10.1146/annurev.med.56.062904.144915 15660527 

  15. Ruckman J. Green L. S. Beeson J. Waugh S. Gillette W. L. Henninger D. D. Claesson-Welsh L. Janjić N. 2′-Fluoropyrimidine RNA-based aptamers to the 165-amino acid form of vascular endothelial growth factor (VEGF165). Inhibition of receptor binding and VEGF-induced vascular permeability through interactions requiring the exon 7-encoded domain J. Biol. Chem. 1998 273 20556 20567 10.1074/jbc.273.32.20556 9685413 

  16. Gold L. and Janjic N. , US Pat. , 669625, 1998 

  17. Potty A. S. R. Kourentzi K. Fang H. Jackson G. W. Zhang X. Legge G. B. Willson R. C. Biophysical characterization of DNA aptamer interactions with vascular endothelial growth factor Biopolymers 2009 91 145 156 10.1002/bip.21097 19025993 

  18. Sarabipour S. Ballmer-Hofer K. Hristova K. VEGFR-2 conformational switch in response to ligand binding eLife 2016 5 e13876 10.7554/eLife.13876 27052508 

  19. Mandell J. G. Roberts V. A. Pique M. E. Kotlovyi V. Mitchell J. C. Nelson E. Tsigelny I. Ten Eyck L. F. Protein docking using continuum electrostatics and geometric fit Protein Eng., Des. Sel. 2001 14 105 113 10.1093/protein/14.2.105 

  20. Roberts V. A. Thompson E. E. Pique M. E. Perez M. S. Ten Eyck L. F. DOT2: macromolecular docking with improved biophysical models J. Comput. Chem. 2013 34 1743 1758 10.1002/jcc.23304 23695987 

  21. Bell D. R. Weber J. K. Yin W. Huynh T. Duan W. Zhou R. In silico design and validation of high-affinity RNA aptamers targeting epithelial cellular adhesion molecule dimers Proc. Natl. Acad. Sci. U. S. A. 2020 117 8486 8493 10.1073/pnas.1913242117 32234785 

  22. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction Nucleic Acids Res. 2003 31 3406 3415 10.1093/nar/gkg595 12824337 

  23. Muller Y. A. Christinger H. W. Keyt B. A. de Vos A. M. The crystal structure of vascular endothelial growth factor (VEGF) refined to 1.93 a resolution: multiple copy flexibility and receptor binding Structure 1993 5 1325 1338 10.1016/S0969-2126(97)00284-0 

  24. Fairbrother W. J. Champe M. A. Christinger H. W. Keyt B. A. Starovasnik M. A. Solution structure of the heparin-binding domain of vascular endothelial growth factor Structure 1998 6 637 648 10.1016/S0969-2126(98)00065-3 9634701 

  25. Verdonk M. L. Cole J. C. Hartshorn M. J. Murray C. W. Taylor R. D. Improved protein–ligand docking using GOLD Proteins 2003 52 609 623 10.1002/prot.10465 12910460 

  26. Gromiha M. M. Yugandhar K. Jemimah S. Protein–protein interactions: scoring schemes and binding affinity Curr. Opin. Struct. Biol. 2017 44 31 38 10.1016/j.sbi.2016.10.016 27866112 

  27. Carlson H. A. Masukawa K. M. McCammon J. A. Method for Including the Dynamic Fluctuations of a Protein in Computer-Aided Drug Design J. Phys. Chem. A 1999 103 10213 10219 10.1021/jp991997z 

  28. Amaro R. E. Baudry J. Chodera J. Demir Ö. McCammon J. A. Miao Y. Smith J. C. Ensemble Docking in Drug Discovery Biophys. J. 2018 114 2271 2278 10.1016/j.bpj.2018.02.038 29606412 

  29. Atilgan A. R. Durell S. R. Jernigan R. L. Demirel M. C. Keskin O. Bahar I. Anisotropy of fluctuation dynamics of proteins with an elastic network model Biophys. J. 2001 80 505 515 10.1016/S0006-3495(01)76033-X 11159421 

  30. Doruker P. Atilgan A. R. Bahar I. Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: application to α-amylase inhibitor Proteins: Struct., Funct., Bioinf. 2000 40 512 524 10.1002/1097-0134(20000815)40:3<512::AID-PROT180>3.0.CO;2-M 

  31. Eyal E. Lum G. Bahar I. The anisotropic network model web server at 2015 (ANM 2.0) Bioinformatics 2015 31 1487 1489 10.1093/bioinformatics/btu847 25568280 

  32. Lee J.-H. Canny M. D. De Erkenez A. Krilleke D. Ng Y.-S. Shima D. T. Pardi A. Jucker F. A therapeutic aptamer inhibits angiogenesis by specifically targeting the heparin binding domain of VEGF165 Proc. Natl. Acad. Sci. U. S. A. 2005 102 18902 18907 10.1073/pnas.0509069102 16357200 

  33. Ahmed A. Rippmann F. Barnickel G. Gohlke H. A normal mode-based geometric simulation approach for exploring biologically relevant conformational transitions in proteins J. Chem. Inf. Model. 2011 51 1604 1622 10.1021/ci100461k 21639141 

  34. Krüger D. M. Ahmed A. Gohlke H. NMSim web server: integrated approach for normal mode-based geometric simulations of biologically relevant conformational transitions in proteins Nucleic Acids Res. 2012 40 W310 W316 10.1093/nar/gks478 22669906 

  35. Goncalves V. Gautier B. Coric P. Bouaziz S. Lenoir C. Garbay C. Vidal M. Inguimbert N. Rational Design, Structure, and Biological Evaluation of Cyclic Peptides Mimicking the Vascular Endothelial Growth Factor J. Med. Chem. 2007 50 5135 5146 10.1021/jm0706970 17900101 

  36. Gautier B. Goncalves V. Diana D. Di Stasi R. Teillet F. Lenoir C. Huguenot F. Garbay C. Fattorusso R. D'Andrea L. D. Vidal M. Inguimbert N. Biochemical and Structural Analysis of the Binding Determinants of a Vascular Endothelial Growth Factor Receptor Peptidic Antagonist J. Med. Chem. 2010 53 4428 4440 10.1021/jm1002167 20462213 

  37. Basile A. Del Gatto A. Diana D. Di Stasi R. Falco A. Festa M. Rosati A. Barbieri A. Franco R. Arra C. Pedone C. Fattorusso R. Turco M. C. D'Andrea L. D. Characterization of a Designed Vascular Endothelial Growth Factor Receptor Antagonist Helical Peptide with Antiangiogenic Activity in Vivo J. Med. Chem. 2011 54 1391 1400 10.1021/jm101435r 21280635 

  38. Wang L. Gagey-Eilstein N. Broussy S. Reille-Seroussi M. Huguenot F. Vidal M. Liu W.-Q. Design and synthesis of C-terminal modified cyclic peptides as VEGFR1 antagonists Materials 2014 19 15391 15407 

  39. De Rosa L. Finetti F. Diana D. Di Stasi R. Auriemma S. Romanelli A. Fattorusso R. Ziche M. Morbidelli L. D'Andrea L. D. Miniaturizing VEGF: Peptides mimicking the discontinuous VEGF receptor-binding site modulate the angiogenic response Sci. Rep. 2016 6 31295 10.1038/srep31295 27498819 

  40. Wang L. Zhou L. Reille-Seroussi M. Gagey-Eilstein N. Broussy S. Zhang T. Ji L. Vidal M. Liu W.-Q. Identification of Peptidic Antagonists of Vascular Endothelial Growth Factor Receptor 1 by Scanning the Binding Epitopes of Its Ligands J. Med. Chem. 2017 60 6598 6606 10.1021/acs.jmedchem.7b00283 28686443 

  41. Sadremomtaz A. Mansouri K. Alemzadeh G. Safa M. Rastaghi A. E. Asghari S. M. Dual blockade of VEGFR1 and VEGFR2 by a novel peptide abrogates VEGF-driven angiogenesis, tumor growth, and metastasis through PI3K/AKT and MAPK/ERK1/2 pathway Biochim. Biophys. Acta, Gen. Subj. 2018 1862 2688 2700 10.1016/j.bbagen.2018.08.013 30251659 

  42. Behelgardi M. F. Zahri S. Mashayekhi F. Mansouri K. Asghari S. M. A peptide mimicking the binding sites of VEGF-A and VEGF-B inhibits VEGFR-1/-2 driven angiogenesis, tumor growth and metastasis Sci. Rep. 2018 8 17924 10.1038/s41598-018-36394-0 30560942 

  43. Markovic-Mueller S. Stuttfeld E. Asthana M. Weinert T. Bliven S. Goldie K. N. Kisko K. Capitani G. Ballmer-Hofer K. Structure of the Full-length VEGFR-1 Extracellular Domain in Complex with VEGF-A Structure 1993 25 341 352 10.1016/j.str.2016.12.012 

  44. Jeddi I. Saiz L. Three-dimensional modeling of single stranded DNA hairpins for aptamer-based biosensors Sci. Rep. 2017 7 1178 10.1038/s41598-017-01348-5 28446765 

  45. Reuter J. S. Mathews D. H. RNAstructure: software for RNA secondary structure prediction and analysis BMC Bioinf. 2010 11 129 10.1186/1471-2105-11-129 

  46. Popenda M. Szachniuk M. Antczak M. Purzycka K. J. Lukasiak P. Bartol N. Blazewicz J. Adamiak R. W. Automated 3D structure composition for large RNAs Nucleic Acids Res. 2012 40 e112 10.1093/nar/gks339 22539264 

  47. Antczak M. Popenda M. Zok T. Sarzynska J. Ratajczak T. Tomczyk K. Adamiak R. W. Szachniuk M. New functionality of RNAComposer: an application to shape the axis of miR160 precursor structure Acta Biochim. Pol. 2016 63 737 744 27741327 

  48. Wang J. Mao K. Zhao Y. Zeng C. Xiang J. Zhang Y. Xiao Y. Optimization of RNA 3D structure prediction using evolutionary restraints of nucleotide–nucleotide interactions from direct coupling analysis Nucleic Acids Res. 2017 45 6299 6309 10.1093/nar/gkx386 28482022 

  49. Magnus M. Boniecki M. J. Dawson W. Bujnicki J. M. SimRNAweb: a web server for RNA 3D structure modeling with optional restraints Nucleic Acids Res. 2016 44 W315 W319 10.1093/nar/gkw279 27095203 

  50. Parisien M. Major F. The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data Nature 2008 452 51 55 10.1038/nature06684 18322526 

  51. Maier J. A. Martinez C. Kasavajhala K. Wickstrom L. Hauser K. E. Simmerling C. ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB J. Chem. Theory Comput. 2015 11 3696 3713 10.1021/acs.jctc.5b00255 26574453 

  52. Still W. C. Tempczyk A. Hawley R. C. Hendrickson T. Semianalytical treatment of solvation for molecular mechanics and dynamics J. Am. Chem. Soc. 1990 112 6127 6129 10.1021/ja00172a038 

  53. Hanwell M. D. Curtis D. E. Lonie D. C. Vandermeersch T. Zurek E. Hutchison G. R. Avogadro: an advanced semantic chemical editor, visualization, and analysis platform J. Cheminf. 2012 4 17 

  54. Jorgensen W. L. Chandrasekhar J. Madura J. D. Impey R. W. Klein M. L. Comparison of Simple Potential Functions for Simulating Liquid Water J. Chem. Phys. 1983 79 926 10.1063/1.445869 

  55. Essmann U. Perera L. Berkowitz M. L. Darden T. Lee H. Pedersen L. G. A smooth particle mesh Ewald method J. Chem. Phys. 1995 103 8577 8593 10.1063/1.470117 

  56. Case D. , Berryman J. , Betz R. , Cerutti D. , Cheatham III T. , Darden T. , Duke R. , Giese T. , Gohlke H. , Goetz A. , Homeyer N. , Izadi S. , Janowski P. , Kaus J. , Kovalenko A. , Lee T. , LeGrand S. , Li P. , Luchko T. , Luo R. , Madej B. , Merz K. , Monard G. , Needham P. , Nguyen H. , Nguyen H. , Omelyan I. , Onufriev A. , Roe D. , Roitberg A. , Solomon-Ferrer R. , Simmerling 

  57. Ryckaert J.-P. Ciccotti G. Berendsen H. J. C. Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n -alkanes J. Comput. Phys. 1977 23 327 341 10.1016/0021-9991(77)90098-5 

  58. Berendsen H. J. C. Postma J. P. M. van Gunsteren W. F. DiNola A. Haak J. R. Molecular dynamics with coupling to an external bath J. Chem. Phys. 1984 81 3684 3690 10.1063/1.448118 

  59. Gouy M. Sur la constitution de la charge électrique à la surface d'un électrolyte J. Phys. Theor. Appl. 1910 9 457 468 10.1051/jphystap:019100090045700 

  60. Chapman D. L. LI. A contribution to the theory of electrocapillarity London, Edinburgh Dublin Philos. Mag. J. Sci. 1913 25 475 481 10.1080/14786440408634187 

  61. Roberts V. A. Case D. A. Tsui V. Predicting interactions of winged-helix transcription factors with DNA Proteins: Struct., Funct., Bioinf. 2004 57 172 187 10.1002/prot.20193 

  62. Roberts V. A. Pique M. E. Ten Eyck L. F. Li S. Predicting protein–DNA interactions by full search computational docking Proteins 2013 81 2106 2118 10.1002/prot.24395 23966176 

  63. Hopfner K. P. Karcher A. Craig L. Woo T. T. Carney J. P. Tainer J. A. Structural biochemistry and interaction architecture of the DNA double-strand break repair Mre11 nuclease and Rad50-ATPase Cell 2001 105 473 485 10.1016/S0092-8674(01)00335-X 11371344 

  64. Fan L. Fuss J. O. Cheng Q. J. Arvai A. S. Hammel M. Roberts V. A. Cooper P. K. Tainer J. A. XPD helicase structures and activities: insights into the cancer and aging phenotypes from XPD mutations Cell 2008 133 789 800 10.1016/j.cell.2008.04.030 18510924 

  65. Hammel M. Rey M. Yu Y. Mani R. S. Classen S. Liu M. Pique M. E. Fang S. Mahaney B. L. Weinfeld M. Schriemer D. C. Lees-Miller S. P. Tainer J. A. XRCC4 Protein Interactions with XRCC4-like Factor (XLF) Create an Extended Grooved Scaffold for DNA Ligation and Double Strand Break Repair J. Biol. Chem. 2011 286 32638 32650 10.1074/jbc.M111.272641 21775435 

  66. Roberts V. A. Pique M. E. Hsu S. Li S. Slupphaug G. Rambo R. P. Jamison J. W. Liu T. Lee J. H. Tainer J. A. Ten Eyck L. F. Woods V. L. Combining H/D exchange mass spectroscopy and computational docking reveals extended DNA-binding surface on uracil–DNA glycosylase Nucleic Acids Res. 2012 40 6070 6081 10.1093/nar/gks291 22492624 

  67. Fan L. Roberts V. A. Complex of linker histone H5 with the nucleosome and its implications for chromatin packing Proc. Natl. Acad. Sci. U. S. A. 2006 103 8384 8389 10.1073/pnas.0508951103 16717183 

  68. Adesokan A. A. Roberts V. A. Lee K. W. Lins R. D. Briggs J. M. Prediction of HIV-1 integrase/viral DNA interactions in the catalytic domain by fast molecular docking J. Med. Chem. 2004 47 821 828 10.1021/jm0301890 14761184 

  69. Roberts V. A. C-Terminal Domain of Integrase Binds between the Two Active Sites J. Chem. Theory Comput. 2015 11 4500 4511 10.1021/ct501125r 26575940 

  70. Weiner S. J. Kollman P. A. Case D. A. Singh U. C. Ghio C. Alagona G. Profeta S. Weiner P. A new force field for molecular mechanical simulation of nucleic acids and proteins J. Am. Chem. Soc. 1984 106 765 784 10.1021/ja00315a051 

  71. Baker N. A. Sept D. Joseph S. Holst M. J. McCammon J. A. Electrostatics of nanosystems: application to microtubules and the ribosome Proc. Natl. Acad. Sci. U. S. A. 2001 98 10037 10041 10.1073/pnas.181342398 11517324 

  72. Sanner M. F. Olson A. J. Spehner J. C. Reduced surface: an efficient way to compute molecular surfaces Biopolymers 1996 38 305 320 10.1002/(SICI)1097-0282(199603)38:3<305::AID-BIP4>3.0.CO;2-Y 8906967 

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