Effect of graphene oxide on the conformational transitions of amyloid beta peptide: A molecular dynamics simulation study

Journal of Molecular Graphics and Modelling

Volumn 61, Issue , 2015, Pages 175-185

  Baweja, Lokesh ^a,b,d   Balamurugan, Kanagasabai ^c   Subramanian, Venkatesan ^b,c   Dhawan, Alok ^b,d  

^a AHMEDABAD UNIVERSITY   (India)

^b ACADEMY OF SCIENTIFIC AND INNOVATIVE RESEARCH ACSIR   (India)

^c CENTRAL LEATHER RESEARCH INSTITUTE   (India)

^d CSIR INDIAN INSTITUTE OF TOXICOLOGY RESEARCH   (India)

Author keywords

Amyloid beta peptide; Graphene oxide; Molecular dynamics simulation; Nanomaterials; Neurodegenerative disorders

Indexed keywords

ADSORPTION; CARBON; DIAGNOSIS; ELECTROSTATICS; GLYCOPROTEINS; MOLECULAR DYNAMICS; MOLECULAR OXYGEN; NANOSTRUCTURED MATERIALS; NEURODEGENERATIVE DISEASES; PEPTIDES; POLYPEPTIDES; PROTEINS; VAN DER WAALS FORCES;

AGGREGATION PATTERNS; AMYLOID-BETA PEPTIDES; CONFORMATIONAL TRANSITIONS; GRAPHENE OXIDES; MOLECULAR DYNAMICS SIMULATIONS; NEURODEGENERATIVE DISORDERS; PLAUSIBLE MECHANISMS; REDUCED GRAPHENE OXIDES (RGO);

GRAPHENE;

AMYLOID BETA PROTEIN; GRAPHENE OXIDE; AMYLOID BETA PROTEIN[1-40]; GRAPHITE; OXIDE; PEPTIDE FRAGMENT; PROTEIN BINDING;

ADSORPTION; ALPHA HELIX; ARTICLE; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; ENTROPY; HYDROGEN BOND; HYDROPHOBICITY; MACROMOLECULE; MICELLE; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN SECONDARY STRUCTURE; STATIC ELECTRICITY; SURFACE AREA; AMINO ACID SEQUENCE; ANTAGONISTS AND INHIBITORS; BINDING SITE; CHEMICAL PHENOMENA; CHEMISTRY; HUMAN; MOLECULAR GENETICS; OXIDATION REDUCTION REACTION; PROTEIN TERTIARY STRUCTURE; STRUCTURAL HOMOLOGY; SURFACE PROPERTY; THERMODYNAMICS;

ADSORPTION; AMINO ACID SEQUENCE; AMYLOID BETA-PEPTIDES; BINDING SITES; GRAPHITE; HUMANS; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; MOLECULAR DYNAMICS SIMULATION; MOLECULAR SEQUENCE DATA; OXIDATION-REDUCTION; OXIDES; PEPTIDE FRAGMENTS; PROTEIN BINDING; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; STATIC ELECTRICITY; STRUCTURAL HOMOLOGY, PROTEIN; SURFACE PROPERTIES; THERMODYNAMICS;

EID: 84939161696     PISSN: 10933263     EISSN: 18734243     Source Type: Journal    
DOI: 10.1016/j.jmgm.2015.07.007     Document Type: Article

References (49)

1. Y. Wang, Z. Li, J. Wang, J. Li, and Y. Lin Graphene and graphene oxide: biofunctionalization and applications in biotechnology Trends Biotechnol. 29 2011 205 212
2. J. Liu, L. Cui, and D. Losic Graphene and graphene oxide as new nanocarriers for drug delivery applications Acta Biomater. 9 2013 9243 9257
3. D.R. Dreyer, S. Park, C.W. Bielawski, and R.S. Ruoff The chemistry of graphene oxide Chem. Soc. Rev. 39 2010 228 240
4. C. Bussy, H. Ali-Boucetta, and K. Kostarelos Safety considerations for graphene: lessons learnt from carbon nanotubes Acc. Chem. Res. 46 2012 692 701
5. S. Sharifi, S. Behzadi, S. Laurent, M.L. Forrest, P. Stroeve, and M. Mahmoudi Toxicity of nanomaterials Chem. Soc. Rev. 41 2012 2323 2343
6. A.A. Shemetov, I. Nabiev, and A. Sukhanova Molecular interaction of proteins and peptides with nanoparticles ACS Nano 6 2012 4585 4602
7. D.M. Zhang, O. Neumann, H. Wang, V.M. Yuwono, A. Barhoumi, M. Perham, J.D. Hartgerink, P. Wittung-Stafshede, and N.J. Halas Gold nanoparticles can induce the formation of protein-based aggregates at physiological pH Nano Lett. 9 2009 666 671
8. C. Li, and R. Mezzenga The interplay between carbon nanomaterials and amyloid fibrils in bio-nanotechnology Nanoscale 5 2013 6207 6218
9. R. Skrabana, J. Sevcik, and M. Novak Intrinsically disordered proteins in the neurodegenerative processes: formation of Tau protein paired helical filaments and their analysis Cell. Mol. Neurobiol. 26 2006 1085 1097
10. A. Albanese, P.S. Tang, and W.C. Chan The effect of nanoparticle size, shape, and surface chemistry on biological systems Annu. Rev. Biomed. Eng. 14 2012 1 16
11. S.S. Sisodia, and D.L. Price Role of the beta-amyloid protein in Alzheimer's disease FASEB J. 9 1995 366 370
12. R. Kayed, E. Head, J.L. Thompson, T.M. McIntire, S.C. Milton, C.W. Cotman, and C.G. Glabe Common structure of soluble amyloid oligomers implies common mechanism of pathogenesis Science 300 2003 486 489
13. S. Gandy, and S.T. DeKosky Toward the treatment and prevention of Alzheimer's disease: rational strategies and recent progress Annu. Rev. Med. 64 2013 367 383
14. D. Brambilla, and et al. PEGylated nanoparticles bind to and alter amyloid-beta peptide conformation: toward engineering of functional nanomedicines for Alzheimer's disease ACS Nano 6 2012 5897 5908
15. L. Fei, and S. Perrett Effect of nanoparticles on protein folding and fibrillogenesis Int. J. Mol. Sci. 10 2009 646 655
16. Y.H. Liao, Y.J. Chang, Y. Yoshiike, Y.C. Chang, and Y.R. Chen Negatively charged gold nanoparticles inhibit Alzheimer's amyloid-beta fibrillization, induce fibril dissociation, and mitigate neurotoxicity Small 8 2013 3631 3639
17. A.R. Ladiwala, J. Litt, R.S. Kane, D.S. Aucoin, S.O. Smith, S. Ranjan, J. Davis, W.E. Van Nostrand, and P.M. Tessier Conformational differences between two amyloid beta oligomers of similar size and dissimilar toxicity J. Biol. Chem. 287 2012 24765 24773
18. M. Mahmoudi, O. Akhavan, M. Ghavami, F. Rezaee, and S.M. Ghiasi Graphene oxide strongly inhibits amyloid beta fibrillation Nanoscale 4 2013 7322 7325
19. X. Pei, J. Wang, and Q. Wan Comment on "Amine-Modified Graphene: Thrombo-protective Safer Alternative to Graphene Oxide for Biomedical Applications" ACS Nano 8 2014 1966
20. L. Baweja, K. Balamurugan, V. Subramanian, and A. Dhawan Hydration patterns of graphene-based nanomaterials (GBNMs) play a major role in the stability of a helical protein: a molecular dynamics simulation study Langmuir 29 2013 14230 14238
21. A.J. Makarucha, N. Todorova, and I. Yarovsky Nanomaterials in biological environment: a review of computer modelling studies Eur. Biophys. J. 40 2011 103 115
22. J.A. Lemkul, and D.R. Bevan The role of molecular simulations in the development of inhibitors of amyloid beta-peptide aggregation for the treatment of Alzheimer's disease ACS Chem. Neurosci. 3 2012 845 856
23. M. Coles, W. Bicknell, A.A. Watson, D.P. Fairlie, and D.J. Craik Solution structure of amyloid beta-peptide (1-40) in a water-micelle environment. Is the membrane-spanning domain where we think it is? Biochemistry 37 1998 11064 11077
24. Y. Xu, J. Shen, X. Luo, W. Zhu, K. Chen, J. Ma, and H. Jiang Conformational transition of amyloid beta-peptide Proc. Natl. Acad. Sci. U. S. A. 102 2005 5403 5407
25. GaussView, Gaussian, Inc., Pittsburgh, PA, 2003.
26. C.J. Shih, S.C. Lin, R. Sharma, M.S. Strano, and D. Blankschtein Understanding the pH-dependent behavior of graphene oxide aqueous solutions: a comparative experimental and molecular dynamics simulation study Langmuir 28 2012 235 241
27. J. Liu, C. Liao, and J. Zhou Multiscale simulations of protein G B1 adsorbed on charged self-assembled monolayers Langmuir 29 2013 11366 11374
28. D. Schneidman-Duhovny, Y. Inbar, R. Nussinov, and H.J. Wolfson PatchDock and SymmDock: servers for rigid and symmetric docking Nucl. Acids Res. 33 2005 363 367
29. E. Lindahl, B. Hess, and D. van der Spoel GROMACS 3.0: a package for molecular simulation and trajectory analysis J. Mol. Model. 7 2001 306 317
30. M. Parrinello, and A. Rahman Polymorphic transitions in single crystals: a new molecular dynamics method J. App. Phys. 52 1981 7182 7190
31. S. Nosé, and M.L. Klein A Unified formulation of the constant temperature molecular dynamics methods Mol. Phys. 50 1983 1055 1076
32. G. Bussi, and D.P.M. Donadio Canonical sampling through velocity rescaling J. Chem. Phys. 126 2007 14101 14107
33. U. Essmann, L. Perera, M.L. Berkowitz, T. Darden, H. Lee, and L.G. Pedersen A smooth particle mesh Ewald method J. Chem. Phys. 103 1995 8577 8593
34. B. Hess, H. Bekker, H.J.C. Berendsen, and J.G.E.M. Fraaije LINCS: a linear constraint solver for molecular simulations J. Comput. Chem. 18 1997 1463 1472
35. W. Humphrey, A. Dalke, and K. Schulten VMD: visual molecular dynamics J. Mol. Graph. 14 1996 33 38 27-8
36. O.O. Olubiyi, and B. Strodel Structures of the amyloid (-peptides A(1-40 and A(1-42 as influenced by pH and a D-peptide J. Phys. Chem. B 116 2012 3280 3291
37. W. Kabsch, and C. Sander Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features Biopolymers 22 1983 2577 2637
38. D.M. Smith, T.P. Straatsma, and T.C. Squier Retention of conformational entropy upon calmodulin binding to target peptides is driven by transient salt-bridges Biophys. J. 103 2012 1576 1584
39. K. Martin, and J.N. Kushick Method for estimating the configurational entropy of macromolecules Macromolecules 14 1981 325 332
40. C. Matteo, S. Hoefinger, and F. Zerbetto Probing the structure of lysozyme-carbon-nanotube hybrids with molecular dynamics Chemis.: A Eur. J. 18 2012 4308 4313
41. J.C. Jose, P. Chatterjee, and N. Sengupta Cross dimerization of amyloid-beta and alphasynuclein proteins in aqueous environment: a molecular dynamics simulations study PloS One 9 9 2014 e106883
42. N. Basdevant, H. Weinstein, and M. Ceruso Thermodynamic basis for promiscuity and selectivity in protein-protein interactions: PDZ domains, a case study J. Am. Chem. Soc. 128 39 2006 12766 12777
43. E.B. Walton, and K.J. Vanvliet Equilibration of experimentally determined protein structures for molecular dynamics simulation Phys. Rev. E 74 2006 061901 61908
44. S. Genheden, and U. Ryde Will molecular dynamics simulations of proteins ever reach equilibrium? Phys. Chem. Chem. Phys. PCCP 14 2012 8662 8677
45. J. Luo, S.K. Warmlander, A. Graslund, and J.P. Abrahams Human lysozyme inhibits the in vitro aggregation of Aβ peptides, which in vivo are associated with Alzheimer's disease Chem. Commun. 49 2013 6507 6509
46. J. Guo, J. Li, Y. Zhang, X. Jin, H. Liu, and X. Yao Exploring the influence of carbon nanoparticles on the formation of beta-sheet-rich oligomers of IAPP(2)(2)(-)(2)(8) peptide by molecular dynamics simulation PloS One 8 2013 e65579
47. B. Moores, E. Drolle, S.J. Attwood, J. Simons, and Z. Leonenko Effect of surfaces on amyloid fibril formation PLoS One 6 2011 e25954
48. T.L. Williams, and L.C. Serpell Membrane and surface interactions of Alzheimer's Aβ peptide - insights into the mechanism of cytotoxicity FEBS J. 278 2011 3905 3917
49. F. Huang, J. Wang, A. Qu, L. Shen, J. Liu, J. Liu, Z. Zhang, Y. An, and L. Shi Maintenance of amyloid beta peptide homeostasis by artificial chaperones based on mixed-shell polymeric micelles Angew. Chem. Int. Ed. 34 2014 8985 8990