Molecular dynamics simulation analysis of anti-MUC1 aptamer and mucin 1 peptide binding

Journal of Physical Chemistry B

Volumn 119, Issue 22, 2015, Pages 6571-6583

  Rhinehardt, Kristen L ^a   Srinivas, Goundla ^a   Mohan, Ram V ^a  

^a NORTH CAROLINA A AND T STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; ARGININE; BINS; BIOINFORMATICS; BIOSENSORS; COMPUTATION THEORY; HYDROGEN BONDS; LOCATION; MOLECULAR DYNAMICS; MOLECULAR ORIENTATION; MOLECULES; PROTEINS;

ARGININE RESIDUE; COMPUTATIONAL MODEL; DISTANCE DISTRIBUTIONS; HIGH SPECIFICITY; MOLECULAR DYNAMICS SIMULATIONS; MOLECULAR INSIGHTS; PEPTIDE SEQUENCES; PHYSIOLOGICAL CONDITION;

PEPTIDES;

APTAMER; MUCIN 1; OLIGOPEPTIDE; PROTEIN BINDING; SOLVENT;

AMINO ACID SEQUENCE; CHEMISTRY; CONFORMATION; HYDROGEN BOND; METABOLISM; MOLECULAR DYNAMICS; PROTEIN CONFORMATION;

AMINO ACID SEQUENCE; APTAMERS, NUCLEOTIDE; HYDROGEN BONDING; MOLECULAR DYNAMICS SIMULATION; MUCIN-1; NUCLEIC ACID CONFORMATION; OLIGOPEPTIDES; PROTEIN BINDING; PROTEIN CONFORMATION; SOLVENTS;

EID: 84930616735     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/acs.jpcb.5b02483     Document Type: Article

References (76)

1. Jain, K. K. The Handbook of Biomarkers; Springer: New York, 2010.
2. Scognamiglio, V. Nanotechnology in glucose monitoring: Advances and challenges in the last 10 years Biosens. Bioelectron. 2013, 47, 12-25
3. Chang, K.; Pi, Y.; Lu, W.; Wang, F.; Pan, F.; Li, F.; Jia, S.; Shi, J.; Deng, S.; Chen, M. Label-free and high-sensitive detection of human breast cancer cells by aptamer-based leaky surface acoustic wave biosensor array Biosens. Bioelectron. 2014, 60, 318-324
4. Ma, F.; Ho, C.; Cheng, A. K. H.; Yu, H.-Z. Immobilization of redox-labeled hairpin DNA aptamers on gold: Electrochemical quantitation of epithelial tumor marker mucin 1 Electrochim. Acta 2013, 110, 139-145
5. Shum, K. T.; Zhou, J.; Rossi, J. J. Nucleic acid aptamers as potential therapeutic and diagnostic agents for lymphoma J. Cancer Ther. 2013, 4, 872-890
6. Malic, L.; Sandros, M. G.; Tabrizian, M. Designed biointerface using near-infrared quantum dots for ultrasensitive surface plasmon resonance imaging biosensors Anal. Chem. 2011, 83, 5222-9
7. Bohunicky, B.; Mousa, S. A. Biosensors: The new wave in cancer diagnosis Nanotechnol., Sci. Appl. 2011, 4, 1-10
8. Turner, A. P. Biosensors: Sense and sensibility Chem. Soc. Rev. 2013, 42, 3184-3196
9. Hu, M.; Zhang, K. The application of aptamers in cancer research: An up-to-date review Future Oncol. 2013, 9, 369-376
10. Ahmed, M. U.; Saaem, I.; Wu, P. C.; Brown, A. S. Personalized diagnostics and biosensors: A review of the biology and technology needed for personalized medicine Crit. Rev. Biotechnol. 2013, 34, 180-196
11. Bertucci, C.; De Simone, A. Optical biosensors and applications to drug discovery and development in cancer research. In Biosensors and Cancer; Preedy, V. R.; Patel, V. B., Eds.; CRC Press: Boca Raton, FL, 2012; pp 321-336.
12. Baruch, A.; Hartmann, M.-l.; Yoeli, M.; Adereth, Y.; Greenstein, S.; Stadler, Y.; Skornik, Y.; Zaretsky, J.; Smorodinsky, N. I.; Keydar, I. The breast cancer-associated MUC1 gene generates both a receptor and its cognate binding protein Cancer Res. 1999, 59, 1552-1561
13. Gendler, S. J. MUC1, the renaissance molecule J. Mammary Gland Biol. Neoplasia 2001, 6, 339-353
14. Dokurno, P.; Bates, P. A.; Band, H. A.; Stewart, L. M. D.; Lally, J. M.; Burchell, J. M.; Taylor-Papadimitriou, J.; Snary, D.; Sternberg, M. J. E.; Freemont, P. S. Crystal structure at 1.95 Å resolution of the breast tumour-specific antibody SM3 complexed with its peptide epitope reveals novel hypervariable loop recognition J. Mol. Biol. 1998, 284, 713-728
15. Taylor-Papadimitriou, J.; Burchell, J. M.; Plunkett, T.; Graham, R.; Correa, I.; Miles, D.; Smith, M. MUC1 and the immunobiology of cancer J. Mammary Gland Biol. Neoplasia 2002, 7, 209-221
16. Kirnarsky, L.; Prakash, O.; Vogen, S. M.; Nomoto, M.; Hollingsworth, M. A.; Sherman, S. Structural effects of O-glycosylation on a 15-residue peptide from the mucin (MUC1) core protein Biochemistry 2000, 39, 12076-12082
17. von Mensdorff-Pouilly, S.; Gourevitch, M. M.; Kenemans, P.; Verstraeten, A. A.; van Kamp, G. J.; Kok, A.; van Uffelen, K.; Snijdewint, F. G. M.; Paul, M. A.; Meijer, S. An enzyme-linked immunosorbent assay for the measurement of circulating antibodies to polymorphic epithelial mucin (MUC1) Tumor Biol. 1998, 19, 186-195
18. Pichinuk, E.; Benhar, I.; Jacobi, O.; Chalik, M.; Weiss, L.; Ziv, R.; Sympson, C.; Karwa, A.; Smorodinsky, N. I.; Rubinstein, D. B. Antibody targeting of cell-bound MUC1 SEA domain kills tumor cells Cancer Res. 2012, 72, 3324-3336
19. Hamanaka, Y.; Suehiro, Y.; Fukui, M.; Shikichi, K.; Imai, K.; Hinoda, Y. Circulating anti-MUC1 IgG antibodies as a favorable prognostic factor for pancreatic cancer Int. J. Cancer 2003, 103, 97-100
20. Strehlitz, B.; Nikolaus, N.; Stoltenburg, R. Protein detection with aptamer biosensors Sensors 2008, 8, 4296-4307
21. Erickson, D.; Mandal, S.; Yang, A.; Cordovez, B. Nanobiosensors: Optofluidic, electrical and mechanical approaches to biomolecular detection at the nanoscale Microfluid. Nanofluid. 2008, 4, 33-52
22. Han, K.; Liang, Z.; Zhou, N. Design strategies for aptamer-based biosensors Sensors 2010, 10, 4541-4557
23. Wang, J. From DNA biosensors to gene chips Nucleic Acid Res. 2000, 28, 3011-3016
24. Song, S.; Wang, L.; Li, J.; Fan, C.; Zhao, J. Aptamer-based biosensors TrAC, Trends Anal. Chem. 2008, 27, 108-117
25. McCauley, T. G.; Hamaguchi, N.; Stanton, M. Aptamer-based biosensor arrays for detection and quantification of biological macromolecules Anal. Biochem. 2003, 319, 244-250
26. He, P.; Oncescu, V.; Lee, S.; Choi, I.; Erickson, D. Label-free electrochemical monitoring of vasopressin in aptamer-based microfluidic biosensors Anal. Chim. Acta 2013, 759, 74-80
27. Palchetti, I.; Mascini, M. Aptamer-based biosensors for cancer studies. In Biosensors and Cancer; Preedy, V. R.; Patel, V. B., Eds.; CRC Press: Boca Raton, FL, 2012; pp 85-100.
28. Clark, S. L.; Remcho, V. T. Aptamers as analytical reagents Electrophoresis 2002, 23, 1335-1340
29. Stoltenburg, R.; Reinemann, C.; Strehlitz, B. SELEX - A (r)evolutionary method to generate high-affinity nucleic acid ligands Biomol. Eng. 2007, 24, 381-403
30. Tuerk, C.; Gold, L. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase Science 1990, 249, 505-510
31. Kolmodin, L. A.; Birch, D. E. Polymerase chain reaction. Basic principles and routine practice Methods Mol. Biol. 2002, 192, 3-18
32. Bartlett, J. S.; Stirling, D. A Short history of the polymerase chain reaction. In PCR Protocols; Bartlett, J. S.; Stirling, D., Eds.; Humana Press: New York, 2003; Vol. 226; pp 3-6.
33. Saiki, R.; Gelfand, D.; Stoffel, S.; Scharf, S.; Higuchi, R.; Horn, G.; Mullis, K.; Erlich, H. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase Science 1988, 239, 487-491
34. Chai, C.; Xie, Z.; Grotewold, E. SELEX (Systematic Evolution of Ligands by EXponential Enrichment), as a powerful tool for deciphering the protein-DNA interaction space Methods Mol. Biol. 2011, 754, 249-58
35. Wan, Y.; Su, Y.; Zhu, X.; Liu, G.; Fan, C. Development of electrochemical immunosensors towards point of care diagnostics Biosens. Bioelectron. 2013, 47, 1-11
36. Ziegler, C.; Göpel, W. Biosensor development Curr. Opin. Chem. Biol. 1998, 2, 585-591
37. Hosseini, S.; Ibrahim, F.; Djordjevic, I.; Koole, L. H. Recent advances in surface functionalization techniques on polymethacrylate materials for optical biosensor applications Analyst 2014, 139, 2933-2943
38. Chen, H.; Huang, J.; Lee, J.; Hwang, S.; Koh, K. Surface plasmon resonance spectroscopic characterization of antibody orientation and activity on the calixarene monolayer Sens. Actuators, B 2010, 147, 548-553
39. Ferreira, C. S.; Matthews, C. S.; Missailidis, S. DNA aptamers that bind to MUC1 tumour marker: design and characterization of MUC1-binding single-stranded DNA aptamers Tumor Biol. 2006, 27, 289-301
40. Nguyen, T. H. T.; Liu, Z.; Moore, P. B. Molecular dynamics simulations of homo-oligomeric bundles embedded within a lipid bilayer Biophys. J. 2013, 105, 1569-1580
41. Kim, S.; Lee, J.; Lee, S. J.; Lee, H. J. Ultra-sensitive detection of IgE using biofunctionalized nanoparticle-enhanced SPR Talanta 2010, 81, 1755-1759
42. Ozsoz, M. S. Electrochemical DNA Biosensors; Pan Stanford: Singapore, 2012.
43. Cheng, X.; Ivanov, I. Molecular dynamics. In Computational Toxicology; Reisfeld, B.; Mayeno, A. N., Eds.; Humana Press: New York, 2012; Vol. 929; pp 243-285.
44. Ivanov, I.; Chapados, B. R.; McCammon, J. A.; Tainer, J. A. Proliferating cell nuclear antigen loaded onto double-stranded DNA: Dynamics, minor groove interactions and functional implications Nucleic Acids Res. 2006, 34, 6023-6033
45. Palermo, G.; Rothlisberger, U.; Cavalli, A.; De Vivo, M. Computational insights into function and inhibition of fatty acid amide hydrolase Eur. J. Med. Chem. 2015, 91, 15-26
46. Rhinehardt, K.; Mohan, R.; Srinivas, G.; Kelkar, A. Computational modeling of peptide-Aptamer binding in biosensor applications Int. J. Biosci., Biochem. Bioinf. 2013, 3, 639-642
47. The PyMOL Molecular Graphics System, version 1.3; Schrödinger, LLC: New York, 2010.
48. Hornak, V.; Abel, R.; Okur, A.; Strockbine, B.; Roitberg, A.; Simmerling, C. Comparison of multiple Amber force fields and development of improved protein backbone parameters Proteins: Struct., Funct., Bioinf. 2006, 65, 712-725
49. Van Der Spoel, D.; Lindahl, E.; Hess, B.; Groenhof, G.; Mark, A. E.; Berendsen, H. J. C. GROMACS: Fast, flexible, and free J. Comput. Chem. 2005, 26, 1701-1718
50. Lange, O. F.; van der Spoel, D.; de Groot, B. L. Scrutinizing molecular mechanics force fields on the submicrosecond timescale with NMR Data Biophys. J. 2010, 99, 647-655
51. Wickstrom, L.; Okur, A.; Simmerling, C. Evaluating the performance of the ff99SB force field based on NMR scalar coupling data Biophys. J. 2009, 97, 853-856
52. Kumar, P. S.; Mukherjee, A.; Hazra, A. Theoretical study of structural changes in DNA under high external hydrostatic pressure J. Phys. Chem. B 2015, 119, 3348-3355
53. Junlang, C.; Liang, C.; Yu, W.; Shude, C. Molecular dynamics simulations of the adsorption of DNA segments onto graphene oxide J. Phys. D: Appl. Phys. 2014, 47, 505401
54. Berendsen, H. J. C.; van der Spoel, D.; van Drunen, R. GROMACS: A message-passing parallel molecular dynamics implementation Comput. Phys. Commun. 1995, 91, 43-56
55. Hess, B.; Kutzner, C.; van der Spoel, D.; Lindahl, E. GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation J. Chem. Theory Comput. 2008, 4, 435-447
56. Nosé, S.; Klein, M. L. Constant pressure molecular dynamics for molecular systems Mol. Phys. 1983, 50, 1055-1076
57. Humphrey, W.; Dalke, A.; Schulten, K. VMD: Visual molecular dynamics J. Mol. Graphics 1996, 14, 33-38
58. Carugo, O. How root-mean-square distance (r.m.s.d.) values depend on the resolution of protein structures that are compared J. Appl. Crystallogr. 2003, 36, 125-128
59. de Gennes, P.-G. Scaling Concepts in Polymer Physics; Cornell University Press: Ithaca, NY, 1979.
60. Berg, J. M.; Deis, F. H.; Tymoczko, J. L.; Stryer, L.; Gerber, N. C.; Gumport, R.; Koeppe, R. E. Biochemistry Student Companion; W. H. Freeman: New York, 2011.
61. Farrell, S.; Taylor, L. Experiments in Biochemistry: A Hands-On Approach; Cengage Learning: Boston, MA, 2005.
62. Schalley, C. A. Analytical Methods in Supramolecular Chemistry: Vol. 1; Wiley-VCH Verlag GmbH & Company KGaA: Weinheim, Germany, 2012.
63. Bondi, A. Van der Waals volumes and radii J. Phys. Chem. 1964, 68, 441-451
64. Pal, S.; Maiti, P. K.; Bagchi, B. Exploring DNA groove water dynamics through hydrogen bond lifetime and orientational relaxation J. Chem. Phys. 2006, 125, 234903
65. Van der Spoel, D.; Lindahl, E.; Hess, B.; van Buuren, A. R.; Apol, E.; Meulenhoff, P. J.; Tieleman, D. P.; Sijbers, A. L. T. M.; Feenstra, K. A.; van Drunen, R.; Berendsen, H. J. C. Gromacs User Manual version 4.5.4, www.gromacs.org (2010).
66. Bernard Da Costa, J.; Dieckmann, T. Entropy and Mg2+ control ligand affinity and specificity in the malachite green binding RNA aptamer Mol. BioSyst. 2011, 7, 2156-2163
67. Hayashi, T.; Oshima, H.; Mashima, T.; Nagata, T.; Katahira, M.; Kinoshita, M. Binding of an RNA aptamer and a partial peptide of a prion protein: Crucial importance of water entropy in molecular recognition Nucleic Acids Res. 2014, 42, 6861-6875
68. Betts, M. J.; Russell, R. B. Amino acid properties and consequences of substitutions. In Bioinformatics for Geneticists; John Wiley & Sons, Ltd.: Chichester, U.K., 2003; pp 289-316.
69. Tramontano, A. Protein Structure Prediction: Concepts and Applications; Wiley-VCH: Weinheim, Germany, 2006.
70. Buxbaum, E. Fundamentals of Protein Structure and Function; Springer US: New York, 2007.
71. Vance, S. A.; Sandros, M. G. Zeptomole detection of C-reactive protein in serum by a nanoparticle amplified surface plasmon resonance imaging aptasensor Sci. Rep. 2014, 4, 5129
72. Pilolli, R.; Monaci, L.; Visconti, A. Advances in biosensor development based on integrating nanotechnology and applied to food-allergen management TrAC, Trends Anal. Chem. 2013, 47, 12-26
73. Andreasen, M.; Skeby, K. K.; Zhang, S.; Nielsen, E. H.; Klausen, L. H.; Frahm, H.; Christiansen, G.; Skrydstrup, T.; Dong, M.; Schiott, B.; Otzen, D. The importance of being capped: Terminal capping of an amyloidogenic peptide affects fibrillation propensity and fibril morphology Biochemistry 2014, 53, 6968-6980
74. Cino, E. A.; Choy, W. Y.; Karttunen, M. Comparison of secondary structure dormation using 10 different force fields in microsecond molecular dynamics simulations J. Chem. Theory Comput. 2012, 8, 2725-2740
75. Marrink, S. J.; Risselada, H. J.; Yefimov, S.; Tieleman, D. P.; de Vries, A. H. The MARTINI force field: Coarse grained model for biomolecular simulations J. Phys. Chem. B 2007, 111, 7812-7824
76. Sim, A. Y. L.; Minary, P.; Levitt, M. Modeling nucleic acids Curr. Opin. Struct. Biol. 2012, 22, 273-278