181
Views
2
CrossRef citations to date
0
Altmetric
Research Articles

A molecular dynamics investigation on transporting mechanism of glucose through a cyclic peptide nanotube

&
Pages 2230-2241 | Received 22 Dec 2019, Accepted 16 Mar 2020, Published online: 15 Apr 2020

Reference

  • Aida, T., Meijer, E., & Stupp, S. I. (2012). Functional supramolecular polymers. Science, 335(6070), 813–817. doi:10.1126/science.1205962
  • Becke, A. D. (1997). Density-functional thermochemistry. V. Systematic optimization of exchange-correlation functionals. The Journal of Chemical Physics, 107(20), 8554–8560. doi:10.1063/1.475007
  • Berendsen, H. J., van der Spoel, D., & van Drunen, R. (1995). GROMACS: A message-passing parallel molecular dynamics implementation. Computer Physics Communications, 91(1-3), 43–56. doi: $SD10010-4655 (95) 00042-9 doi:10.1016/0010-4655(95)00042-E
  • Bjelkmar, P., Larsson, P., Cuendet, M. A., Hess, B., & Lindahl, E. (2010). Implementation of the CHARMM force field in GROMACS: Analysis of protein stability effects from correction maps, virtual interaction sites, and water models. Journal of Chemical Theory and Computation, 6(2), 459–466. doi:10.1021/ct900549r
  • Bussi, G., Donadio, D., & Parrinello, M. (2007). Canonical sampling through velocity rescaling. The Journal of Chemical Physics, 126(1), 014101. doi:10.1063/1.2408420
  • Comer, J., Dehez, F. O., Cai, W., & Chipot, C. (2013). Water conduction through a peptide nanotube. The Journal of Physical Chemistry C, 117(50), 26797–26803. doi:10.1021/jp4088223
  • Cuerva, M., García-Fandiño, R., Vázquez-Vázquez, C., López-Quintela, M. A., Montenegro, J., & Granja, J. R. (2015). Self-assembly of silver metal clusters of small atomicity on cyclic peptide nanotubes. ACS Nano, 9(11), 10834–10843. doi:10.1021/acsnano.5b03445
  • Darden, T., York, D., & Pedersen, L. (1993). Particle mesh Ewald: An N⋅ log (N) method for Ewald sums in large systems. The Journal of Chemical Physics, 98(12), 10089–10092. doi:10.1063/1.464397
  • Dashnau, J. L., Sharp, K. A., & Vanderkooi, J. M. (2005). Carbohydrate intramolecular hydrogen bonding cooperativity and its effect on water structure. The Journal of Physical Chemistry B, 109(50), 24152–24159. doi:10.1021/jp0543072
  • De La Rica, R., Mendoza, E., Lechuga, L. M., & Matsui, H. (2008). Label‐free pathogen detection with sensor chips assembled from peptide nanotubes. Angewandte Chemie International Edition, 47(50), 9752–9755. doi:10.1002/anie.200804299
  • Engels, M., Bashford, D., & Ghadiri, M. R. (1995). Structure and dynamics of self-assembling peptide nanotubes and the channel-mediated water organization and self-diffusion. A molecular dynamics study. Journal of the American Chemical Society, 117(36), 9151–9158. doi:10.1021/ja00141a005
  • Farrokhpour, H., Mansouri, A., & Najafi Chermahini, A. (2017). Transport behavior of the enantiomers of lactic acid through the cyclic peptide nanotube: Enantiomer discrimination. The Journal of Physical Chemistry C, 121(14), 8165–8176. doi:10.1021/acs.jpcc.7b00010
  • Farrokhpour, H., Mansouri, A., Rajabi, A. R., & Najafi Chermahini, A. (2019). The effect of the diameter of cyclic peptide nanotube on its chirality discrimination. Journal of Biomolecular Structure and Dynamics, 37(3), 691–701. doi:10.1080/07391102.2018.1436090
  • Fenniri, H., Mathivanan, P., Vidale, K. L., Sherman, D. M., Hallenga, K., Wood, K. V., & Stowell, J. G. (2001). Helical rosette nanotubes: Design, self-assembly, and characterization. Journal of the American Chemical Society, 123(16), 3854–3855. doi:10.1021/ja005886l
  • Fuertes, A., Ozores, H. L., Amorín, M., & Granja, J. R. (2017). Self-assembling Venturi-like peptide nanotubes. Nanoscale, 9(2), 748–753. doi:10.1039/C6NR08174F
  • Ghadiri, M. R., Granja, J. R., & Buehler, L. K. (1994). Artificial transmembrane ion channels from self-assembling peptide nanotubes. Nature, 369(6478), 301–304. doi:10.1038/369301a0
  • Ghadiri, M. R., Granja, J. R., Milligan, R. A., McRee, D. E., & Khazanovich, N. (1993). Self-assembling organic nanotubes based on a cyclic peptide architecture. Nature, 366(6453), 324–327. doi:10.1038/366324a0
  • Gomes, S., Leonor, I. B., Mano, J. F., Reis, R. L., & Kaplan, D. L. (2012). Natural and genetically engineered proteins for tissue engineering. Progress in Polymer Science, 37(1), 1–17. doi:10.1016/j.progpolymsci.2011.07.003
  • Granja, J. R., & Ghadiri, M. R. (1994). Channel-mediated transport of glucose across lipid bilayers. Journal of the American Chemical Society, 116(23), 10785–10786. doi:10.1021/ja00102a054
  • Hartgerink, J. D., Granja, J. R., Milligan, R. A., & Ghadiri, M. R. (1996). Self-assembling peptide nanotubes. Journal of the American Chemical Society, 118(1), 43–50. doi:10.1021/ja953070s
  • Hess, B., Bekker, H., Berendsen, H. J., & Fraaije, J. G. (1997). LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry, 18(12), 1463–1472. doi:10.1002/(SICI)1096-987X(199709)
  • Hsieh, W.-H., Chang, S.-F., Chen, H.-M., Chen, J.-H., & Liaw, J. (2012). Oral gene delivery with cyclo-(D-Trp-Tyr) peptide nanotubes. Molecular Pharmaceutics, 9(5), 1231–1249. doi:10.1021/mp200523n
  • Huck, W. T. (2005). Nanoscale assembly: chemical techniques. Springer. doi:10.1007/b106927
  • Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics, 14(1), 33–38. doi:10.1016/0263-7855(96)00018-5
  • Jo, S., Kim, T., & Im, W. (2007). Automated builder and database of protein/membrane complexes for molecular dynamics simulations. PloS One., 2(9), e880. doi:10.1371/journal.pone.0000880
  • Kim, S., Lee, J., Jo, S., Brooks, C. L., III, Lee, H. S., & Im, W. (2017). CHARMM‐GUI ligand reader and modeler for CHARMM force field generation of small molecules. Journal of Computational Chemistry, 38(21), 1879–1886. doi:10.1002/jcc.24829
  • Kirkwood, J. G., & Boggs, E. M. (1942). The radial distribution function in liquids. The Journal of Chemical Physics, 10(6), 394–402. doi:10.1063/1.1723737
  • Krieger, E., & Vriend, G. (2014). YASARA View—molecular graphics for all devices—from smartphones to workstations. Bioinformatics, 30(20), 2981–2982. doi:10.1093/bioinformatics/btu426
  • Lakshmanan, A., Zhang, S., & Hauser, C. A. (2012). Short self-assembling peptides as building blocks for modern nanodevices. Trends in Biotechnology, 30(3), 155–165. doi:10.1016/j.tibtech.2011.11.001
  • Lemkul, J. A., & Bevan, D. R. (2010). Assessing the stability of Alzheimer’s amyloid protofibrils using molecular dynamics. The Journal of Physical Chemistry B, 114(4), 1652–1660. doi:10.1021/jp9110794
  • Lin, H., Fan, J., Weng, P., Si, X., & Zhao, X. (2017). Molecular Dynamics Simulations on the Behaviors of Hydrophilic/Hydrophobic Cyclic Peptide Nanotubes at the Water/Hexane Interface. The Journal of Physical Chemistry A, 121(37), 6863–6873. doi:10.1021/acs.jpca.7b02465
  • Liu, H., Chen, J., Shen, Q., Fu, W., & Wu, W. (2010). Molecular insights on the cyclic peptide nanotube-mediated transportation of antitumor drug 5-fluorouracil. Molecular Pharmaceutics, 7(6), 1985–1994. doi:10.1021/mp100274f
  • Loo, Y., Zhang, S., & Hauser, C. A. (2012). From short peptides to nanofibers to macromolecular assemblies in biomedicine. Biotechnology Advances, 30(3), 593–603. doi:10.1016/j.biotechadv.2011.10.004
  • Makin, O. S., Sikorski, P., & Serpell, L. C. (2006). Diffraction to study protein and peptide assemblies. Current Opinion in Chemical Biology, 10(5), 417–422. doi:10.1016/j.cbpa.2006.08.009
  • Maroli, N., & Kolandaivel, P. (2018). Structure, stability and water permeation of ([D-Leu-L-Lys-(D-Gln-L-Ala). Molecular Simulation, 44(3), 225–235. doi:10.1080/08927022.2017.1366653
  • Maroli, N., & Kolandaivel, P. (2020). Comparative study of stability and transport of molecules through cyclic peptide nanotube and aquaporin: A molecular dynamics simulation approach. Journal of Biomolecular Structure and Dynamics, 38(1), 186–199. doi:10.1080/07391102.2019.1570341
  • Mehralitabar, H., Taghdir, M., & Naderi-Manesh, H. (2019). A combination of bioactive and nonbioactive alkyl-peptides form a more stable nanofiber structure for differentiating neural stem cells: A molecular dynamics simulation survey. Journal of Biomolecular Structure and Dynamics, 37(13), 3434–3444. doi:10.1080/07391102.2018.1516571
  • Montenegro, J., Ghadiri, M. R., & Granja, J. R. (2013). Ion channel models based on self-assembling cyclic peptide nanotubes. Accounts of Chemical Research, 46(12), 2955–2965. doi:10.1021/ar400061d
  • Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., & Olson, A. J. (2009). AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of Computational Chemistry, 30(16), 2785–2791. doi:10.1002/jcc.21256
  • Mortazavifar, A., Raissi, H., & Shahabi, M. (2019). Comparative prediction of binding affinity of Hydroxyurea anti-cancer to boron nitride and carbon nanotubes as smart targeted drug delivery vehicles. Journal of Biomolecular Structure and Dynamics, 37(18), 4852–4862. doi:10.1080/07391102.2019.1567385
  • Mueckler, M. (1994). Facilitative glucose transporters. European Journal of Biochemistry, 219(3), 713–725. doi:10.1111/j.1432-1033.1994.tb18550.x
  • Nuraje, N., Banerjee, I. A., MacCuspie, R. I., Yu, L., & Matsui, H. (2004). Biological bottom-up assembly of antibody nanotubes on patterned antigen arrays. Journal of the American Chemical Society, 126(26), 8088–8089. doi:10.1021/ja048617u
  • Pakdel, M., Raissi, H., & Shahabi, M. (2020). Predicting doxorubicin drug delivery by single-walled carbon nanotube through cell membrane in the absence and presence of nicotine molecules: A molecular dynamics simulation study. Journal of Biomolecular Structure and Dynamics, 38(5), 1488–1498. doi:10.1080/07391102.2019.1611474
  • Panda, J. J., & Chauhan, V. S. (2014). Short peptide based self-assembled nanostructures: Implications in drug delivery and tissue engineering. Polymer Chemistry, 5(15), 4418–4436. doi:10.1039/c4py00173g
  • Parrinello, M., & Rahman, A. (1981). Polymorphic transitions in single crystals: A new molecular dynamics method. Journal of Applied Physics, 52(12), 7182–7190. doi:10.1063/1.328693
  • Pérez, C. M. R., Stephanopoulos, N., Sur, S., Lee, S. S., Newcomb, C., & Stupp, S. I. (2015). The powerful functions of peptide-based bioactive matrices for regenerative medicine. Annals of Biomedical Engineering, 43(3), 501–514. doi:10.1007/s10439-014-1166-6
  • Petrov, A., & Audette, G. F. (2012). Peptide and protein‐based nanotubes for nanobiotechnology. Wiley Interdisciplinary Reviews: Nanomedicine and Nanobiotechnology, 4(5), 575–585. doi:10.1002/wnan.1180
  • Rodríguez-Vázquez, N., Amorín, M., & Granja, J. (2017). Recent advances in controlling the internal and external properties of self-assembling cyclic peptide nanotubes and dimers. Organic & Biomolecular Chemistry, 15(21), 4490–4505. doi:10.1039/C7OB00351J
  • Sánchez-Quesada, J., Sun Kim, H., & Ghadiri, M. R. (2001). A synthetic pore‐mediated transmembrane transport of glutamic acid. Angewandte Chemie International Edition, 40(13), 2503–2506. doi:10.1002/1521-3773(20010702)40:13<2503::AID-ANIE2503>3.0.CO;2-E
  • Schmidt, M. W., Baldridge, K. K., Boatz, J. A., Elbert, S. T., Gordon, M. S., Jensen, J. H., Koseki, S., Matsunaga, N., Nguyen, K. A., Su, S., Windus, T. L., Dupuis, M., & Montgomery, J. A. (1993). General atomic and molecular electronic structure system. Journal of Computational Chemistry, 14(11), 1347–1363. doi:10.1002/jcc.540141112
  • Seo, Y., Song, Y., Schatz, G. C., & Hwang, H. (2018). Conformational Effects in the Transport of Glucose through a Cyclic Peptide Nanotube: A Molecular Dynamics Simulation Study. The Journal of Physical Chemistry B, 122(34), 8174–8184. doi:10.1021/acs.jpcb.8b05591
  • Shahabi, M., & Raissi, H. (2019). Theoretical investigation insights into the temperature triggered tegafur anticancer drug release from the surface of graphene oxide nanosheet. Journal of Biomolecular Structure and Dynamics, 1–9. doi:10.1080/07391102.2019.1630004
  • Shekhar, S., Anjia, L., Matsui, H., & Khondaker, S. I. (2011). Electrical transport properties of peptide nanotubes coated with gold nanoparticles via peptide-induced biomineralization. Nanotechnology, 22(9), 095202. doi:10.1088/0957-4484/22/9/095202
  • Shuaib, S., Saini, R. K., Goyal, D., & Goyal, B. (2020). Impact of K16A and K28A mutation on the structure and dynamics of amyloid-β42 peptide in Alzheimer’s disease: Key insights from molecular dynamics simulations. Journal of Biomolecular Structure and Dynamics, 38(3), 708–721. doi:10.1080/07391102.2019.1586587
  • Sun, L., Fan, Z., Wang, Y., Huang, Y., Schmidt, M., & Zhang, M. (2015). Tunable synthesis of self-assembled cyclic peptide nanotubes and nanoparticles. Soft Matter., 11(19), 3822–3832. doi:10.1039/C5SM00533G
  • Suzuki, T. (2008). The hydration of glucose: The local configurations in sugar–water hydrogen bonds. Physical Chemistry Chemical Physics, 10(1), 96–105. doi:10.1039/B708719E
  • Tarek, M., Maigret, B., & Chipot, C. (2003). Molecular dynamics investigation of an oriented cyclic peptide nanotube in DMPC bilayers. Biophysical Journal, 85(4), 2287–2298. doi:10.1016/S0006-3495(03)74653-0
  • Trott, O., & Olson, A. J. (2010). AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, 31(2), 455–461. doi:10.1002/jcc.21334
  • Tsai, C.-J., Zheng, J., & Nussinov, R. (2006). Designing a nanotube using naturally occurring protein building blocks. PLoS Computational Biology, 2(4), e42. doi:10.1371/journal.pcbi.0020042
  • Tsai, C. J., Zheng, J., Zanuy, D., Haspel, N., Wolfson, H., Alemán, C., & Nussinov, R. (2007). Principles of nanostructure design with protein building blocks. Proteins: Structure, Function, and Bioinformatics, 68(1), 1–12. doi:10.1002/prot.21413
  • Vijayaraj, R., Van Damme, S., Bultinck, P., & Subramanian, V. (2013). Theoretical studies on the transport mechanism of 5-fluorouracil through cyclic peptide based nanotubes. Physical Chemistry Chemical Physics, 15(4), 1260–1270. doi:10.1039/C2CP42038D
  • Wallace, A. C., Laskowski, R. A., & Thornton, J. M. (1995). LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions. "Protein Engineering, Design and Selection"", 8(2), 127–134. doi:10.1093/protein/8.2.127
  • Wright, E. M. (2001). Renal Na+-glucose cotransporters. American Journal of Physiology-Renal Physiology, 280(1), F10–F18. doi:10.1152/ajprenal.2001.280.1.F10
  • Yan, X., Fan, J., Yu, Y., Xu, J., & Zhang, M. (2015). Transport behavior of a single Ca2+, K+, and Na + in a water-filled transmembrane cyclic peptide nanotube. Journal of Chemical Information and Modeling, 55(5), 998–1011. doi:10.1021/acs.jcim.5b00025
  • Yan, X., He, Q., Wang, K., Duan, L., Cui, Y., & Li, J. (2007). Transition of cationic dipeptide nanotubes into vesicles and oligonucleotide delivery. Angewandte Chemie International Edition, 46(14), 2431–2434. doi:10.1002/anie.200603387
  • Zhu, J., Cheng, J., Liao, Z., Lai, Z., & Liu, B. (2008). Investigation of structures and properties of cyclic peptide nanotubes by experiment and molecular dynamics. Journal of Computer-Aided Molecular Design, 22(11), 773–781. doi:10.1007/s10822-008-9212-9

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.