Structure, stability and water permeation of ([D-Leu-L-Lys-(D-Gln-L-Ala)₃]) cyclic peptide nanotube: a molecular dynamics study

References

• Williams AJ. The functions of two species of calcium channel in cardiac muscle excitation-contraction coupling. Eur Heart J. 1997;18:27–35.10.1093/eurheartj/18.suppl_A.27
   Web of Science ®Google Scholar
• Lodish H, Baltimore D, Berk A, et al. Molecular cell biology. vol. 3. New York (NY): Scientific American Books; 1995.
   Google Scholar
• Montenegro J, Ghadiri MR, Granja JR. Ion channel models based on self-assembling cyclic peptide nanotubes. Acc Chem Res. 2013;46:2955–2965.10.1021/ar400061d
   PubMed Web of Science ®Google Scholar
• de Guadalupe Chávez-López M, Zúñiga-García V. Camacho J. 6. Ion channels in cervical cancer: new perspectives in diagnosis and therapy.
   Google Scholar
• Dolowy K, Dworakowska B. Ion channels-related diseases. Acta Biochim Polonica. 2000;47(3):685–703.
   PubMed Web of Science ®Google Scholar
• Tabushi I, Kuroda Y, Yokota K. A, B, D, F- tetrasubstituted β-cyclodextrin as artificial channel compound. Tetrahedron Lett. 1982;23:4601–4604.10.1016/S0040-4039(00)85664-6
   Web of Science ®Google Scholar
• Sakai N, Matile S. Synthetic ion channels. Langmuir 2013;29:9031–9040.10.1021/la400716c
   PubMed Web of Science ®Google Scholar
• Kennedy SJ, Roeske RW, Freeman AR, et al. Synthetic peptides form ion channels in artificial lipid bilayer membranes. Science. 1977;196:1341–1342.10.1126/science.867034
   PubMed Web of Science ®Google Scholar
• Lear JD, Schneider JP, Kienker PK, et al. Electrostatic effects on ion selectivity and rectification in designed ion channel peptides. J Am Chem Soc. 1997;119:3212–3217.10.1021/ja9629672
   Web of Science ®Google Scholar
• Neevel JG, Nolte RJM. Ion transport across vesicle bilayers mediated by an artificial channel compound. Tetrahedron Lett. 1984;25:2263–2266.10.1016/S0040-4039(01)80228-8
   Web of Science ®Google Scholar
• Nakano A, Xie Q, Mallen JV, et al. Synthesis of a membrane-insertable, sodium cation conducting channel: kinetic analysis by dynamic sodium-23 NMR. J Am Chem Soc. 1990;112:1287–1289.10.1021/ja00159a083
   Web of Science ®Google Scholar
• Ghadiri MR, Granja JR, Buehler LK. Artificial transmembrane ion channels from self-assembling peptide nanotubes. Nature. 1994;369:301.10.1038/369301a0
   PubMed Web of Science ®Google Scholar
• Ghadiri MR, Granja JR, Milligan RA, et al. Self-assembling organic nanotubes based on a cyclic peptide architecture. Nature. 1993;366:324.10.1038/366324a0
   PubMed Web of Science ®Google Scholar
• Granja JR, Ghadiri MR. Channel-mediated transport of glucose across lipid bilayers. J Am Chem Soc. 1994;116:10785–10786.10.1021/ja00102a054
   Web of Science ®Google Scholar
• Sanchez-Quesada J, Ghadiri MR, Bayley H, et al. Cyclic peptides as molecular adapters for a pore-forming protein. J Am Chem Soc. 2000;122:11757–11766.10.1021/ja002436 k
   Web of Science ®Google Scholar
• Liu H, Chen J, Shen Q, et al. Molecular insights on the cyclic peptide nanotube-mediated transportation of antitumor drug 5-fluorouracil. Mol Pharm. 2010;7:1985–1994.10.1021/mp100274f
   PubMed Web of Science ®Google Scholar
• Asthagiri D, Bashford D. Continuum and atomistic modeling of ion partitioning into a peptide nanotube. Biophys J. 2002;82:1176–1189.10.1016/S0006-3495(02)75475-1
   PubMed Web of Science ®Google Scholar
• Hwang H, Schatz GC, Ratner MA. Ion current calculations based on three dimensional Poisson- Nernst- Planck theory for a cyclic peptide nanotube. J Phys Chem B. 2006;110:6999–7008.10.1021/jp055740e
   PubMed Web of Science ®Google Scholar
• Liu J, Fan J, Tang M, et al. Water diffusion behaviors and transportation properties in transmembrane cyclic hexa-, octa- and decapeptide nanotubes. J Phys Chem B. 2010;114:12183–12192.10.1021/jp1039207
   PubMed Web of Science ®Google Scholar
• Yan X, Fan J, Yu Y, et al. Transport behavior of a single Ca2+, K+, and Na+ in a water-filled transmembrane cyclic peptide nanotube. J Chem Inf Model. 2015;55:998–1011.10.1021/acs.jcim.5b00025
   PubMed Web of Science ®Google Scholar
• Engels M, Bashford D, Ghadiri MR. Structure and dynamics of self-assembling peptide nanotubes and the channel-mediated water organization and self-diffusion. a molecular dynamics study. J Am Chem Soc. 1995;117:9151–9158.10.1021/ja00141a005
   Web of Science ®Google Scholar
• Tarek M. Membrane electroporation: a molecular dynamics simulation. Biophys J. 2005;88:4045–4053.10.1529/biophysj.104.050617
   PubMed Web of Science ®Google Scholar
• Tarek M, Maigret B, Chipot C. Molecular dynamics investigation of an oriented cyclic peptide nanotube in DMPC bilayers. Biophys J. 2003;85:2287–2298.10.1016/S0006-3495(03)74653-0
   PubMed Web of Science ®Google Scholar
• Vijayaraj R, Van Damme S, Bultinck P, et al. Theoretical studies on the transport mechanism of 5-fluorouracil through cyclic peptide based nanotubes. Phys Chem Chem Phys. 2013;15:1260–1270.10.1039/C2CP42038D
   PubMed Web of Science ®Google Scholar
• Chapman R, Danial M, Koh ML, et al. Design and properties of functional nanotubes from the self-assembly of cyclic peptide templates. Chem Soc Rev. 2012;41:6023–6041.10.1039/c2cs35172b
   PubMed Web of Science ®Google Scholar
• Duan Y, Wu C, Chowdhury S, et al. A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J Comput Chem. 2003;24:1999–2012.10.1002/(ISSN)1096-987X
   PubMed Web of Science ®Google Scholar
• Finkelstein, A. Water movement through lipid bilayer, pores and plasma membranes. Theory and Reality. 1987;4.
   Google Scholar
• Jorgensen WL, Chandrasekhar J, Madura JD, et al. Comparison of simple potential functions for simulating liquid water. J Chem Phys. 1983;79:926–935.10.1063/1.445869
   Web of Science ®Google Scholar
• Vanommeslaeghe K, Hatcher E, Acharya C, et al. CHARMM general force field: a force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields. J. Comput. Chem. 2010;31:671–690.
   PubMed Web of Science ®Google Scholar
• Jo S, Kim T, Im W. Automated builder and database of protein/membrane complexes for molecular dynamics simulations. PLoS ONE. 2007;2:e880.10.1371/journal.pone.0000880
   PubMed Web of Science ®Google Scholar
• Jo S, Kim T, Iyer VG, et al. CHARMM-GUI: a web-based graphical user interface for CHARMM. J Comput Chem. 2008;29:1859–1865.10.1002/jcc.20945
   PubMed Web of Science ®Google Scholar
• Essmann U, Perera L, Berkowitz ML, et al. A smooth particle mesh Ewald method. J Chem Phys. 1995;103:8577–8593.10.1063/1.470117
   Web of Science ®Google Scholar
• Hess B, Bekker H, Berendsen HJC, et al. LINCS: a linear constraint solver for comparative protein modeling. J Comput Chem. 1997;18:1463–1472.10.1002/(ISSN)1096-987X
   Web of Science ®Google Scholar
• Hess B, Kutzner C, van der Spoel D, et al. GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theory Comput. 2008;4:435–447.10.1021/ct700301q
   PubMed Web of Science ®Google Scholar
• Pettersen EF, Goddard TD, Huang CC, et al. UCSF Chimera? a visualization system for exploratory research and analysis. J Comput Chem. 2004;25:1605–1612.10.1002/(ISSN)1096-987X
   PubMed Web of Science ®Google Scholar
• Humphrey W, Dalke A, Schulten K. VMD: visual molecular dynamics. J Mol Graph. 1996;14:33–38.10.1016/0263-7855(96)00018-5
   PubMed Web of Science ®Google Scholar
• Zhu F, Tajkhorshid E, Schulten K. Theory and simulation of water permeation in aquaporin-1. Biophys J. 2004;86:50–57.10.1016/S0006-3495(04)74082-5
   PubMed Web of Science ®Google Scholar
• Zhu F, Tajkhorshid E, Schulten K. Collective diffusion model for water permeation through microscopic channels. Phys Rev Lett. 2004;93:50.10.1103/PhysRevLett.93.224501
   Web of Science ®Google Scholar
• Smart OS, Goodfellow JM, Wallace BA. The pore dimensions of gramicidin A. Biophys J. 1993;65:2455–2460.10.1016/S0006-3495(93)81293-1
   PubMed Web of Science ®Google Scholar
• Michaud-Agrawal N, Denning EJ, Woolf TB, et al. MD analysis: a toolkit for the analysis of molecular dynamics simulations. J Comput Chem. 2011;32:2319–2327.10.1002/jcc.21787
   PubMed Web of Science ®Google Scholar
• Liu J, Fan J, Cen M, et al. Dependences of water permeation through cyclic octa-peptide nanotubes on channel length and membrane thickness. J Chem Inf Model. 2012;52:2132–2138.10.1021/ci300185c
   PubMed Web of Science ®Google Scholar