97
Views
0
CrossRef citations to date
0
Altmetric
Articles

Modelling of Ca2+-promoted structural effects in wild type and post-translationally modified Connexin26

ORCID Icon, ORCID Icon, ORCID Icon, ORCID Icon & ORCID Icon
Pages 235-245 | Received 24 Jul 2019, Accepted 04 Nov 2019, Published online: 27 Nov 2019

References

  • Kumar NM, Gilula NB. The gap junction communication channel. Cell. 1996;84(3):381–388.
  • Locke D, Bian S, Li H, et al. Post-translational modifications of connexin26 revealed by mass spectrometry. Biochem J. Dec. 2009;424(3):385–398.
  • Maeda S, Nakagawa S, Suga M, et al. Structure of the connexin 26 gap junction channel at 3.5 A resolution. Nature. 2009;458(7238):597–602.
  • Unger VM, Kumar NM, Gilula NB, et al. Three-dimensional structure of a recombinant gap junction membrane channel. Science. 1999;283(5405):1176–1180.
  • Fleishman SJ, Unger VM, Yeager M, et al. A Cα model for the transmembrane α helices of gap junction intercellular channels. Mol Cell. 2004;15(6):879–888.
  • Oshima A, Tani K, Hiroaki Y, et al. Three-dimensional structure of a human connexin26 gap junction channel reveals a plug in the vestibule. Proc Natl Acad Sci USA. Jun. 2007;104(24):10034–10039.
  • Kwon T, Harris AL, Rossi A, et al. Molecular dynamics simulations of the Cx26 hemichannel: evaluation of structural models with brownian dynamics. J Gen Physiol. 2011;138(5):475–493.
  • Alizadeh H, Davoodi J, Rafii-Tabar H. Deconstruction of the human connexin 26 hemichannel due to an applied electric field; A molecular dynamics simulation study. J Mol Graph Model. May 2017;73:108–114.
  • Alizadeh H, Davoodi J, Zeilinger C, et al. Molecular dynamics simulation of the thermosensitivity of the human connexin 26 hemichannel. Chem Phys. Jan. 2018;500:7–14.
  • Valdez Capuccino JM, Chatterjee P, García IE, et al. The connexin26 human mutation N14 K disrupts cytosolic intersubunit interactions and promotes channel opening. J Gen Physiol. Mar. 2019;151(3):328–341.
  • Zonta F, Polles G, Zanotti G, et al. Permeation pathway of homomeric connexin 26 and connexin 30 channels investigated by molecular dynamics. J Biomol Struct Dyn. Jan. 2012;29(5):985–998.
  • Zonta F, Buratto D, Cassini C, et al. Molecular dynamics simulations highlight structural and functional alterations in deafness–related M34 T mutation of connexin 26. Front Physiol. 2014;5(85):1–9.
  • Zonta F, Mammano F, Torsello M, et al. Role of gamma carboxylated Glu47 in connexin 26 hemichannel regulation by extracellular Ca2+: insight from a local quantum chemistry study. Biochem Biophys Res Commun. 2014;445(1):10–15.
  • Zonta F, Polles G, Sanasi MF, et al. The 3.5 {{}{å}{}}ngstr{{}{ö}{}}m X-ray structure of the human connexin26 gap junction channel is unlikely that of a fully open channel. Cell Commun Signal. 2013;11(1):1–9.
  • Zonta F, Girotto G, Buratto D, et al. The p.Cys169Tyr variant of connexin 26 is not a polymorphism. Hum Mol Genet. May 2015;24(9):2641–2648.
  • Müller DJ, Hand GM, Engel A, et al. Conformational changes in surface structures of isolated connexin 26 gap junctions. EMBO J. Jul. 2002;21(14):3598–3607.
  • Thimm J, Mechler A, Lin H, et al. Calcium-dependent open/closed conformations and interfacial energy maps of reconstituted hemichannels. J Biol Chem. Mar. 2005;280(11):10646–10654.
  • Srinivas M, Kronengold J, Bukauskas FF, et al. Correlative Studies of gating in Cx46 and Cx50 hemichannels and Gap junction channels. Biophys J. Mar. 2005;88(3):1725–1739.
  • Bennett BC, Purdy MD, Baker KA, et al. An electrostatic mechanism for Ca2+-mediated regulation of gap junction channels. Nat Commun. Jan. 2016;7:8770.
  • Walsh CT, Garneau-Tsodikova S, Gatto GJ. Protein Posttranslational modifications: The Chemistry of Proteome Diversifications. Angew Chem Int Ed. Nov. 2005;44(45):7342–7372.
  • Axelsen LN, Calloe K, Holstein-Rathlou N-H, et al. Managing the complexity of communication: regulation of gap junctions by post-translational modification. Front Pharmacol. 2013;4(130):1–18.
  • Solan JL, Lampe PD. Key connexin 43 phosphorylation events regulate the gap junction life cycle. J Membr Biol. Jun. 2007;217(1–3):35–41.
  • Lampe PD, Lau AF. The effects of connexin phosphorylation on gap junctional communication. Int J Biochem Cell Biol. Jul. 2004;36(7):1171–1186.
  • Locke D, Koreen IV, Harris AL. Isoelectric points and post-translational modifications of connexin26 and connexin32. FASEB J. Jun. 2006;20(8):1221–1223.
  • Petrov D, Margreitter C, Grandits M, et al. A systematic framework for molecular dynamics simulations of protein post-translational modifications. PLOS Comput Biol. Jul. 2013;9(7):e1003154.
  • Margreitter C, Petrov D, Zagrovic B. Vienna-PTM web server: a toolkit for MD simulations of protein post-translational modifications. Nucleic Acids Res. Jul. 2013;41(W1):W422–W426.
  • Khoury GA, Thompson JP, Smadbeck J, et al. Forcefield_PTM: Ab initio charge and AMBER forcefield parameters for frequently occurring post-translational modifications. J Chem Theory Comput. Dec. 2013;9(12):5653–5674.
  • Bortoli M, Torsello M, Bickelhaupt FM, et al. Role of the chalcogen (S, Se, Te) in the oxidation mechanism of the glutathione peroxidase active site. ChemPhysChem. 2017;18(21):2990–2998.
  • Torsello M, Pimenta AC, Wolters LP, et al. General AMBER force field parameters for diphenyl diselenides and diphenyl ditellurides. J Phys Chem A. Jun. 2016;120(25):4389–4400.
  • Calligari PA, Calandrini V, Ollivier J, et al. Adaptation of extremophilic proteins with temperature and pressure: evidence from initiation factor 6. J Phys Chem B. Jun. 2015;119(25):7860–7873.
  • Calligari P, Gerolin M, Abergel D, et al. Decomposition of proteins into dynamic units from atomic cross-correlation functions. J Chem Theory Comput. Jan. 2017;13(1):309–319.
  • Lopez W, Ramachandran J, Alsamarah A, et al. Mechanism of gating by calcium in connexin hemichannels. Proc Natl Acad Sci. Dec. 2016;113(49):E7986–E7995.
  • Becke AD. Density-functional thermochemistry. III. The role of exact exchange. J Chem Phys. Apr. 1993;98(7):5648.
  • Lee C, Yang W, Parr RG. Development of the colle-salvetti correlation-energy formula into a functional of the electron density. Phys Rev B. Jan. 1988;37(2):785–789.
  • Vosko SH, Wilk L, Nusair M. Accurate spin-dependent electron liquid correlation energies for local spin density calculations: a critical analysis. Can J Phys. Aug. 1980;58(8):1200–1211.
  • Stephens PJ, Devlin FJ, Chabalowski CF, et al. Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields. J Phys Chem. Nov. 1994;98(45):11623–11627.
  • Vanquelef E, Simon S, Marquant G, et al. R.E.D. Server: A web service for deriving RESP and ESP charges and building force field libraries for new molecules and molecular fragments. Nucleic Acids Res. Jul. 2011;39(Web Server issue):W511–W517.
  • Wang F, Becker JP, Cieplak P, et al. R.E.D. Python: Object oriented programming for AMBER force fields. Sanford Burnham Prebys Medical Discovery Institute: Université de Picardie - Jules Verne; 2013.
  • Dupradeau FY, Pigache A, Zaffran T, et al. The R.E.D. tools: advances in RESP and ESP charge derivation and force field library building. Phys Chem Chem Phys PCCP. Jul. 2010;12(28):7821–7839.
  • Bayly CCI, Cieplak P, Cornell WD, et al. A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model. J Phys Chem. Oct. 1993;97(40):10269–10280.
  • Hornak V, Abel R, Okur A, et al. Comparison of multiple amber force fields and development of improved protein backbone parameters. Proteins Struct Funct Bioinforma. 2006;65(3):712–725.
  • Besler BH, Merz KM, Kollman PA. Atomic charges derived from semiempirical methods. J Comput Chem. 1990;11(4):431–439.
  • Betz RM, Walker RC. Paramfit: Automated optimization of force field parameters for molecular dynamics simulations. J Comput Chem. 2015;36(2):79–87.
  • Ling S, Yu W, Huang Z, et al. Gaseous arginine conformers and their unique intramolecular interactions. J Phys Chem A. 2006;110(44):12282–12291.
  • Maier JA, Martinez C, Kasavajhala K, et al. ff14SB: Improving the Accuracy of protein side chain and backbone parameters from ff99SB. J Chem Theory Comput. Aug. 2015;11(8):3696–3713.
  • Shen M, Sali A. Statistical potential for assessment and prediction of protein structures. Protein Sci. 2006;15(11):2507–2524.
  • Šali A, Blundell TL. Comparative protein modelling by Satisfaction of Spatial restraints. J Mol Biol. 1993;234(3):779–815.
  • Jo S, Kim T, Iyer VG, et al. CHARMM-GUI: A web-based graphical user interface for CHARMM. J Comput Chem. 2008;29(11):1859–1865.
  • Jo S, Cheng X, Islam SM, et al. Chapter eight - CHARMM-GUI PDB Manipulator for Advanced modeling and simulations of proteins Containing Nonstandard residues. In: Karabencheva-Christova SB, editor. Biomolecular Modelling and simulations. Cambridge, USA: Academic Press; 2014. p. 235–265.
  • Jo S, Kim T, Im W. Automated builder and database of protein/membrane complexes for molecular dynamics simulations. PLoS One. Sep. 2007;2(9):e880.
  • Jo S, Lim JB, Klauda JB, et al. CHARMM-GUI membrane builder for mixed bilayers and its application to yeast membranes. Biophys J. 2009;97(1):50–58.
  • Wu EL, Cheng X, Jo S, et al. CHARMM-GUI membrane builder toward realistic biological membrane simulations. J Comput Chem. 2014;35(27):1997–2004.
  • Lee J, Cheng X, Swails JM, et al. CHARMM-GUI input generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM simulations using the CHARMM36 additive force field. J Chem Theor Comp. 2016;12(1):405–413.
  • Jorgensen WL, Chandrasekhar J, Madura JD, et al. Comparison of simple potential functions for simulating liquid water. J Chem Phys. Jul. 1983;79(2):926.
  • Joung IS, Cheatham III TE. Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations. J Phys Chem B. 2008;112(30):9020–9041.
  • Joung IS, Cheatham III TE. Molecular dynamics simulations of the dynamic and energetic properties of alkali and halide ions using water-model-specific ion parameters. J Phys Chem B. 2009;113(40):13279–13290.
  • Case P, Darden DA, Cheatham TA, et al. AMBER. San Francisco: University of California; 2008.
  • Dickson CJ, Madej BD, Skjevik ÅA, et al. Lipid14: The amber lipid force field. J Chem Theor Comp. 2014;10(2):865–879.
  • Essmann U, Perera L, Berkowitz ML, et al. A smooth particle mesh ewald method. J Chem Phys. 1995;103(19):8577–8593.
  • Darden T, York D, Pedersen L. Particle mesh ewald: An N⋅log(N) method for ewald sums in large systems. J Chem Phys. 1993;98(12):10089–10092.
  • Crowley MF, Darden TA, Cheatham TE, et al. Adventures in improving the scaling and accuracy of a parallel molecular dynamics program. J Supercomput. 1997;11(3):255–278.
  • Sagui C, Darden TA. P3m and PME: A comparison of the two methods. AIP Conf Proc. 1999;492(1):104–113.
  • Chevrot G, Calligari P, Hinsen K, et al. Least constraint approach to the extraction of internal motions from molecular dynamics trajectories of flexible macromolecules. J Chem Phys. Jan. 2011;135(8):084110.
  • Brezovsky J, Chovancova E, Gora A, et al. Software tools for identification, visualization and analysis of protein tunnels and channels. Biotechnol Adv. 2013;31(1):38–49.
  • Smart OS, Neduvelil JG, Wang X, et al. HOLE: A program for the analysis of the pore dimensions of ion channel structural models. J Mol Graph. 1996;14(6):354–360.
  • Kneller GR, Calligari P. Efficient characterization of protein secondary structure in terms of screw motions. Acta Cryst D. 2006;62(3):302–311.
  • Calligari PA, Kneller GR. Screwfit: combining localization and description of protein secondary structure. Acta Cryst D. 2012;68:1690–1693.
  • Calligari PA, Kneller GR, Giansanti A, et al. Inhibition of viral group-1 and group-2 neuraminidases by oseltamivir: A comparative structural analysis by the ScrewFit algorithm. Biophys Chem. 2009;141(1):117–123.
  • Kumar S, Nussinov R. Relationship between Ion pair geometries and electrostatic strengths in proteins. Biophys J. 2002;83(3):1595–1612.
  • Tran AT, Sadet A, Calligari P, et al. Targeting the pentose phosphate pathway: Characterization of a new 6PGL inhibitor. Biophys J. Dec. 2018;115(11):2114–2126.
  • Kumar S, Nussinov R. Close-Range electrostatic interactions in proteins. ChemBioChem. 2002;3(7):604–617.
  • Oshima A. Structure and closure of connexin gap junction channels. Febs Lett. 2014;588:1230–1237.
  • Oshima A, Doi T, Mitsuoka K, et al. Roles of Met-34, Cys-64, and Arg-75 in the assembly of human connexin 26. implication for key amino acid residues for channel formation and function. J Biol Chem. Jan. 2003;278(3):1807–1816.
  • Kumar S, Nussinov R. Salt bridge stability in monomeric proteins. J Mol Biol. 1999;293:1241–1255.

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.