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The Journal of Membrane Biology

, Volume 252, Issue 1, pp 17–29 | Cite as

Presence of Intra-helical Salt-Bridge in Loop E Half-Helix Can Influence the Transport Properties of AQP1 and GlpF Channels: Molecular Dynamics Simulations of In Silico Mutants

  • Alok Jain
  • Ravi Kumar Verma
  • Ramasubbu SankararamakrishnanEmail author
Article
  • 159 Downloads

Abstract

Major intrinsic protein (MIP) superfamily contains water-transporting AQP1 and glycerol-specific GlpF belonging to two major phylogenetic groups, namely aquaporins (AQPs) and aquaglyceroporins (AQGPs). MIP channels have six transmembrane helices (TM1 to TM6) and two half-helices (LB and LE). LE region contributes two residues to the aromatic/arginine (Ar/R) selectivity filter (SF) within the MIP channel. Bioinformatics analyses have shown that all AQGPs have an intra-helical salt-bridge (IHSB) in LE half-helix and all AQGPs and majority of AQPs have helix destabilizing Gly and/or Pro in the same region. In this paper, we mutated in silico the acidic and basic residues in GlpF to Ser and introduced salt-bridge interaction in AQP1 LE half-helix by substituting Ser residues at the equivalent positions with acidic and basic residues. We investigated the influence of IHSB in LE half-helix on the transport properties of GlpF and AQP1 mutant channels using molecular dynamics simulations. With IHSB abolished in LE half-helix, the GlpF mutant exhibited a significantly reduced water transport. In contrast, the introduction of IHSB in the two AQP1 mutants has increased water transport. Absence of salt-bridge in LE half-helix alters the SF geometry and results in a higher energy barrier for the solutes in the Ar/R selectivity filter. Presence/absence of IHSB in LE half-helix influences the channel transport properties and it is evident especially for the AQGPs. By modulating its helical flexibility, LE half-helix can perhaps play a regulatory role in transport either on its own or in conjunction with other extracellular regions.

Keywords

Water channels Transport mechanism Potential of mean force Channel regulation Membrane protein simulation 

Notes

Acknowledgements

We gratefully acknowledge Prof. Bert de Groot for sharing the Berger lipid parameters compatible with the OPLS-AA force-field. We thank the High Performance Computing facility of IIT-Kanpur supported by DST and MHRD, Government of India. RS is Pradeep Sindhu Chair Professor. RKV thanks Council of Scientific and Industrial Research (CSIR) for a Senior Research Fellowship. We thank all our lab members for suggestions and useful discussions.

Compliance with Ethical Standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

232_2018_54_MOESM1_ESM.pdf (1.8 mb)
Supplementary Material (PDF 1865 kb)

References

  1. Abascal F, Irisarri I, Zardoya R (2014) Diversity and evolution of membrane intrinsic proteins. Biochim Biophys Acta 1840:1468–1481CrossRefGoogle Scholar
  2. Alberga D, Nicolotti O, Lattanzi G, Nicchia GP, Frigeri A, Pisani F, Benfenati V, Mangiatordi GF (2014) A new gating site in human aquaporin-4: insights from molecular dynamics simulations. Biochim Biophys Acta 1838:3052–3060CrossRefGoogle Scholar
  3. Aponte-Santamaria C, Hub JS, de Groot BL (2010) Dynamics and energetics of solute permeation through the Plasmodium falciparum aquaglyceroporin. Phys Chem Chem Phys 12:10246–10254CrossRefGoogle Scholar
  4. Araya-Secchi R, Garate JA, Holmes DS, Perez-Acle T (2011) Molecular dynamics study of the archaeal aquaporin AqpM. BMC Genom 12(4):S8CrossRefGoogle Scholar
  5. Azad AK, Yoshikawa N, Ishikawa T, Sawa Y, Shibata H (2012) Substitution of a single amino acid residue in the aromatic/arginine selectivity filter alters the transport profiles of tonoplast aquaporin homologs. Biochim Biophys Acta 1818:1–11CrossRefGoogle Scholar
  6. Ballesteros JA, Weinstein H (1995) Integrated methods for the construction of three-dimensional models and computational probing of structure-function relations in G protein-coupled receptors. Methods Neurosci 25:366–428CrossRefGoogle Scholar
  7. Bansal A, Sankararamakrishnan R (2007) Homology modeling of major intrinsic proteins in rice, maize and Arabidopsis: comparative analysis of transmembrane helix association and aromatic/arginine selectivity filters. BMC Struct Biol 7:Art. No. 27Google Scholar
  8. Beitz E, Wu B, Holm LM, Schultz JE, Zeuthen T (2006) Point mutations in the aromatic/arginine region in aquaporin 1 allow passage of urea, glycerol, ammonia, and protons. Proc Natl Acad Sci USA 103:269–274CrossRefGoogle Scholar
  9. Berger O, Edholm O, Jahnig F (1997) Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature. Biophys J 72:2002–2013CrossRefGoogle Scholar
  10. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) The Protein Data Bank. Nucleic Acids Res 28:235–242CrossRefGoogle Scholar
  11. Beuming T, Shi L, Javitch JA, Weinstein H (2006) A comprehensive structure-based alignment of prokaryotic and eukaryotic neurotransmitter/Na + symporters (NSS) aids in the use of the LeuT structure to probe NSS structure and function. Mol Pharmacol 70:1630–1642CrossRefGoogle Scholar
  12. Cheng AL, Merz KM (1996) Application of the Nose-Hoover chain algorithm to the study of protein dynamics. J Phys Chem 100:1927–1937CrossRefGoogle Scholar
  13. de Groot BL, Grubmuller H (2001) Water permeation across biological membranes: mechanism and dynamics of aquaporin-1 and GlpF. Science 294:2353–2357CrossRefGoogle Scholar
  14. Essmann U, Perera L, Berkowitz ML, Darden T, Lee H, Pedersen LG (1995) A smooth particle mesh Ewald method. J Chem Phys 103:8577–8593CrossRefGoogle Scholar
  15. Fischer G, Kosinska-Eriksson U, Aponte-Santamaria C, Palmgren M, Geijer C, Hedfalk K, Hohmann S, de Groot BL, Neutze R, Lindkvist-Petersson K (2009) Crystal structure of a yeast aquaporin at 1.15 angstrom reveals a novel gating mechanism. PLoS Biol 7(6):e1000130CrossRefGoogle Scholar
  16. Fu D, Libson A, Miercke LJ, Weitzman C, Nollert P, Krucinski J, Stroud RM (2000) Structure of a glycerol-conducting channel and the basis for its selectivity. Science 290:481–486CrossRefGoogle Scholar
  17. Gonen T, Sliz P, Kistler J, Cheng Y, Walz T (2004) Aquaporin-0 membrane junctions reveal the structure of a closed water pore. Nature 429:193–197CrossRefGoogle Scholar
  18. Gonen T, Walz T (2006) The structure of aquaporins. Quart Rev Biophys 39:361–396CrossRefGoogle Scholar
  19. Gupta A, Sankararamakrishnan R (2018) dbSWEET: an integrated resource for SWEET superfamily to understand, analyze and predict the function of sugar transporters in prokaryotes and eukaryotes. J Mol Biol 430:2203–2211CrossRefGoogle Scholar
  20. Gupta AB, Sankararamakrishnan R (2009) Genome-wide analysis of major intrinsic proteins in the tree plant Populus trichocarpa: Characterization of XIP subfamily of aquaporins from evolutionary perspective. BMC Plant Biol 9:134CrossRefGoogle Scholar
  21. Gupta AB, Verma RK, Agarwal V, Vajpai M, Bansal V, Sankararamakrishnan R (2012) MIPModDB: a central resource for the superfamily of major intrinsic proteins. Nucleic Acids Res 40:D362–D369CrossRefGoogle Scholar
  22. Hashido M, Ikeguchi M, Kidera A (2005) Comparative simulations of aquaporin family: AQP1, AQPZ, AQP0 and GlpF. FEBS Lett 579:5549–5552CrossRefGoogle Scholar
  23. Hashido M, Kidera A, Ikeguchi M (2007) Water transport in aquaporins: osmatic permeability matrix analysis of molecular dynamics simulations. Biophys J 93:373–385CrossRefGoogle Scholar
  24. Hess B, Kutzner C, van der Spoel D, Lindahl E (2008) GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theoy Comput 4:435–447CrossRefGoogle Scholar
  25. Ho JD, Yeh R, Sandstrom A, Chorny I, Harries WEC, Robbins RA, Miercke LJW, Stroud RM (2009) Crystal structure of human aquaporin 4 at 1.8 angstrom and its mechansim of conductance. Proc Natl Acad Sci USA 106:7437–7442CrossRefGoogle Scholar
  26. Hu GD, Chen LY, Wang J (2012) Insights into the mechanisms of the selectivity filter of Escherichia coli aquaporin Z. J Mol Model 18:3731–3741CrossRefGoogle Scholar
  27. Hub JS, de Groot BL (2006) Does CO2 permeate through aquaporin-1? Biophys J 91:842–848CrossRefGoogle Scholar
  28. Hub JS, de Groot BL (2008) Mechanism of selectivity in aquaporins and aquaglyceroporins. Proc Natl Acad Sci USA 105:1198–1203CrossRefGoogle Scholar
  29. Janosi L, Ceccarelli M (2013) The gating mechanism of the human aquaporin 5 revealed by molecular dynamics simulations. PLoS ONE 8:e59897CrossRefGoogle Scholar
  30. Jensen MO, Dror RO, Xu HF, Borhani DW, Arkin IT, Eastwood MP, Shaw DE (2008) Dynamic control of slow water transport by aquaporin 0: Implications for hydration and junction stability in the eye lens. Proc Natl Acad Sci USA 105:14430–14435CrossRefGoogle Scholar
  31. Jiang JS, Daniels BV, Fu D (2006) Crystal structure of AqpZ tetramer reveals two distinct Arg-189 conformations associated with water permeation through the narrowest constriction of the water-conducting channel. J Biol Chem 281:454–460CrossRefGoogle Scholar
  32. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML (1983) Comparison of simple potential functions for simulating water. J Chem Phys 79:926–935CrossRefGoogle Scholar
  33. Jorgensen WL, Maxwell DS, Tirado-Rives J (1996) Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J Am Chem Soc 118:11225–11236CrossRefGoogle Scholar
  34. Kabsch W, Sander C (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22:2577–2637CrossRefGoogle Scholar
  35. Kandt C, Ash WL, Tieleman DP (2007) Setting up and running molecular dynamics simulations of membrane proteins. Methods 41:475–488CrossRefGoogle Scholar
  36. Khandelia H, Jensen MO, Mouritsen OG (2009) To gate or not to gate: using molecular dynamics simulations to morph gated plant aquaporins into constitutively open conformations. J Phys Chem B 113:5239–5244CrossRefGoogle Scholar
  37. Li T, Choi WG, Wallace IS, Baudry J, Roberts DM (2011) Arabidopsis thaliana NIP7;1: an anther-specific boric acid transporter of the aquaporin superfamily regulated by an unusual tyrosine in helix 2 of the transport pore. Biochemistry 50:6633–6641CrossRefGoogle Scholar
  38. Mitani-Ueno N, Yamaji N, Zhao FJ, Ma JF (2011) The aromatic/arginine selectivity filter of NIP aquaporins plays a critical role in substrate selectivity for silicon, boron, and arsenic. J Exp Botany 62:4391–4398CrossRefGoogle Scholar
  39. Parrinello M, Rahman A (1981) Polymorphic transitions in single-crystals—a new molecular dynamics method. J Appl Phys 52:7182–7190CrossRefGoogle Scholar
  40. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE (2004) UCSF Chimera—a visualization system for exploratory research and analysis. J Comp Chem 25:1605–1612CrossRefGoogle Scholar
  41. Smart OS, Neduvelil JG, Wang X, Wallace B, Sansom MSP (1996) HOLE: a program for the analysis of the pore dimensions of ion channel structural models. J Mol Graph Model 14:354–360CrossRefGoogle Scholar
  42. Sui H, Han BG, Lee JK, Walian P, Jap BK (2001) Structural basis of water-specific transport through the AQP1 water channel. Nature 414:872–878CrossRefGoogle Scholar
  43. Tajkhorshid E, Nollert P, Jensen MO, Miercke LJ, O’Connell J, Stroud RM, Schulten K (2002) Control of the selectivity of the aquaporin water channel family by global orientational tuning. Science 296:525–530CrossRefGoogle Scholar
  44. Tieleman DP, Berendsen HJC (1998) A molecular dynamics study of the pores formed by Escherichia coli OmpF porin in a fully hydrated palmitoyloleoylphosphatidylcholine bilayer. Biophys J 74:2786–2801CrossRefGoogle Scholar
  45. Tornroth-Horsefield S, Wang Y, Hedfalk K, Johanson U, Karlsson M, Tajkhorshid E, Neutze R, Kjellbom P (2006) Structural mechanism of plant aquaporin gating. Nature 439:688–694CrossRefGoogle Scholar
  46. Verma RK, Gupta AB, Sankararamakrishnan R (2015a) Major intrinsic protein superfamily: channels with unique structural features and diverse selectivity filters. Methods Enzymol 557:485–520CrossRefGoogle Scholar
  47. Verma RK, Prabh ND, Sankararamakrishnan R (2014) New subfamilies of major intrinsic proteins in fungi suggest novel transport properties in fungal channels: Implications for the host-fungal interactions. BMC Evol Biol 14:Art. No. 173Google Scholar
  48. Verma RK, Prabh ND, Sankararamakrishnan R (2015b) Intra-helical salt-bridge and helix destabilizing residues within the same helical turn: Role of functionally important loop E half-helix in channel regulation of major intrinsic proteins. Biochim Biophys Acta 1848:1436–1449CrossRefGoogle Scholar
  49. Wang Y, Schulten K, Tajkhorshid E (2005) What makes an aquaporin a glycerol channel? A comparative study of AqpZ and GlpF. Structure 13:1107–1118CrossRefGoogle Scholar
  50. Xin L, Su HB, Nielsen CH, Tang CY, Torres J, Mu YG (2011) Water permeation dynamics of AqpZ: a tale of two states. Biochim Biophys Acta 1808:1581–1586CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Department of Biological Sciences and BioengineeringIndian Institute of Technology KanpurKanpurIndia
  2. 2.National Institute of Pharmaceutical Education and ResearchAhmedabadIndia
  3. 3.Bioinformatics InstituteSingaporeSingapore

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