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


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.


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



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)


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© 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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