Dynamics and energetics of water transport through aquaporin mutants causing nephrogenic diabetes insipidus (NDI): A molecular dynamics study

Water Migration through Enzyme Tunnels Is Sensitive to the Choice of Explicit Water Model

The utilization of tunnels and water transport within enzymes is crucial for their catalytic function as water molecules can stabilize bound substrates and help with unbinding processes of products and inhibitors. Since the choice of water models for molecular dynamics simulations was shown to determine the accuracy of various calculated properties of the bulk solvent and solvated proteins, we have investigated if and to what extent water transport through the enzyme tunnels depends on the selection of the water model. Here, we focused on simulating enzymes with various well-defined tunnel geometries. In a systematic investigation using haloalkane dehalogenase as a model system, we focused on the well-established TIP3P, OPC, and TIP4P-Ew water models to explore their impact on the use of tunnels for water molecule transport. The TIP3P water model showed significantly faster migration, resulting in the transport of approximately 2.5 times more water molecules compared to that of the OPC and 1.7 times greater than that of the TIP4P-Ew. Finally, the transport was 1.4-fold more pronounced in TIP4P-Ew than in OPC. The increase in migration of TIP3P water molecules was mainly due to faster transit times through dehalogenase tunnels. We observed similar behavior in two different enzymes with buried active sites and different tunnel network topologies, i.e., alditol oxidase and cytochrome P450, indicating that our findings are likely not restricted to a particular enzyme family. Overall, this study showcases the critical importance of water models in comprehending the use of enzyme tunnels for small molecule transport. Given the significant role of water availability in various stages of the catalytic cycle and the solvation of substrates, products, and drugs, choosing an appropriate water model may be crucial for accurate simulations of complex enzymatic reactions, rational enzyme design, and predicting drug residence times.

Expression Regulation and Trafficking of Aquaporins

Aquaporins (AQPs) mediate the bidirectional water flow driven by an osmotic gradient. Either gating or trafficking allows for rapid and specific AQP regulation in a tissue-dependent manner. The regulatory mechanisms of AQP2 are discussed mainly in this chapter, as the mechanisms controlling the regulation and trafficking of AQP2 have been very well studied. The targeting of AQP2 to the apical plasma membrane of collecting duct principal cells is mainly regulated by the action of arginine vasopressin (AVP) on the type 2 AVP receptor (V2R), which cause increased intracellular cAMP or elevated intracellular calcium levels. Activation of these intracellular signaling pathways results in vesicles bearing AQP2 transport, docking and fusion with the apical membrane, which increase density of AQP2 on the membrane. The removal of AQP2 from the membrane requires dynamic cytoskeletal remodeling. AQP2 is degraded through the ubiquitin proteasome pathway and lysosomal proteolysis pathway. Finally, we review updated findings in transcriptional and epigenetic regulation of AQP2.

Non-equilibrium molecular dynamics study of human aquaporin-2 in the static external electric fields

In this paper, non-equilibrium MD simulations (NEMD) of human aquaporin-2 (AQP2) in the presence of an external static electric field have been performed along + z and - z directions of the pore axis. The impacts of the electric field direction on the gating mechanism corresponding to the selectivity filter (SF) region of AQP2 have been studied. Besides, the effects of applied external electric field on the PMF profile of water molecules translocation, water permeability, and molecules dipole orientation are investigated. Our results showed that when the external electric field is implemented along the + z direction of the channels, the selectivity filter region is kept in the wide conformation for the majority of the time. Therefore, a remarkable increase in the overall water permeability can be seen compared to the case without any external electric field. This is in contrast to the effects of - z-directed electric field on the conformations of the selectivity filter, which induces mostly narrow conformations in this constriction region. A substantial higher energy barrier emerged in the middle of the AQP2's pores under the effect of -z-directed electric field in comparison with the zero and + z-directed electric field strengths, which is mainly ascribed to the deviation from bipolar dipole orientation within the AQP2's pores.Communicated by Ramaswamy H. Sarma.

Deciphering the role of aquaporin 1 in the adaptation of the stinging catfish Heteropneustes fossilis to environmental hypertonicity by molecular dynamics simulation studies

A thorough investigation of the water permeability of H. fossilis aquaporin 1 (hfAQP1) in a hypertonic environment can provide a useful insight into the understanding of the underlying molecular mechanism of its high tolerance to salinity. Here, we constructed a 3 D homology model of hfAQP1 by taking Bos taurus AQP1, AQP0, and human AQP2 as templates using I-TASSER. The model obtained has similar structural organizations with mammalian AQP1s in all aspects. We investigated the water permeability of the modeled hfAQP1 in a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) membrane under neutral and 100 mM hypersalinity by subjecting each system to a 100 ns molecular dynamics simulation. Our results show that hypersalinity hinders water permeation across the membrane through the hfAQP1 channel. A change in the intermolecular distance between key residues of the ar/R selectivity filter along with charge redistribution resulted in the accommodation of only 2-6 water molecules inside the channel at once under hypersaline conditions. We investigated the mRNA expression pattern of hfaqp1 in osmoregulatory organs of H. fossilis in response to 100 mM hypertonicity by using qPCR analysis. The transcript was downregulated in kidney and GI tract, but upregulated in the Gills. Thus, the catfish survive in a hypertonic environment by reducing the transport of water in its cellular systems and downregulating the expression of the hfaqp1 gene. The results observed in our study can shed more light on the functionality of AQP1 in catfishes under salinity stress and aid in future researches on solving more gating mechanisms involved in its regulation.Communicated by Ramaswamy H. Sarma.

Molecular dynamics study of water transport through AQP5-R188C mutant causing palmoplantar keratoderma (PPK) using the gating mechanism concept

It is widely known that any disruption to the water regulation in aquaporins (AQPs) leads to numerous important diseases. However, studies of dynamics and energetics of disease-causing mutations in the aquaporins on the molecular level are still limited. In the present work, the effects of a skin disease-causing mutant, R188C, on the structure of AQP5 and water transport mechanism within this mutated aquaporin are investigated using the concept of gating mechanism. Our results have revealed that the R188C mutation causes a remarkable increase in the pore radius inside the selectivity filter (SF) region facilitating the passage of water molecules. This observation is supported by plotting the free energy profiles of water molecules transport and calculating permeability values through AQP5-R188C, such that the energy barrier in the SF region of the pores was substantially reduced by this mutation, and therefore, the translocation of water molecules was improved. The total averaged osmotic permeability for R188C has been computed as about 11-fold of the wild-type permeability. However, a comparison between the osmotic permeability values related to the open conformation of CE revealed that this coefficient for AQP5-R188C is about 6.5 times larger than that of wt-AQP5, which can be a more accurate value according to the gating mechanism associated with the constriction region of the aquaporin.