Year: 2023
Type: article
Abstract: NarK nitrate/nitrite antiporter imports nitrate (a mineral form of the essential element nitrogen) into the cell and exports nitrite (a metabolite that can be toxic in high concentrations) out of the cell. However, many details about its operational mechanism remain poorly understood. In this work, we performed steered molecular dynamics simulations of anion translocations and quantum-chemistry model calculations of the binding sites to study the wild-type NarK protein and its R89K mutant. Our results shed light on the importance of the two strictly conserved binding-site arginine residues (R89 and R305) and two glycine-rich signature motifs (G164-M176 and G408-F419) in anion movement through the pore. We also observe conformational changes of the protein during anion migration. For the R89K mutant, our quantum calculations reveal a competition for a proton between the anion (especially nitrite) and lysine, which can potentially slow down or even trap the anion in the pore. Our findings provide a possible explanation for the striking experimental finding that the arginine-to-lysine mutation, despite preserving the charge, impedes or abolishes anion transport in such mutants of NarK and other similar nitrate/nitrite exchangers.
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: hybrid
Estimated APC paid: $5,000
Awards: G1374583926, G1453181110, G1555197637, G1787346651, Track 4: Advanced CI Coordination Ecosystem: Monitoring and Measurement Services, Operation Mechanism of CLCF Fluoride/Proton Antiporter, Mechanistic studies of prokaryotic and eukaryotic nitrate/nitrite transport, G3147773666, G3226045097, G338811424, G34258105, G3562386289, XSEDE 2.0: Integrating, Enabling and Enhancing National Cyberinfrastructure with Expanding Community Involvement, Track 1: ACCESS Resource Allocations Marketplace and Platform Services (RAMPS), G4010157413, G4275568664, ACO: An Open CI Ecosystem to Advance Scientific Discovery (OpenCI), G5047595966, G5054405183, Track 3: COre National Ecosystem for CyberinfrasTructure (CONECT), G5156331529, G5367127336, G5464919783, G6577206003, G7526614437, G7916508619, Track 2: Customized Multi-tier Assistance, Training, and Computational Help (MATCH) for End User ACCESS to CI, G8499740153, G8994211811, Adaptive Multi-Layer Simulations of NarK Transport Protein
OpenAlex ID: W4385857715