Structural assessment of OsNIP2;1 highlighted critical residues defining solute specificity and functionality of NIP class aquaporins

• Published in: Journal of advanced research Vol. 58; pp. 1 - 11
• Main Authors: Sharma, Yogesh, Thakral, Vandana, Raturi, Gaurav, Dutta Dubey, Kshatresh, Sonah, Humira, Pareek, Ashwani, Sharma, Tilak Raj, Deshmukh, Rupesh
• Format: Journal Article
• Language: English
• Published: Egypt Elsevier B.V 01.04.2024; Elsevier
• Subjects: Aquaporins - chemistry; Aquaporins - genetics; Aquaporins - metabolism; Arsenic; Arsenic - metabolism; Arsenites; Arsenous acid; Metalloid; Metalloids - metabolism; Molecular dynamics; Original; Orthosilicic acid; plant aquaporins; Saccharomyces cerevisiae - metabolism; Silicic Acid - metabolism; Silicon; Silicon - metabolism; Solute specificity; plant aquaporins; Arsenic; Molecular dynamics; Orthosilicic acid; Silicon; Arsenous acid; Metalloid; Solute specificity
• ISSN: 2090-1232; 2090-1224
• DOI: 10.1016/j.jare.2023.04.020

[Display omitted] •The free energy landscape for silicon and arsenic permeation was traced.•The transport cycle reveals novel energy constraints onsilicon and arsenic permeation.•Predicted functionally important residues were validated in yeast.•Altering conserved amino acids in loop C and loop D directly influenced metalloid uptake of OsNIP2;1.•Protein variants with lower arsenic uptake were identified to reduce arsenic levels with minimum counterproductive effects. Nodulin-26-like intrinsic proteins (NIPs) are integral membrane proteins belonging to the aquaporin family, that facilitate the transport of neutral solutes across the bilayer. The OsNIP2;1 a member of NIP-III class of aquaporins is permeable to beneficial elements like silicon and hazardous arsenic. However, the atomistic cross-talk of these molecules traversing the OsNIP2;1 channel is not well understood. Due to the lack of genomic variation but the availability of high confidence crystal structure, this study aims to highlight structural determinants of metalloid permeation through OsNIP2;1. The molecular simulations, combined with site-directed mutagenesis were used to probe the role of specific residues in the metalloid transport activity of OsNIP2;1. We drew energetic landscape of OsNIP2;1, for silicic and arsenous acid transport. Potential Mean Force (PMF) construction illuminate three prominent energetic barriers for metalloid passage through the pore. One corresponds to the extracellular molecular entry in the channel, the second located on ar/R filter, and the third size constriction in the cytoplasmic half. Comparative PMF for silicic acid and arsenous acid elucidate a higher barrier for silicic acid at the cytoplasmic constrict resulting in longer residence time for silicon. Furthermore, our simulation studies explained the importance of conserved residues in loop-C and loop-D with a direct effect on pore dynamics and metalloid transport. Next we assessed contribution of predicted key residues for arsenic uptake, by functional complementation in yeast. With the aim of reducing arsenic uptake while maintaining beneficial elements uptake, we identified novel OsNIP2;1 mutants with substantial reduction in arsenic uptake in yeast. We provide a comprehensive assessment of pore lining residues of OsNIP2;1 with respect to metalloid uptake. The findings will expand mechanistic understanding of aquaporin’s metalloid selectivity and facilitate variant interpretation to develop novel alleles with preference for beneficial metalloid species and reducing hazardous ones.