Structures of KcsA in Complex with Symmetrical Quaternary Ammonium Compounds Reveal a Hydrophobic Binding Site

Abstract

Potassium channels allow for the passive movement of potassium ions across the cell membrane and are instrumental in controlling the membrane potential in all cell types. Quaternary ammonium (QA) compounds block potassium channels and have long been used to study the functional and structural properties of these channels. Here we describe the interaction between three symmetrical hydrophobic QAs and the prokaryotic potassium channel KcsA. The structures demonstrate the presence of a hydrophobic pocket between the inner helices of KcsA and provide insight into the binding site and blocking mechanism of hydrophobic QAs. The structures also reveal a structurally hidden pathway between the central cavity and the outside membrane environment reminiscent of the lateral fenestration observed in sodium channels that can be accessed through small conformational changes in the pore wall. We propose that the hydrophobic binding pocket stabilizes the alkyl chains of long-chain QA molecules and may play a key role in hydrophobic drug binding in general.

Unravelling the Biological Activities of the Byttneria pilosa Leaves Using Experimental and Computational Approaches

“…The docking analysis was followed by the protocol of Sastry et al (2013) [ 50 ] and explained in detail in our previous studies [ 11 , 51 ]. Protein data bank was used to derive the 3D structures of the subsequent proteins: cyclooxygenase (COX)-1 (PDB ID: 2OYE) [ 52 ], cyclooxygenase (COX)-2 (PDB ID: 6COX) [ 53 ], serotonin transporter (PDB ID: 5I6X) [ 54 ], potassium channel (PDB ID: 4UUJ) [ 55 ], PDE4 complexed with inhibitor (PDB ID: 4WCU) [ 56 ], bromodomain of human BRD4 (PDB ID: 3U5J) [ 57 ], V. cholerae MARTX toxin and (PDB ID: 3CJB) [ 58 ], and bromodomain of human BRD4 in complex with midazolam (PDB ID: 3U5K) [ 57 ]. The molecular docking analysis was assessed by Schrodinger Maestro version 11.1 and the amino acid residues of the active sites of each receptor were given as follows: for 2OYE receptor, the amino acid residues were Val116, Arg120, Glu524, Leu531, Ala527, Gly526, Trp387, Met522, Leu384, Tyr385, Ser530, Val349, Leu352, Ile523, Ser353, Phe518, Tyr355, and Leu93; for 6COX receptor, the amino acid residues were Trp387, Tyr385, Gly526, Ala527, Leu384, Met522, Leu352, Phe518, Ala516, Gln192, Arg513, Ser353, Tyr355, Val116, Arg120, Leu531, Leu359, Val349, Val523, and Ser530; for 5I6X receptor, the amino acid residues were Val501, Phe335, Gly338, Ser336, Asp98, Ala96, Tyr95, Tyr176, Ser438, Ser439, Ile172, Ala169, Gly442, and Phe341; for 4UUJ receptor, the amino acid residues were Val93, Arg89, and Leu86; for 4WCU receptor, the amino acid residues were Phe432, Met273, Thr271, Asp318, Leu319, Tyr159, Trp332, Asn321, Thr333, Ile336, Phe340, Met337, Gln433, Gln369, Met357, Ile376, Phe372, and Leu436; for 3U5J receptor, the amino acid residues were Pro82, Trp81, Leu92, Met149, Ile146, Leu94, Asn140, and Phe83; for 3CJB receptor, the amino acid residues were Gly158, Leu16, Val159, Gly13, Gly15, Ser14, Gly302, Lys336, Tyr306, Met305, Glu214, Lys213, Thr303, Asp157, Gly301, Lys18, Gly156, and Asp154; and for 3U5K receptor, the amino acid residues were Asn140, Leu94, Leu92, Met149, Ile146, Trp81, Pro82, Val87, and Phe83.…”

Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory

“…Ion channels are fundamental molecular components of signaling in our nervous system, and have been the subject of major advances in structural determination over the last decade (see, for example (Brohawn, del Marmol & MacKinnon, 2012; Chen, Durr & Gouaux, 2014; Cuello et al, 2010; Gonzales, Kawate & Gouaux, 2009; Karakas & Furukawa, 2014; Kato et al, 2012; Lenaeus et al, 2014; Payandeh et al, 2012). The perspective of the community on the role played by lipids in channel modulation has recently started to shift: whereas earlier work only considered the membrane as an adaptable matrix for protein functioning, recent data suggest that lipid molecules play fundamental structural and functional roles in ion transport.…”

Intervention in Neuropsychiatric Disorders by Suppressing Inflammatory and Oxidative Stress Signal and Exploration of In Silico Studies for Potential Lead Compounds from Holigarna caustica (Dennst.) Oken leaves

“…Three-dimensional crystallographic structures of enzyme/receptors were obtained from the Protein Data Bank RCSB PDB [36]: potassium channel receptor (PDB: 4UUJ) [37], human serotonin receptor (PDB: 5I6X) [38], cyclooxygenase-1 (COX-1, PDB: 2OYE) [39], cyclooxygenase-2 (COX-2, PDB: 3HS5) [40], and xanthine oxidoreductase enzyme (PDB: 1R4U) [41]. The enzyme/receptor was prepared for a docking experiment using Protein Preparation Wizard [42], which embedded in Schrödinger suite-Maestro v 10.1, as we described previously [43].…”