Docking flexible ligands in proteins with a solvent exposure- and distance-dependent dielectric function

Garden, Daniel P.; Zhorov, Boris S.

doi:10.1007/s10822-009-9317-9

Cited by 84 publications

(77 citation statements)

References 59 publications

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“…Our computational methodology allows one to reproduce structural details of known complexes of proteins with organic ligands (38) and calcium ions (31). However a homology model, which includes only a part of a large transmembrane protein and lacks membrane lipids, is not expected to correspond to the global energy minimum.…”

Section: Discussionmentioning

confidence: 99%

Possible Roles of Exceptionally Conserved Residues around the Selectivity Filters of Sodium and Calcium Channels

Tikhonov

Zhorov

2011

Journal of Biological Chemistry

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In the absence of x-ray structures of sodium and calcium channels their homology models are used to rationalize experimental data and design new experiments. A challenge is to model the outer-pore region that folds differently from potassium channels. Here we report a new model of the outer-pore region of the NaV1.4 channel, which suggests roles of highly conserved residues around the selectivity filter. The model takes from our previous study (Tikhonov, D. B., and Zhorov, B. S. (2005) Biophys. J. 88, 184 -197) the general disposition of the P-helices, selectivity filter residues, and the outer carboxylates, but proposes new intra-and inter-domain contacts that support structural stability of the outer pore. Glycine residues downstream from the selectivity filter are proposed to participate in knob-into-hole contacts with the P-helices and S6s. These contacts explain the adapted tetrodotoxin resistance of snakes that feed on toxic prey through valine substitution of isoleucine in the P-helix of repeat IV. Polar residues five positions upstream from the selectivity filter residues form H-bonds with the ascending-limb backbones. Exceptionally conserved tryptophans are engaged in inter-repeat H-bonds to form a ring whose -electrons would facilitate passage of ions from the outer carboxylates to the selectivity filter. The outerpore model of CaV1.2 derived from the NaV1.4 model is also stabilized by the ring of exceptionally conservative tryptophans and H-bonds between the P-helices and ascending limbs. In this model, the exceptionally conserved aspartate downstream from the selectivity-filter glutamate in repeat II facilitates passage of calcium ions to the selectivity-filter ring through the tryptophan ring. Available experimental data are discussed in view of the models.Voltage-gated ion channels are involved in the control of many physiological functions. Upon membrane depolarization, channels rapidly transit from the resting to the open state, then close to inactivated state(s), and return to the resting state upon membrane repolarization. The human genome encodes nine voltage-gated sodium (NaV1.1-NaV1.9) and ten voltage-gated calcium channels categorized as L (CaV1.1-CaV1.4), P/Q (CaV2.1), N (CaV2.2), R (CaV2.3), and T (CaV3.1-CaV3.3) types. The pore-forming ␣ 1 -subunit of calcium and sodium channels folds from a single polypeptide chain of four homologous repeats (Fig. 1A). Repeats I to IV are arranged clockwise when viewed extracellularly (1). Each repeat contains a voltage-sensing domain S1-S4, an outer helix S5, an inner helix S6, and a membrane-diving P-loop between S5 and S6. The P-loop includes a P-helix, a P-turn, and an ascending limb. Four ascending limbs, which line the outer pore, contain selectivity-filter residues in positions p50 (see Footnote 2 for residue labels). 2 Repeats I, II, III, and IV contain selectivity-filter glutamates in calcium channels (the EEEE ring) and Asp, Glu, Lys, and Ala residues in sodium channels (the DEKA ring). The ascending limbs also contain the outer carboxylates t...

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Section: Discussionmentioning

confidence: 99%

Possible Roles of Exceptionally Conserved Residues around the Selectivity Filters of Sodium and Calcium Channels

Tikhonov

Zhorov

2011

Journal of Biological Chemistry

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“…1. Homology modeling and ligand docking were performed using the ZMM program (www.zmmsoft.com; see Garden and Zhorov, 2010) and Monte Carlo minimization (MCM) protocol (Li and Scheraga, 1987), as described in our previous study . Molecular images were created using the PyMol Molecular Graphics System, version 0.99rc6 (Schrödinger, New York, NY).…”

Section: Computer Modelingmentioning

confidence: 99%

Rotational Symmetry of Two Pyrethroid Receptor Sites in the Mosquito Sodium Channel

Nomura

Zhorov

et al. 2015

Mol Pharmacol

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Voltage-gated sodium channels are the primary target of pyrethroid insecticides. Although it is well known that specific mutations in insect sodium channels confer knockdown resistance (kdr) to pyrethroids, the atomic mechanisms of pyrethroid-sodium channel interactions are not clearly understood. Previously, computer modeling and mutational analysis predicted two pyrethroid receptors, pyrethroid receptor site 1 (PyR1) (initial) and pyrethroid receptor site 2 (PyR2), located in the domain interfaces II/III and I/II, respectively. The models differ in ligand orientation and the number of transmembrane helices involved. In this study, we elaborated a revised PyR1 model of the mosquito sodium channel. Computational docking in the K v 1.2-based open channel model yielded a complex in which a pyrethroid (deltamethrin) binds between the linker helix IIL45 and transmembrane helices IIS5, IIS6, and IIIS6 with its dibromoethenyl and diphenylether moieties oriented in the intra-and extracellular directions, respectively. The PyR2 and revised PyR1 models explained recently discovered kdr mutations and predicted new deltamethrin-channel contacts. Further model-driven mutagenesis identified seven new pyrethroid-sensing residues, three in the revised PyR1 and four in PyR2. Our data support the following conclusions: 1) each pyrethroid receptor is formed by a linker-helix L45 and three transmembrane helices (S5 and two S6s); 2) IIS6 contains four residues that contribute to PyR1 and another four to PyR2; 3) seven pairs of pyrethroid-sensing residues are located in symmetric positions within PyR1 and PyR2; and 4) pyrethroids bind to PyR1 and PyR2 in similar orientations, penetrating deeply into the respective domain interfaces. Our study elaborates the dual pyrethroid-receptor sites concept and provides a structural background for rational development of new insecticides.

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“…The Monte Carlo-energy minimization method (39) was used to optimize the channel model and dock BTX. The energy was calculated using the AMBER force field (40, 41) and a solvent exposure-and distance-dependent dielectric function (42). Atomic charges at the BTX molecule were calculated using the AM1 method (43) realized in MOPAC.…”

Section: Expression Of Bgna V Sodium Channels In Xenopus Oocytes-mentioning

confidence: 99%

“…an H-bond or a cation-contact). To search for low energy binding modes of BTX, we employed our three-stage flexible docking protocol (42). In the first stage, a library of BTX conformers was generated by randomly sampling BTX torsions, followed by energy minimizations to ensure that all the rings were closed.…”

Section: Expression Of Bgna V Sodium Channels In Xenopus Oocytes-mentioning

confidence: 99%

“…Hands-free docking of semiflexible BTX in the channel with flexible side chains is possible (42), but the lowest energy binding mode may or may not correspond to the native ligandchannel conformation. Indeed, even when high resolution x-ray structures of proteins are used to dock flexible ligands, the probability that the ligand conformation and orientation in the apparent global minimum would match those in the x-ray structure does not exceed 70% (47)(48)(49).…”

Section: G 3i14 a And F 3i16 A/k Substitutions Reduce Action Of Btx Omentioning

confidence: 99%

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Identification of New Batrachotoxin-sensing Residues in Segment IIIS6 of the Sodium Channel

Garden

Wang

et al. 2011

Journal of Biological Chemistry

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Ion permeation through voltage-gated sodium channels is modulated by various drugs and toxins. The atomistic mechanisms of action of many toxins are poorly understood. A steroidal alkaloid batrachotoxin (BTX) causes persistent channel activation by inhibiting inactivation and shifting the voltage dependence of activation to more negative potentials. Traditionally, BTX is considered to bind at the channel-lipid interface and allosterically modulate the ion permeation. However, amino acid residues critical for BTX action are found in the inner helices of all four repeats, suggesting that BTX binds in the pore. In the octapeptide segment IFGSFFTL in IIIS6 of a cockroach sodium channel BgNa V , besides Ser_3i15 and Leu_3i19, which correspond to known BTX-sensing residues of mammalian sodium channels, we found that Gly_3i14 and Phe_3i16 are critical for BTX action. Using these data along with published data as distance constraints, we docked BTX in the Kv1.2-based homology model of the open BgNa V channel. We arrived at a model in which BTX adopts a horseshoe conformation with the horseshoe plane normal to the pore axis. The BTX ammonium group is engaged in cation-interactions with Phe_3i16 and BTX moieties interact with known BTX-sensing residues in all four repeats. Oxygen atoms at the horseshoe inner surface constitute a transient binding site for permeating cations, whereas the bulky BTX molecule would resist the pore closure, thus causing persistent channel activation. Our study reinforces the concept that steroidal sodium channel agonists bind in the inner pore of sodium channels and elaborates the atomistic mechanism of BTX action.Voltage-gated sodium channels (Na V ) are responsible for the rapid rising phase of the action potential in nerve and muscle cells. The pore-forming ␣-subunit of Na V channels contains four repeats, and each repeat has six transmembrane helices (S1-S6). The S1-S4 helices form the voltage sensor domain.Positively charged S4 helices move outward in response to membrane depolarization. The S5 and S6 helices contribute to the pore-forming domain. The extracellular linkers connecting S5 and S6 helices form the four re-entrant P-loops, which contain the selectivity filter residues. In the absence of x-ray structures of Na V channels, their homology models, which are based on x-ray structures of potassium channels, are used to explain structure-activity relationships of various sodium channel ligands, including local anesthetics (1-4), steroidal activators (5-8), and pyrethroid insecticides (9, 10). Recent reinterpretation of data on substituted cysteine accessibility of the Ca V 2.1 channel (11) in view of a the channel homology model, which is based on the x-ray structure of the open voltage-gated potassium channel Kv1.2 (12), further supports a general similarity of the inner pore architecture in different voltage-gated cationic channels (13).Sodium channels are targets for numerous drugs and naturally occurring toxins. Batrachotoxin (BTX) 4 is a steroidal sodium-channel agonist, which...

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Docking flexible ligands in proteins with a solvent exposure- and distance-dependent dielectric function

Cited by 84 publications

References 59 publications

Possible Roles of Exceptionally Conserved Residues around the Selectivity Filters of Sodium and Calcium Channels

Possible Roles of Exceptionally Conserved Residues around the Selectivity Filters of Sodium and Calcium Channels

Rotational Symmetry of Two Pyrethroid Receptor Sites in the Mosquito Sodium Channel

Identification of New Batrachotoxin-sensing Residues in Segment IIIS6 of the Sodium Channel

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