Substrate-Driven Conformational Changes in CLC-ec1 Observed by Fluorine NMR

Elvington, Shelley; Liu, Corey; Maduke, Merritt

doi:10.1016/j.bpj.2009.12.1740

Cited by 18 publications

(29 citation statements)

References 38 publications

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“…Interestingly, chlorideproton exchangers (ClCs) (6) were thought, until recently, to be an exception to this rule because transport seemed to be associated only with the local movements of side chains within a rigid protein scaffold (7)(8)(9). However, new data suggest that global structural transitions are also likely to be part of the ClC mechanism (10)(11)(12). It should be noted that small perturbations, such as mutations or the binding of small molecules, can turn some transporters into channels, presumably by stabilizing the states in which both the extracellular and intracellular gates are open (e.g., a double mutant of the Escherichia coli ClC transporter becomes a channel) (6,13,14).…”

Section: The Alternating-access Mechanismmentioning

confidence: 99%

Shared Molecular Mechanisms of Membrane Transporters

Drew

Boudker

2016

Annu. Rev. Biochem.

452

482

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The determination of the crystal structures of small-molecule transporters has shed light on the conformational changes that take place during structural isomerization from outward- to inward-facing states. Rather than using a simple rocking movement of two bundles around a central substrate-binding site, it has become clear that even the most simplistic transporters utilize rearrangements of nonrigid bodies. In the most dramatic cases, one bundle is fixed while the other, structurally divergent, bundle carries the substrate some 18 Å across the membrane, which in this review is termed an elevator alternating-access mechanism. Here, we compare and contrast rocker-switch, rocking-bundle, and elevator alternating-access mechanisms to highlight shared features and novel refinements to the basic alternating-access model.

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Section: The Alternating-access Mechanismmentioning

confidence: 99%

Shared Molecular Mechanisms of Membrane Transporters

Drew

Boudker

2016

Annu. Rev. Biochem.

452

482

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“…These studies concluded that such behavior could only be explained by conformational changes occurring at the inner gate, in conjunction with the side chain rotation of GLU ex at the outer gate [77]. Using the CLC transporter structures as a guide, these inner-gate residues correspond to conserved SER cen and TYR cen residues that physically prevent Cl − from entering the pore [13,25,[27][28][29]. Consistent with the conclusion that these residues must move in order to open the channel, the recent CLC-K channel structures show that these residues adopt a more open configuration that results from rotation of a loop containing the intracellular SER cen gate.…”

Section: Resultsmentioning

confidence: 99%

“…When mutated to GLN (to resemble the protonated GLU), this side chain rotates outwards and partially unblocks the Cl − permeation pathway [19]. The inner gate is formed by conserved SER (SER cen ) and TYR residues [13,[27][28][29] that physically obstruct the Cl − translocation pathway from the intracellular side.…”

Section: Introductionmentioning

confidence: 99%

Dynamical model of the CLC-2 ion channel exhibits a two-step gating mechanism

McKiernan

Koster

Maduke

et al. 2017

Preprint

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AbstractThis work reports a dynamical Markov state model of CLC-2 “fast” (pore) gating, based on 600 microseconds of molecular dynamics (MD) simulation. In the starting conformation of our CLC-2 model, both outer and inner channel gates are closed. The first conformational change in our dataset involves rotation of the inner-gate backbone along residues S168-G169-I170. This change is strikingly similar to that observed in the cryo-EM structure of the bovine CLC-K channel, though the volume of the intracellular (inner) region of the ion conduction pathway is further expanded in our model. From this state (inner gate open and outer gate closed), two additional states are observed, each involving a unique rotameric flip of the outer-gate residue GLUex. Both additional states involve conformational changes that orient GLUex away from the extracellular (outer) region of the ion conduction pathway. In the first additional state, the rotameric flip of GLUex results in an open, or near-open, channel pore. The equilibrium population of this state is low (∼1%), consistent with the low open probability of CLC-2 observed experimentally in the absence of a membrane potential stimulus (0 mV). In the second additional state, GLUex rotates to occlude the channel pore. This state, which has a low equilibrium population (∼1%), is only accessible when GLUex is protonated. Together, these pathways model the opening of both an inner and outer gate within the CLC-2 selectivity filter, as a function of GLUex protonation. Collectively, our findings are consistent with published experimental analyses of CLC-2 gating and provide a high-resolution structural model to guide future investigations.Author summaryIn the brain, the roles and mechanisms of sodium-, potassium-, and calcium-selective ion channels are well established. In contrast, chloride-selective channels have been studied much less and are not sufficiently understood, despite known associations of chloride-channel defects with brain disorders. The most broadly expressed voltage-activated chloride channel in the brain is CLC-2 (one of 9 human CLC homologs). In this work, we use simulations to model the conformational dynamics of the CLC-2 chloride ion channel selectivity filter (SF), which is the part of the protein that controls whether the channel is in an ion-conducting or non-conducting state. Our analysis identifies four primary conformational states and a specific progression through these states. Our results are consistent with structural and functional data in the literature and provide a high-resolution model for guiding further studies of CLC-2. These results will inform our understanding of how CLC-2 governs electrical activity and ion homeostasis in the brain.

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“…) and in another region distal to the permeation pathway (at the residue Y419 in the loop between helix P and Q) (Elvington et al . ). Very recently, Accardi and coworkers showed that the movement of helix O, which does not directly line the transport pathway, is an important component in the transport activity of EcClC‐1 (Basilio et al .…”

Section: Introductionmentioning

confidence: 97%

A tale of two CLCs: biophysical insights toward understanding ClC‐5 and ClC‐7 function in endosomes and lysosomes

Zifarelli

2015

The Journal of Physiology

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The CLC protein family comprises both Cl − channels and H + -coupled anion transporters. The understanding of the critical role of CLC proteins in a number of physiological functions has greatly contributed to a revision of the classical paradigm that attributed to Cl − ions only a marginal role in human physiology. The endosomal ClC-5 and the lysosomal ClC-7 are the best characterized human CLC transporters. Their dysfunction causes Dent's disease and osteopetrosis, respectively. It had been originally proposed that they would provide a Cl − shunt conductance allowing efficient acidification of intracellular compartments. However, this model seems to conflict with the transport properties of these proteins and with recent physiological evidence. Currently, there is no consensus on their specific physiological role. CLC proteins present also a number of peculiar biophysical properties, such as the dimeric architecture, the co-existence of intrinsically different thermodynamic modes of transport based on similar structural principles, and the gating mechanism recently emerging for the transporters, just to name a few. This review focuses on the biophysical properties and physiological roles of ClC-5 and ClC-7.

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Substrate-Driven Conformational Changes in CLC-ec1 Observed by Fluorine NMR

Cited by 18 publications

References 38 publications

Shared Molecular Mechanisms of Membrane Transporters

Shared Molecular Mechanisms of Membrane Transporters

Dynamical model of the CLC-2 ion channel exhibits a two-step gating mechanism

A tale of two CLCs: biophysical insights toward understanding ClC‐5 and ClC‐7 function in endosomes and lysosomes

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