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Liu J, Li X, Xu N, Han H, Li X. Role of ion channels in the mechanism of proteinuria (Review). Exp Ther Med 2022; 25:27. [PMID: 36561615 PMCID: PMC9748662 DOI: 10.3892/etm.2022.11726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 10/10/2022] [Indexed: 11/25/2022] Open
Abstract
Proteinuria is a common clinical manifestation of kidney diseases, such as glomerulonephritis, nephrotic syndrome, immunoglobulin A nephropathy and diabetic nephropathy. Therefore, proteinuria is considered to be a risk factor for renal dysfunction. Furthermore, proteinuria is also significantly associated with the progression of kidney diseases and increased mortality. Its occurrence is closely associated with damage to the structure of the glomerular filtration membrane. An impaired glomerular filtration membrane can affect the selective filtration function of the kidneys; therefore, several macromolecular substances, such as proteins, may pass through the filtration membrane and promote the manifestation of proteinuria. It has been reported that ion channels play a significant role in the mechanisms underlying proteinuria. Ion channel mutations or other dysfunctions have been implicated in several diseases, therefore ion channels could be used as major therapeutic targets. The mechanisms underlying the action of ion channels and ion transporters in proteinuria have been overlooked in the literature, despite their importance in identifying novel targets for treating proteinuria and delaying the progression of kidney diseases. The current review article focused on the four key ion channel groups, namely Na+, Ca2+, Cl- and K+ ion channels and the associated ion transporters.
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Affiliation(s)
- Jie Liu
- Department of Nephrology, Affiliated Hospital of Weifang Medical University, Weifang, Shandong 261000, P.R. China
| | - Xuewei Li
- Department of Rheumatology, Affiliated Hospital of Weifang Medical University, Weifang, Shandong 261000, P.R. China
| | - Ning Xu
- Department of Nephrology, Affiliated Hospital of Weifang Medical University, Weifang, Shandong 261000, P.R. China
| | - Huirong Han
- Department of Anesthesiology, Weifang Medical University, Weifang, Shandong 261000, P.R. China
| | - Xiangling Li
- Department of Nephrology, Affiliated Hospital of Weifang Medical University, Weifang, Shandong 261000, P.R. China,Correspondence to: Professor Xiangling Li, Department of Nephrology, Affiliated Hospital of Weifang Medical University, 2428 Yu He Road, Weifang, Shandong 261000, P.R. China
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Zhang J, Han J, Li L, Zhang Q, Feng Y, Jiang Y, Deng F, Zhang Y, Wu Q, Chen B, Hu J. Inwardly rectifying potassium channel 5.1: Structure, function, and possible roles in diseases. Genes Dis 2020; 8:272-278. [PMID: 33997174 PMCID: PMC8093645 DOI: 10.1016/j.gendis.2020.03.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 03/02/2020] [Accepted: 03/13/2020] [Indexed: 11/30/2022] Open
Abstract
Inwardly rectifying potassium (Kir) channels make it easier for K+ to enter into a cell and subsequently regulate cellular biological functions. Kir5.1 (encoded by KCNJ16) alone can form a homotetramer and can form heterotetramers with Kir4.1 (encoded by KCNJ10) or Kir4.2 (encoded by KCNJ15). In most cases, homomeric Kir5.1 is non-functional, while heteromeric Kir5.1 on the cell membrane contributes to the inward flow of K+ ions, which can be regulated by intracellular pH and a variety of signaling mechanisms. In the form of a heterotetramer, Kir5.1 regulates Kir4.1/4.2 activity and is involved in the maintenance of nephron function. Actually, homomeric Kir5.1 may also play a very important role in diseases, including in the ventilatory response to hypoxia and hypercapnia, hearing impairment, cardiovascular disease and cancer. With an increase in the number of studies into the roles of Kir channels, researchers are paying more attention to the pathophysiological functions of Kir5.1. This minireview provides an overview regarding these Kir5.1 roles.
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Affiliation(s)
- Junhui Zhang
- Institute of Burn Research, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China.,State Key Laboratory of Trauma, Burns and Combined Injury, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China.,Department of Endocrinology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China
| | - Jian Han
- Department of Obstetrics and Gynecology, Daping Hospital, Third Military Medical University (Army Medical University), Chongqing, 400042, PR China
| | - Lingfei Li
- Department of Dermatology, Daping Hospital, Third Military Medical University (Army Medical University), Chongqing, 400042, PR China
| | - Qiong Zhang
- Institute of Burn Research, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China.,State Key Laboratory of Trauma, Burns and Combined Injury, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China
| | - Yanhai Feng
- Institute of Burn Research, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China.,State Key Laboratory of Trauma, Burns and Combined Injury, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China
| | - Youzhao Jiang
- Department of Endocrinology, People's Hospital of Banan District, Chongqing, 401320, PR China
| | - Fang Deng
- Department of Endocrinology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China
| | - Yuping Zhang
- Department of Endocrinology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China
| | - Qinan Wu
- Department of Endocrinology, Chongqing Cancer Hospital (Chongqing University Cancer Hospital), Chongqing, 40030, PR China
| | - Bing Chen
- Department of Endocrinology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China
| | - Jiongyu Hu
- Institute of Burn Research, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China.,State Key Laboratory of Trauma, Burns and Combined Injury, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China.,Department of Endocrinology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China
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3
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Sun H, Huang R, Xia M, Shahane S, Southall N, Wang Y. Prediction of hERG Liability - Using SVM Classification, Bootstrapping and Jackknifing. Mol Inform 2017; 36:10.1002/minf.201600126. [PMID: 28000393 PMCID: PMC5382096 DOI: 10.1002/minf.201600126] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 11/14/2016] [Indexed: 12/11/2022]
Abstract
Drug-induced QT prolongation leads to life-threatening cardiotoxicity, mostly through blockage of the human ether-à-go-go-related gene (hERG) encoded potassium ion (K+ ) channels. The hERG channel is one of the most important antitargets to be addressed in the early stage of drug discovery process, in order to avoid more costly failures in the development phase. Using a thallium flux assay, 4,323 molecules were screened for hERG channel inhibition in a quantitative high throughput screening (qHTS) format. Here, we present support vector classification (SVC) models of hERG channel inhibition with the averaged area under the receiver operator characteristics curve (AUC-ROC) of 0.93 for the tested compounds. Both Jackknifing and bootstrapping have been employed to rebalance the heavily biased training datasets, and the impact of these two under-sampling rebalance methods on the performance of the predictive models is discussed. Our results indicated that the rebalancing techniques did not enhance the predictive power of the resulting models; instead, adoption of optimal cutoffs could restore the desirable balance of sensitivity and specificity of the binary classifiers. In an external validation set of 66 drug molecules, the SVC model exhibited an AUC-ROC of 0.86, further demonstrating the utility of this modeling approach to predict hERG liabilities.
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Affiliation(s)
- Hongmao Sun
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Bethesda, MD 20892, USA
| | - Ruili Huang
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Bethesda, MD 20892, USA
| | - Menghang Xia
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Bethesda, MD 20892, USA
| | - Sampada Shahane
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Bethesda, MD 20892, USA
| | - Noel Southall
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Bethesda, MD 20892, USA
| | - Yuhong Wang
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Bethesda, MD 20892, USA
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Valverde P, Kawai T, Taubman MA. Potassium Channel-blockers as Therapeutic Agents to Interfere with Bone Resorption of Periodontal Disease. J Dent Res 2016; 84:488-99. [PMID: 15914584 DOI: 10.1177/154405910508400603] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Inflammatory lesions of periodontal disease contain all the cellular components, including abundant activated/memory T- and B-cells, necessary to control immunological interactive networks and to accelerate bone resorption by RANKL-dependent and -independent mechanisms. Blockade of RANKL function has been shown to ameliorate periodontal bone resorption and other osteopenic disorders without affecting inflammation. Development of therapies aimed at decreasing the expression of RANKL and pro-inflammatory cytokines by T-cells constitutes a promising strategy to ameliorate not only bone resorption, but also inflammation. Several reports have demonstrated that the potassium channels Kv1.3 and IKCa1, through the use of selective blockers, play important roles in T-cell-mediated events, including T-cell proliferation and the production of pro-inflammatory cytokines. More recently, a potassium channel-blocker for Kv1.3 has been shown to down-regulate bone resorption by decreasing the ratio of RANKL-to-OPG expression by memory-activated T-cells. In this article, we first summarize the mechanisms by which chronically activated/memory T-cells, in concert with B-cells and macrophages, trigger inflammatory bone resorption. Then, we describe the main structural and functional characteristics of potassium channels Kv1.3 and IKCa1 in some of the cells implicated in periodontal disease progression. Finally, this review elucidates some recent advances in the use of potassium channel-blockers of Kv1.3 and IKCa1 to ameliorate the clinical signs or side-effects of several immunological disorders and to decrease inflammatory bone resorption in periodontal disease. ABBREVIATIONS: AICD, activation-induced cell death; APC, antigen-presenting cells; B(K), large conductance; CRAC, calcium release-activated calcium channels; DC, dendritic cell; GAPDH, glyceraldehyde-3-phosphate dehydrogenase; IFN-γ, interferon-γ; IP3, inositol (1,4,5)-triphosphate; (K)ir, inward rectifier; JNK, c-Jun N-terminal kinase; I(K), intermediate conductance; LPS, lipopolysaccharide; L, ligand; MCSF, macrophage colony-stimulating factor; MHC, major histocompatibility complex; NFAT, nuclear factor of activated T-cells; RANK, receptor activator of nuclear factor-κB; TCM, central memory T-cells; TEM, effector memory T-cells; TNF, tumor necrosis factor; TRAIL, TNF-related apoptosis-inducing ligand; OPG, osteoprotegerin; Omp29, 29-kDa outer membrane protein; PKC, protein kinase C; PLC, phospholipase C; RT-PCR, reverse-transcriptase polymerase chain-reaction; S(K), small conductance; TCR, T-cell receptor; and (K)v, voltage-gated.
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Affiliation(s)
- P Valverde
- Tufts University School of Dental Medicine, One Kneeland Street, Boston, MA 02111, USA.
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Nekouzadeh A, Rudy Y. Conformational changes of an ion-channel during gating and emerging electrophysiologic properties: Application of a computational approach to cardiac Kv7.1. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2015; 120:18-27. [PMID: 26743208 DOI: 10.1016/j.pbiomolbio.2015.12.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 12/23/2015] [Accepted: 12/28/2015] [Indexed: 10/22/2022]
Abstract
Ion channels are the "building blocks" of the excitation process in excitable tissues. Despite advances in determining their molecular structure, understanding the relationship between channel protein structure and electrical excitation remains a challenge. The Kv7.1 potassium channel is an important determinant of the cardiac action potential and its adaptation to rate changes. It is subject to beta adrenergic regulation, and many mutations in the channel protein are associated with the arrhythmic long QT syndrome. In this theoretical study, we use a novel computational approach to simulate the conformational changes that Kv7.1 undergoes during activation gating and compute the resulting electrophysiologic function in terms of single-channel and macroscopic currents. We generated all possible conformations of the S4-S5 linker that couples the S3-S4 complex (voltage sensor domain, VSD) to the pore, and all associated conformations of VSD and the pore (S6). Analysis of these conformations revealed that VSD-to-pore mechanical coupling during activation gating involves outward translation of the voltage sensor, accompanied by a translation away from the pore and clockwise twist. These motions cause pore opening by moving the S4-S5 linker upward and away from the pore, providing space for the S6 tails to move away from each other. Single channel records, computed from the simulated motion trajectories during gating, have stochastic properties similar to experimentally recorded traces. Macroscopic current through an ensemble of channels displays two key properties of Kv7.1: an initial delay of activation and fast inactivation. The simulations suggest a molecular mechanism for fast inactivation; a large twist of the VSD following its outward translation results in movement of the base of the S4-S5 linker toward the pore, eliminating open pore conformations to cause inactivation.
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Affiliation(s)
- Ali Nekouzadeh
- Cardiac Bioelectricity and Arrhythmia Center and Departments of Biomedical Engineering and Cell Biology & Physiology, Washington University in St. Louis, 290 Whitaker Hall, 1 Brooking Dr., St. Louis, MO 63130, USA.
| | - Yoram Rudy
- Cardiac Bioelectricity and Arrhythmia Center and Departments of Biomedical Engineering and Cell Biology & Physiology, Washington University in St. Louis, 290 Whitaker Hall, 1 Brooking Dr., St. Louis, MO 63130, USA.
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Renigunta V, Schlichthörl G, Daut J. Much more than a leak: structure and function of K₂p-channels. Pflugers Arch 2015; 467:867-94. [PMID: 25791628 DOI: 10.1007/s00424-015-1703-7] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 03/09/2015] [Indexed: 11/27/2022]
Abstract
Over the last decade, we have seen an enormous increase in the number of experimental studies on two-pore-domain potassium channels (K2P-channels). The collection of reviews and original articles compiled for this special issue of Pflügers Archiv aims to give an up-to-date summary of what is known about the physiology and pathophysiology of K2P-channels. This introductory overview briefly describes the structure of K2P-channels and their function in different organs. Its main aim is to provide some background information for the 19 reviews and original articles of this special issue of Pflügers Archiv. It is not intended to be a comprehensive review; instead, this introductory overview focuses on some unresolved questions and controversial issues, such as: Do K2P-channels display voltage-dependent gating? Do K2P-channels contribute to the generation of action potentials? What is the functional role of alternative translation initiation? Do K2P-channels have one or two or more gates? We come to the conclusion that we are just beginning to understand the extremely complex regulation of these fascinating channels, which are often inadequately described as 'leak channels'.
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Affiliation(s)
- Vijay Renigunta
- Institute of Physiology and Pathophysiology, Marburg University, 35037, Marburg, Germany
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7
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Efremov RG, Leitner A, Aebersold R, Raunser S. Architecture and conformational switch mechanism of the ryanodine receptor. Nature 2014; 517:39-43. [DOI: 10.1038/nature13916] [Citation(s) in RCA: 250] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2014] [Accepted: 10/06/2014] [Indexed: 12/11/2022]
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Sumino A, Sumikama T, Iwamoto M, Dewa T, Oiki S. The open gate structure of the membrane-embedded KcsA potassium channel viewed from the cytoplasmic side. Sci Rep 2013; 3:1063. [PMID: 23323207 PMCID: PMC3545221 DOI: 10.1038/srep01063] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Accepted: 12/06/2012] [Indexed: 01/24/2023] Open
Abstract
Crystallographic studies of channel proteins have provided insight into the molecular mechanisms of ion channels, even though these structures are obtained in the absence of the membrane and some structural portions have remained unsolved. Here we report the gating structure of the membrane-embedded KcsA potassium channel using atomic force microscopy (AFM). The activation gate of the KcsA channel is located on the intracellular side, and the cytoplasmic domain was truncated to clear the view of this location. Once opened, the individual subunits in the tetramer were resolved with the pore open at the center. Furthermore, AFM was able to capture the previously unsolved bulge helix at the entrance. A molecular dynamics simulation revealed that the bulge helices fluctuated dramatically at the open entryway. This dynamic behavior was observed as vigorous open-channel noise in the single-channel current recordings. The role of the bulge helices in the open gate structure is discussed.
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Affiliation(s)
- Ayumi Sumino
- Department of Frontier Materials, Graduate School of Engineering, Nagoya Institute of Technology, Nagoya, Japan
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Waller KL, McBride SM, Kim K, McDonald TV. Characterization of two putative potassium channels in Plasmodium falciparum. Malar J 2008; 7:19. [PMID: 18218136 PMCID: PMC2263067 DOI: 10.1186/1475-2875-7-19] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2007] [Accepted: 01/24/2008] [Indexed: 11/23/2022] Open
Abstract
Background Potassium channels are essential for cell survival and participate in the regulation of cell membrane potential and electrochemical gradients. During its lifecycle, Plasmodium falciparum parasites must successfully traverse widely diverse environmental milieus, in which K+ channel function is likely to be critical. Dramatically differing conditions will be presented to the parasite in the mosquito mid-gut, red blood cell (RBC) cytosol and the human circulatory system. Methods In silico sequence analyses identified two open-reading frames in the P. falciparum genome that are predicted to encode for proteins with high homology to K+ channels. To further analyse these putative channels, specific antisera were generated and used in immunoblot and immunofluorescence analyses of P. falciparum-infected RBCs. Recombinant genome methods in cultured P. falciparum were used to create genetic knock outs of each K+ channel gene to asses the importance of their expression. Results Immunoblot and IFA analyses confirmed the expression of the two putative P. falciparum K+ channels (PfK1 and PfK2). PfK1 is expressed in all asexual stage parasites, predominantly in late stages and localizes to the RBC membrane. Conversely, PfK2 is predominantly expressed in late schizont and merozoite stage parasites and remains primarily localized to the parasite. Repeated attempts to knockout PfK1 and PfK2 expression by targeted gene disruption proved unsuccessful despite evidence of recombinant gene integration, indicating that pfk1 and pfk2 are apparently refractory to genetic disruption. Conclusion Putative K+ channel proteins PfK1 and PfK2 are expressed in cultured P. falciparum parasites with differing spatial and temporal patterns. Eventual functional characterization of these channels may reveal future pharmacological targets.
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Affiliation(s)
- Karena L Waller
- Department of Medicine (Cardiology), Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx NY 10461, USA.
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Abstract
Many plant and animal toxins cause aversive behaviors in animals due to their pungent or unpleasant taste or because they cause other unpleasant senstations like pain. This article reviews the current state of knowledge of toxins that act at the TRPV1 ion channel, which is expressed in primary sensory neurons, is activated by multiple painful stimuli and is thought to be a key pain sensor and integrator. The recent finding that painful peptide "vanillotoxin" components of tarantula toxin activate the TRPV1 ion channel to cause pain led us to survey what is known about toxins that act at this receptor. Toxins from plants, spiders and jellyfish are considered. Where possible, structural information about sites of interaction is considered in relation to toxin-binding sites on the Kv ion channel, for which more structural information exists. We discuss a developing model where toxin agonists such as resiniferatoxin and vanillotoxins are proposed to interact with a region of TRPV1 that is homologous to the "voltage sensor" in the Kv1.2 ion channel, to open the channel and activate primary sensory nerves, causing pain.
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Chekmenev EY, Waddell KW, Hu J, Gan Z, Wittebort RJ, Cross TA. Ion-binding study by 17O solid-state NMR spectroscopy in the model peptide Gly-Gly-Gly at 19.6 T. J Am Chem Soc 2007; 128:9849-55. [PMID: 16866542 DOI: 10.1021/ja060191r] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Li(+) and Ca(2+) binding to the carbonyl oxygen sites of a model peptide system has been studied by (17)O solid-state NMR spectroscopy. (17)O chemical shift (CS) and quadrupole coupling (QC) tensors are determined in four Gly-(Gly-(17)O)-Gly polymorphs by a combination of stationary and fast magic-angle spinning (MAS) methods at high magnetic field, 19.6 T. In the crystal lattice, the carbonyl oxygen of the central glycyl residue in two gly-gly-gly polymorphs form intermolecular hydrogen bonds with amides, whereas the corresponding carbonyl oxygens of the other two polymorphs form interactions with Li(+) and Ca(2+) ions. This permits a comparison of perturbations on (17)O NMR properties by ion binding and intermolecular hydrogen bonding. High quality spectra are augmented by density functional theory (DFT) calculations on large molecular clusters to gain additional theoretical insights and to aid in the spectral simulations. Ion binding significantly decreases the two (17)O chemical shift tensor components in the peptide plane, delta(11) and delta(22), and, thus, a substantial change in the isotropic chemical shift. In addition, quadrupole coupling constants are decreased by up to 1 MHz. The effects of ion binding are found to be almost an order of magnitude greater than those induced by hydrogen bonding.
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Affiliation(s)
- Eduard Y Chekmenev
- NMR Program, National High Magnetic Field Laboratory (NHMFL), Tallahassee, Florida 32310, USA
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Boiteux C, Kraszewski S, Ramseyer C, Girardet C. Ion conductance vs. pore gating and selectivity in KcsA channel: Modeling achievements and perspectives. J Mol Model 2007; 13:699-713. [PMID: 17415597 DOI: 10.1007/s00894-007-0202-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2006] [Revised: 03/08/2007] [Accepted: 03/19/2007] [Indexed: 12/29/2022]
Abstract
KcsA potassium channel belongs to a wide family of allosteric proteins that switch between closed and open states conformations in response to a stimulus, and act as a regulator of cation activity in living cells. The gating mechanism and cation selectivity of such channels have been extensively studied in the literature, with a revival emphasis these latter years, due to the publication of the crystallized structure of KcsA. Despite the increasing number of research and review papers on these topics, quantitative interpretation of these processes at the atomic scale is far from achieved. On the basis of available experimental and theoretical data, and by including our recent results, we review the progresses in this field of activity and discuss the weaknesses that should be corrected. In this spirit, we partition the channel into the filter, cavity, extra and intracellular media, in order to analyze separately the specificity of each region. Special emphasis is brought to the study of an open state for the channel and to the different properties generated by the opening. The influence of water as a structural and dynamical component of the channel properties in closed and open states, as well as in the sequential motions of the cations, is analyzed using molecular dynamics simulations and ab initio calculations. The polarization and charge transfer effects on the ions' dynamics and kinetics are discussed in terms of partial charge models.
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Affiliation(s)
- Céline Boiteux
- Laboratoire de Physique Moléculaire UMR CNRS 6624, Université de Franche-Comté, La Bouloie, 25030, Besançon Cedex, France
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Yi H, Cao Z, Yin S, Dai C, Wu Y, Li W. Interaction Simulation of hERG K+ Channel with Its Specific BeKm-1 Peptide: Insights into the Selectivity of Molecular Recognition. J Proteome Res 2006; 6:611-20. [PMID: 17269718 DOI: 10.1021/pr060368g] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Potassium channels show a huge variability in the affinity when recognizing enormous bioactive peptides, and the elucidation of their recognition mechanism remains a great challenge due to an undetermined peptide-channel complex structure. Here, we employed combined computation methods to study the specific binding of BeKm-1 peptide to the hERG potassium channel, which is an essential determinant of the long-QT syndrome. By the use of a segment-assembly homology modeling method, the closed-state hERG structure containing unusual longer S5P linker was successfully constructed. It has a "petunia" shape, while four "petals" of symmetrically distributed S5P segments always decentralize. Starting from the hERG and BeKm-1 structures, a considerably reasonable BeKm-1-hERG complex structure was then screened out and identified by protein-protein docking, molecular dynamics (MD) simulations, and calculation of relative binding free energies. The validity of this predicted complex was further assessed by computational alanine-scanning, with the results correlating reasonably well with experimental data. In the novel complex structure, four considerably flexible S5P linkers are far from the BeKm-1 peptide. The BeKm-1 mainly uses its helical region to associate the channel outer vestibule, except for the S5P linker region; however, structural analysis further implies this neutral pore region with wiggling S5P linker is highly beneficial to the binding of BeKm-1 with lower positive charges. The most critical Lys18 of BeKm-1 plugs its side chain into the channel selectivity filter, while the secondarily important Arg20 forms three hydrogen bonds with spatially neighboring residues in the hERG channel. Different from the classical peptide-K+ channel interaction mainly induced by electrostatic interaction, a synergetic effect of the electrostatic and van der Waals interactions was found to mediate the molecular recognition between BeKm-1 and the hERG channel. And this specific binding process is revealed to be a dynamic change of reduction of binding free energy and conformational rearrangement mainly in the interface of both BeKm-1 and the hERG channel. All these structural and energy features yield deep insights on the high selective binding mechanism of hERG-specific peptides, present a diversity of peptide-K+ channel interactions, and also provide important clues to further study structure-function relationships of the hERG channel.
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Affiliation(s)
- Hong Yi
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, People's Republic of China
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Bingham JP, Bian S, Tan ZY, Takacs Z, Moczydlowski E. Synthesis of a biotin derivative of iberiotoxin: binding interactions with streptavidin and the BK Ca2+-activated K+ channel expressed in a human cell line. Bioconjug Chem 2006; 17:689-99. [PMID: 16704206 PMCID: PMC2505059 DOI: 10.1021/bc060002u] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Iberiotoxin (IbTx) is a scorpion venom peptide that inhibits BK Ca2+-activated K+ channels with high affinity and specificity. Automated solid-phase synthesis was used to prepare a biotin-labeled derivative (IbTx-LC-biotin) of IbTx by substitution of Asp19 of the native 37-residue peptide with N--(D-biotin-6-amidocaproate)-L-lysine. Both IbTx-LC-biotin and its complex with streptavidin (StrAv) block single BK channels from rat skeletal muscle with nanomolar affinity, indicating that the biotin-labeled residue, either alone or in complex with StrAv, does not obstruct the toxin binding interaction with the BK channel. IbTx-LC-biotin exhibits high affinity (KD = 26 nM) and a slow dissociation rate (koff = 5.4 x 10(-4) s(-1)) in a macroscopic blocking assay of whole-cell current of the cloned human BK channel. Titration of IbTx-LC-biotin with StrAv monitored by high performance size exclusion chromatography is consistent with a stoichiometry of two binding sites for IbTx-LC-biotin per StrAv tetramer, indicating that steric interference hinders simultaneous binding of two toxin molecules on each of the two biotin-binding faces of StrAv. In combination with fluorescent conjugates of StrAv or anti-biotin antibody, IbTx-LC-biotin was used to image the surface distribution of BK channels on a transfected cell line. Fluorescence microscopy revealed a patch-like surface distribution of BK channel protein. The results support the feasibility of using IbTx-LC-biotin and similar biotin-tagged K+ channel toxins for diverse applications in cellular neurobiology. .
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Affiliation(s)
| | - Shumin Bian
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven CT 06520
| | - Zhi-Yong Tan
- Department of Internal Medicine, University of Iowa, Iowa City IA 52242
| | - Zoltan Takacs
- The Department of Pediatrics; University of Chicago, Chicago, IL 60637
| | - Edward Moczydlowski
- Department of Biology, Clarkson University, Potsdam, NY 13699
- Corresponding Author: Edward Moczydlowski, Department of Biology, Box 5805, Clarkson University, Potsdam, NY 13699-5805; Tel.: 315-268-6641; Fax: 315-268-7118; e-mail:
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15
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Chill JH, Louis JM, Miller C, Bax A. NMR study of the tetrameric KcsA potassium channel in detergent micelles. Protein Sci 2006; 15:684-98. [PMID: 16522799 PMCID: PMC2242490 DOI: 10.1110/ps.051954706] [Citation(s) in RCA: 145] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Nuclear magnetic resonance (NMR) studies of large membrane-associated proteins are limited by the difficulties in preparation of stable protein-detergent mixed micelles and by line broadening, which is typical of these macroassemblies. We have used the 68-kDa homotetrameric KcsA, a thermostable N-terminal deletion mutant of a bacterial potassium channel from Streptomyces lividans, as a model system for applying NMR methods to membrane proteins. Optimization of measurement conditions enabled us to perform the backbone assignment of KcsA in SDS micelles and establish its secondary structure, which was found to closely agree with the KcsA crystal structure. The C-terminal cytoplasmic domain, absent in the original structure, contains a 14-residue helix that could participate in tetramerization by forming an intersubunit four-helix bundle. A quantitative estimate of cross- relaxation between detergent and KcsA backbone amide protons, together with relaxation and light scattering data, suggests SDS-KcsA mixed micelles form an oblate spheroid with approximately 180 SDS molecules per channel. K(+) ions bind to the micelle-solubilized channel with a K(D) of 3 +/- 0.5 mM, resulting in chemical shift changes in the selectivity filter. Related pH-induced changes in chemical shift along the "outer" transmembrane helix and the cytoplasmic membrane interface hint at a possible structural explanation for the observed pH-gating of the potassium channel.
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Affiliation(s)
- Jordan H Chill
- Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, Maryland 20892, USA
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16
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Leng Q, MacGregor GG, Dong K, Giebisch G, Hebert SC. Subunit-subunit interactions are critical for proton sensitivity of ROMK: evidence in support of an intermolecular gating mechanism. Proc Natl Acad Sci U S A 2006; 103:1982-7. [PMID: 16446432 PMCID: PMC1413660 DOI: 10.1073/pnas.0510610103] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The tetrameric K channel ROMK provides an important pathway for K secretion by the mammalian kidney, and the gating of this channel is highly sensitive to changes in cytosolic pH. Although charge-charge interactions have been implicated in pH sensing by this K channel tetramer, the molecular mechanism linking pH sensing and the gating of ion channels is poorly understood. The x-ray crystal structure KirBac1.1, a prokaryotic ortholog of ROMK, has suggested that channel gating involves intermolecular interactions of the N- and C-terminal domains of adjacent subunits. Here we studied channel gating behavior to changes in pH using giant patch clamping of Xenopus laevis oocytes expressing WT or mutant ROMK, and we present evidence that no single charged residue provides the pH sensor. Instead, we show that N-C- and C-C-terminal subunit-subunit interactions form salt bridges, which function to stabilize ROMK in the open state and which are modified by protons. We identify a highly conserved C-C-terminal arginine-glutamate (R-E) ion pair that forms an intermolecular salt bridge and responds to changes in proton concentration. Our results support the intermolecular model for pH gating of inward rectifier K channels.
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Affiliation(s)
- Qiang Leng
- *Department of Cellular and Molecular Physiology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520-8026; and
| | - Gordon G. MacGregor
- *Department of Cellular and Molecular Physiology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520-8026; and
- Department of Cell Biology and Physiology, University of Pittsburgh, Pittsburgh, PA 15261
| | - Ke Dong
- *Department of Cellular and Molecular Physiology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520-8026; and
| | - Gerhard Giebisch
- *Department of Cellular and Molecular Physiology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520-8026; and
| | - Steven C. Hebert
- *Department of Cellular and Molecular Physiology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520-8026; and
- To whom correspondence should be addressed. E-mail:
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17
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Encinar JA, Molina ML, Poveda JA, Barrera FN, Renart ML, Fernández AM, González-Ros JM. The influence of a membrane environment on the structure and stability of a prokaryotic potassium channel, KcsA. FEBS Lett 2005; 579:5199-204. [PMID: 16150445 DOI: 10.1016/j.febslet.2005.08.038] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2005] [Revised: 08/22/2005] [Accepted: 08/22/2005] [Indexed: 11/22/2022]
Abstract
The lack of a membrane environment in membrane protein crystals is considered one of the major limiting factors to fully imply X-ray structural data to explain functional properties of ion channels [Gulbis, J.M. and Doyle, D. (2004) Curr. Opin. Struct. Biol. 14, 440-446]. Here, we provide infrared spectroscopic evidence that the structure and stability of the potassium channel KcsA and its chymotryptic derivative 1-125 KcsA reconstituted into native-like membranes differ from those exhibited by these proteins in detergent solution, the latter taken as an approximation of the mixed detergent-protein crystal conditions.
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Affiliation(s)
- J A Encinar
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, 03202 Alicante, Spain
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18
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Lai HC, Grabe M, Jan YN, Jan LY. The S4 voltage sensor packs against the pore domain in the KAT1 voltage-gated potassium channel. Neuron 2005; 47:395-406. [PMID: 16055063 DOI: 10.1016/j.neuron.2005.06.019] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2004] [Revised: 03/09/2005] [Accepted: 06/09/2005] [Indexed: 10/25/2022]
Abstract
In voltage-gated ion channels, the S4 transmembrane segment responds to changes in membrane potential and controls channel opening. The local environment of S4 is still unknown, even regarding the basic question as to whether S4 is close to the pore domain. Relying on the ability of functional KAT1 channels to rescue potassium (K+) transport-deficient yeast, we have performed an unbiased mutagenesis screen aimed at determining whether S4 packs against S5 of the pore domain. Starting with semilethal mutations of surface-exposed S5 residues of the KAT1 pore domain, we have screened randomly mutagenized libraries of S4 or S1-S3 for second-site suppressors. Our study identifies two S4 residues that interact in a highly specific manner with two S5 residues in the middle of the membrane-spanning regions, supporting a model in which the S4 voltage sensor packs against the pore domain in the hyperpolarized, or "down," state of S4.
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Affiliation(s)
- Helen C Lai
- Graduate Group in Biophysics, University of California, San Francisco, San Francisco, California 94143, USA
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19
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Dong K, Tang LQ, MacGregor GG, Leng Q, Hebert SC. Novel nucleotide-binding sites in ATP-sensitive potassium channels formed at gating interfaces. EMBO J 2005; 24:1318-29. [PMID: 15775962 PMCID: PMC1142547 DOI: 10.1038/sj.emboj.7600626] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2004] [Accepted: 02/15/2005] [Indexed: 11/09/2022] Open
Abstract
The coupling of cell metabolism to membrane electrical activity is a vital process that regulates insulin secretion, cardiac and neuronal excitability and the responses of cells to ischemia. ATP-sensitive potassium channels (K(ATP); Kir6.x) are a major part of this metabolic-electrical coupling system and translate metabolic signals such as the ATP:ADP ratio to changes in the open or closed state (gate) of the channel. The localization of the nucleotide-binding site (NBS) on Kir6.x channels and how nucleotide binding gates these K(ATP) channels remain unclear. Here, we use fluorescent nucleotide binding to purified Kir6.x proteins to define the peptide segments forming the NBS on Kir6.x channels and show that unique N- and C-terminal interactions from adjacent subunits are required for high-affinity nucleotide binding. The short N- and C-terminal segments comprising the novel intermolecular NBS are next to helices that likely move with channel opening/closing, suggesting a lock-and-key model for ligand gating.
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Affiliation(s)
- Ke Dong
- Department of Cellular and Molecular Physiology, School of Medicine, Yale University, New Haven, CT, USA
| | - Lie-Qi Tang
- Department of Cellular and Molecular Physiology, School of Medicine, Yale University, New Haven, CT, USA
| | - Gordon G MacGregor
- Department of Cellular and Molecular Physiology, School of Medicine, Yale University, New Haven, CT, USA
| | - Qiang Leng
- Department of Cellular and Molecular Physiology, School of Medicine, Yale University, New Haven, CT, USA
| | - Steven C Hebert
- Department of Cellular and Molecular Physiology, School of Medicine, Yale University, New Haven, CT, USA
- Department of Cellular and Molecular Physiology, School of Medicine, Yale University, 333 Cedar Street, New Haven, CT 06520, USA. Tel.: +1 203 785 4041; Fax: +1 203 785 7678; E-mail:
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