1
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Qiao P, Odenkirk MT, Zheng W, Wang Y, Chen J, Xu W, Baker ES. Elucidating the role of lipid interactions in stabilizing the membrane protein KcsA. Biophys J 2024:S0006-3495(24)00478-8. [PMID: 39030907 DOI: 10.1016/j.bpj.2024.07.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 06/12/2024] [Accepted: 07/15/2024] [Indexed: 07/22/2024] Open
Abstract
The significant effects of lipid binding on the functionality of potassium channel KcsA have been validated by brilliant studies. However, the specific interactions between lipids and KcsA, such as binding parameters for each binding event, have not been fully elucidated. In this study, we employed native mass spectrometry to investigate the binding of lipids to KcsA and their effects on the channel. The tetrameric structure of KcsA remains intact even in the absence of lipid binding. However, the subunit architecture of the E71A mutant, which is constantly open at low pH, relies on tightly associated copurified lipids. Furthermore, we observed that lipids exhibit weak binding to KcsA at high pH when the channel is at a closed/inactivation state in the absence of permeant cation K+. This feeble interaction potentially facilitates the association of K+ ions, leading to the transition of the channel to a resting closed/open state. Interestingly, both anionic and zwitterionic lipids strongly bind to KcsA at low pH when the channel is in an open/inactivation state. We also investigated the binding patterns of KcsA with natural lipids derived from E. coli and Streptomyces lividans. Interestingly, lipids from E. coli exhibited much stronger binding affinity compared to the lipids from S. lividans. Among the natural lipids from S. lividans, free fatty acids and triacylglycerols demonstrated the tightest binding to KcsA, whereas no detectable binding events were observed with natural phosphatidic acid lipids. These findings suggest that the lipid association pattern in S. lividans, the natural host for KcsA, warrants further investigation. In conclusion, our study sheds light on the role of lipids in stabilizing KcsA and highlights the importance of specific lipid-protein interactions in modulating its conformational states.
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Affiliation(s)
- Pei Qiao
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China; Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas.
| | - Melanie T Odenkirk
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina
| | - Weiyi Zheng
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Yuchen Wang
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Jinhui Chen
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Wenhao Xu
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, China
| | - Erin S Baker
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
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2
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Renart ML, Giudici AM, González-Ros JM, Poveda JA. Steady-state and time-resolved fluorescent methodologies to characterize the conformational landscape of the selectivity filter of K + channels. Methods 2024; 225:89-99. [PMID: 38508347 DOI: 10.1016/j.ymeth.2024.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 02/02/2024] [Accepted: 02/23/2024] [Indexed: 03/22/2024] Open
Abstract
A variety of equilibrium and non-equilibrium methods have been used in a multidisciplinary approach to study the conformational landscape associated with the binding of different cations to the pore of potassium channels. These binding processes, and the conformational changes resulting therefrom, modulate the functional properties of such integral membrane properties, revealing these permeant and blocking cations as true effectors of such integral membrane proteins. KcsA, a prototypic K+ channel from Streptomyces lividans, has been extensively characterized in this regard. Here, we revise several fluorescence-based approaches to monitor cation binding under different experimental conditions in diluted samples, analyzing the advantages and disadvantages of each approach. These studies have contributed to explain the selectivity, conduction, and inactivation properties of K+ channels at the molecular level, together with the allosteric communication between the two gates that control the ion channel flux, and how they are modulated by lipids.
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Affiliation(s)
- María Lourdes Renart
- IDiBE-Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, 03202 Elche, Spain.
| | - Ana Marcela Giudici
- IDiBE-Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, 03202 Elche, Spain.
| | - José M González-Ros
- IDiBE-Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, 03202 Elche, Spain.
| | - José A Poveda
- IDiBE-Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, 03202 Elche, Spain.
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3
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Renart ML, Giudici AM, Coll-Díez C, González-Ros JM, Poveda JA. Anionic Phospholipids Shift the Conformational Equilibrium of the Selectivity Filter in the KcsA Channel to the Conductive Conformation: Predicted Consequences on Inactivation. Biomedicines 2023; 11:biomedicines11051376. [PMID: 37239046 DOI: 10.3390/biomedicines11051376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/19/2023] [Accepted: 05/03/2023] [Indexed: 05/28/2023] Open
Abstract
Here, we report an allosteric effect of an anionic phospholipid on a model K+ channel, KcsA. The anionic lipid in mixed detergent-lipid micelles specifically induces a change in the conformational equilibrium of the channel selectivity filter (SF) only when the channel inner gate is in the open state. Such change consists of increasing the affinity of the channel for K+, stabilizing a conductive-like form by maintaining a high ion occupancy in the SF. The process is highly specific in several aspects: First, lipid modifies the binding of K+, but not that of Na+, which remains unperturbed, ruling out a merely electrostatic phenomenon of cation attraction. Second, no lipid effects are observed when a zwitterionic lipid, instead of an anionic one, is present in the micelles. Lastly, the effects of the anionic lipid are only observed at pH 4.0, when the inner gate of KcsA is open. Moreover, the effect of the anionic lipid on K+ binding to the open channel closely emulates the K+ binding behaviour of the non-inactivating E71A and R64A mutant proteins. This suggests that the observed increase in K+ affinity caused by the bound anionic lipid should result in protecting the channel against inactivation.
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Affiliation(s)
- María Lourdes Renart
- IDiBE-Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, 03202 Elche, Spain
| | - Ana Marcela Giudici
- IDiBE-Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, 03202 Elche, Spain
| | - Carlos Coll-Díez
- IDiBE-Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, 03202 Elche, Spain
| | - José M González-Ros
- IDiBE-Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, 03202 Elche, Spain
| | - José A Poveda
- IDiBE-Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, 03202 Elche, Spain
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4
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Abrahamyan A, Eldstrom J, Sahakyan H, Karagulyan N, Mkrtchyan L, Karapetyan T, Sargsyan E, Kneussel M, Nazaryan K, Schwarz JR, Fedida D, Vardanyan V. Mechanism of external K+ sensitivity of KCNQ1 channels. J Gen Physiol 2023; 155:213880. [PMID: 36809486 PMCID: PMC9960071 DOI: 10.1085/jgp.202213205] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 12/20/2022] [Accepted: 01/31/2023] [Indexed: 02/23/2023] Open
Abstract
KCNQ1 voltage-gated K+ channels are involved in a wide variety of fundamental physiological processes and exhibit the unique feature of being markedly inhibited by external K+. Despite the potential role of this regulatory mechanism in distinct physiological and pathological processes, its exact underpinnings are not well understood. In this study, using extensive mutagenesis, molecular dynamics simulations, and single-channel recordings, we delineate the molecular mechanism of KCNQ1 modulation by external K+. First, we demonstrate the involvement of the selectivity filter in the external K+ sensitivity of the channel. Then, we show that external K+ binds to the vacant outermost ion coordination site of the selectivity filter inducing a diminution in the unitary conductance of the channel. The larger reduction in the unitary conductance compared to whole-cell currents suggests an additional modulatory effect of external K+ on the channel. Further, we show that the external K+ sensitivity of the heteromeric KCNQ1/KCNE complexes depends on the type of associated KCNE subunits.
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Affiliation(s)
- Astghik Abrahamyan
- Molecular Neuroscience Group, Institute of Molecular Biology, National Academy of Sciences of the Republic of Armenia , Yerevan, Armenia
| | - Jodene Eldstrom
- Department of Anesthesiology, Pharmacology and Therapeutics, University of British Columbia , Vancouver, BC, Canada
| | - Harutyun Sahakyan
- Laboratory of Computational Modeling of Biological Processes, Institute of Molecular Biology of National Academy of Sciences of the Republic of Armenia , Yerevan, Armenia
| | - Nare Karagulyan
- Molecular Neuroscience Group, Institute of Molecular Biology, National Academy of Sciences of the Republic of Armenia , Yerevan, Armenia
| | - Liana Mkrtchyan
- Molecular Neuroscience Group, Institute of Molecular Biology, National Academy of Sciences of the Republic of Armenia , Yerevan, Armenia
| | - Tatev Karapetyan
- Molecular Neuroscience Group, Institute of Molecular Biology, National Academy of Sciences of the Republic of Armenia , Yerevan, Armenia
| | - Ernest Sargsyan
- Molecular Neuroscience Group, Institute of Molecular Biology, National Academy of Sciences of the Republic of Armenia , Yerevan, Armenia
| | - Matthias Kneussel
- Institute for Molecular Neurogenetics, Center for Molecular Neurobiology Hamburg , Hamburg, Germany
| | - Karen Nazaryan
- Laboratory of Computational Modeling of Biological Processes, Institute of Molecular Biology of National Academy of Sciences of the Republic of Armenia , Yerevan, Armenia
| | - Jürgen R Schwarz
- Institute for Molecular Neurogenetics, Center for Molecular Neurobiology Hamburg , Hamburg, Germany
| | - David Fedida
- Department of Anesthesiology, Pharmacology and Therapeutics, University of British Columbia , Vancouver, BC, Canada
| | - Vitya Vardanyan
- Molecular Neuroscience Group, Institute of Molecular Biology, National Academy of Sciences of the Republic of Armenia , Yerevan, Armenia
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5
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Kurauskas V, Tonelli M, Henzler-Wildman K. Full opening of helix bundle crossing does not lead to NaK channel activation. J Gen Physiol 2022; 154:213659. [PMID: 36326620 PMCID: PMC9640265 DOI: 10.1085/jgp.202213196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 08/11/2022] [Accepted: 10/10/2022] [Indexed: 11/05/2022] Open
Abstract
A critical part of ion channel function is the ability to open and close in response to stimuli and thus conduct ions in a regulated fashion. While x-ray diffraction studies of ion channels suggested a general steric gating mechanism located at the helix bundle crossing (HBC), recent functional studies on several channels indicate that the helix bundle crossing is wide-open even in functionally nonconductive channels. Two NaK channel variants were crystallized in very different open and closed conformations, which served as important models of the HBC gating hypothesis. However, neither of these NaK variants is conductive in liposomes unless phenylalanine 92 is mutated to alanine (F92A). Here, we use NMR to probe distances at near-atomic resolution of the two NaK variants in lipid bicelles. We demonstrate that in contrast to the crystal structures, both NaK variants are in a fully open conformation, akin to Ca2+-bound MthK channel structure where the HBC is widely open. While we were not able to determine what a conductive NaK structure is like, our further inquiry into the gating mechanism suggests that the selectivity filter and pore helix are coupled to the M2 helix below and undergo changes in the structure when F92 is mutated. Overall, our data show that NaK exhibits coupling between the selectivity filter and HBC, similar to K+ channels, and has a more complex gating mechanism than previously thought, where the full opening of HBC does not lead to channel activation.
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Affiliation(s)
- Vilius Kurauskas
- Department of Biochemistry, University of Wisconsin—Madison, Madison, WI
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison, University of Wisconsin—Madison, Madison, WI
| | - Katherine Henzler-Wildman
- Department of Biochemistry, University of Wisconsin—Madison, Madison, WI
- National Magnetic Resonance Facility at Madison, University of Wisconsin—Madison, Madison, WI
- Correspondence to Katherine Henzler-Wildman:
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6
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Do HQ, Jansen M. Cell-Free Expression of Proton-Coupled Folate Transporter in the Presence of Nanodiscs. Methods Mol Biol 2022; 2507:425-444. [PMID: 35773596 DOI: 10.1007/978-1-0716-2368-8_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Proton coupled folate transporter (PCFT) is an integral membrane protein with 12 transmembrane segments localized to the plasma membrane. PCFT is the main route by which folate, vitamin B9, from dietary sources enters mammalian cells in the small intestine. Loss-of-function mutations in this membrane transport protein cause hereditary folate malabsorption, and upregulation of PCFT has been reported in cancer cells. Currently, a complete translocation mechanism of folate via PCFT is still missing. To reveal this mechanism via studies of structural architecture and structure-function relationships, soluble and stable PCFT in a phospholipid bilayer environment is needed. We therefore develop an approach to screen lipid environments in which PCFT is most soluble. Traditional in vitro expression and reconstitution into lipid bilayers of integral membrane proteins requires separate steps, which are costly and time-consuming. In this chapter, we describe a protocol for in vitro translation of PCFT into preformed lipid nanodiscs using a cell-free expression system, which helps to accelerate and reduce the cost of the sample preparation.
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Affiliation(s)
- Hoa Quynh Do
- Department of Cell Physiology and Molecular Biophysics and Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Michaela Jansen
- Department of Cell Physiology and Molecular Biophysics and Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA.
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7
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Reddi R, Matulef K, Riederer E, Moenne-Loccoz P, Valiyaveetil FI. Structures of Gating Intermediates in a K + channel. J Mol Biol 2021; 433:167296. [PMID: 34627789 DOI: 10.1016/j.jmb.2021.167296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 09/16/2021] [Accepted: 09/16/2021] [Indexed: 11/30/2022]
Abstract
Regulation of ion conduction through the pore of a K+ channel takes place through the coordinated action of the activation gate at the bundle crossing of the inner helices and the inactivation gate located at the selectivity filter. The mechanism of allosteric coupling of these gates is of key interest. Here we report new insights into this allosteric coupling mechanism from studies on a W67F mutant of the KcsA channel. W67 is in the pore helix and is highly conserved in K+ channels. The KcsA W67F channel shows severely reduced inactivation and an enhanced rate of activation. We use continuous wave EPR spectroscopy to establish that the KcsA W67F channel shows an altered pH dependence of activation. Structural studies on the W67F channel provide the structures of two intermediate states: a pre- open state and a pre-inactivated state of the KcsA channel. These structures highlight key nodes in the allosteric pathway. The structure of the KcsA W67F channel with the activation gate open shows altered ion occupancy at the second ion binding site (S2) in the selectivity filter. This finding in combination with previous studies strongly support a requirement for ion occupancy at the S2 site for the channel to inactivate.
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Affiliation(s)
- Ravikumar Reddi
- Program in Chemical Biology, Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd, Portland, OR 97239, United States. https://twitter.com/Ravi_K_Reddi
| | - Kimberly Matulef
- Program in Chemical Biology, Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd, Portland, OR 97239, United States
| | - Erika Riederer
- Program in Chemical Biology, Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd, Portland, OR 97239, United States
| | - Pierre Moenne-Loccoz
- Program in Chemical Biology, Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd, Portland, OR 97239, United States
| | - Francis I Valiyaveetil
- Program in Chemical Biology, Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd, Portland, OR 97239, United States.
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8
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Do HQ, Bassil CM, Andersen EI, Jansen M. Impact of nanodisc lipid composition on cell-free expression of proton-coupled folate transporter. PLoS One 2021; 16:e0253184. [PMID: 34793461 PMCID: PMC8601550 DOI: 10.1371/journal.pone.0253184] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 10/31/2021] [Indexed: 01/19/2023] Open
Abstract
The Proton-Coupled Folate Transporter (PCFT) is a transmembrane transport protein that controls the absorption of dietary folates in the small intestine. PCFT also mediates uptake of chemotherapeutically used antifolates into tumor cells. PCFT has been identified within lipid rafts observed in phospholipid bilayers of plasma membranes, a micro environment that is altered in tumor cells. The present study aimed at investigating the impact of different lipids within Lipid-protein nanodiscs (LPNs), discoidal lipid structures stabilized by membrane scaffold proteins, to yield soluble PCFT expression in an E. coli lysate-based cell-free transcription/translation system. In the absence of detergents or lipids, we observed PCFT quantitatively as precipitate in this system. We then explored the ability of LPNs to support solubilized PCFT expression when present during in-vitro translation. LPNs consisted of either dimyristoyl phosphatidylcholine (DMPC), palmitoyl-oleoyl phosphatidylcholine (POPC), or dimyristoyl phosphatidylglycerol (DMPG). While POPC did not lead to soluble PCFT expression, both DMPG and DMPC supported PCFT translation directly into LPNs, the latter in a concentration dependent manner. The results obtained through this study provide insights into the lipid preferences of PCFT. Membrane-embedded or solubilized PCFT will enable further studies with diverse biophysical approaches to enhance the understanding of the structure and molecular mechanism of folate transport through PCFT.
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Affiliation(s)
- Hoa Quynh Do
- Department of Cell Physiology and Molecular Biophysics and Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Carla M. Bassil
- Department of Cell Physiology and Molecular Biophysics and Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
- The Clark Scholar Program, Texas Tech University, Lubbock, TX, United States of America
| | - Elizabeth I. Andersen
- Department of Cell Physiology and Molecular Biophysics and Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Michaela Jansen
- Department of Cell Physiology and Molecular Biophysics and Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
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9
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Díaz-García C, Renart ML, Poveda JA, Giudici AM, González-Ros JM, Prieto M, Coutinho A. Probing the Structural Dynamics of the Activation Gate of KcsA Using Homo-FRET Measurements. Int J Mol Sci 2021; 22:ijms222111954. [PMID: 34769384 PMCID: PMC8584343 DOI: 10.3390/ijms222111954] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/18/2021] [Accepted: 10/29/2021] [Indexed: 12/16/2022] Open
Abstract
The allosteric coupling between activation and inactivation processes is a common feature observed in K+ channels. Particularly, in the prokaryotic KcsA channel the K+ conduction process is controlled by the inner gate, which is activated by acidic pH, and by the selectivity filter (SF) or outer gate, which can adopt non-conductive or conductive states. In a previous study, a single tryptophan mutant channel (W67 KcsA) enabled us to investigate the SF dynamics using time-resolved homo-Förster Resonance Energy Transfer (homo-FRET) measurements. Here, the conformational changes of both gates were simultaneously monitored after labelling the G116C position with tetramethylrhodamine (TMR) within a W67 KcsA background. At a high degree of protein labeling, fluorescence anisotropy measurements showed that the pH-induced KcsA gating elicited a variation in the homo-FRET efficiency among the conjugated TMR dyes (TMR homo-FRET), while the conformation of the SF was simultaneously tracked (W67 homo-FRET). The dependence of the activation pKa of the inner gate with the ion occupancy of the SF unequivocally confirmed the allosteric communication between the two gates of KcsA. This simple TMR homo-FRET based ratiometric assay can be easily extended to study the conformational dynamics associated with the gating of other ion channels and their modulation.
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Affiliation(s)
- Clara Díaz-García
- iBB, Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal; (C.D.-G.); (M.P.)
- Associate Laboratory i4HB, Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal
| | - Maria Lourdes Renart
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, 03202 Elche, Spain; (J.A.P.); (A.M.G.); (J.M.G.-R.)
- Correspondence: (M.L.R.); (A.C.)
| | - José Antonio Poveda
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, 03202 Elche, Spain; (J.A.P.); (A.M.G.); (J.M.G.-R.)
| | - Ana Marcela Giudici
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, 03202 Elche, Spain; (J.A.P.); (A.M.G.); (J.M.G.-R.)
| | - José M. González-Ros
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, 03202 Elche, Spain; (J.A.P.); (A.M.G.); (J.M.G.-R.)
| | - Manuel Prieto
- iBB, Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal; (C.D.-G.); (M.P.)
- Associate Laboratory i4HB, Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal
| | - Ana Coutinho
- iBB, Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal; (C.D.-G.); (M.P.)
- Associate Laboratory i4HB, Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal
- Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
- Correspondence: (M.L.R.); (A.C.)
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10
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Puiggalí-Jou A, Molina BG, Lopes-Rodrigues M, Michaux C, Perpète EA, Zanuy D, Alemán C. Self-standing, conducting and capacitive biomimetic hybrid nanomembranes for selective molecular ion separation. Phys Chem Chem Phys 2021; 23:16157-16164. [PMID: 34297025 DOI: 10.1039/d1cp01840j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hybrid free-standing biomimetic materials are developed by integrating the VDAC36 β-barrel protein into robust and flexible three-layered polymer nanomembranes. The first and third layers are prepared by spin-coating a mixture of poly(lactic acid) (PLA) and poly(vinyl alcohol) (PVA). PVA nanofeatures are transformed into controlled nanoperforations by solvent-etching. The two nanoperforated PLA layers are separated by an electroactive layer, which is successfully electropolymerized by introducing a conducting sacrificial substrate under the first PLA nanosheet. Finally, the nanomaterial is consolidated by immobilizing the VDAC36 protein, active as an ion channel, into the nanoperforations of the upper layer. The integration of the protein causes a significant reduction of the material resistance, which decreases from 21.9 to 3.9 kΩ cm2. Electrochemical impedance spectroscopy studies using inorganic ions and molecular metabolites (i.e.l-lysine and ATP) not only reveal that the hybrid films behave as electrochemical supercapacitors but also indicate the most appropriate conditions to obtain selective responses against molecular ions as a function of their charge. The combination of polymers and proteins is promising for the development of new devices for engineering, biotechnological and biomedical applications.
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Affiliation(s)
- Anna Puiggalí-Jou
- Departament d'Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, C/Eduard Maristany 10-14, Edif. I2, 08019, Barcelona, Spain.
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11
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Abstract
K+ channels enable potassium to flow across the membrane with great selectivity. There are four K+ channel families: voltage-gated K (Kv), calcium-activated (KCa), inwardly rectifying K (Kir), and two-pore domain potassium (K2P) channels. All four K+ channels are formed by subunits assembling into a classic tetrameric (4x1P = 4P for the Kv, KCa, and Kir channels) or tetramer-like (2x2P = 4P for the K2P channels) architecture. These subunits can either be the same (homomers) or different (heteromers), conferring great diversity to these channels. They share a highly conserved selectivity filter within the pore but show different gating mechanisms adapted for their function. K+ channels play essential roles in controlling neuronal excitability by shaping action potentials, influencing the resting membrane potential, and responding to diverse physicochemical stimuli, such as a voltage change (Kv), intracellular calcium oscillations (KCa), cellular mediators (Kir), or temperature (K2P).
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12
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Jing Z, Rackers JA, Pratt LR, Liu C, Rempe SB, Ren P. Thermodynamics of ion binding and occupancy in potassium channels. Chem Sci 2021; 12:8920-8930. [PMID: 34257893 PMCID: PMC8246295 DOI: 10.1039/d1sc01887f] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 06/01/2021] [Indexed: 12/15/2022] Open
Abstract
Potassium channels modulate various cellular functions through efficient and selective conduction of K+ ions. The mechanism of ion conduction in potassium channels has recently emerged as a topic of debate. Crystal structures of potassium channels show four K+ ions bound to adjacent binding sites in the selectivity filter, while chemical intuition and molecular modeling suggest that the direct ion contacts are unstable. Molecular dynamics (MD) simulations have been instrumental in the study of conduction and gating mechanisms of ion channels. Based on MD simulations, two hypotheses have been proposed, in which the four-ion configuration is an artifact due to either averaged structures or low temperature in crystallographic experiments. The two hypotheses have been supported or challenged by different experiments. Here, MD simulations with polarizable force fields validated by ab initio calculations were used to investigate the ion binding thermodynamics. Contrary to previous beliefs, the four-ion configuration was predicted to be thermodynamically stable after accounting for the complex electrostatic interactions and dielectric screening. Polarization plays a critical role in the thermodynamic stabilities. As a result, the ion conduction likely operates through a simple single-vacancy and water-free mechanism. The simulations explained crystal structures, ion binding experiments and recent controversial mutagenesis experiments. This work provides a clear view of the mechanism underlying the efficient ion conduction and demonstrates the importance of polarization in ion channel simulations. Polarization shapes the energy landscape of ion conduction in potassium channels.![]()
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Affiliation(s)
- Zhifeng Jing
- Department of Biomedical Engineering, The University of Texas at Austin Austin Texas 78712 USA
| | - Joshua A Rackers
- Center for Integrated Nanotechnologies, Sandia National Laboratories Albuquerque New Mexico 87185 USA
| | - Lawrence R Pratt
- Department of Chemical and Biomolecular Engineering, Tulane University New Orleans Louisiana 70118 USA
| | - Chengwen Liu
- Department of Biomedical Engineering, The University of Texas at Austin Austin Texas 78712 USA
| | - Susan B Rempe
- Center for Integrated Nanotechnologies, Sandia National Laboratories Albuquerque New Mexico 87185 USA
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin Austin Texas 78712 USA
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13
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Mironenko A, Zachariae U, de Groot BL, Kopec W. The Persistent Question of Potassium Channel Permeation Mechanisms. J Mol Biol 2021; 433:167002. [PMID: 33891905 DOI: 10.1016/j.jmb.2021.167002] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 04/14/2021] [Accepted: 04/15/2021] [Indexed: 02/09/2023]
Abstract
Potassium channels play critical roles in many physiological processes, providing a selective permeation route for K+ ions in and out of a cell, by employing a carefully designed selectivity filter, evolutionarily conserved from viruses to mammals. The structure of the selectivity filter was determined at atomic resolution by x-ray crystallography, showing a tight coordination of desolvated K+ ions by the channel. However, the molecular mechanism of K+ ions permeation through potassium channels remains unclear, with structural, functional and computational studies often providing conflicting data and interpretations. In this review, we will present the proposed mechanisms, discuss their origins, and will critically assess them against all available data. General properties shared by all potassium channels are introduced first, followed by the introduction of two main mechanisms of ion permeation: soft and direct knock-on. Then, we will discuss critical computational and experimental studies that shaped the field. We will especially focus on molecular dynamics (MD) simulations, that provided mechanistic and energetic aspects of K+ permeation, but at the same time created long-standing controversies. Further challenges and possible solutions are presented as well.
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Affiliation(s)
- Andrei Mironenko
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Ulrich Zachariae
- Computational Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Bert L de Groot
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Wojciech Kopec
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.
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14
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Cosseddu SM, Choe EJ, Khovanov IA. Unraveling of a Strongly Correlated Dynamical Network of Residues Controlling the Permeation of Potassium in KcsA Ion Channel. ENTROPY (BASEL, SWITZERLAND) 2021; 23:E72. [PMID: 33418985 PMCID: PMC7825352 DOI: 10.3390/e23010072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/23/2020] [Accepted: 01/02/2021] [Indexed: 12/26/2022]
Abstract
The complicated patterns of the single-channel currents in potassium ion channel KcsA are governed by the structural variability of the selectivity filter. A comparative analysis of the dynamics of the wild type KcsA channel and several of its mutants showing different conducting patterns was performed. A strongly correlated dynamical network of interacting residues is found to play a key role in regulating the state of the wild type channel. The network is centered on the aspartate D80 which plays the role of a hub by strong interacting via hydrogen bonds with residues E71, R64, R89, and W67. Residue D80 also affects the selectivity filter via its backbones. This network further compromises ions and water molecules located inside the channel that results in the mutual influence: the permeation depends on the configuration of residues in the network, and the dynamics of network's residues depends on locations of ions and water molecules inside the selectivity filter. Some features of the network provide a further understanding of experimental results describing the KcsA activity. In particular, the necessity of anionic lipids to be present for functioning the channel is explained by the interaction between the lipids and the arginine residues R64 and R89 that prevents destabilizing the structure of the selectivity filter.
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Affiliation(s)
| | | | - Igor A. Khovanov
- School of Engineering, University of Warwick, Coventry CV4 7AL, UK; (S.M.C.); (E.J.C.)
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15
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Lolicato M, Natale AM, Abderemane-Ali F, Crottès D, Capponi S, Duman R, Wagner A, Rosenberg JM, Grabe M, Minor DL. K 2P channel C-type gating involves asymmetric selectivity filter order-disorder transitions. SCIENCE ADVANCES 2020; 6:6/44/eabc9174. [PMID: 33127683 PMCID: PMC7608817 DOI: 10.1126/sciadv.abc9174] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 09/10/2020] [Indexed: 05/05/2023]
Abstract
K2P potassium channels regulate cellular excitability using their selectivity filter (C-type) gate. C-type gating mechanisms, best characterized in homotetrameric potassium channels, remain controversial and are attributed to selectivity filter pinching, dilation, or subtle structural changes. The extent to which such mechanisms control C-type gating of innately heterodimeric K2Ps is unknown. Here, combining K2P2.1 (TREK-1) x-ray crystallography in different potassium concentrations, potassium anomalous scattering, molecular dynamics, and electrophysiology, we uncover unprecedented, asymmetric, potassium-dependent conformational changes that underlie K2P C-type gating. These asymmetric order-disorder transitions, enabled by the K2P heterodimeric architecture, encompass pinching and dilation, disrupt the S1 and S2 ion binding sites, require the uniquely long K2P SF2-M4 loop and conserved "M3 glutamate network," and are suppressed by the K2P C-type gate activator ML335. These findings demonstrate that two distinct C-type gating mechanisms can operate in one channel and underscore the SF2-M4 loop as a target for K2P channel modulator development.
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Affiliation(s)
- Marco Lolicato
- Cardiovascular Research Institute, University of California, San Francisco, CA 93858-2330, USA
| | - Andrew M Natale
- Cardiovascular Research Institute, University of California, San Francisco, CA 93858-2330, USA
| | - Fayal Abderemane-Ali
- Cardiovascular Research Institute, University of California, San Francisco, CA 93858-2330, USA
| | - David Crottès
- Department of Physiology, University of California, San Francisco, CA 93858-2330, USA
| | - Sara Capponi
- Cardiovascular Research Institute, University of California, San Francisco, CA 93858-2330, USA
| | - Ramona Duman
- Science Division, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
| | - Armin Wagner
- Science Division, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
| | - John M Rosenberg
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Michael Grabe
- Cardiovascular Research Institute, University of California, San Francisco, CA 93858-2330, USA.
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 93858-2330, USA
| | - Daniel L Minor
- Cardiovascular Research Institute, University of California, San Francisco, CA 93858-2330, USA.
- Departments of Biochemistry and Biophysics, and Cellular and Molecular Pharmacology, University of California, San Francisco, CA 93858-2330, USA
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, CA 93858-2330, USA
- Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, CA, 93858-2330, USA
- Molecular Biophysics and Integrated Bio-imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720 USA
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16
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Modulation of Function, Structure and Clustering of K + Channels by Lipids: Lessons Learnt from KcsA. Int J Mol Sci 2020; 21:ijms21072554. [PMID: 32272616 PMCID: PMC7177331 DOI: 10.3390/ijms21072554] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 04/02/2020] [Accepted: 04/05/2020] [Indexed: 12/19/2022] Open
Abstract
KcsA, a prokaryote tetrameric potassium channel, was the first ion channel ever to be structurally solved at high resolution. This, along with the ease of its expression and purification, made KcsA an experimental system of choice to study structure–function relationships in ion channels. In fact, much of our current understanding on how the different channel families operate arises from earlier KcsA information. Being an integral membrane protein, KcsA is also an excellent model to study how lipid–protein and protein–protein interactions within membranes, modulate its activity and structure. In regard to the later, a variety of equilibrium and non-equilibrium methods have been used in a truly multidisciplinary effort to study the effects of lipids on the KcsA channel. Remarkably, both experimental and “in silico” data point to the relevance of specific lipid binding to two key arginine residues. These residues are at non-annular lipid binding sites on the protein and act as a common element to trigger many of the lipid effects on this channel. Thus, processes as different as the inactivation of channel currents or the assembly of clusters from individual KcsA channels, depend upon such lipid binding.
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17
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Sun Z, Xu Y, Zhang D, McDermott AE. Probing allosteric coupling in a constitutively open mutant of the ion channel KcsA using solid-state NMR. Proc Natl Acad Sci U S A 2020; 117:7171-7175. [PMID: 32188782 PMCID: PMC7132268 DOI: 10.1073/pnas.1908828117] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Transmembrane allosteric coupling is a feature of many critical biological signaling events. Here we test whether transmembrane allosteric coupling controls the potassium binding affinity of the prototypical potassium channel KcsA in the context of C-type inactivation. Activation of KcsA is initiated by proton binding to the pH gate upon an intracellular drop in pH. Numerous studies have suggested that this proton binding also prompts a conformational switch, leading to a loss of affinity for potassium ions at the selectivity filter and therefore to channel inactivation. We tested this mechanism for inactivation using a KcsA mutant (H25R/E118A) that exhibits an open pH gate across a broad range of pH values. We present solid-state NMR measurements of this open mutant at neutral pH to probe the affinity for potassium at the selectivity filter. The potassium binding affinity in the selectivity filter of this mutant, 81 mM, is about four orders of magnitude weaker than that of wild-type KcsA at neutral pH and is comparable to the value for wild-type KcsA at low pH (pH ≈ 3.5). This result strongly supports our assertion that the open pH gate allosterically affects the potassium binding affinity of the selectivity filter. In this mutant, the protonation state of a glutamate residue (E120) in the pH sensor is sensitive to potassium binding, suggesting that this mutant also has flexibility in the activation gate and is subject to transmembrane allostery.
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Affiliation(s)
- Zhiyu Sun
- Department of Chemistry, Columbia University, New York, NY 10027
| | - Yunyao Xu
- Department of Chemistry, Columbia University, New York, NY 10027
| | - Dongyu Zhang
- Department of Chemistry, Columbia University, New York, NY 10027
| | - Ann E McDermott
- Department of Chemistry, Columbia University, New York, NY 10027
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18
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Bernsteiner H, Zangerl-Plessl EM, Chen X, Stary-Weinzinger A. Conduction through a narrow inward-rectifier K + channel pore. J Gen Physiol 2019; 151:1231-1246. [PMID: 31511304 PMCID: PMC6785732 DOI: 10.1085/jgp.201912359] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 07/25/2019] [Accepted: 08/13/2019] [Indexed: 12/17/2022] Open
Abstract
G-protein–gated inwardly rectifying potassium channels are important mediators of inhibitory neurotransmission. Based on microsecond-scale molecular dynamics simulations, Bernsteiner et al. propose novel gating details that may enable K+ flux via a direct knock-on mechanism. Inwardly rectifying potassium (Kir) channels play a key role in controlling membrane potentials in excitable and unexcitable cells, thereby regulating a plethora of physiological processes. G-protein–gated Kir channels control heart rate and neuronal excitability via small hyperpolarizing outward K+ currents near the resting membrane potential. Despite recent breakthroughs in x-ray crystallography and cryo-EM, the gating and conduction mechanisms of these channels are poorly understood. MD simulations have provided unprecedented details concerning the gating and conduction mechanisms of voltage-gated K+ and Na+ channels. Here, we use multi-microsecond–timescale MD simulations based on the crystal structures of GIRK2 (Kir3.2) bound to phosphatidylinositol-4,5-bisphosphate to provide detailed insights into the channel’s gating dynamics, including insights into the behavior of the G-loop gate. The simulations also elucidate the elementary steps that underlie the movement of K+ ions through an inward-rectifier K+ channel under an applied electric field. Our simulations suggest that K+ permeation might occur via direct knock-on, similar to the mechanism recently shown for Kv channels.
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Affiliation(s)
- Harald Bernsteiner
- Department of Pharmacology and Toxicology, University of Vienna, Vienna, Austria
| | | | - Xingyu Chen
- Department of Pharmacology and Toxicology, University of Vienna, Vienna, Austria
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19
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Xu Y, McDermott AE. Inactivation in the potassium channel KcsA. JOURNAL OF STRUCTURAL BIOLOGY-X 2019; 3:100009. [PMID: 32647814 PMCID: PMC7337057 DOI: 10.1016/j.yjsbx.2019.100009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 05/17/2019] [Accepted: 06/04/2019] [Indexed: 12/17/2022]
Abstract
C-type inactivation in potassium channels is a nearly universal regulatory mechanism. A major hypothesis states that C-type inactivation involves ion loss at the selectivity filter as an allosteric response to activation. NMR is used to probe protein conformational changes in response to pH and [K+], demonstrating that H+ and K+ binding are allosterically coupled in KcsA. The lipids are integrated parts of potassium channels in terms of structure, energetics and function.
Inactivation, the slow cessation of transmission after activation, is a general feature of potassium channels. It is essential for their function, and malfunctions in inactivation leads to numerous pathologies. The detailed mechanism for the C-type inactivation, distinct from the N-type inactivation, remains an active area of investigation. Crystallography, computational simulations, and NMR have greatly enriched our understanding of the process. Here we review the major hypotheses regarding C-type inactivation, particularly focusing on the key role played by NMR studies of the prokaryotic potassium channel KcsA, which serves as a good model for voltage gated mammalian channels.
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Affiliation(s)
- Yunyao Xu
- Department of Chemistry, Columbia University, New York, NY 10027, United States
| | - Ann E McDermott
- Department of Chemistry, Columbia University, New York, NY 10027, United States
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20
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Conformational plasticity in the KcsA potassium channel pore helix revealed by homo-FRET studies. Sci Rep 2019; 9:6215. [PMID: 30996281 PMCID: PMC6470172 DOI: 10.1038/s41598-019-42405-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 03/29/2019] [Indexed: 11/24/2022] Open
Abstract
Potassium channels selectivity filter (SF) conformation is modulated by several factors, including ion-protein and protein-protein interactions. Here, we investigate the SF dynamics of a single Trp mutant of the potassium channel KcsA (W67) using polarized time-resolved fluorescence measurements. For the first time, an analytical framework is reported to analyze the homo-Förster resonance energy transfer (homo-FRET) within a symmetric tetrameric protein with a square geometry. We found that in the closed state (pH 7), the W67-W67 intersubunit distances become shorter as the average ion occupancy of the SF increases according to cation type and concentration. The hypothesis that the inactivated SF at pH 4 is structurally similar to its collapsed state, detected at low K+, pH 7, was ruled out, emphasizing the critical role played by the S2 binding site in the inactivation process of KcsA. This homo-FRET approach provides complementary information to X-ray crystallography in which the protein conformational dynamics is usually compromised.
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21
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Righetto RD, Biyani N, Kowal J, Chami M, Stahlberg H. Retrieving high-resolution information from disordered 2D crystals by single-particle cryo-EM. Nat Commun 2019; 10:1722. [PMID: 30979902 PMCID: PMC6461647 DOI: 10.1038/s41467-019-09661-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 03/22/2019] [Indexed: 12/14/2022] Open
Abstract
Electron crystallography can reveal the structure of membrane proteins within 2D crystals under close-to-native conditions. High-resolution structural information can only be reached if crystals are perfectly flat and highly ordered. In practice, such crystals are difficult to obtain. Available image unbending algorithms correct for disorder, but only perform well on images of non-tilted, flat crystals, while out-of-plane distortions are not addressed. Here, we present an approach that employs single-particle refinement procedures to locally unbend crystals in 3D. With this method, density maps of the MloK1 potassium channel with a resolution of 4 Å were obtained from images of 2D crystals that do not diffract beyond 10 Å. Furthermore, 3D classification allowed multiple structures to be resolved, revealing a series of MloK1 conformations within a single 2D crystal. This conformational heterogeneity explains the poor diffraction observed and is related to channel function. The approach is implemented in the FOCUS package.
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Affiliation(s)
- Ricardo D Righetto
- Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, Mattenstrasse 26, CH-4058, Basel, Switzerland
| | - Nikhil Biyani
- Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, Mattenstrasse 26, CH-4058, Basel, Switzerland
| | - Julia Kowal
- Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, Mattenstrasse 26, CH-4058, Basel, Switzerland
- Institute for Molecular Biology and Biophysics, ETH Zürich, Otto-Stern-Weg 5, CH-8093, Zürich, Switzerland
| | - Mohamed Chami
- Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, Mattenstrasse 26, CH-4058, Basel, Switzerland
| | - Henning Stahlberg
- Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, Mattenstrasse 26, CH-4058, Basel, Switzerland.
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22
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Giudici AM, Renart ML, Díaz-García C, Morales A, Poveda JA, González-Ros JM. Accessibility of Cations to the Selectivity Filter of KcsA in the Inactivated State: An Equilibrium Binding Study. Int J Mol Sci 2019; 20:ijms20030689. [PMID: 30764559 PMCID: PMC6387330 DOI: 10.3390/ijms20030689] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 01/25/2019] [Accepted: 01/25/2019] [Indexed: 12/29/2022] Open
Abstract
Cation binding under equilibrium conditions has been used as a tool to explore the accessibility of permeant and nonpermeant cations to the selectivity filter in three different inactivated models of the potassium channel KcsA. The results show that the stack of ion binding sites (S1 to S4) in the inactivated filter models remain accessible to cations as they are in the resting channel state. The inactivated state of the selectivity filter is therefore “resting-like” under such equilibrium conditions. Nonetheless, quantitative differences in the apparent KD’s of the binding processes reveal that the affinity for the binding of permeant cations to the inactivated channel models, mainly K+, decreases considerably with respect to the resting channel. This is likely to cause a loss of K+ from the inactivated filter and consequently, to promote nonconductive conformations. The most affected site by the affinity loss seems to be S4, which is interesting because S4 is the first site to accommodate K+ coming from the channel vestibule when K+ exits the cell. Moreover, binding of the nonpermeant species, Na+, is not substantially affected by inactivation, meaning that the inactivated channels are also less selective for permeant versus nonpermeant cations under equilibrium conditions.
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Affiliation(s)
- Ana Marcela Giudici
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDiBE), and Instituto de Biología Molecular y Celular (IBMC), Universidad Miguel Hernández, Elche, E-03202 Alicante, Spain.
| | - Maria Lourdes Renart
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDiBE), and Instituto de Biología Molecular y Celular (IBMC), Universidad Miguel Hernández, Elche, E-03202 Alicante, Spain.
| | - Clara Díaz-García
- CQFM-IN and IBB-Institute for Bioengineering and Bioscience, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal.
| | - Andrés Morales
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, E-03080 Alicante, Spain.
| | - José Antonio Poveda
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDiBE), and Instituto de Biología Molecular y Celular (IBMC), Universidad Miguel Hernández, Elche, E-03202 Alicante, Spain.
| | - José Manuel González-Ros
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDiBE), and Instituto de Biología Molecular y Celular (IBMC), Universidad Miguel Hernández, Elche, E-03202 Alicante, Spain.
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23
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Delemotte L. Opening leads to closing: Allosteric crosstalk between the activation and inactivation gates in KcsA. J Gen Physiol 2018; 150:1356-1359. [PMID: 30143551 PMCID: PMC6168244 DOI: 10.1085/jgp.201812161] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Delemotte appraises new computational work revealing that the intracellular activation gate must open for C-type inactivation to occur in K+ channels.
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Affiliation(s)
- Lucie Delemotte
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
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24
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Li J, Ostmeyer J, Cuello LG, Perozo E, Roux B. Rapid constriction of the selectivity filter underlies C-type inactivation in the KcsA potassium channel. J Gen Physiol 2018; 150:1408-1420. [PMID: 30072373 PMCID: PMC6168234 DOI: 10.1085/jgp.201812082] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 07/12/2018] [Indexed: 12/27/2022] Open
Abstract
C-type inactivation in K+ channels is thought to be a result of constriction of the selectivity filter. By using MD simulations, Li et al. show that rapid constriction occurs within 1–2 s when the intracellular activation gate is fully open, but not when the gate is closed or partially open. C-type inactivation is a time-dependent process observed in many K+ channels whereby prolonged activation by an external stimulus leads to a reduction in ionic conduction. While C-type inactivation is thought to be a result of a constriction of the selectivity filter, the local dynamics of the process remain elusive. Here, we use molecular dynamics (MD) simulations of the KcsA channel to elucidate the nature of kinetically delayed activation/inactivation gating coupling. Microsecond-scale MD simulations based on the truncated form of the KcsA channel (C-terminal domain deleted) provide a first glimpse of the onset of C-type inactivation. We observe over multiple trajectories that the selectivity filter consistently undergoes a spontaneous and rapid (within 1–2 µs) transition to a constricted conformation when the intracellular activation gate is fully open, but remains in the conductive conformation when the activation gate is closed or partially open. Multidimensional umbrella sampling potential of mean force calculations and nonequilibrium voltage-driven simulations further confirm these observations. Electrophysiological measurements show that the truncated form of the KcsA channel inactivates faster and greater than full-length KcsA, which is consistent with truncated KcsA opening to a greater degree because of the absence of the C-terminal domain restraint. Together, these results imply that the observed kinetics underlying activation/inactivation gating reflect a rapid conductive-to-constricted transition of the selectivity filter that is allosterically controlled by the slow opening of the intracellular gate.
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Affiliation(s)
- Jing Li
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL
| | - Jared Ostmeyer
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL
| | - Luis G Cuello
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, TX
| | - Eduardo Perozo
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL
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25
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Abstract
Sodium (Na+) is a ubiquitous and important inorganic salt mediating many critical biological processes such as neuronal excitation, signaling, and facilitation of various transporters. The hydration states of Na+ are proposed to play critical roles in determining the conductance and the selectivity of Na+ channels, yet they are rarely captured by conventional structural biology means. Here we use the emerging cryo-electron microscopy (cryoEM) method micro-electron diffraction (MicroED) to study the structure of a prototypical tetrameric Na+-conducting channel, NaK, to 2.5 Å resolution from nano-crystals. Two new conformations at the external site of NaK are identified, allowing us to visualize a partially hydrated Na+ ion at the entrance of the channel pore. A process of dilation coupled with Na+ movement is identified leading to valuable insights into the mechanism of ion conduction and gating. This study lays the ground work for future studies using MicroED in membrane protein biophysics. Through a MicroED structure of NaK ion channel, Shian Liu and Tamir Gonen identify a process of dilation coupled with Na+ movement, providing mechanistic insights into ion conduction and gating. This study lays the ground work for future studies using MicroED in membrane protein biophysics.
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26
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Jalily Hasani H, Ganesan A, Ahmed M, Barakat KH. Effects of protein-protein interactions and ligand binding on the ion permeation in KCNQ1 potassium channel. PLoS One 2018; 13:e0191905. [PMID: 29444113 PMCID: PMC5812580 DOI: 10.1371/journal.pone.0191905] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 01/12/2018] [Indexed: 12/23/2022] Open
Abstract
The voltage-gated KCNQ1 potassium ion channel interacts with the type I transmembrane protein minK (KCNE1) to generate the slow delayed rectifier (IKs) current in the heart. Mutations in these transmembrane proteins have been linked with several heart-related issues, including long QT syndromes (LQTS), congenital atrial fibrillation, and short QT syndrome. Off-target interactions of several drugs with that of KCNQ1/KCNE1 ion channel complex have been known to cause fatal cardiac irregularities. Thus, KCNQ1/KCNE1 remains an important avenue for drug-design and discovery research. In this work, we present the structural and mechanistic details of potassium ion permeation through an open KCNQ1 structural model using the combined molecular dynamics and steered molecular dynamics simulations. We discuss the processes and key residues involved in the permeation of a potassium ion through the KCNQ1 ion channel, and how the ion permeation is affected by (i) the KCNQ1-KCNE1 interactions and (ii) the binding of chromanol 293B ligand and its derivatives into the complex. The results reveal that interactions between KCNQ1 with KCNE1 causes a pore constriction in the former, which in-turn forms small energetic barriers in the ion-permeation pathway. These findings correlate with the previous experimental reports that interactions of KCNE1 dramatically slows the activation of KCNQ1. Upon ligand-binding onto the complex, the energy-barriers along ion permeation path are more pronounced, as expected, therefore, requiring higher force in our steered-MD simulations. Nevertheless, pulling the ion when a weak blocker is bound to the channel does not necessitate high force in SMD. This indicates that our SMD simulations have been able to discern between strong and week blockers and reveal their influence on potassium ion permeation. The findings presented here will have some implications in understanding the potential off-target interactions of the drugs with the KCNQ1/KCNE1 channel that lead to cardiotoxic effects.
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Affiliation(s)
- Horia Jalily Hasani
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Aravindhan Ganesan
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Marawan Ahmed
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Khaled H. Barakat
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Alberta, Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta, Canada
- Li Ka Shing Applied Virology Institute, University of Alberta, Edmonton, Alberta, Canada
- * E-mail:
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McClenaghan C, Schewe M, Aryal P, Carpenter EP, Baukrowitz T, Tucker SJ. Polymodal activation of the TREK-2 K2P channel produces structurally distinct open states. J Gen Physiol 2017; 147:497-505. [PMID: 27241700 PMCID: PMC4886281 DOI: 10.1085/jgp.201611601] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 05/09/2016] [Indexed: 01/08/2023] Open
Abstract
TREK channels, which are gated open by a wide range of stimuli, exist in at least two conformations known as “up” and “down.” McClenaghan et al. show that the channel can be open in both of these conformations and that gating is primarily achieved by the channel’s selectivity filter. The TREK subfamily of two-pore domain (K2P) K+ channels exhibit polymodal gating by a wide range of physical and chemical stimuli. Crystal structures now exist for these channels in two main states referred to as the “up” and “down” conformations. However, recent studies have resulted in contradictory and mutually exclusive conclusions about the functional (i.e., conductive) status of these two conformations. To address this problem, we have used the state-dependent TREK-2 inhibitor norfluoxetine that can only bind to the down state, thereby allowing us to distinguish between these two conformations when activated by different stimuli. Our results reconcile these previously contradictory gating models by demonstrating that activation by pressure, temperature, voltage, and pH produce more than one structurally distinct open state and reveal that channel activation does not simply involve switching between the up and down conformations. These results also highlight the diversity of structural mechanisms that K2P channels use to integrate polymodal gating signals.
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Affiliation(s)
- Conor McClenaghan
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, England, UK OXION Initiative in Ion Channels and Disease, University of Oxford, Oxford OX1 3PU, England, UK
| | - Marcus Schewe
- Department of Physiology, University of Kiel, 24118 Kiel, Germany
| | - Prafulla Aryal
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, England, UK OXION Initiative in Ion Channels and Disease, University of Oxford, Oxford OX1 3PU, England, UK
| | - Elisabeth P Carpenter
- OXION Initiative in Ion Channels and Disease, University of Oxford, Oxford OX1 3PU, England, UK Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, England, UK
| | | | - Stephen J Tucker
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, England, UK OXION Initiative in Ion Channels and Disease, University of Oxford, Oxford OX1 3PU, England, UK
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Jalily Hasani H, Ahmed M, Barakat K. A comprehensive structural model for the human KCNQ1/KCNE1 ion channel. J Mol Graph Model 2017; 78:26-47. [PMID: 28992529 DOI: 10.1016/j.jmgm.2017.09.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 09/25/2017] [Accepted: 09/26/2017] [Indexed: 10/18/2022]
Abstract
The voltage-gated KCNQ1/KCNE1 potassium ion channel complex, forms the slow delayed rectifier (IKs) current in the heart, which plays an important role in heart signaling. The importance of KCNQ1/KCNE1 channel's function is further implicated by the linkage between loss-of-function and gain-of-function mutations in KCNQ1 or KCNE1, and long QT syndromes, congenital atrial fibrillation, and short QT syndrome. Also, KCNQ1/KCNE1 channels are an off-target for many non-cardiovascular drugs, leading to fatal cardiac irregularities. One solution to address and study the mentioned aspects of KCNQ1/KNCE1 channel would be the structural studies using a validated and accurate model. Along the same line in this study, we have used several top-notch modeling approaches to build a structural model for the open state of KCNQ1 protein, which is both accurate and compatible with available experimental data. Next, we included the KCNE1 protein components using data-driven protein-protein docking simulations, encompassing a 4:2 stoichiometry to complete the picture of the channel complex formed by these two proteins. All the protein systems generated through these processes were refined by long Molecular Dynamics simulations. The refined models were analyzed extensively to infer data about the interaction of KCNQ1 channel with its accessory KCNE1 beta subunits.
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Affiliation(s)
- Horia Jalily Hasani
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Marawan Ahmed
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Khaled Barakat
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Alberta, Canada; Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta, Canada; Li Ka Shing Applied Virology Institute, University of Alberta, Edmonton, Alberta, Canada.
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van der Cruijsen EAW, Prokofyev AV, Pongs O, Baldus M. Probing Conformational Changes during the Gating Cycle of a Potassium Channel in Lipid Bilayers. Biophys J 2017; 112:99-108. [PMID: 28076820 DOI: 10.1016/j.bpj.2016.12.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 11/08/2016] [Accepted: 12/01/2016] [Indexed: 01/10/2023] Open
Abstract
Ion conduction across the cellular membrane requires the simultaneous opening of activation and inactivation gates of the K+ channel pore. The bacterial KcsA channel has served as a powerful system for dissecting the structural changes that are related to four major functional states associated with K+ gating. Yet, the direct observation of the full gating cycle of KcsA has remained structurally elusive, and crystal structures mimicking these gating events require mutations in or stabilization of functionally relevant channel segments. Here, we found that changes in lipid composition strongly increased the KcsA open probability. This enabled us to probe all four major gating states in native-like membranes by combining electrophysiological and solid-state NMR experiments. In contrast to previous crystallographic views, we found that the selectivity filter and turret region, coupled to the surrounding bilayer, were actively involved in channel gating. The increase in overall steady-state open probability was accompanied by a reduction in activation-gate opening, underscoring the important role of the surrounding lipid bilayer in the delicate conformational coupling of the inactivation and activation gates.
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Affiliation(s)
- Elwin A W van der Cruijsen
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | - Alexander V Prokofyev
- Department of Physiology, Institute of Cellular Neurophysiology, University of the Saarland, Homburg, Germany
| | - Olaf Pongs
- Department of Physiology, Institute of Cellular Neurophysiology, University of the Saarland, Homburg, Germany.
| | - Marc Baldus
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands.
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Kratochvil HT, Maj M, Matulef K, Annen AW, Ostmeyer J, Perozo E, Roux B, Valiyaveetil FI, Zanni MT. Probing the Effects of Gating on the Ion Occupancy of the K + Channel Selectivity Filter Using Two-Dimensional Infrared Spectroscopy. J Am Chem Soc 2017; 139:8837-8845. [PMID: 28472884 DOI: 10.1021/jacs.7b01594] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The interplay between the intracellular gate and the selectivity filter underlies the structural basis for gating in potassium ion channels. Using a combination of protein semisynthesis, two-dimensional infrared (2D IR) spectroscopy, and molecular dynamics (MD) simulations, we probe the ion occupancy at the S1 binding site in the constricted state of the selectivity filter of the KcsA channel when the intracellular gate is open and closed. The 2D IR spectra resolve two features, whose relative intensities depend on the state of the intracellular gate. By matching the experiment to calculated 2D IR spectra of structures predicted by MD simulations, we identify the two features as corresponding to states with S1 occupied or unoccupied by K+. We learn that S1 is >70% occupied when the intracellular gate is closed and <15% occupied when the gate is open. Comparison of MD trajectories show that opening of the intracellular gate causes a structural change in the selectivity filter, which leads to a change in the ion occupancy. This work reveals the complexity of the conformational landscape of the K+ channel selectivity filter and its dependence on the state of the intracellular gate.
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Affiliation(s)
- Huong T Kratochvil
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Michał Maj
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Kimberly Matulef
- Program in Chemical Biology, Department of Physiology and Pharmacology, Oregon Health and Science University , Portland, Oregon 97239, United States
| | - Alvin W Annen
- Program in Chemical Biology, Department of Physiology and Pharmacology, Oregon Health and Science University , Portland, Oregon 97239, United States
| | - Jared Ostmeyer
- Department of Biochemistry and Molecular Biology, The University of Chicago , Chicago, Illinois 60637, United States
| | - Eduardo Perozo
- Department of Biochemistry and Molecular Biology, The University of Chicago , Chicago, Illinois 60637, United States
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, The University of Chicago , Chicago, Illinois 60637, United States
| | - Francis I Valiyaveetil
- Program in Chemical Biology, Department of Physiology and Pharmacology, Oregon Health and Science University , Portland, Oregon 97239, United States
| | - Martin T Zanni
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
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31
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The Synergetic Effects of Combining Structural Biology and EPR Spectroscopy on Membrane Proteins. CRYSTALS 2017. [DOI: 10.3390/cryst7040117] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Protein structures as provided by structural biology such as X-ray crystallography, cryo-electron microscopy and NMR spectroscopy are key elements to understand the function of a protein on the molecular level. Nonetheless, they might be error-prone due to crystallization artifacts or, in particular in case of membrane-imbedded proteins, a mostly artificial environment. In this review, we will introduce different EPR spectroscopy methods as powerful tools to complement and validate structural data gaining insights in the dynamics of proteins and protein complexes such that functional cycles can be derived. We will highlight the use of EPR spectroscopy on membrane-embedded proteins and protein complexes ranging from receptors to secondary active transporters as structural information is still limited in this field and the lipid environment is a particular challenge.
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32
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Ion and inhibitor binding of the double-ring ion selectivity filter of the mitochondrial calcium uniporter. Proc Natl Acad Sci U S A 2017; 114:E2846-E2851. [PMID: 28325874 DOI: 10.1073/pnas.1620316114] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The calcium (Ca2+) uniporter of mitochondria is a holocomplex consisting of the Ca2+-conducting channel, known as mitochondrial calcium uniporter (MCU), and several accessory and regulatory components. A previous electrophysiology study found that the uniporter has high Ca2+ selectivity and conductance and this depends critically on the conserved amino acid sequence motif, DXXE (Asp-X-X-Glu) of MCU. A recent NMR structure of the MCU channel from Caenorhabditis elegans revealed that the DXXE forms two parallel carboxylate rings at the channel entrance that seem to serve as the ion selectivity filter, although direct ion interaction of this structural motif has not been addressed. Here, we use a paramagnetic probe, manganese (Mn2+), to investigate ion and inhibitor binding of this putative selectivity filter. Our paramagnetic NMR data show that mutants with a single carboxylate ring, NXXE (Asn-X-X-Glu) and DXXQ (Asp-X-X-Gln), each can bind Mn2+ specifically, whereas in the WT the two rings bind Mn2+ cooperatively, resulting in ∼1,000-fold higher apparent affinity. Ca2+ can specifically displace the bound Mn2+ at the DXXE site in the channel. Furthermore, titrating the sample with the known channel inhibitor ruthenium 360 (Ru360) can displace Mn2+ binding from the solvent-accessible Asp site but not the inner Glu site. The NMR titration data, together with structural analysis of the DXXE motif and molecular dynamics simulation, indicate that the double carboxylate rings at the apex of the MCU pore constitute the ion selectivity filter and that Ru360 directly blocks ion entry into the filter by binding to the outer carboxylate ring.
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33
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Tellinghuisen J. Analysis of multitemperature isothermal titration calorimetry data at very low c: Global beats van't Hoff. Anal Biochem 2016; 513:43-46. [PMID: 27567993 DOI: 10.1016/j.ab.2016.08.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 08/06/2016] [Accepted: 08/23/2016] [Indexed: 10/21/2022]
Abstract
Isothermal titration calorimetry data for very low c (≡K[M]0) must normally be analyzed with the stoichiometry parameter n fixed - at its known value or at any reasonable value if the system is not well characterized. In the latter case, ΔH° (and hence n) can be estimated from the T-dependence of the binding constant K, using the van't Hoff (vH) relation. An alternative is global or simultaneous fitting of data at multiple temperatures. In this Note, global analysis of low-c data at two temperatures is shown to estimate ΔH° and n with double the precision of the vH method.
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Affiliation(s)
- Joel Tellinghuisen
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, United States.
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34
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Bian X, Lockless SW. Preparation To Minimize Buffer Mismatch in Isothermal Titration Calorimetry Experiments. Anal Chem 2016; 88:5549-53. [PMID: 27092566 DOI: 10.1021/acs.analchem.6b01319] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
There is a growing need to study ligand binding to proteins in native or complex solution using isothermal titration calorimetry (ITC). For example, it is desirable to measure ligand binding to membrane proteins in more native lipid-like environments such as bicelles, where ligands can access both sides of the membrane in a homogeneous environment. A critical step to obtain high signal-to-noise is matching the reaction chamber solution to the ligand solution, typically through a final dialysis or gel filtration step. However, to obtain reproducible bicelles, the lipid concentrations must be carefully controlled which eliminates the use of dialysis that can disrupt these parameters. Here, we report and validate a rapid preparation ITC (RP-ITC) approach to measure ligand binding without the need for a dialysis step. This general approach is used to quantify ion binding to a K(+) channel embedded in bicelles and can be applied to complex, less defined systems.
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Affiliation(s)
- Xuelin Bian
- Department of Biology, Texas A&M University , 3474 TAMU, College Station, Texas 77843-3474, United States
| | - Steve W Lockless
- Department of Biology, Texas A&M University , 3474 TAMU, College Station, Texas 77843-3474, United States
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