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Wu Y, Yan Y, Yang Y, Bian S, Rivetta A, Allen K, Sigworth FJ. Cryo-EM structures of Kv1.2 potassium channels, conducting and non-conducting. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.02.543446. [PMID: 37398110 PMCID: PMC10312591 DOI: 10.1101/2023.06.02.543446] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
We present near-atomic-resolution cryo-EM structures of the mammalian voltage-gated potassium channel Kv1.2 in open, C-type inactivated, toxin-blocked and sodium-bound states at 3.2 Å, 2.5 Å, 3.2 Å, and 2.9Å. These structures, all obtained at nominally zero membrane potential in detergent micelles, reveal distinct ion-occupancy patterns in the selectivity filter. The first two structures are very similar to those reported in the related Shaker channel and the much-studied Kv1.2-2.1 chimeric channel. On the other hand, two new structures show unexpected patterns of ion occupancy. First, the toxin α-Dendrotoxin, like Charybdotoxin, is seen to attach to the negatively-charged channel outer mouth, and a lysine residue penetrates into the selectivity filter, with the terminal amine coordinated by carbonyls, partially disrupting the outermost ion-binding site. In the remainder of the filter two densities of bound ions are observed, rather than three as observed with other toxin-blocked Kv channels. Second, a structure of Kv1.2 in Na+ solution does not show collapse or destabilization of the selectivity filter, but instead shows an intact selectivity filter with ion density in each binding site. We also attempted to image the C-type inactivated Kv1.2 W366F channel in Na+ solution, but the protein conformation was seen to be highly variable and only a low-resolution structure could be obtained. These findings present new insights into the stability of the selectivity filter and the mechanism of toxin block of this intensively studied, voltage-gated potassium channel.
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Affiliation(s)
- Yangyu Wu
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, Connecticut USA
| | - Yangyang Yan
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, Connecticut USA
| | - Youshan Yang
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, Connecticut USA
| | - Shumin Bian
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, Connecticut USA
| | - Alberto Rivetta
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, Connecticut USA
| | - Ken Allen
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, Connecticut USA
| | - Fred J Sigworth
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, Connecticut USA
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Zhao X, Ding W, Wang H, Wang Y, Liu Y, Li Y, Liu C. Structural Insights and Influence of Terahertz Waves in Midinfrared Region on Kv1.2 Channel Selectivity Filter. ACS OMEGA 2024; 9:9702-9713. [PMID: 38434859 PMCID: PMC10905694 DOI: 10.1021/acsomega.3c09801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/16/2024] [Accepted: 01/23/2024] [Indexed: 03/05/2024]
Abstract
Potassium ion channels are the structural basis for excitation transmission, heartbeat, and other biological processes. The selectivity filter is a critical structural component of potassium ion channels, whose structure is crucial to realizing their function. As biomolecules vibrate and rotate at frequencies in the terahertz band, potassium ion channels are sensitive to terahertz waves. Therefore, it is worthwhile to investigate how the terahertz wave influences the selectivity filter of the potassium channels. In this study, we investigate the structure of the selectivity filter of Kv1.2 potassium ion channels using molecular dynamics simulations. The effect of an electric field on the channel has been examined at four different resonant frequencies of the carbonyl group in SF: 36.75 37.06, 37.68, and 38.2 THz. As indicated by the results, 376GLY appears to be the critical residue in the selectivity filter of the Kv1.2 channel. Its dihedral angle torsion is detrimental to the channel structural stability and the transmembrane movement of potassium ions. 36.75 THz is the resonance frequency of the carbonyl group of 376GLY. Among all four frequencies explored, the applied terahertz electric field of this frequency has the most significant impact on the channel structure, negatively impacting the channel stability and reducing the ion permeability by 20.2% compared to the absence of fields. In this study, we simulate that terahertz waves in the mid-infrared frequency region can significantly alter the structure and function of potassium ion channels and that the effects of terahertz waves differ greatly based on frequency.
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Affiliation(s)
- Xiaofei Zhao
- Key Laboratory
for Physical
Electronics and Devices of the Ministry of Education, School of Electronic
and Information Engineering, Xi’an
Jiaotong University, Xi’an, Shaanxi 710049, China
| | - Wen Ding
- Key Laboratory
for Physical
Electronics and Devices of the Ministry of Education, School of Electronic
and Information Engineering, Xi’an
Jiaotong University, Xi’an, Shaanxi 710049, China
| | - Hongguang Wang
- Key Laboratory
for Physical
Electronics and Devices of the Ministry of Education, School of Electronic
and Information Engineering, Xi’an
Jiaotong University, Xi’an, Shaanxi 710049, China
| | - Yize Wang
- Key Laboratory
for Physical
Electronics and Devices of the Ministry of Education, School of Electronic
and Information Engineering, Xi’an
Jiaotong University, Xi’an, Shaanxi 710049, China
| | - Yanjiang Liu
- Key Laboratory
for Physical
Electronics and Devices of the Ministry of Education, School of Electronic
and Information Engineering, Xi’an
Jiaotong University, Xi’an, Shaanxi 710049, China
| | - Yongdong Li
- Key Laboratory
for Physical
Electronics and Devices of the Ministry of Education, School of Electronic
and Information Engineering, Xi’an
Jiaotong University, Xi’an, Shaanxi 710049, China
| | - Chunliang Liu
- Key Laboratory
for Physical
Electronics and Devices of the Ministry of Education, School of Electronic
and Information Engineering, Xi’an
Jiaotong University, Xi’an, Shaanxi 710049, China
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Li J, Shen R, Rohaim A, Mendoza Uriarte R, Fajer M, Perozo E, Roux B. Computational study of non-conductive selectivity filter conformations and C-type inactivation in a voltage-dependent potassium channel. J Gen Physiol 2021; 153:212541. [PMID: 34357375 PMCID: PMC8352720 DOI: 10.1085/jgp.202112875] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 06/01/2021] [Accepted: 07/13/2021] [Indexed: 12/25/2022] Open
Abstract
C-type inactivation is a time-dependent process of great physiological significance that is observed in a large class of K+ channels. Experimental and computational studies of the pH-activated KcsA channel show that the functional C-type inactivated state, for this channel, is associated with a structural constriction of the selectivity filter at the level of the central glycine residue in the signature sequence, TTV(G)YGD. The structural constriction is allosterically promoted by the wide opening of the intracellular activation gate. However, whether this is a universal mechanism for C-type inactivation has not been established with certainty because similar constricted structures have not been observed for other K+ channels. Seeking to ascertain the general plausibility of the constricted filter conformation, molecular dynamics simulations of a homology model of the pore domain of the voltage-gated potassium channel Shaker were performed. Simulations performed with an open intracellular gate spontaneously resulted in a stable constricted-like filter conformation, providing a plausible nonconductive state responsible for C-type inactivation in the Shaker channel. While there are broad similarities with the constricted structure of KcsA, the hypothetical constricted-like conformation of Shaker also displays some subtle differences. Interestingly, those are recapitulated by the Shaker-like E71V KcsA mutant, suggesting that the residue at this position along the pore helix plays a pivotal role in determining the C-type inactivation behavior. Free energy landscape calculations show that the conductive-to-constricted transition in Shaker is allosterically controlled by the degree of opening of the intracellular activation gate, as observed with the KcsA channel. The behavior of the classic inactivating W434F Shaker mutant is also characterized from a 10-μs MD simulation, revealing that the selectivity filter spontaneously adopts a nonconductive conformation that is constricted at the level of the second glycine in the signature sequence, TTVGY(G)D.
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Affiliation(s)
- Jing Li
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL.,Department of BioMolecular Sciences, Division of Medicinal Chemistry, School of Pharmacy, University of Mississippi, Oxford, MS
| | - Rong Shen
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL
| | - Ahmed Rohaim
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL
| | - Ramon Mendoza Uriarte
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL
| | - Mikolai Fajer
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL
| | - Eduardo Perozo
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL
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Agostini A, Bortolus M, Ferlez B, Walters K, Golbeck JH, van der Est A, Carbonera D. Differential sensitivity to oxygen among the bacteriochlorophylls g in the type-I reaction centers of Heliobacterium modesticaldum. Photochem Photobiol Sci 2021; 20:747-759. [PMID: 34018156 DOI: 10.1007/s43630-021-00049-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 04/28/2021] [Indexed: 11/27/2022]
Abstract
The type-I, homodimeric photosynthetic reaction center (RC) of Heliobacteria (HbRC) is the only known RC in which bacteriochlorophyll g (BChl g) is found. It is also simpler than other RCs, having the smallest number of protein subunits and bound chromophores of any type-I RC. In the presence of oxygen, BChl g isomerizes to 81-hydroxychlorophyll aF (Chl aF). This naturally occurring process provides a way of altering the chlorophylls and studying the effect of these changes on energy and electron transfer. Transient absorbance difference spectroscopy reveals that triplet-state formation occurs in the antenna chlorophylls of HbRCs but does not provide site-specific information. Here, we report on an extended optically detected magnetic resonance (ODMR) study of the antenna triplet states in HbRCs with differing levels of conversion of BChl g to Chl aF. The data reveal pools of BChl g molecules with different triplet zero-field splitting parameters and different susceptibilities to chemical oxidation. By relating the detailed spectroscopic characteristics derived from the ODMR data to the recently solved crystallographic structure, we have tentatively identified BChl g molecules in which the probability of triplet formation is high and sites at which BChl g conversion is more likely, providing useful information about the fate of the excitation in the complex.
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Affiliation(s)
- Alessandro Agostini
- Department of Chemical Sciences, University of Padova, Via Marzolo, 1, 35131, Padua, Italy.,Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branisovska 31, 37005, České Budějovice, Czechia
| | - Marco Bortolus
- Department of Chemical Sciences, University of Padova, Via Marzolo, 1, 35131, Padua, Italy
| | - Bryan Ferlez
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA.,Department of Biochemistry and Molecular Biology and MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, USA
| | - Karim Walters
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - John H Golbeck
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Art van der Est
- Department of Chemistry, Brock University, 1812 Sir Isaac Brock, Way, Saint Catharines, ON, L2S 3A1, Canada.
| | - Donatella Carbonera
- Department of Chemical Sciences, University of Padova, Via Marzolo, 1, 35131, Padua, Italy.
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