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Salas-Estrada LA, Leioatts N, Romo TD, Grossfield A. Lipids Alter Rhodopsin Function via Ligand-like and Solvent-like Interactions. Biophys J 2018; 114:355-367. [PMID: 29401433 PMCID: PMC5984976 DOI: 10.1016/j.bpj.2017.11.021] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 09/20/2017] [Accepted: 11/09/2017] [Indexed: 10/18/2022] Open
Abstract
Rhodopsin, a prototypical G protein-coupled receptor, is a membrane protein that can sense dim light. This highly effective photoreceptor is known to be sensitive to the composition of its lipidic environment, but the molecular mechanisms underlying this fine-tuned modulation of the receptor's function and structural stability are not fully understood. There are two competing hypotheses to explain how this occurs: 1) lipid modulation occurs via solvent-like interactions, where lipid composition controls membrane properties like hydrophobic thickness, which in turn modulate the protein's conformational equilibrium; or 2) protein-lipid interactions are ligand-like, with specific hot spots and long-lived binding events. By analyzing an ensemble of all-atom molecular dynamics simulations of five different states of rhodopsin, we show that a local ordering effect takes place in the membrane upon receptor activation. Likewise, docosahexaenoic acid acyl tails and phosphatidylethanolamine headgroups behave like weak ligands, preferentially binding to the receptor in inactive-like conformations and inducing subtle but significant structural changes.
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Affiliation(s)
- Leslie A Salas-Estrada
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York
| | - Nicholas Leioatts
- Department of Theoretical and Computational Biophysics, Max Plank Institute for Biophysical Chemistry, Göttingen, Germany
| | - Tod D Romo
- Center for Integrated Research Computing, University of Rochester, Rochester, New York
| | - Alan Grossfield
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York.
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Gu Z, Plant LD, Meng XY, Perez-Aguilar JM, Wang Z, Dong M, Logothetis DE, Zhou R. Exploring the Nanotoxicology of MoS 2: A Study on the Interaction of MoS 2 Nanoflakes and K + Channels. ACS NANO 2018; 12:705-717. [PMID: 29236481 DOI: 10.1021/acsnano.7b07871] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Molybdenum disulfide (MoS2) nanomaterial has recently found various applications in the biomedical field mainly due to its outstanding physicochemical properties. However, little is known about its interactions with biological systems at the atomic level, which intimately relates to the biocompatibility of the material. To provide insights into the effects of MoS2 in biological entities, we investigated the interactions of MoS2 with proteins from a functionally important membrane family, the ubiquitous potassium (K+) channels. Here, we study four representative K+ channels-KcsA, Kir3.2, the Kv1.2 paddle chimera, and K2P2-to investigate their interactions with a triangular MoS2 nanoflake using Molecular Dynamics (MD) simulations combined with electrophysiology experiments. These particular K+ channels were selected based on the diversity in their structure; that is, although these K+ channels display similar structural motifs, they also contain significant differences related to their particular function. Our results indicate that the MoS2 nanoflake is able to stably bind to three out of the four channels, albeit through distinct binding modes. The binding mode between each channel and MoS2 underlies the specific deleterious influence on the channel's basic physiological function: For KcsA, MoS2 binds on the extracellular loops, which indirectly destroys the delicate structure of the selectivity filter causing a strong leak of K+ ions. In the binding mode with Kir3.2, the MoS2 nanoflake completely covers the entrance to the channel pore affecting the normal ion conduction. For the Kv1.2 chimera, the MoS2 nanoflake prefers to bind into a crevice located at the extracellular side of the Voltage Sensor Domain (VSD). Interestingly, the crevice involves the N-terminal segment of S4, a crucial transmembrane helix which directly controls the gating process of the Kv1.2 chimera channel by electromechanical coupling the VSD to the transmembrane electric field. MoS2 in contact with S4 from the Kv1.2 chimera, potentially influences the channel's gating process from open to closed states. In all three systems, the van der Waals contribution to the total energy dominates the binding interactions; also, hydrophobic residues contribute the most contact points, which agrees with the strong hydrophobic character of the MoS2 nanomaterial. Electrophysiology recordings using two-electrode voltage-clamp show that currents of Kir3.2 and Kv1.2 are both blocked by the MoS2 nanoflakes in a concentration-dependent way. While the background K+ channel, K2P2 (TREK-1), identified as a negative control, is not blocked by the MoS2 nanoflakes. The large and rigid extracellular domain of K2P2 appears to protect the channel from disturbance by the nanoflakes. Intrinsic chemical properties of MoS2, together with the specific features of the channels, such as the electrostatic character and complex surface architecture, determine the critical details of the binding events. These findings might shed light on the potential nanotoxicology of MoS2 nanomaterials and help us to understand the underlying molecular mechanism.
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Affiliation(s)
- Zonglin Gu
- Institute of Quantitative Biology and Medicine, SRMP and RAD-X, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University , Suzhou 215123, China
| | - Leigh D Plant
- Department of Pharmaceutical Sciences in the School of Pharmacy, Bouvé College of Health Sciences, Northeastern University , Boston, Massachusetts 02115, United States
| | - Xuan-Yu Meng
- Institute of Quantitative Biology and Medicine, SRMP and RAD-X, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University , Suzhou 215123, China
| | - Jose Manuel Perez-Aguilar
- Computational Biological Center, IBM Thomas J. Watson Research Center , Yorktown Heights, New York 10598, United States
| | - Zegao Wang
- Interdisciplinary Nanoscience Center, Aarhus University , DK-8000 Aarhus C, Denmark
| | - Mingdong Dong
- Interdisciplinary Nanoscience Center, Aarhus University , DK-8000 Aarhus C, Denmark
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Diomedes E Logothetis
- Department of Pharmaceutical Sciences in the School of Pharmacy, Bouvé College of Health Sciences, Northeastern University , Boston, Massachusetts 02115, United States
| | - Ruhong Zhou
- Institute of Quantitative Biology and Medicine, SRMP and RAD-X, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University , Suzhou 215123, China
- Computational Biological Center, IBM Thomas J. Watson Research Center , Yorktown Heights, New York 10598, United States
- Department of Chemistry, Columbia University , New York, New York 10027, United States
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53
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Gaburjakova J, Gaburjakova M. Reconstitution of Ion Channels in Planar Lipid Bilayers: New Approaches. ADVANCES IN BIOMEMBRANES AND LIPID SELF-ASSEMBLY 2018. [DOI: 10.1016/bs.abl.2017.12.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Polymer Nanodiscs: Discoidal Amphiphilic Block Copolymer Membranes as a New Platform for Membrane Proteins. Sci Rep 2017; 7:15227. [PMID: 29123151 PMCID: PMC5680229 DOI: 10.1038/s41598-017-15151-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 10/18/2017] [Indexed: 12/23/2022] Open
Abstract
Lipid nanodiscs are playing increasingly important roles in studies of the structure and function of membrane proteins. Development of lipid nanodiscs as a membrane-protein-supporting platform, or a drug targeting and delivery vehicle in general, is undermined by the fluidic and labile nature of lipid bilayers. Here, we report the discovery of polymer nanodiscs, i.e., discoidal amphiphilic block copolymer membrane patches encased within membrane scaffold proteins, as a novel two-dimensional nanomembrane that maintains the advantages of lipid nanodiscs while addressing their weaknesses. Using MsbA, a bacterial ATP-binding cassette transporter as a membrane protein prototype, we show that the protein can be reconstituted into the polymer nanodiscs in an active state. As with lipid nanodiscs, reconstitution of detergent-solubilized MsbA into the polymer nanodiscs significantly enhances its activity. In contrast to lipid nanodiscs that undergo time- and temperature-dependent structural changes, the polymer nanodiscs experience negligible structural evolution under similar environmental stresses, revealing a critically important property for the development of nanodisc-based characterization methodologies or biotechnologies. We expect that the higher mechanical and chemical stability of block copolymer membranes and their chemical versatility for adaptation will open new opportunities for applications built upon diverse membrane protein functions, or involved with drug targeting and delivery.
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Kuć M, Cieślik-Boczula K, Rospenk M. Anesthetic-dependent changes in the chain-melting phase transition of DPPG liposomes studied using near-infrared spectroscopy supported by PCA. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 186:37-43. [PMID: 28605687 DOI: 10.1016/j.saa.2017.06.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 05/18/2017] [Accepted: 06/05/2017] [Indexed: 06/07/2023]
Abstract
The effect of inhalation anesthetics (enflurane, isoflurane, sevoflurane or halothane) on the lipid chain-melting phase transition of negatively charged phospholipid membranes was studied using near-infrared (NIR) spectroscopy supported by Principal Component Analysis (PCA). NIR spectra of anesthetics-mixed dipalmitoylphosphatidylglycerol (DPPG) membranes were recorded in a range of the first overtone of the symmetric and antisymmetric stretching vibrations of CH2 groups of lipid aliphatic chains as a function of increasing temperature. Anesthetic-dependent changes in the trans to gauche conformers ratio of CH2 groups in the hydrocarbon lipid chains were characterized in detail and compared with the zwitterionic lipid membranes, which were built of dipalmitoylphosphatidylcholine (DPPC) molecules.
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Affiliation(s)
- Marta Kuć
- Faculty of Chemistry, University of Wroclaw, Joliot- Curie 14, 50-383 Wroclaw, Poland
| | | | - Maria Rospenk
- Faculty of Chemistry, University of Wroclaw, Joliot- Curie 14, 50-383 Wroclaw, Poland
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56
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Transmembrane allosteric energetics characterization for strong coupling between proton and potassium ion binding in the KcsA channel. Proc Natl Acad Sci U S A 2017; 114:8788-8793. [PMID: 28768808 DOI: 10.1073/pnas.1701330114] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The slow spontaneous inactivation of potassium channels exhibits classic signatures of transmembrane allostery. A variety of data support a model in which the loss of K+ ions from the selectivity filter is a major factor in promoting inactivation, which defeats transmission, and is allosterically coupled to protonation of key channel activation residues, more than 30 Å from the K+ ion binding site. We show that proton binding at the intracellular pH sensor perturbs the potassium affinity at the extracellular selectivity filter by more than three orders of magnitude for the full-length wild-type KcsA, a pH-gated bacterial channel, in membrane bilayers. Studies of F103 in the hinge of the inner helix suggest an important role for its bulky sidechain in the allosteric mechanism; we show that the energetic strength of coupling of the gates is strongly altered when this residue is mutated to alanine. These results provide quantitative site-specific measurements of allostery in a bilayer environment, and highlight the power of describing ion channel gating through the lens of allosteric coupling.
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57
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Oz M, El Nebrisi EG, Yang KHS, Howarth FC, Al Kury LT. Cellular and Molecular Targets of Menthol Actions. Front Pharmacol 2017; 8:472. [PMID: 28769802 PMCID: PMC5513973 DOI: 10.3389/fphar.2017.00472] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 07/03/2017] [Indexed: 02/04/2023] Open
Abstract
Menthol belongs to monoterpene class of a structurally diverse group of phytochemicals found in plant-derived essential oils. Menthol is widely used in pharmaceuticals, confectionary, oral hygiene products, pesticides, cosmetics, and as a flavoring agent. In addition, menthol is known to have antioxidant, anti-inflammatory, and analgesic effects. Recently, there has been renewed awareness in comprehending the biological and pharmacological effects of menthol. TRP channels have been demonstrated to mediate the cooling actions of menthol. There has been new evidence demonstrating that menthol can significantly influence the functional characteristics of a number of different kinds of ligand and voltage-gated ion channels, indicating that at least some of the biological and pharmacological effects of menthol can be mediated by alterations in cellular excitability. In this article, we examine the results of earlier studies on the actions of menthol with voltage and ligand-gated ion channels.
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Affiliation(s)
- Murat Oz
- Department of Pharmacology, College of Medicine and Health Sciences, United Arab Emirates UniversityAl Ain, United Arab Emirates.,Department of Basic Medical Sciences, College of Medicine, Qatar UniversityDoha, Qatar
| | - Eslam G El Nebrisi
- Department of Pharmacology, College of Medicine and Health Sciences, United Arab Emirates UniversityAl Ain, United Arab Emirates
| | - Keun-Hang S Yang
- Department of Biological Sciences, Schmid College of Science and Technology, Chapman UniversityOrange, CA, United States
| | - Frank C Howarth
- Department of Physiology, College of Medicine and Health Sciences, United Arab Emirates UniversityAl Ain, United Arab Emirates
| | - Lina T Al Kury
- Department of Health Sciences, College of Natural and Health Sciences, Zayed UniversityAbu Dhabi, United Arab Emirates
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58
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Borrell JH, Domènech Ò. Critical Temperature of 1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine Monolayers and Its Possible Biological Relevance. J Phys Chem B 2017. [PMID: 28636818 DOI: 10.1021/acs.jpcb.7b04021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Because transmembrane proteins (TMPs) can be obtained with sufficient purity for X-ray diffraction studies more frequently than decades ago, their mechanisms of action may now be elucidated. One of the pending issues is the actual interplay between transmembrane proteins and membrane lipids. There is strong evidence of the involvement of specific lipids with some membrane proteins, such as the potassium crystallographically sited activation channel (KcsA) of Streptomyces lividans and the secondary transporter of lactose LacY of Escherichia coli, the activities of which are associated with the presence of anionic phospholipids such as the phosphatidylglycerol (PG) and phosphatidyethanolamine (PE), respectively. Other proteins such as the large conductance mechanosensitive channel (MscL) of E. coli seem to depend on the adaptation of specific phospholipids to the irregular surface of the integral membrane protein. In this work we investigated the lateral compressibility of two homoacid phosphatidylethanolamines (one with both acyl chains unsaturated (DOPE), the other with the acyl chains saturated (DPPE)) and the heteroacid phosphatidyletanolamine (POPE) and their mixtures with POPG. The liquid expanded (LE) to liquid condensed (LC) transition was observed in POPE at a temperature below its critical temperature (Tc = 36 °C). Because Tc lies below the physiological temperature, the occurrence of this phase transition may have something to do with the functioning of LacY. This magnitude is discussed within the context of the experiments carried out at temperatures below the Tc of POPE at which the activity of Lac Y and other TMPs are frequently studied.
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Affiliation(s)
- Jordi H Borrell
- Department of Pharmacy, Pharmaceutical Technology and Physical Chemistry, Faculty of Pharmacy and Food Sciences and ‡Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona (UB) , E-08028 Barcelona, Spain
| | - Òscar Domènech
- Department of Pharmacy, Pharmaceutical Technology and Physical Chemistry, Faculty of Pharmacy and Food Sciences and ‡Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona (UB) , E-08028 Barcelona, Spain
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59
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Abstract
To study integral membrane proteins, one has to extract them from the membrane—the step that is typically achieved by the application of detergents. In this mini-review, we summarize the top 10 detergents used for the structural analysis of membrane proteins based on the published results. The aim of this study is to provide the reader with an overview of the main properties of available detergents (critical micelle concentration (CMC) value, micelle size, etc.) and provide an idea of what detergents to may merit further study. Furthermore, we briefly discuss alternative solubilization and stabilization agents, such as polymers.
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60
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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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61
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Oligomeric Structure of Anabaena Sensory Rhodopsin in a Lipid Bilayer Environment by Combining Solid-State NMR and Long-range DEER Constraints. J Mol Biol 2017; 429:1903-1920. [DOI: 10.1016/j.jmb.2017.05.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 04/27/2017] [Accepted: 05/06/2017] [Indexed: 11/22/2022]
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Poveda JA, Marcela Giudici A, Lourdes Renart M, Morales A, González-Ros JM. Towards understanding the molecular basis of ion channel modulation by lipids: Mechanistic models and current paradigms. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:1507-1516. [PMID: 28408206 DOI: 10.1016/j.bbamem.2017.04.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Revised: 03/27/2017] [Accepted: 04/09/2017] [Indexed: 10/19/2022]
Abstract
Research on ion channel modulation has become a hot topic because of the key roles these membrane proteins play in both prokaryotic and eukaryotic organisms. In this respect, lipid modulation adds to the overall modulatory mechanisms as a potential via to find new pharmacological targets for drug design based on interfering with lipid/channel interactions. However, our knowledge in this field is scarce and often circumscribed to the sites where lipids bind and/or its final functional consequences. To fully understand this process it is necessary to improve our knowledge on its molecular basis, from the binding sites to the signalling pathways that derive in structural and functional effects on the ion channel. In this review, we have compiled information about such mechanisms and established a classification into four different modes of action. Afterwards, we have revised in more detail the lipid modulation of Cys-loop receptors and of the potassium channel KcsA, which were chosen as model channels modulated by specific lipids. This article is part of a Special Issue entitled: Membrane Lipid Therapy: Drugs Targeting Biomembranes edited by Pablo V. Escribá.
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Affiliation(s)
- José A Poveda
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, 03202 Alicante, Spain.
| | - A Marcela Giudici
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, 03202 Alicante, Spain
| | - M Lourdes Renart
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, 03202 Alicante, Spain
| | - Andrés Morales
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, 03080 Alicante, Spain
| | - José M González-Ros
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, 03202 Alicante, Spain.
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63
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Altrichter S, Haase M, Loh B, Kuhn A, Leptihn S. Mechanism of the Spontaneous and Directional Membrane Insertion of a 2-Transmembrane Ion Channel. ACS Chem Biol 2017; 12:380-388. [PMID: 27960258 DOI: 10.1021/acschembio.6b01085] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Protein insertion into membranes is a process occurring in every cell and every cellular compartment. Yet, many thermodynamic aspects of this fundamental biophysical process are not well understood. We investigated physicochemical parameters that influence protein insertion using the model protein KcsA, a 2-transmembrane ion channel. To understand what drives insertion and to identify individual steps of protein integration into a highly apolar environment, we investigated the contribution of electrostatic interactions and lipid composition on protein insertion on a single molecule level. We show that insertion of KcsA is spontaneous and directional as the cytosolic part of the protein does not translocate across the membrane barrier. Surprisingly, not hydrophobic residues but charged amino acids are crucial for the insertion of the unfolded protein into the membrane. Our results demonstrate the importance of electrostatic interactions between membrane and protein during the insertion process of hydrophobic polypeptides into the apolar membrane. On the basis of the observation that negatively charged lipids increase insertion events while high ionic strength in the surrounding aqueous phase decreases insertion events, a two-step mechanism is proposed. Here, an initial electrostatic attraction between membrane and protein represents the first step prior to insertion of hydrophobic residues into the hydrocarbon core of the membrane.
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Affiliation(s)
- Steffen Altrichter
- Institute of Microbiology
and Molecular Biology, University of Hohenheim, Garbenstrasse 30, 70599 Stuttgart, Germany
| | - Maximilian Haase
- Institute of Microbiology
and Molecular Biology, University of Hohenheim, Garbenstrasse 30, 70599 Stuttgart, Germany
| | - Belinda Loh
- Institute of Microbiology
and Molecular Biology, University of Hohenheim, Garbenstrasse 30, 70599 Stuttgart, Germany
| | - Andreas Kuhn
- Institute of Microbiology
and Molecular Biology, University of Hohenheim, Garbenstrasse 30, 70599 Stuttgart, Germany
| | - Sebastian Leptihn
- Institute of Microbiology
and Molecular Biology, University of Hohenheim, Garbenstrasse 30, 70599 Stuttgart, Germany
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64
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D'Angelo G, Conti Nibali V, Crupi C, Rifici S, Wanderlingh U, Paciaroni A, Sacchetti F, Branca C. Probing Intermolecular Interactions in Phospholipid Bilayers by Far-Infrared Spectroscopy. J Phys Chem B 2017; 121:1204-1210. [PMID: 28118017 DOI: 10.1021/acs.jpcb.6b10323] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fast thermal fluctuations and low frequency phonon modes are thought to play a part in the dynamic mechanisms of many important biological functions in cell membranes. Here we report a detailed far-infrared study of the molecular subpicosecond motions of phospholipid bilayers at various hydrations. We show that these systems sustain several low frequency collective modes and deduce that they arise from vibrations of different lipids interacting through intermolecular van der Waals forces. Furthermore, we observe that the low frequency vibrations of lipid membrane have strong similarities with the subpicosecond motions of liquid water and suggest that resonance mechanisms are an important element to the dynamics coupling between membranes and their hydration water.
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Affiliation(s)
- Giovanna D'Angelo
- Dipartimento di Fisica e Scienze della Terra, Università degli Studi di Messina , 98122 Messina, Italy
| | - Valeria Conti Nibali
- Institute for Physical Chemistry II, Ruhr-University Bochum , 44801 Bochum, Germany
| | - Cristina Crupi
- Dipartimento di Fisica e Scienze della Terra, Università degli Studi di Messina , 98122 Messina, Italy
| | - Simona Rifici
- Dipartimento di Fisica e Scienze della Terra, Università degli Studi di Messina , 98122 Messina, Italy
| | - Ulderico Wanderlingh
- Dipartimento di Fisica e Scienze della Terra, Università degli Studi di Messina , 98122 Messina, Italy
| | - Alessandro Paciaroni
- Dipartimento di Fisica, Università degli Studi di Perugia , 06123 Perugia, Italy
| | - Francesco Sacchetti
- Dipartimento di Fisica, Università degli Studi di Perugia , 06123 Perugia, Italy
| | - Caterina Branca
- Dipartimento di Fisica e Scienze della Terra, Università degli Studi di Messina , 98122 Messina, Italy
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65
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Crystallogenesis of Membrane Proteins Mediated by Polymer-Bounded Lipid Nanodiscs. Structure 2017; 25:384-392. [DOI: 10.1016/j.str.2016.12.004] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 09/20/2016] [Accepted: 12/12/2016] [Indexed: 11/20/2022]
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66
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Combining NMR Spectroscopy and Molecular Dynamics Simulation to Investigate the Structure and Dynamics of Membrane-Associated Proteins. SPRINGER SERIES IN BIOPHYSICS 2017. [DOI: 10.1007/978-3-319-66601-3_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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67
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Miller DM, Findlay HE, Ces O, Templer RH, Booth PJ. Light-activated control of protein channel assembly mediated by membrane mechanics. NANOTECHNOLOGY 2016; 27:494004. [PMID: 27831930 DOI: 10.1088/0957-4484/27/49/494004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Photochemical processes provide versatile triggers of chemical reactions. Here, we use a photoactivated lipid switch to modulate the folding and assembly of a protein channel within a model biological membrane. In contrast to the information rich field of water-soluble protein folding, there is only a limited understanding of the assembly of proteins that are integral to biological membranes. It is however possible to exploit the foreboding hydrophobic lipid environment and control membrane protein folding via lipid bilayer mechanics. Mechanical properties such as lipid chain lateral pressure influence the insertion and folding of proteins in membranes, with different stages of folding having contrasting sensitivities to the bilayer properties. Studies to date have relied on altering bilayer properties through lipid compositional changes made at equilibrium, and thus can only be made before or after folding. We show that light-activation of photoisomerisable di-(5-[[4-(4-butylphenyl)azo]phenoxy]pentyl)phosphate (4-Azo-5P) lipids influences the folding and assembly of the pentameric bacterial mechanosensitive channel MscL. The use of a photochemical reaction enables the bilayer properties to be altered during folding, which is unprecedented. This mechanical manipulation during folding, allows for optimisation of different stages of the component insertion, folding and assembly steps within the same lipid system. The photochemical approach offers the potential to control channel assembly when generating synthetic devices that exploit the mechanosensitive protein as a nanovalve.
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Affiliation(s)
- David M Miller
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia. Department of Medical Biology, The University of Melbourne, 3052, Australia
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Taylor KC, Sanders CR. Regulation of KCNQ/Kv7 family voltage-gated K + channels by lipids. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1859:586-597. [PMID: 27818172 DOI: 10.1016/j.bbamem.2016.10.023] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 10/24/2016] [Accepted: 10/31/2016] [Indexed: 12/19/2022]
Abstract
Many years of studies have established that lipids can impact membrane protein structure and function through bulk membrane effects, by direct but transient annular interactions with the bilayer-exposed surface of protein transmembrane domains, and by specific binding to protein sites. Here, we focus on how phosphatidylinositol 4,5-bisphosphate (PIP2) and polyunsaturated fatty acids (PUFAs) impact ion channel function and how the structural details of the interactions of these lipids with ion channels are beginning to emerge. We focus on the Kv7 (KCNQ) subfamily of voltage-gated K+ channels, which are regulated by both PIP2 and PUFAs and play a variety of important roles in human health and disease. This article is part of a Special Issue entitled: Lipid order/lipid defects and lipid-control of protein activity edited by Dirk Schneider.
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Affiliation(s)
- Keenan C Taylor
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Charles R Sanders
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN, USA; Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
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69
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Focke PJ, Hein C, Hoffmann B, Matulef K, Bernhard F, Dötsch V, Valiyaveetil FI. Combining in Vitro Folding with Cell Free Protein Synthesis for Membrane Protein Expression. Biochemistry 2016; 55:4212-9. [PMID: 27384110 DOI: 10.1021/acs.biochem.6b00488] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cell free protein synthesis (CFPS) has emerged as a promising methodology for protein expression. While polypeptide production is very reliable and efficient using CFPS, the correct cotranslational folding of membrane proteins during CFPS is still a challenge. In this contribution, we describe a two-step protocol in which the integral membrane protein is initially expressed by CFPS as a precipitate followed by an in vitro folding procedure using lipid vesicles for converting the protein precipitate to the correctly folded protein. We demonstrate the feasibility of using this approach for the K(+) channels KcsA and MVP and the amino acid transporter LeuT. We determine the crystal structure of the KcsA channel obtained by CFPS and in vitro folding to show the structural similarity to the cellular expressed KcsA channel and to establish the feasibility of using this two-step approach for membrane protein production for structural studies. Our studies show that the correct folding of these membrane proteins with complex topologies can take place in vitro without the involvement of the cellular machinery for membrane protein biogenesis. This indicates that the folding instructions for these complex membrane proteins are contained entirely within the protein sequence.
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Affiliation(s)
- Paul J Focke
- Program in Chemical Biology, Department of Physiology and Pharmacology, Oregon Health & Science University , 3181 Southwest Sam Jackson Park Road, Portland, Oregon 97239, United States
| | - Christopher Hein
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University , Max-von-Laue Strasse 9, 60438 Frankfurt am Main, Germany
| | - Beate Hoffmann
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University , Max-von-Laue Strasse 9, 60438 Frankfurt am Main, Germany
| | - Kimberly Matulef
- Program in Chemical Biology, Department of Physiology and Pharmacology, Oregon Health & Science University , 3181 Southwest Sam Jackson Park Road, Portland, Oregon 97239, United States
| | - Frank Bernhard
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University , Max-von-Laue Strasse 9, 60438 Frankfurt am Main, Germany
| | - Volker Dötsch
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University , Max-von-Laue Strasse 9, 60438 Frankfurt am Main, Germany
| | - Francis I Valiyaveetil
- Program in Chemical Biology, Department of Physiology and Pharmacology, Oregon Health & Science University , 3181 Southwest Sam Jackson Park Road, Portland, Oregon 97239, United States
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70
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Kim DM, Dikiy I, Upadhyay V, Posson DJ, Eliezer D, Nimigean CM. Conformational heterogeneity in closed and open states of the KcsA potassium channel in lipid bicelles. J Gen Physiol 2016; 148:119-32. [PMID: 27432996 PMCID: PMC4969796 DOI: 10.1085/jgp.201611602] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 06/27/2016] [Indexed: 12/27/2022] Open
Abstract
The process of ion channel gating-opening and closing-involves local and global structural changes in the channel in response to external stimuli. Conformational changes depend on the energetic landscape that underlies the transition between closed and open states, which plays a key role in ion channel gating. For the prokaryotic, pH-gated potassium channel KcsA, closed and open states have been extensively studied using structural and functional methods, but the dynamics within each of these functional states as well as the transition between them is not as well understood. In this study, we used solution nuclear magnetic resonance (NMR) spectroscopy to investigate the conformational transitions within specific functional states of KcsA. We incorporated KcsA channels into lipid bicelles and stabilized them into a closed state by using either phosphatidylcholine lipids, known to favor the closed channel, or mutations designed to trap the channel shut by disulfide cross-linking. A distinct state, consistent with an open channel, was uncovered by the addition of cardiolipin lipids. Using selective amino acid labeling at locations within the channel that are known to move during gating, we observed at least two different slowly interconverting conformational states for both closed and open channels. The pH dependence of these conformations and the predictable disruptions to this dependence observed in mutant channels with altered pH sensing highlight the importance of conformational heterogeneity for KcsA gating.
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Affiliation(s)
- Dorothy M Kim
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY 10065
| | - Igor Dikiy
- Department of Biochemistry, Weill Cornell Medical College, New York, NY 10065
| | - Vikrant Upadhyay
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY 10065
| | - David J Posson
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY 10065 Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065
| | - David Eliezer
- Department of Biochemistry, Weill Cornell Medical College, New York, NY 10065 Brain and Mind Research Institute, Weill Cornell Medical College, New York, NY 10065
| | - Crina M Nimigean
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY 10065 Department of Biochemistry, Weill Cornell Medical College, New York, NY 10065 Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065
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71
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Tong S, Lin Y, Lu S, Wang M, Bogdanov M, Zheng L. Structural Insight into Substrate Selection and Catalysis of Lipid Phosphate Phosphatase PgpB in the Cell Membrane. J Biol Chem 2016; 291:18342-52. [PMID: 27405756 DOI: 10.1074/jbc.m116.737874] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Indexed: 12/19/2022] Open
Abstract
PgpB belongs to the lipid phosphate phosphatase protein family and is one of three bacterial integral membrane phosphatases catalyzing dephosphorylation of phosphatidylglycerol phosphate (PGP) to generate phosphatidylglycerol. Although the structure of its apo form became recently available, the mechanisms of PgpB substrate binding and catalysis are still unclear. We found that PgpB was inhibited by phosphatidylethanolamine (PE) in a competitive mode in vitro Here we report the crystal structure of the lipid-bound form of PgpB. The structure shows that a PE molecule is stabilized in a membrane-embedded tunnel formed by TM3 and the "PSGH" fingerprint peptide near the catalytic site, providing structural insight into PgpB substrate binding mechanism. Noteworthy, in silico docking of varied lipid phosphates exhibited similar substrate binding modes to that of PE, and the residues in the lipid tunnel appear to be important for PgpB catalysis. The catalytic triad in the active site is essential for dephosphorylating substrates lysophosphatidic acid, phosphatidic acid, or sphingosine-1-phosphate but surprisingly not for the native substrate PGP. Remarkably, residue His-207 alone is sufficient to hydrolyze PGP, indicating a specific catalytic mechanism for PgpB in PG biosynthesis. We also identified two novel sensor residues, Lys-93 and Lys-97, on TM3. Our data show that Lys-97 is essential for the recognition of lyso-form substrates. Modification at the Lys-93 position may alter substrate specificity of lipid phosphate phosphatase proteins in prokaryotes versus eukaryotes. These studies reveal new mechanisms of lipid substrate selection and catalysis by PgpB and suggest that the enzyme rests in a PE-stabilized state in the bilayer.
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Affiliation(s)
- Shuilong Tong
- From the Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Houston Medical School, Houston, Texas 77030 and
| | - Yibin Lin
- From the Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Houston Medical School, Houston, Texas 77030 and
| | - Shuo Lu
- From the Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Houston Medical School, Houston, Texas 77030 and
| | - Meitian Wang
- Swiss Light Source, Paul Scherrer Institute, CH-5232 Villigen PSI, Switzerland
| | - Mikhail Bogdanov
- From the Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Houston Medical School, Houston, Texas 77030 and
| | - Lei Zheng
- From the Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Houston Medical School, Houston, Texas 77030 and
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72
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Klein N, Hellmann N, Schneider D. Anionic Lipids Modulate the Activity of the Aquaglyceroporin GlpF. Biophys J 2016; 109:722-31. [PMID: 26287624 DOI: 10.1016/j.bpj.2015.06.063] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 06/11/2015] [Accepted: 06/15/2015] [Indexed: 01/30/2023] Open
Abstract
The structure and composition of a biological membrane can severely influence the activity of membrane-embedded proteins. Here, we show that the E. coli aquaglyceroporin GlpF has only little activity in lipid bilayers formed from native E. coli lipids. Thus, at first glance, GlpF appears to not be optimized for its natural membrane environment. In fact, we found that GlpF activity was severely affected by negatively charged lipids regardless of the exact chemical nature of the lipid headgroup, whereas GlpF was not sensitive to changes in the lateral membrane pressure. These observations illustrate a potential mechanism by which the activity of an α-helical membrane protein is modulated by the negative charge density around the protein.
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Affiliation(s)
- Noreen Klein
- Institut für Pharmazie und Biochemie, Johannes Gutenberg Universität Mainz, Mainz, Germany
| | - Nadja Hellmann
- Institut für Molekulare Biophysik, Johannes Gutenberg Universität Mainz, Mainz, Germany
| | - Dirk Schneider
- Institut für Pharmazie und Biochemie, Johannes Gutenberg Universität Mainz, Mainz, Germany.
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73
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Combs DJ, Lu Z. Sphingomyelinase D inhibits store-operated Ca2+ entry in T lymphocytes by suppressing ORAI current. ACTA ACUST UNITED AC 2016. [PMID: 26216860 PMCID: PMC4516786 DOI: 10.1085/jgp.201511359] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Sphingomyelinase D suppresses Orai current in human T cells and decreases cytokine production, providing a mechanism whereby certain bacteria could inhibit the immune system. Infections caused by certain bacteria including Mycobacterium tuberculosis and Corynebacterium pseudotuberculosis provoke inflammatory responses characterized by the formation of granulomas with necrotic foci—so-called caseous necrosis. The granulomas of infected animals show prominent infiltration by T lymphocytes, and T cell depletion increases host mortality. Notorious zoonotic C. pseudotuberculosis secretes sphingomyelinase (SMase) D, a phospholipase that cleaves off the choline moiety of sphingomyelin, a phospholipid found primarily in the outer leaflet of host cell plasma membranes. Experimental C. pseudotuberculosis strains that lack SMase D are markedly less infectious and unable to spread in hosts, indicating that this enzyme is a crucial virulence factor for sustaining the caseous lymphadenitis infections caused by this microbe. However, the molecular mechanism by which SMase D helps bacteria evade the host’s immune response remains unknown. Here, we find that SMase D inhibits store-operated Ca2+ entry (SOCE) in human T cells and lowers the production of the SOCE-dependent cytokines interleukin-2, which is critical for T cell growth, proliferation, and differentiation, and tumor necrosis factor α, which is crucial for the formation and maintenance of granulomas in microbial infections. SMase D inhibits SOCE through a previously unknown mechanism, namely, suppression of Orai1 current, rather than through altering gating of voltage-gated K+ channels. This finding suggests that, whereas certain genetic mutations abolish Orai1 activity causing severe combined immunodeficiency (SCID), bacteria have the ability to suppress Orai1 activity with SMase D to create an acquired, chronic SCID-like condition that allows persistent infection. Thus, in an example of how virulence factors can disrupt key membrane protein function by targeting phospholipids in host cell membranes, our study has uncovered a novel molecular mechanism that bacteria can use to thwart host immunity.
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Affiliation(s)
- David J Combs
- Department of Physiology, Howard Hughes Medical Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Zhe Lu
- Department of Physiology, Howard Hughes Medical Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
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74
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Skeby KK, Andersen OJ, Pogorelov TV, Tajkhorshid E, Schiøtt B. Conformational Dynamics of the Human Islet Amyloid Polypeptide in a Membrane Environment: Toward the Aggregation Prone Form. Biochemistry 2016; 55:2031-42. [PMID: 26953503 PMCID: PMC5733697 DOI: 10.1021/acs.biochem.5b00507] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Human islet amyloid polypeptide (hIAPP) is a 37-residue peptide hormone, which upon misfolding changes from the physiologically active monomer into pathological amyloid fibril aggregates in the pancreas of type 2 diabetes mellitus patients. During this process, the insulin-producing pancreatic β-cells are damaged; however, the underlying mechanism of this mode of cytotoxicity remains elusive. It is known that anionic lipids accelerate amyloid fibril formation, implicating the importance of the cellular membrane in the process, and that a pH close to the level in the β-cell secretory granules (pH 5.5) inhibits amyloid fibril formation. Using all-atom molecular dynamics simulations, we have investigated the membrane-associated monomer state of α-helical hIAPP, analyzed specific interactions of hIAPP with a mixed anionic-zwitterionic lipid membrane and examined the influence of pH on the structure and dynamics of hIAPP and its interaction with the membrane. We find that hIAPP primarily interacts with the membrane by forming favorable interactions between anionic lipids and the positively charged residues in the N-terminal part of the peptide. Rationalizing experimental findings, the simulations show that the N-terminal part of the peptide interacts with the membrane in the lipid headgroup region. At neutral pH, the C-terminal part of the peptide, which contains the residues that initiate fibril formation, displays a highly dynamic, unfolded state, which interacts with the membrane significantly less than the N-terminal part. Such an unfolded form can be proposed to contribute to the acceleration of fibril formation. At low pH, protonation of His18 mediates a stronger interaction of the C-terminal part with the membrane, resulting in the immobilization of the C-terminal part on the membrane surface that might constitute a mechanism by which low pH inhibits fibril formation.
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Affiliation(s)
- Katrine Kirkeby Skeby
- Center for Insoluble Protein Structures (inSPIN) and Interdisciplinary Nanoscience Center (iNANO) and the Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus, Denmark
| | - Ole Juul Andersen
- Center for Insoluble Protein Structures (inSPIN) and Interdisciplinary Nanoscience Center (iNANO) and the Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus, Denmark
| | - Taras V. Pogorelov
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- School of Chemical Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Emad Tajkhorshid
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Birgit Schiøtt
- Center for Insoluble Protein Structures (inSPIN) and Interdisciplinary Nanoscience Center (iNANO) and the Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus, Denmark
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75
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Rivera-Torres IO, Jin TB, Cadene M, Chait BT, Poget SF. Discovery and characterisation of a novel toxin from Dendroaspis angusticeps, named Tx7335, that activates the potassium channel KcsA. Sci Rep 2016; 6:23904. [PMID: 27044983 PMCID: PMC4820689 DOI: 10.1038/srep23904] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 03/16/2016] [Indexed: 02/07/2023] Open
Abstract
Due to their central role in essential physiological processes, potassium channels are common targets for animal toxins. These toxins in turn are of great value as tools for studying channel function and as lead compounds for drug development. Here, we used a direct toxin pull-down assay with immobilised KcsA potassium channel to isolate a novel KcsA-binding toxin (called Tx7335) from eastern green mamba snake (Dendroaspis angusticeps) venom. Sequencing of the toxin by Edman degradation and mass spectrometry revealed a 63 amino acid residue peptide with 4 disulphide bonds that belongs to the three-finger toxin family, but with a unique modification of its disulphide-bridge scaffold. The toxin induces a dose-dependent increase in both open probabilities and mean open times on KcsA in artificial bilayers. Thus, it unexpectedly behaves as a channel activator rather than an inhibitor. A charybdotoxin-sensitive mutant of KcsA exhibits similar susceptibility to Tx7335 as wild-type, indicating that the binding site for Tx7335 is distinct from that of canonical pore-blocker toxins. Based on the extracellular location of the toxin binding site (far away from the intracellular pH gate), we propose that Tx7335 increases potassium flow through KcsA by allosterically reducing inactivation of the channel.
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Affiliation(s)
- Iván O. Rivera-Torres
- LaGuardia Community College, City University of New York, Long Island City, NY 11101, USA
| | - Tony B. Jin
- Department of Chemistry, CUNY Graduate Center and Institute for Macromolecular Assemblies, College of Staten Island, City University of New York, Staten Island, NY 10314, USA
| | | | | | - Sébastien F. Poget
- Department of Chemistry, CUNY Graduate Center and Institute for Macromolecular Assemblies, College of Staten Island, City University of New York, Staten Island, NY 10314, USA
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76
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Setiadi J, Kuyucak S. Computational Investigation of the Effect of Lipid Membranes on Ion Permeation in Gramicidin A. MEMBRANES 2016; 6:membranes6010020. [PMID: 26999229 PMCID: PMC4812426 DOI: 10.3390/membranes6010020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 03/08/2016] [Accepted: 03/08/2016] [Indexed: 06/05/2023]
Abstract
Membrane proteins are embedded in a lipid bilayer and interact with the lipid molecules in subtle ways. This can be studied experimentally by examining the effect of different lipid bilayers on the function of membrane proteins. Understanding the causes of the functional effects of lipids is difficult to dissect experimentally but more amenable to a computational approach. Here we perform molecular dynamics simulations and free energy calculations to study the effect of two lipid types (POPC and NODS) on the conductance of the gramicidin A (gA) channel. A larger energy barrier is found for the K⁺ potential of mean force in gA embedded in POPC compared to that in NODS, which is consistent with the enhanced experimental conductance of cations in gA embedded in NODS. Further analysis of the contributions to the potential energy of K⁺ reveals that gA and water molecules in gA make similar contributions in both bilayers but there are significant differences between the two bilayers when the lipid molecules and interfacial waters are considered. It is shown that the stronger dipole moments of the POPC head groups create a thicker layer of interfacial waters with better orientation, which ultimately is responsible for the larger energy barrier in the K⁺ PMF in POPC.
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Affiliation(s)
- Jeffry Setiadi
- School of Physics, University of Sydney, Sydney NSW 2006, Australia.
| | - Serdar Kuyucak
- School of Physics, University of Sydney, Sydney NSW 2006, Australia.
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77
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Lipid interaction sites on channels, transporters and receptors: Recent insights from molecular dynamics simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2390-2400. [PMID: 26946244 DOI: 10.1016/j.bbamem.2016.02.037] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 02/25/2016] [Accepted: 02/28/2016] [Indexed: 11/22/2022]
Abstract
Lipid molecules are able to selectively interact with specific sites on integral membrane proteins, and modulate their structure and function. Identification and characterization of these sites are of importance for our understanding of the molecular basis of membrane protein function and stability, and may facilitate the design of lipid-like drug molecules. Molecular dynamics simulations provide a powerful tool for the identification of these sites, complementing advances in membrane protein structural biology and biophysics. We describe recent notable biomolecular simulation studies which have identified lipid interaction sites on a range of different membrane proteins. The sites identified in these simulation studies agree well with those identified by complementary experimental techniques. This demonstrates the power of the molecular dynamics approach in the prediction and characterization of lipid interaction sites on integral membrane proteins. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
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78
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Dörr JM, Scheidelaar S, Koorengevel MC, Dominguez JJ, Schäfer M, van Walree CA, Killian JA. The styrene-maleic acid copolymer: a versatile tool in membrane research. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2016; 45:3-21. [PMID: 26639665 PMCID: PMC4698303 DOI: 10.1007/s00249-015-1093-y] [Citation(s) in RCA: 275] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 10/12/2015] [Accepted: 10/14/2015] [Indexed: 10/28/2022]
Abstract
A new and promising tool in membrane research is the detergent-free solubilization of membrane proteins by styrene-maleic acid copolymers (SMAs). These amphipathic molecules are able to solubilize lipid bilayers in the form of nanodiscs that are bounded by the polymer. Thus, membrane proteins can be directly extracted from cells in a water-soluble form while conserving a patch of native membrane around them. In this review article, we briefly discuss current methods of membrane protein solubilization and stabilization. We then zoom in on SMAs, describe their physico-chemical properties, and discuss their membrane-solubilizing effect. This is followed by an overview of studies in which SMA has been used to isolate and investigate membrane proteins. Finally, potential future applications of the methodology are discussed for structural and functional studies on membrane proteins in a near-native environment and for characterizing protein-lipid and protein-protein interactions.
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Affiliation(s)
- Jonas M Dörr
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research and Institute of Biomembranes, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
| | - Stefan Scheidelaar
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research and Institute of Biomembranes, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Martijn C Koorengevel
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research and Institute of Biomembranes, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Juan J Dominguez
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research and Institute of Biomembranes, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Marre Schäfer
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research and Institute of Biomembranes, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Cornelis A van Walree
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research and Institute of Biomembranes, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, 5001, Australia
| | - J Antoinette Killian
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research and Institute of Biomembranes, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
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79
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Ma QL, Xia H, Zhang ST, Qin DD, Devaramani S, Shan DL, Lu XQ. Investigation of proton-driven amine functionalized tube array as ion responsive biomimetic nanochannels. RSC Adv 2016. [DOI: 10.1039/c5ra25114a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A simple amine embellished tube array was assembled at the liquid–liquid interface to study ion transfer behavior.
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Affiliation(s)
- Qiao-Ling Ma
- Key Laboratory of Bioelectrochemistry & Environmental Analysis of Gansu Province
- College of Chemistry & Chemical Engineering
- Northwest Normal University
- Lanzhou
- China
| | - Hong Xia
- Key Laboratory of Bioelectrochemistry & Environmental Analysis of Gansu Province
- College of Chemistry & Chemical Engineering
- Northwest Normal University
- Lanzhou
- China
| | - Shou-Ting Zhang
- Key Laboratory of Bioelectrochemistry & Environmental Analysis of Gansu Province
- College of Chemistry & Chemical Engineering
- Northwest Normal University
- Lanzhou
- China
| | - Dong-Dong Qin
- Key Laboratory of Bioelectrochemistry & Environmental Analysis of Gansu Province
- College of Chemistry & Chemical Engineering
- Northwest Normal University
- Lanzhou
- China
| | - Samrat Devaramani
- Key Laboratory of Bioelectrochemistry & Environmental Analysis of Gansu Province
- College of Chemistry & Chemical Engineering
- Northwest Normal University
- Lanzhou
- China
| | - Duo-Liang Shan
- Key Laboratory of Bioelectrochemistry & Environmental Analysis of Gansu Province
- College of Chemistry & Chemical Engineering
- Northwest Normal University
- Lanzhou
- China
| | - Xiao-Quan Lu
- Key Laboratory of Bioelectrochemistry & Environmental Analysis of Gansu Province
- College of Chemistry & Chemical Engineering
- Northwest Normal University
- Lanzhou
- China
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80
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Snijder HJA, Hakulinen J. Membrane Protein Production in E. coli for Applications in Drug Discovery. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 896:59-77. [PMID: 27165319 DOI: 10.1007/978-3-319-27216-0_5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Producing high quality purified membrane proteins for structure-based drug design and biophysical assays compatible with typical timelines in drug discovery is a significant challenge. Escherichia coli has been an expression host of the utmost importance for soluble proteins and has applications for membrane proteins as well. However, membrane protein overexpression in E. coli may lead to toxicity and low yields of functional product. Here, we review the challenges encountered with heterologous overproduction of α-helical membrane proteins in E. coli and a range of strategies to overcome them. A detailed protocol is also provided for expression and screening of membrane proteins in E. coli using a His-specific fluorescent probe and fluorescent size-exclusion chromatography.
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Affiliation(s)
| | - Jonna Hakulinen
- Discovery Sciences, AstraZeneca R&D, SE-43183, Mölndal, Sweden
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81
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Ando M, Akiyama M, Okuno D, Hirano M, Ide T, Sawada S, Sasaki Y, Akiyoshi K. Liposome chaperon in cell-free membrane protein synthesis: one-step preparation of KcsA-integrated liposomes and electrophysiological analysis by the planar bilayer method. Biomater Sci 2016; 4:258-64. [DOI: 10.1039/c5bm00285k] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Chaperoning functions of liposomes were investigated using cell-free membrane protein synthesis.
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Affiliation(s)
- M. Ando
- Department of Polymer Chemistry
- Graduate School of Engineering
- Kyoto University
- Kyoto
- Japan
| | - M. Akiyama
- Department of Polymer Chemistry
- Graduate School of Engineering
- Kyoto University
- Kyoto
- Japan
| | - D. Okuno
- Laboratory for Cell Dynamics Observation
- Quantitative Biology Center
- RIKEN
- Osaka 565-0874
- Japan
| | - M. Hirano
- Laboratory for Cell Dynamics Observation
- Quantitative Biology Center
- RIKEN
- Osaka 565-0874
- Japan
| | - T. Ide
- Graduate School of Natural Science and Technology
- Okayama University
- Okayama 700-8530
- Japan
| | - S. Sawada
- Department of Polymer Chemistry
- Graduate School of Engineering
- Kyoto University
- Kyoto
- Japan
| | - Y. Sasaki
- Department of Polymer Chemistry
- Graduate School of Engineering
- Kyoto University
- Kyoto
- Japan
| | - K. Akiyoshi
- Department of Polymer Chemistry
- Graduate School of Engineering
- Kyoto University
- Kyoto
- Japan
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82
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Ion-binding properties of a K+ channel selectivity filter in different conformations. Proc Natl Acad Sci U S A 2015; 112:15096-100. [PMID: 26598654 DOI: 10.1073/pnas.1510526112] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
K(+) channels are membrane proteins that selectively conduct K(+) ions across lipid bilayers. Many voltage-gated K(+) (KV) channels contain two gates, one at the bundle crossing on the intracellular side of the membrane and another in the selectivity filter. The gate at the bundle crossing is responsible for channel opening in response to a voltage stimulus, whereas the gate at the selectivity filter is responsible for C-type inactivation. Together, these regions determine when the channel conducts ions. The K(+) channel from Streptomyces lividians (KcsA) undergoes an inactivation process that is functionally similar to KV channels, which has led to its use as a practical system to study inactivation. Crystal structures of KcsA channels with an open intracellular gate revealed a selectivity filter in a constricted conformation similar to the structure observed in closed KcsA containing only Na(+) or low [K(+)]. However, recent work using a semisynthetic channel that is unable to adopt a constricted filter but inactivates like WT channels challenges this idea. In this study, we measured the equilibrium ion-binding properties of channels with conductive, inactivated, and constricted filters using isothermal titration calorimetry (ITC). EPR spectroscopy was used to determine the state of the intracellular gate of the channel, which we found can depend on the presence or absence of a lipid bilayer. Overall, we discovered that K(+) ion binding to channels with an inactivated or conductive selectivity filter is different from K(+) ion binding to channels with a constricted filter, suggesting that the structures of these channels are different.
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83
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Molina ML, Giudici AM, Poveda JA, Fernández-Ballester G, Montoya E, Renart ML, Fernández AM, Encinar JA, Riquelme G, Morales A, González-Ros JM. Competing Lipid-Protein and Protein-Protein Interactions Determine Clustering and Gating Patterns in the Potassium Channel from Streptomyces lividans (KcsA). J Biol Chem 2015; 290:25745-55. [PMID: 26336105 DOI: 10.1074/jbc.m115.669598] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Indexed: 11/06/2022] Open
Abstract
There is increasing evidence to support the notion that membrane proteins, instead of being isolated components floating in a fluid lipid environment, can be assembled into supramolecular complexes that take part in a variety of cooperative cellular functions. The interplay between lipid-protein and protein-protein interactions is expected to be a determinant factor in the assembly and dynamics of such membrane complexes. Here we report on a role of anionic phospholipids in determining the extent of clustering of KcsA, a model potassium channel. Assembly/disassembly of channel clusters occurs, at least partly, as a consequence of competing lipid-protein and protein-protein interactions at nonannular lipid binding sites on the channel surface and brings about profound changes in the gating properties of the channel. Our results suggest that these latter effects of anionic lipids are mediated via the Trp(67)-Glu(71)-Asp(80) inactivation triad within the channel structure and its bearing on the selectivity filter.
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Affiliation(s)
- M Luisa Molina
- From the Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, 03202 Alicante, Spain
| | - A Marcela Giudici
- From the Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, 03202 Alicante, Spain
| | - José A Poveda
- From the Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, 03202 Alicante, Spain
| | | | - Estefanía Montoya
- From the Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, 03202 Alicante, Spain
| | - M Lourdes Renart
- From the Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, 03202 Alicante, Spain
| | - Asia M Fernández
- From the Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, 03202 Alicante, Spain
| | - José A Encinar
- From the Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, 03202 Alicante, Spain
| | - Gloria Riquelme
- the Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, 1027 Santiago, Chile, and
| | - Andrés Morales
- the Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, 03080 Alicante, Spain
| | - José M González-Ros
- From the Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, 03202 Alicante, Spain,
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84
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Lindholm L, Ariöz C, Jawurek M, Liebau J, Mäler L, Wieslander Å, von Ballmoos C, Barth A. Effect of lipid bilayer properties on the photocycle of green proteorhodopsin. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:698-708. [DOI: 10.1016/j.bbabio.2015.04.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 04/17/2015] [Accepted: 04/21/2015] [Indexed: 01/20/2023]
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85
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Rice AJ, Alvarez FJD, Davidson AL, Pinkett HW. Effects of lipid environment on the conformational changes of an ABC importer. Channels (Austin) 2015; 8:327-33. [PMID: 24852576 PMCID: PMC4203734 DOI: 10.4161/chan.29294] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
In order to shuttle substrates across the lipid bilayer, membrane proteins undergo a series of conformation changes that are influenced by protein structure, ligands, and the lipid environment. To test the effect of lipid on conformation change of the ABC transporter MolBC, EPR studies were conducted in lipids and detergents of variable composition. In both a detergent and lipid environment, MolBC underwent the same general conformation changes as detected by site-directed EPR spectroscopy. However, differences in activity and the details of the EPR analysis indicate conformational rigidity that is dependent on the lipid environment. From these observations, we conclude that native-like lipid mixtures provide the transporter with greater activity and conformational flexibility as well as technical advantages such as reconstitution efficiency and protein stability.
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86
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Kuang Q, Purhonen P, Hebert H. Structure of potassium channels. Cell Mol Life Sci 2015; 72:3677-93. [PMID: 26070303 PMCID: PMC4565861 DOI: 10.1007/s00018-015-1948-5] [Citation(s) in RCA: 167] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Revised: 05/09/2015] [Accepted: 06/03/2015] [Indexed: 12/25/2022]
Abstract
Potassium channels ubiquitously exist in nearly all kingdoms of life and perform diverse but important functions. Since the first atomic structure of a prokaryotic potassium channel (KcsA, a channel from Streptomyces lividans) was determined, tremendous progress has been made in understanding the mechanism of potassium channels and channels conducting other ions. In this review, we discuss the structure of various kinds of potassium channels, including the potassium channel with the pore-forming domain only (KcsA), voltage-gated, inwardly rectifying, tandem pore domain, and ligand-gated ones. The general properties shared by all potassium channels are introduced first, followed by specific features in each class. Our purpose is to help readers to grasp the basic concepts, to be familiar with the property of the different domains, and to understand the structure and function of the potassium channels better.
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Affiliation(s)
- Qie Kuang
- Department of Biosciences and Nutrition, Karolinska Institutet, Novum, 14183, Huddinge, Sweden.
- School of Technology and Health, KTH Royal Institute of Technology, Novum, 14183, Huddinge, Sweden.
| | - Pasi Purhonen
- Department of Biosciences and Nutrition, Karolinska Institutet, Novum, 14183, Huddinge, Sweden
| | - Hans Hebert
- Department of Biosciences and Nutrition, Karolinska Institutet, Novum, 14183, Huddinge, Sweden
- School of Technology and Health, KTH Royal Institute of Technology, Novum, 14183, Huddinge, Sweden
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87
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Effects of monoterpenes on ion channels of excitable cells. Pharmacol Ther 2015; 152:83-97. [PMID: 25956464 DOI: 10.1016/j.pharmthera.2015.05.006] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 04/23/2015] [Indexed: 11/20/2022]
Abstract
Monoterpenes are a structurally diverse group of phytochemicals and a major constituent of plant-derived 'essential oils'. Monoterpenes such as menthol, carvacrol, and eugenol have been utilized for therapeutical purposes and food additives for centuries and have been reported to have anti-inflammatory, antioxidant and analgesic actions. In recent years there has been increasing interest in understanding the pharmacological actions of these molecules. There is evidence indicating that monoterpenes can modulate the functional properties of several types of voltage and ligand-gated ion channels, suggesting that some of their pharmacological actions may be mediated by modulations of ion channel function. In this report, we review the literature concerning the interaction of monoterpenes with various ion channels.
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88
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Stangl M, Schneider D. Functional competition within a membrane: Lipid recognition vs. transmembrane helix oligomerization. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:1886-96. [PMID: 25791349 DOI: 10.1016/j.bbamem.2015.03.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 03/09/2015] [Accepted: 03/09/2015] [Indexed: 12/27/2022]
Abstract
Binding of specific lipids to large, polytopic membrane proteins is well described, and it is clear that such lipids are crucial for protein stability and activity. In contrast, binding of defined lipid species to individual transmembrane helices and regulation of transmembrane helix monomer-oligomer equilibria by binding of distinct lipids is a concept, which has emerged only lately. Lipids bind to single-span membrane proteins, both in the juxta-membrane region as well as in the hydrophobic membrane core. While some interactions counteract transmembrane helix oligomerization, in other cases lipid binding appears to enhance oligomerization. As reversible oligomerization is involved in activation of many membrane proteins, binding of defined lipids to single-span transmembrane proteins might be a mechanism to regulate and/or fine-tune the protein activity. But how could lipid binding trigger the activity of a protein? How can binding of a single lipid molecule to a transmembrane helix affect the structure of a transmembrane helix oligomer, and consequently its signaling state? These questions are discussed in the present article based on recent results obtained with simple, single-span transmembrane proteins. This article is part of a Special Issue entitled: Lipid-protein interactions.
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Affiliation(s)
- Michael Stangl
- Department of Pharmacy and Biochemistry, Johannes-Gutenberg-University Mainz, Johann-Joachim-Becher-Weg 30, 55128 Mainz, Germany
| | - Dirk Schneider
- Department of Pharmacy and Biochemistry, Johannes-Gutenberg-University Mainz, Johann-Joachim-Becher-Weg 30, 55128 Mainz, Germany.
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89
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McIlwain BC, Vandenberg RJ, Ryan RM. Transport rates of a glutamate transporter homologue are influenced by the lipid bilayer. J Biol Chem 2015; 290:9780-8. [PMID: 25713135 DOI: 10.1074/jbc.m114.630590] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Indexed: 11/06/2022] Open
Abstract
The aspartate transporter from Pyrococcus horikoshii (GltPh) is a model for the structure of the SLC1 family of amino acid transporters. Crystal structures of GltPh provide insight into mechanisms of ion coupling and substrate transport; however, structures have been solved in the absence of a lipid bilayer so they provide limited information regarding interactions that occur between the protein and lipids of the membrane. Here, we investigated the effect of the lipid environment on aspartate transport by reconstituting GltPh into liposomes of defined lipid composition where the primary lipid is phosphatidylethanolamine (PE) or its methyl derivatives. We showed that the rate of aspartate transport and the transmembrane orientation of GltPh were influenced by the primary lipid in the liposomes. In PE liposomes, we observed the highest transport rate and showed that 85% of the transporters were orientated right-side out, whereas in trimethyl PE liposomes, 50% of transporters were right-side out, and we observed a 4-fold reduction in transport rate. Differences in orientation can only partially explain the lipid composition effect on transport rate. Crystal structures of GltPh revealed a tyrosine residue (Tyr-33) that we propose interacts with lipid headgroups during the transport cycle. Based on site-directed mutagenesis, we propose that a cation-π interaction between Tyr-33 and the lipid headgroups can influence conformational flexibility of the trimerization domain and thus the rate of transport. These results provide a specific example of how interactions between membrane lipids and membrane-bound proteins can influence function and highlight the importance of the role of the membrane in transporter function.
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Affiliation(s)
- Benjamin C McIlwain
- From the Transporter Biology Group, Discipline of Pharmacology and Bosch Institute, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Robert J Vandenberg
- From the Transporter Biology Group, Discipline of Pharmacology and Bosch Institute, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Renae M Ryan
- From the Transporter Biology Group, Discipline of Pharmacology and Bosch Institute, University of Sydney, Sydney, New South Wales 2006, Australia
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90
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Focke PJ, Annen AW, Valiyaveetil FI. Engineering the glutamate transporter homologue GltPh using protein semisynthesis. Biochemistry 2015; 54:1694-702. [PMID: 25649707 DOI: 10.1021/bi501477y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Glutamate transporters catalyze the concentrative uptake of glutamate from synapses and are essential for normal synaptic function. Despite extensive investigations of glutamate transporters, the mechanisms underlying substrate recognition, ion selectivity, and the coupling of substrate and ion transport are not well-understood. Deciphering these mechanisms requires the ability to precisely engineer the transporter. In this study, we describe the semisynthesis of GltPh, an archaeal homologue of glutamate transporters. Semisynthesis allows the precise engineering of GltPh through the incorporation of unnatural amino acids and peptide backbone modifications. In the semisynthesis, the GltPh polypeptide is initially assembled from a recombinantly expressed thioester peptide and a chemically synthesized peptide using the native chemical ligation reaction followed by in vitro folding to the native state. We have developed a robust procedure for the in vitro folding of GltPh. Biochemical characterization of the semisynthetic GltPh indicates that it is similar to the native transporter. We used semisynthesis to substitute Arg397, a highly conserved residue in the substrate binding site, with the unnatural analogue, citrulline. Our studies demonstrate that Arg397 is required for high-affinity substrate binding, and on the basis of our results, we propose that Arg397 is involved in a Na+-dependent remodeling of the substrate binding site required for high-affinity Asp binding. We anticipate that the semisynthetic approach developed in this study will be extremely useful in investigating functional mechanisms in GltPh. Further, the approach developed in this study should also be applicable to other membrane transport proteins.
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Affiliation(s)
- Paul J Focke
- Program in Chemical Biology, Department of Physiology and Pharmacology, Oregon Health & Science University , 3181 Southwest Sam Jackson Park Road, Portland, Oregon 97239, United States
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91
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Hong H. Role of Lipids in Folding, Misfolding and Function of Integral Membrane Proteins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 855:1-31. [DOI: 10.1007/978-3-319-17344-3_1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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92
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Dörr JM, Koorengevel MC, Schäfer M, Prokofyev AV, Scheidelaar S, van der Cruijsen EAW, Dafforn TR, Baldus M, Killian JA. Detergent-free isolation, characterization, and functional reconstitution of a tetrameric K+ channel: the power of native nanodiscs. Proc Natl Acad Sci U S A 2014; 111:18607-12. [PMID: 25512535 PMCID: PMC4284610 DOI: 10.1073/pnas.1416205112] [Citation(s) in RCA: 244] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
A major obstacle in the study of membrane proteins is their solubilization in a stable and active conformation when using detergents. Here, we explored a detergent-free approach to isolating the tetrameric potassium channel KcsA directly from the membrane of Escherichia coli, using a styrene-maleic acid copolymer. This polymer self-inserts into membranes and is capable of extracting membrane patches in the form of nanosize discoidal proteolipid particles or "native nanodiscs." Using circular dichroism and tryptophan fluorescence spectroscopy, we show that the conformation of KcsA in native nanodiscs is very similar to that in detergent micelles, but that the thermal stability of the protein is higher in the nanodiscs. Furthermore, as a promising new application, we show that quantitative analysis of the co-isolated lipids in purified KcsA-containing nanodiscs allows determination of preferential lipid-protein interactions. Thin-layer chromatography experiments revealed an enrichment of the anionic lipids cardiolipin and phosphatidylglycerol, indicating their close proximity to the channel in biological membranes and supporting their functional relevance. Finally, we demonstrate that KcsA can be reconstituted into planar lipid bilayers directly from native nanodiscs, which enables functional characterization of the channel by electrophysiology without first depriving the protein of its native environment. Together, these findings highlight the potential of the use of native nanodiscs as a tool in the study of ion channels, and of membrane proteins in general.
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Affiliation(s)
- Jonas M Dörr
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands;
| | - Martijn C Koorengevel
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Marre Schäfer
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Alexander V Prokofyev
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands; and
| | - Stefan Scheidelaar
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Elwin A W van der Cruijsen
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands; and
| | - Timothy R Dafforn
- School of Bio Sciences, University of Birmingham, Edgbaston Birmingham B15 2TT, United Kingdom
| | - Marc Baldus
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands; and
| | - J Antoinette Killian
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
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93
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Folding membrane proteins in vitro: A table and some comments. Arch Biochem Biophys 2014; 564:314-26. [DOI: 10.1016/j.abb.2014.06.029] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 06/17/2014] [Accepted: 06/23/2014] [Indexed: 12/23/2022]
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94
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Folding energetics and oligomerization of polytopic α-helical transmembrane proteins. Arch Biochem Biophys 2014; 564:281-96. [DOI: 10.1016/j.abb.2014.07.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 06/26/2014] [Accepted: 07/14/2014] [Indexed: 01/06/2023]
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95
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Rusinova R, Kim DM, Nimigean CM, Andersen OS. Regulation of ion channel function by the host lipid bilayer examined by a stopped-flow spectrofluorometric assay. Biophys J 2014; 106:1070-8. [PMID: 24606931 DOI: 10.1016/j.bpj.2014.01.027] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 01/03/2014] [Accepted: 01/07/2014] [Indexed: 01/16/2023] Open
Abstract
To examine the function of ligand-gated ion channels in a defined membrane environment, we developed a robust sequential-mixing fluorescence-based stopped-flow assay. Channel activity is determined using a channel-permeable quencher (e.g., thallium, Tl(+)) of a water-soluble fluorophore (8-aminonaphthalene-1,3,6-trisulfonic acid) encapsulated in large unilamellar vesicles in which the channel of interest has been reconstituted, which allows for rapid solution changes. To validate the method, we explored the activation of wild-type KcsA channel, as well as it's noninactivating (E71A) KcsA mutant, by extravesicular protons (H(+)). For both channel types, the day-to-day variability in the reconstitution yield (as judged from the time course of fluorescence quenching) is <10%. The activation curve for E71A KcsA is similar to that obtained previously using single-channel electrophysiology, and the activation curves for wild-type and E71A KcsA are indistinguishable, indicating that channel activation and inactivation are separate processes. We then investigated the regulation of KcsA activation by changes in lipid bilayer composition. Increasing the acyl chain length (from C18:1 to C22:1 in diacylphosphatidylcholine), but not the mole fraction of POPG (>0.25) in the bilayer-forming phospholipid mixture, alters KcsA H(+) gating. The bilayer-thickness-dependent shift in the activation curve is suggestive of a decrease in an apparent H(+) affinity and cooperativity. The control over bilayer environment and time resolution makes this method a powerful assay for exploring ligand activation and inactivation of ion channels, and how channel gating varies with changes in the channels' lipid bilayer environment or other regulatory processes.
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Affiliation(s)
- Radda Rusinova
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York; Department of Anesthesiology, Weill Cornell Medical College, New York, New York.
| | - Dorothy M Kim
- Department of Anesthesiology, Weill Cornell Medical College, New York, New York
| | - Crina M Nimigean
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York; Department of Anesthesiology, Weill Cornell Medical College, New York, New York
| | - Olaf S Andersen
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York
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96
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Yuan C, Velázquez-Marrero C, Bernardo A, Treistman SN. Lipids modulate the increase of BK channel calcium sensitivity by the β1 subunit. PLoS One 2014; 9:e107917. [PMID: 25254644 PMCID: PMC4177886 DOI: 10.1371/journal.pone.0107917] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 08/24/2014] [Indexed: 11/18/2022] Open
Abstract
Co-expression of the auxiliary β1 subunit with the pore forming α subunit of BK dramatically alters apparent calcium sensitivity. Investigation of the mechanism underlying the increase in calcium sensitivity of BK in smooth muscle has concentrated on the energetic effect of β1's interaction with α. We take a novel approach, exploring whether β1 modification of calcium sensitivity reflects altered interaction between the channel protein and surrounding lipids. We reconstituted hSlo BK α and BK α+β1 channels into two sets of bilayers. One set contained POPE with POPS, POPG, POPA and POPC, where the length of acyl chains is constant, but surface charge differs. The second set is a series of neutral bilayers formed from DOPE with phosphatidylcholines (PCs) of varying acyl chain lengths: C (14:1), C (18:1), C (22:1) and C (24:1), and with brain sphingomyelin (SPM), in which surface charge is constant, but bilayer thickness varies. The increase in calcium sensitivity caused by the β1 subunit was preserved in negatively charged lipid bilayers but not in neutral bilayers, indicating that modification of apparent Ca(2+) sensitivity by β1 is modulated by membrane lipids, requiring negatively charged lipids in the membrane. Moreover, the presence of β1 reduces BK activity in thin bilayers of PC 14:1 and thick bilayers containing SPM, but has no significant effect on activity of BK in PC 18:1, PC 22:1 and PC 24:1 bilayers. These data suggest that auxiliary β1 subunits fine-tune channel gating not only through direct subunit-subunit interactions but also by modulating lipid-protein interactions.
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Affiliation(s)
- Chunbo Yuan
- Institute of Neurobiology, University of Puerto Rico, San Juan, Puerto Rico
| | | | - Alexandra Bernardo
- Institute of Neurobiology, University of Puerto Rico, San Juan, Puerto Rico
| | - Steven N. Treistman
- Institute of Neurobiology, University of Puerto Rico, San Juan, Puerto Rico
- * E-mail:
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97
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Sachse R, Dondapati SK, Fenz SF, Schmidt T, Kubick S. Membrane protein synthesis in cell-free systems: From bio-mimetic systems to bio-membranes. FEBS Lett 2014; 588:2774-81. [DOI: 10.1016/j.febslet.2014.06.007] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 05/30/2014] [Accepted: 06/02/2014] [Indexed: 01/28/2023]
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98
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Olguín Y, Carrascosa LG, Lechuga LM, Young M. The effects of lipids and surfactants on TLR5-proteoliposome functionality for flagellin detection using surface plasmon resonance biosensing. Talanta 2014; 126:136-44. [PMID: 24881544 DOI: 10.1016/j.talanta.2014.03.065] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 03/25/2014] [Accepted: 03/27/2014] [Indexed: 12/15/2022]
Abstract
The use of proteoliposomes as affinity elements in conjunction with a surface plasmon resonance sensor is a high-sensitivity alternative for the detection of multiple analytes. However, one of the most important aspects of these conformations is maintaining the functionality of the immobilized protein, which is determined by the choice of lipids and surfactants employed in the reconstitutions. Previously, we demonstrated the functionality of TLR5-proteoliposomes as screening affinity elements of bacterial flagellin. In this new study we change the conditions of immobilization of TLR5 and evaluate how the fluidity of the membrane and the final size of the liposomes affect the functionality of the construct and thus increase their utility as an affinity element for design of new biosensors. In particular, we used reconstructions into preformed liposomes composed of the lipids POPC, POPC-DMPC and POPC-POPE mediated by the use of surfactants OG, Triton X100, and DDM, respectively. The affinity results were evaluated by SPR technology proteoliposomes and were correlated with the anisotropic change in the membrane status; the final sizes of the proteoliposomes were estimated. Our results clearly show the dependence of fluidity and final size of the proteoliposomes with surface plasmon resonance affinity measurements.
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Affiliation(s)
- Y Olguín
- Biotechnology Center, Federico Santa Maria Technical University, Valparaíso, Chile.
| | - L G Carrascosa
- Nanobiosensor and Bioanalytical Applications Group, Institut Catàla de Nanociencia i Nanotecnología (ICN2), CSIC and CIBER-BBN, Bellaterra, Barcelona, Spain
| | - L M Lechuga
- Nanobiosensor and Bioanalytical Applications Group, Institut Catàla de Nanociencia i Nanotecnología (ICN2), CSIC and CIBER-BBN, Bellaterra, Barcelona, Spain
| | - M Young
- Biotechnology Center, Federico Santa Maria Technical University, Valparaíso, Chile
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Poveda J, Giudici A, Renart M, Molina M, Montoya E, Fernández-Carvajal A, Fernández-Ballester G, Encinar J, González-Ros J. Lipid modulation of ion channels through specific binding sites. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:1560-7. [DOI: 10.1016/j.bbamem.2013.10.023] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Revised: 10/24/2013] [Accepted: 10/30/2013] [Indexed: 01/08/2023]
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100
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Zaydman MA, Cui J. PIP2 regulation of KCNQ channels: biophysical and molecular mechanisms for lipid modulation of voltage-dependent gating. Front Physiol 2014; 5:195. [PMID: 24904429 PMCID: PMC4034418 DOI: 10.3389/fphys.2014.00195] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Accepted: 05/08/2014] [Indexed: 12/28/2022] Open
Abstract
Voltage-gated potassium (Kv) channels contain voltage-sensing (VSD) and pore-gate (PGD) structural domains. During voltage-dependent gating, conformational changes in the two domains are coupled giving rise to voltage-dependent opening of the channel. In addition to membrane voltage, KCNQ (Kv7) channel opening requires the membrane lipid phosphatidylinositol 4,5-bisphosphate (PIP2). Recent studies suggest that PIP2 serves as a cofactor to mediate VSD-PGD coupling in KCNQ1 channels. In this review, we put these findings in the context of the current understanding of voltage-dependent gating, lipid modulation of Kv channel activation, and PIP2-regulation of KCNQ channels. We suggest that lipid-mediated coupling of functional domains is a common mechanism among KCNQ channels that may be applicable to other Kv channels and membrane proteins.
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Affiliation(s)
- Mark A Zaydman
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Diseases, Cardiac Bioelectricity and Arrhythmia Center, Washington University in St. Louis St. Louis, MO, USA
| | - Jianmin Cui
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Diseases, Cardiac Bioelectricity and Arrhythmia Center, Washington University in St. Louis St. Louis, MO, USA
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