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Temperini ME, Polito R, Venanzi T, Baldassarre L, Hu H, Ciracì C, Pea M, Notargiacomo A, Mattioli F, Ortolani M, Giliberti V. An Infrared Nanospectroscopy Technique for the Study of Electric-Field-Induced Molecular Dynamics. NANO LETTERS 2024; 24:9808-9815. [PMID: 39089683 PMCID: PMC11328210 DOI: 10.1021/acs.nanolett.4c01387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Static electric fields play a considerable role in a variety of molecular nanosystems as diverse as single-molecule junctions, molecules supporting electrostatic catalysis, and biological cell membranes incorporating proteins. External electric fields can be applied to nanoscale samples with a conductive atomic force microscopy (AFM) probe in contact mode, but typically, no structural information is retrieved. Here we combine photothermal expansion infrared (IR) nanospectroscopy with electrostatic AFM probes to measure nanometric volumes where the IR field enhancement and the static electric field overlap spatially. We leverage the vibrational Stark effect in the polymer poly(methyl methacrylate) for calibrating the local electric field strength. In the relevant case of membrane protein bacteriorhodopsin, we observe electric-field-induced changes of the protein backbone conformation and residue protonation state. The proposed technique also has the potential to measure DC currents and IR spectra simultaneously, insofar enabling the monitoring of the possible interplay between charge transport and other effects.
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Affiliation(s)
- Maria Eleonora Temperini
- Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro 5, I-00185 Roma, Italy
- Center for Life Nano- & Neuro-Science, Istituto Italiano di Tecnologia, Viale Regina Elena 291, I-00161 Roma, Italy
| | - Raffaella Polito
- Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro 5, I-00185 Roma, Italy
| | - Tommaso Venanzi
- Center for Life Nano- & Neuro-Science, Istituto Italiano di Tecnologia, Viale Regina Elena 291, I-00161 Roma, Italy
| | - Leonetta Baldassarre
- Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro 5, I-00185 Roma, Italy
| | - Huatian Hu
- Center for Biomolecular Nanotechnologies, Istituto Italiano di Tecnologia, Via Barsanti 14, I-73010 Arnesano, Italy
| | - Cristian Ciracì
- Center for Biomolecular Nanotechnologies, Istituto Italiano di Tecnologia, Via Barsanti 14, I-73010 Arnesano, Italy
| | - Marialilia Pea
- Istituto di Fotonica e Nanotecnologie, Consiglio Nazionale delle Ricerche, Via del Fosso del Cavaliere 100, I-00133 Roma, Italy
| | - Andrea Notargiacomo
- Istituto di Fotonica e Nanotecnologie, Consiglio Nazionale delle Ricerche, Via del Fosso del Cavaliere 100, I-00133 Roma, Italy
| | - Francesco Mattioli
- Istituto di Fotonica e Nanotecnologie, Consiglio Nazionale delle Ricerche, Via del Fosso del Cavaliere 100, I-00133 Roma, Italy
| | - Michele Ortolani
- Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro 5, I-00185 Roma, Italy
- Center for Life Nano- & Neuro-Science, Istituto Italiano di Tecnologia, Viale Regina Elena 291, I-00161 Roma, Italy
| | - Valeria Giliberti
- Center for Life Nano- & Neuro-Science, Istituto Italiano di Tecnologia, Viale Regina Elena 291, I-00161 Roma, Italy
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Chen X, Al-Mualem ZA, Baiz CR. Lipid Landscapes: Vibrational Spectroscopy for Decoding Membrane Complexity. Annu Rev Phys Chem 2024; 75:283-305. [PMID: 38382566 DOI: 10.1146/annurev-physchem-090722-010230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Cell membranes are incredibly complex environments containing hundreds of components. Despite substantial advances in the past decade, fundamental questions related to lipid-lipid interactions and heterogeneity persist. This review explores the complexity of lipid membranes, showcasing recent advances in vibrational spectroscopy to characterize the structure, dynamics, and interactions at the membrane interface. We include an overview of modern techniques such as surface-enhanced infrared spectroscopy as a steady-state technique with single-bilayer sensitivity, two-dimensional sum-frequency generation spectroscopy, and two-dimensional infrared spectroscopy to measure time-evolving structures and dynamics with femtosecond time resolution. Furthermore, we discuss the potential of multiscale molecular dynamics (MD) simulations, focusing on recently developed simulation algorithms, which have emerged as a powerful approach to interpret complex spectra. We highlight the ongoing challenges in studying heterogeneous environments in multicomponent membranes via current vibrational spectroscopic techniques and MD simulations. Overall, this review provides an up-to-date comprehensive overview of the powerful combination of vibrational spectroscopy and simulations, which has great potential to illuminate lipid-lipid, lipid-protein, and lipid-water interactions in the intricate conformational landscape of cell membranes.
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Affiliation(s)
- Xiaobing Chen
- Department of Chemistry, University of Texas at Austin, Austin, Texas, USA;
| | | | - Carlos R Baiz
- Department of Chemistry, University of Texas at Austin, Austin, Texas, USA;
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Bodine M, Rozyyev V, Elam JW, Tokmakoff A, Lewis NHC. Vibrational Probe at the Electrochemical Interface: Dependence on Plasmon Coupling and Potential of the Lineshape in Two-Dimensional Infrared Spectroscopy. J Phys Chem Lett 2023:11092-11099. [PMID: 38051916 DOI: 10.1021/acs.jpclett.3c02987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Two-dimensional infrared spectroscopy of vibrational probes at an electrode surface shows promise for studying the structural dynamics at an active electrochemical interface. This interface is a complex environment where the solution structures in response to the applied potential. A strategy for achieving the necessary monolayer sensitivity is to use a plasmonically active electrode, which enhances the electromagnetic fields that produce the spectroscopic response. Here, we show how the coupling between the plasmon and the vibrations of the molecular monolayer impacts the FTIR and 2D IR spectroscopy, with an emphasis on the electrochemical potential difference spectra. We show how mixing between the vibrational and plasmonic states gives rise to the distortions that are observed in these measurements. This provides an important step toward 2D IR measurements of vibrational probes at the electrochemical interface as a tool for probing the structural dynamics in the double layer.
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Affiliation(s)
- Melissa Bodine
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Vepa Rozyyev
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois 60637, United States
- Applied Materials Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Jeffrey W Elam
- Applied Materials Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Andrei Tokmakoff
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Nicholas H C Lewis
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
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Ryan M, Gao L, Valiyaveetil FI, Zanni MT, Kananenka AA. Probing Ion Configurations in the KcsA Selectivity Filter with Single-Isotope Labels and 2D IR Spectroscopy. J Am Chem Soc 2023; 145:18529-18537. [PMID: 37578394 PMCID: PMC10450685 DOI: 10.1021/jacs.3c05339] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Indexed: 08/15/2023]
Abstract
The potassium ion (K+) configurations of the selectivity filter of the KcsA ion channel protein are investigated with two-dimensional infrared (2D IR) spectroscopy of amide I vibrations. Single 13C-18O isotope labels are used, for the first time, to selectively probe the S1/S2 or S2/S3 binding sites in the selectivity filter. These binding sites have the largest differences in ion occupancy in two competing K+ transport mechanisms: soft-knock and hard-knock. According to the former, water molecules alternate between K+ ions in the selectivity filter while the latter assumes that K+ ions occupy the adjacent sites. Molecular dynamics simulations and computational spectroscopy are employed to interpret experimental 2D IR spectra. We find that in the closed conductive state of the KcsA channel, K+ ions do not occupy adjacent binding sites. The experimental data is consistent with simulated 2D IR spectra of soft-knock ion configurations. In contrast, the simulated spectra for the hard-knock ion configurations do not reproduce the experimental results. 2D IR spectra of the hard-knock mechanism have lower frequencies, homogeneous 2D lineshapes, and multiple peaks. In contrast, ion configurations of the soft-knock model produce 2D IR spectra with a single peak at a higher frequency and inhomogeneous lineshape. We conclude that under equilibrium conditions, in the absence of transmembrane voltage, both water and K+ ions occupy the selectivity filter of the KcsA channel in the closed conductive state. The ion configuration is central to the mechanism of ion transport through potassium channels.
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Affiliation(s)
- Matthew
J. Ryan
- Department
of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Lujia Gao
- Department
of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Francis I. Valiyaveetil
- Department
of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Martin T. Zanni
- Department
of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Alexei A. Kananenka
- Department
of Physics and Astronomy, University of
Delaware, Newark, Delaware 19716, United States
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Su Z, Leitch JJ, Lipkowski J. Effect of Lipid Composition on the Inhibition Mechanism of Amiloride on Alamethicin Ion Channels in Supported Phospholipid Bilayers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:8398-8406. [PMID: 35749587 DOI: 10.1021/acs.langmuir.2c00953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The inhibition effect of amiloride on alamethicin ion channels was studied in a model zwitterionic floating bilayer lipid membrane (fBLM). The EIS studies indicated that amiloride prevents the transport of ions through the alamethicin channels leading to an overall increase in membrane resistance. The PM-IRRAS data demonstrated that amiloride has no influence on the secondary structure of alamethicin but restricts the insertion of the peptides into the bilayer and blocks ion transport through preformed alamethicin channels. The effect of amiloride on ion channel formation in the floating bilayer formed by a zwitterionic lipid was compared to those of previous studies involving negatively charged fBLMs and tethered zwitterionic lipid bilayers. The findings from these studies show that the effects of amiloride on ion channel formation strongly depend on the mobility and charge of the membrane lipids.
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Affiliation(s)
- ZhangFei Su
- Department of Chemistry, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - J Jay Leitch
- Department of Chemistry, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Jacek Lipkowski
- Department of Chemistry, University of Guelph, Guelph, Ontario N1G 2W1, Canada
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Li S, Wu L, Zhu M, Cheng X, Jiang X. Effect of dipole potential on the orientation of Voltage-gated Alamethicin peptides regulated by chaotropic anions. J Electroanal Chem (Lausanne) 2022. [DOI: 10.1016/j.jelechem.2021.115880] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Czernek J, Brus J. Modeling the Structure of Crystalline Alamethicin and Its NMR Chemical Shift Tensors. Antibiotics (Basel) 2021; 10:1265. [PMID: 34680845 PMCID: PMC8532780 DOI: 10.3390/antibiotics10101265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/11/2021] [Accepted: 10/12/2021] [Indexed: 11/25/2022] Open
Abstract
Alamethicin (ALM) is an antimicrobial peptide that is frequently employed in studies of the mechanism of action of pore-forming molecules. Advanced techniques of solid-state NMR spectroscopy (SSNMR) are important in these studies, as they are capable of describing the alignment of helical peptides, such as ALM, in lipid bilayers. Here, it is demonstrated how an analysis of the SSNMR measurements can benefit from fully periodic calculations, which employ the plane-wave density-functional theory (PW DFT) of the solid-phase geometry and related spectral parameters of ALM. The PW DFT calculations are used to obtain the structure of desolvated crystalline ALM and predict the NMR chemical shift tensors (CSTs) of its nuclei. A variation in the CSTs of the amidic nitrogens and carbonyl carbons along the ALM backbone is evaluated and included in simulations of the orientation-dependent anisotropic 15N and 13C chemical shift components. In this way, the influence of the site-specific structural effects on the experimentally determined orientation of ALM is shown in models of cell membranes.
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Affiliation(s)
- Jiří Czernek
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, 16206 Prague, Czech Republic;
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