1
|
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.
Collapse
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;
| |
Collapse
|
2
|
Sato K, Nakagawa Y, Mori M, Takinoue M, Kinbara K. Transient control of lytic activity via a non-equilibrium chemical reaction system. NANOSCALE 2024. [PMID: 38465880 DOI: 10.1039/d3nr06626f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
The development of artificial non-equilibrium chemical reaction systems has recently attracted considerable attention as a new type of biomimetic. However, due to the lack of bioorthogonality, such reaction systems could not be linked to the regulation of any biological phenomena. Here, we have newly designed a non-equilibrium reaction system based on olefin metathesis to produce the Triton X-mimetic non-ionic amphiphile as a kinetic product. Using phospholipid vesicles encapsulating fluorescent dyes and red blood cells as cell models, we demonstrate that the developed chemical reaction system is applicable for transient control of the resulting lytic activity.
Collapse
Affiliation(s)
- Kohei Sato
- School of Life Science and Technology, International Research Frontiers Initiative, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan.
| | - Yume Nakagawa
- School of Life Science and Technology, International Research Frontiers Initiative, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan.
| | - Miki Mori
- School of Life Science and Technology, International Research Frontiers Initiative, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan.
| | - Masahiro Takinoue
- School of Life Science and Technology, International Research Frontiers Initiative, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan.
- Department of Computer Science, International Research Frontiers Initiative, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
- Living Systems Materialogy Research Group, International Research Frontiers Initiative, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Kazushi Kinbara
- School of Life Science and Technology, International Research Frontiers Initiative, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan.
- Living Systems Materialogy Research Group, International Research Frontiers Initiative, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| |
Collapse
|
3
|
Andersen DG, Pedersen AB, Jørgensen MH, Montasell MC, Søgaard AB, Chen G, Schroeder A, Andersen GR, Zelikin AN. Chemical Zymogens and Transmembrane Activation of Transcription in Synthetic Cells. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2309385. [PMID: 38009384 DOI: 10.1002/adma.202309385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 11/17/2023] [Indexed: 11/28/2023]
Abstract
In this work, synthetic cells equipped with an artificial signaling pathway that connects an extracellular trigger event to the activation of intracellular transcription are engineered. Learning from nature, this is done via an engineering of responsive enzymes, such that activation of enzymatic activity can be triggered by an external biochemical stimulus. Reversibly deactivated creatine kinase to achieve triggered production of adenosine triphosphate, and a reversibly deactivated nucleic acid polymerase for on-demand synthesis of RNA are engineered. An extracellular, enzyme-activated production of a diffusible zymogen activator is also designed. The key achievement of this work is that the importance of cellularity is illustrated whereby the separation of biochemical partners is essential to resolve their incompatibility, to enable transcription within the confines of a synthetic cell. The herein designed biochemical pathway and the engineered synthetic cells are arguably primitive compared to their natural counterpart. Nevertheless, the results present a significant step toward the design of synthetic cells with responsive behavior, en route from abiotic to life-like cell mimics.
Collapse
Affiliation(s)
| | | | | | | | | | - Gal Chen
- Department of Chemical Engineering, Technion, Haifa, 32000, Israel
| | - Avi Schroeder
- Department of Chemical Engineering, Technion, Haifa, 32000, Israel
| | - Gregers Rom Andersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, 8000, Denmark
| | - Alexander N Zelikin
- iNano Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, 8000, Denmark
- Department of Chemistry, Aarhus University, Aarhus, 8000, Denmark
| |
Collapse
|
4
|
Chen J, Brea RJ, Fracassi A, Cho CJ, Wong AM, Salvador-Castell M, Sinha SK, Budin I, Devaraj NK. Rapid Formation of Non-canonical Phospholipid Membranes by Chemoselective Amide-Forming Ligations with Hydroxylamines. Angew Chem Int Ed Engl 2024; 63:e202311635. [PMID: 37919232 PMCID: PMC11179435 DOI: 10.1002/anie.202311635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 10/30/2023] [Accepted: 11/02/2023] [Indexed: 11/04/2023]
Abstract
There has been increasing interest in methods to generate synthetic lipid membranes as key constituents of artificial cells or to develop new tools for remodeling membranes in living cells. However, the biosynthesis of phospholipids involves elaborate enzymatic pathways that are challenging to reconstitute in vitro. An alternative approach is to use chemical reactions to non-enzymatically generate natural or non-canonical phospholipids de novo. Previous reports have shown that synthetic lipid membranes can be formed in situ using various ligation chemistries, but these methods lack biocompatibility and/or suffer from slow kinetics at physiological pH. Thus, it would be valuable to develop chemoselective strategies for synthesizing phospholipids from water-soluble precursors that are compatible with synthetic or living cells Here, we demonstrate that amide-forming ligations between lipid precursors bearing hydroxylamines and α-ketoacids (KAs) or potassium acyltrifluoroborates (KATs) can be used to prepare non-canonical phospholipids at physiological pH conditions. The generated amide-linked phospholipids spontaneously self-assemble into cell-like micron-sized vesicles similar to natural phospholipid membranes. We show that lipid synthesis using KAT ligation proceeds extremely rapidly, and the high selectivity and biocompatibility of the approach facilitates the in situ synthesis of phospholipids and associated membranes in living cells.
Collapse
Affiliation(s)
- Jiyue Chen
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, Natural Sciences Building, La Jolla, CA 92093, USA
| | - Roberto J Brea
- Biomimetic Membrane Chemistry (BioMemChem) Group, CICA-Centro Interdisciplinar de Química e Bioloxía, Universidade da Coruña, Rúa As Carballeiras, 15701, A Coruña, Spain
| | - Alessandro Fracassi
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, Natural Sciences Building, La Jolla, CA 92093, USA
| | - Christy J Cho
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, Natural Sciences Building, La Jolla, CA 92093, USA
| | - Adrian M Wong
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, Natural Sciences Building, La Jolla, CA 92093, USA
| | - Marta Salvador-Castell
- Department of Physics, University of California, San Diego, 9500 Gilman Drive, Building: Mayer Hall Addition 4561, La Jolla, CA 92093, USA
| | - Sunil K Sinha
- Department of Physics, University of California, San Diego, 9500 Gilman Drive, Building: Mayer Hall Addition 4561, La Jolla, CA 92093, USA
| | - Itay Budin
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, Natural Sciences Building, La Jolla, CA 92093, USA
| | - Neal K Devaraj
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, Natural Sciences Building, La Jolla, CA 92093, USA
| |
Collapse
|
5
|
Knittel CH, Devaraj NK. Bioconjugation Strategies for Revealing the Roles of Lipids in Living Cells. Acc Chem Res 2022; 55:3099-3109. [PMID: 36215688 DOI: 10.1021/acs.accounts.2c00511] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The structural boundaries of living cells are composed of numerous membrane-forming lipids. Lipids not only are crucial for the cellular compartmentalization but also are involved in cell signaling as well as energy storage. Abnormal lipid levels have been linked to severe human diseases such as cancer, multiple sclerosis, neurodegenerative diseases, as well as lysosomal storage disorders. Given their biological significance, there is immense interest in studying lipids and their effect on cells. However, limiting factors include the low solubility of lipids, their structural complexity, and the challenge of using genetic techniques to directly manipulate lipid structure. Current methods to study lipids rely mostly on lipidomics, which analyzes the composition of lipid extracts using mass spectrometry. Although, these efforts have successfully catalogued and profiled a great number of lipids in cells, many aspects about their exact functional role and subcellular distribution remain enigmatic.In this Account, we outline how our laboratory developed and applied different bioconjugation strategies to study the role of lipids and lipid modifications in cells. Inspired by our ongoing work on developing lipid bioconjugation strategies to generate artificial cell membranes, we developed a ceramide synthesis method in live cells using a salicylaldehyde ester that readily reacts with sphingosine in form of a traceless ceramide ligation. Our study not only confirmed existing knowledge about the association of ceramides with cell death, but also gave interesting new findings about the structure-function relationship of ceramides in apoptosis. Our initial efforts led us to investigate probes that detect endogenous sphingolipids using live cell imaging. We describe the development of a fluorogenic probe that reacts chemoselectively with sphingosine in living cells, enabling the detection of elevated endogenous levels of this biomarker in human disease. Building on our interest in the fluorescence labeling of lipids, we have also explored the use of bioorthogonal reactions to label chemically synthesized lipid probes. We discuss the development of photocaged dihydrotetrazine lipids, where the initiation of the bioorthogonal reaction can be triggered by visible light, allowing for live cell modification of membranes with spatiotemporal control.Finally, proteins are often post-translationally modified by lipids, which have important effects on protein subcellular localization and function. Controlling lipid modifications with small molecule probes could help reveal the function of lipid post-translational modifications and could potentially inspire novel therapeutic strategies. We describe how our previous studies on synthetic membrane formation inspired us to develop an amphiphilic cysteine derivative that depalmitoylates membrane-bound S-acylated proteins in live cells. Ultimately, we applied this amphiphile mediated depalmitoylation (AMD) in studies investigating the palmitoylation of cancer relevant palmitoylated proteins in healthy and diseased cells.
Collapse
Affiliation(s)
- Caroline H Knittel
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Neal K Devaraj
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| |
Collapse
|