1
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Doerner B, Della Sala F, Wang S, Webb SJ. Reaction, Recognition, Relay: Anhydride Hydrolysis Reported by Conformationally Responsive Fluorinated Foldamers in Micelles. Angew Chem Int Ed Engl 2024; 63:e202405924. [PMID: 38703400 DOI: 10.1002/anie.202405924] [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: 03/27/2024] [Revised: 04/23/2024] [Accepted: 04/29/2024] [Indexed: 05/06/2024]
Abstract
Natural membrane receptors are proteins that can report on changes in the concentration of external chemical messengers. Messenger binding to a receptor produces conformational changes that are relayed through the membrane into the cell; this information allows cells to adapt to changes in their environment. Artificial membrane receptors (R)-1 and (S)-1 are helical α-aminoisobutyric acid (Aib) foldamers that replicate key parts of this information relay. Solution-phase 19F NMR spectroscopy of zinc(II)-capped receptor 1, either in organic solvent or in membrane-mimetic micelles, showed messenger binding produced an enrichment of either left- or right-handed screw-sense; the chirality of the bound messenger was relayed to the other receptor terminus. Furthermore, in situ production of a chemical messenger in the external aqueous environment could be detected in real-time by a racemic mixture of receptor 1 in micelles. The hydrolysis of insoluble anhydrides produced carboxylate in the aqueous phase, which bound to the receptors and gave a distinct 19F NMR output from inside the hydrophobic region of the micelles.
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Affiliation(s)
- Benedicte Doerner
- Department of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Flavio Della Sala
- Department of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Siyuan Wang
- Department of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Simon J Webb
- Department of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
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2
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Weber DK, Reddy UV, Robia SL, Veglia G. Pathological mutations in the phospholamban cytoplasmic region affect its topology and dynamics modulating the extent of SERCA inhibition. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024:184370. [PMID: 38986894 DOI: 10.1016/j.bbamem.2024.184370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 06/26/2024] [Accepted: 07/02/2024] [Indexed: 07/12/2024]
Abstract
Phospholamban (PLN) is a 52 amino acid regulin that allosterically modulates the activity of the sarco(endo)plasmic reticulum Ca2+-ATPase (SERCA) in the heart muscle. In its unphosphorylated form, PLN binds SERCA within its transmembrane (TM) domains, approximately 20 Å away from the Ca2+ binding site, reducing SERCA's apparent Ca2+ affinity (pKCa) and decreasing cardiac contractility. During the enzymatic cycle, the inhibitory TM domain of PLN remains anchored to SERCA, whereas its cytoplasmic region transiently binds the ATPase's headpiece. Phosphorylation of PLN at Ser16 by protein kinase A increases the affinity of its cytoplasmic domain to SERCA, weakening the TM interactions with the ATPase, reversing its inhibitory function, and augmenting muscle contractility. How the structural changes caused by pathological mutations in the PLN cytoplasmic region are transmitted to its inhibitory TM domain is still unclear. Using solid-state NMR spectroscopy and activity assays, we analyzed structural and functional effects of a series of mutations and their phosphorylated forms located in the PLN cytoplasmic region and linked to dilated cardiomyopathy. We found that these missense mutations affect the overall topology and dynamics of PLN and ultimately modulate its inhibitory potency. Also, the changes in the TM tilt angle and cytoplasmic dynamics of PLN caused by these mutations correlate well with the extent of SERCA inhibition. Our study unveils new molecular determinants for designing variants of PLN that outcompete endogenous PLN to regulate SERCA in a tunable manner.
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Affiliation(s)
- Daniel K Weber
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - U Venkateswara Reddy
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Seth L Robia
- Department of Cell and Molecular Physiology, Loyola University Chicago, Maywood, IL, USA
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
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3
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Karanth S, Benthin J, Wiesenfarth M, Somoza V, Koehler M. Nanodisc Technology: Direction toward Physicochemical Characterization of Chemosensory Membrane Proteins in Food Flavor Research. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:14521-14529. [PMID: 38906535 PMCID: PMC11228972 DOI: 10.1021/acs.jafc.4c01827] [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: 02/29/2024] [Revised: 05/31/2024] [Accepted: 06/11/2024] [Indexed: 06/23/2024]
Abstract
Chemosensory membrane proteins such as G-protein-coupled receptors (GPCRs) drive flavor perception of food formulations. To achieve this, a detailed understanding of the structure and function of these membrane proteins is needed, which is often limited by the extraction and purification methods involved. The proposed nanodisc methodology helps overcome some of these existing challenges such as protein stability and solubilization along with their reconstitution from a native cell-membrane environment. Being well-established in structural biology procedures, nanodiscs offer this elegant solution by using, e.g., a membrane scaffold protein (MSP) or styrene-maleic acid (SMA) polymer, which interacts directly with the cell membrane during protein reconstitution. Such derived proteins retain their biophysical properties without compromising the membrane architecture. Here, we seek to show that these lipidic systems can be explored for insights with a focus on chemosensory membrane protein morphology and structure, conformational dynamics of protein-ligand interactions, and binding kinetics to answer pending questions in flavor research. Additionally, the compatibility of nanodiscs across varied (labeled or label-free) techniques offers significant leverage, which has been highlighted here.
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Affiliation(s)
- Sanjai Karanth
- Leibniz
Institute for Food Systems Biology at the Technical University of
Munich, Lise-Meitner-Strasse 34, 85354 Freising, Germany
| | - Julia Benthin
- Leibniz
Institute for Food Systems Biology at the Technical University of
Munich, Lise-Meitner-Strasse 34, 85354 Freising, Germany
- TUM
Graduate School, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Alte Akademie 8, 85354 Freising, Germany
| | - Marina Wiesenfarth
- Leibniz
Institute for Food Systems Biology at the Technical University of
Munich, Lise-Meitner-Strasse 34, 85354 Freising, Germany
- TUM
Graduate School, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Alte Akademie 8, 85354 Freising, Germany
| | - Veronika Somoza
- Leibniz
Institute for Food Systems Biology at the Technical University of
Munich, Lise-Meitner-Strasse 34, 85354 Freising, Germany
- Chair
of Nutritional Systems Biology, Technical
University of Munich, 85354 Freising, Germany
- Department
of Physiological Chemistry, Faculty of Chemistry, University of Vienna, Vienna 1090, Austria
| | - Melanie Koehler
- Leibniz
Institute for Food Systems Biology at the Technical University of
Munich, Lise-Meitner-Strasse 34, 85354 Freising, Germany
- TUM
Junior Fellow at the Chair of Nutritional Systems Biology, Technical University of Munich, 85354 Freising, Germany
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4
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Krishnarjuna B, Sharma G, Hiiuk VM, Struppe J, Nagorny P, Ivanova MI, Ramamoorthy A. Nanodisc Reconstitution and Characterization of Amyloid-β Precursor Protein C99. Anal Chem 2024; 96:9362-9369. [PMID: 38826107 DOI: 10.1021/acs.analchem.3c05727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Amyloid precursor protein (APP) plays a pivotal role in the pathology of Alzheimer's disease (AD). Since the fragmentation of the membrane-bound APP that results in the production of amyloid-β peptides is the starting point for amyloid toxicity in AD, it is important to investigate the structure and dynamics of APP in a near-native lipid-bilayer environment. However, the reconstitution of APP into a stable and suitable membrane-mimicking lipid environment is a challenging task. In this study, the 99-residue C-terminal domain of APP is successfully reconstituted into polymer nanodiscs and characterized using size-exclusion chromatography, mass spectrometry, solution NMR, and magic-angle spinning solid-state NMR. In addition, the feasibility of using lipid-solubilizing polymers for isolating and characterizing APP in the native Escherichia. coli membrane environment is demonstrated.
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Affiliation(s)
- Bankala Krishnarjuna
- Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Gaurav Sharma
- Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Volodymyr M Hiiuk
- Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jochem Struppe
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, Massachusetts 01821, United States
| | - Pavel Nagorny
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Magdalena I Ivanova
- Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Neurology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Ayyalusamy Ramamoorthy
- Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
- Department of Chemical and Biomedical Engineering, FAMU-FSU College of Engineering, Florida State University, Tallahassee, Florida 32310, United States
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5
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Dong Y, Li M, Kang L, Wang W, Li Z, Wang Y, Wu Z, Zhu C, Zhu L, Zheng X, Qian D, Dai H, Wu B, Zhao H, Wang J. A new preparation method of covalent annular nanodiscs based on MTGase. Arch Biochem Biophys 2024; 756:109997. [PMID: 38621443 DOI: 10.1016/j.abb.2024.109997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 03/11/2024] [Accepted: 04/12/2024] [Indexed: 04/17/2024]
Abstract
The preservation of the native conformation and functionality of membrane proteins has posed considerable challenges. While detergents and liposome reconstitution have been traditional approaches, nanodiscs (NDs) offer a promising solution by embedding membrane proteins in phospholipids encircled by an amphipathic helical protein MSP belt. Nevertheless, a drawback of commonly used NDs is their limited homogeneity and stability. In this study, we present a novel approach to construct covalent annular nanodiscs (cNDs) by leveraging microbial transglutaminase (MTGase) to catalyze isopeptide bond formation between the side chains of terminal amino acids, specifically Lysine (K) and Glutamine (Q). This methodology significantly enhances the homogeneity and stability of NDs. Characterization of cNDs and the assembly of membrane proteins within them validate the successful reconstitution of membrane proteins with improved homogeneity and stability. Our findings suggest that cNDs represent a more suitable tool for investigating interactions between membrane proteins and lipids, as well as for analyzing membrane protein structures.
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Affiliation(s)
- Yingkui Dong
- Institute of Physical Science and Information Technology, Anhui University, Hefei, Anhui, 230039, China; High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, 230031, China
| | - Ming Li
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, 230031, China; University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Li Kang
- Institute of Physical Science and Information Technology, Anhui University, Hefei, Anhui, 230039, China; High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, 230031, China
| | - Wanxue Wang
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, 230031, China; School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Zehua Li
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, 230031, China; University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Yizhuo Wang
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, 230031, China; University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Ziwei Wu
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, 230031, China; University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Chenchen Zhu
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, 230031, China; University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Lei Zhu
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, 230031, China
| | - Xinwei Zheng
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, 230031, China
| | - Dongming Qian
- Hefei China Science Longwood Biological Technology Co., Ltd. Hefei, Anhui, 230088, China
| | - Han Dai
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, 230031, China; Hefei China Science Longwood Biological Technology Co., Ltd. Hefei, Anhui, 230088, China
| | - Bo Wu
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, 230031, China.
| | - Hongxin Zhao
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, 230031, China; Hefei China Science Longwood Biological Technology Co., Ltd. Hefei, Anhui, 230088, China.
| | - Junfeng Wang
- Institute of Physical Science and Information Technology, Anhui University, Hefei, Anhui, 230039, China; High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, 230031, China; University of Science and Technology of China, Hefei, Anhui, 230026, China.
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6
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Umegawa Y, Kato S, Seo S, Shinoda W, Kawatake S, Matsuoka S, Murata M. Protein-lipid acyl chain interactions: Depth-dependent changes of segmental mobility of phospholipid in contact with bacteriorhodopsin. Biophys Chem 2024; 308:107204. [PMID: 38412762 DOI: 10.1016/j.bpc.2024.107204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 01/31/2024] [Accepted: 02/20/2024] [Indexed: 02/29/2024]
Abstract
Boundary lipids surrounding membrane proteins play an essential role in protein function and structure. These protein-lipid interactions are mainly divided into electrostatic interactions between the polar amino acids of proteins and polar heads of phospholipids, and hydrophobic interactions between protein transmembrane sites and phospholipid acyl chains. Our previous report (Kawatake et al., Biochim. Biophys. Acta 1858 [2016] 2106-2115) covered a method for selectively analyzing boundary lipid interactions and showed differences in membrane protein-peripheral lipid interactions due to differences in their head group. Interactions in the hydrophobic acyl chains of phospholipids are relatively consistent among proteins, but the details of these interactions have not been elucidated. In this study, we reconstituted bacteriorhodopsin as a model protein into phospholipid membranes labeled with 2H and 13C for solid-state NMR measurement to investigate the depth-dependent effect of the head group structure on the lipid bilayer. The results showed that the position of the phospholipid near the carbonyl carbon was affected by the head group in terms of selectivity for protein surfaces, whereas in the deep interior of the bilayer near the leaflet interface, there was little difference between the head groups, indicating that the dependence of their interactions on the head group was much reduced.
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Affiliation(s)
- Yuichi Umegawa
- JST-ERATO, Lipid Active Structure Project, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan; Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan; Forefront Research Center, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan.
| | - Sho Kato
- JST-ERATO, Lipid Active Structure Project, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan; Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Sangjae Seo
- Department of Materials Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan; Division of Supercomputing, Korea Institute of Science and Technology Information, 245 Daehak-ro, Yuseong-gu, Daejeon 34141, South Korea
| | - Wataru Shinoda
- Department of Materials Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan; Research Institute for Interdisciplinary Science, Okayama University, 3-1-1, Tsushima-naka, Okayama 700-8530, Japan
| | - Satoshi Kawatake
- JST-ERATO, Lipid Active Structure Project, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan; Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan; Forefront Research Center, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Shigeru Matsuoka
- JST-ERATO, Lipid Active Structure Project, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan; Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan; Forefront Research Center, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Michio Murata
- JST-ERATO, Lipid Active Structure Project, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan; Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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7
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Krishnarjuna B, Sharma G, Hiiuk VM, Struppe J, Nagorny P, Ivanova MI, Ramamoorthy A. Nanodisc reconstitution and characterization of amyloid-β precursor protein C99. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.21.590446. [PMID: 38659865 PMCID: PMC11042261 DOI: 10.1101/2024.04.21.590446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Amyloid precursor protein (APP) plays a pivotal role in the pathology of Alzheimer's disease. Since the fragmentation of the membrane-bound APP that results in the production of amyloid-beta peptides is the starting point for amyloid toxicity in AD, it is important to investigate the structure and dynamics of APP in a near-native lipid-bilayer environment. However, the reconstitution of APP into a stable/suitable membrane-mimicking lipid environment is a challenging task. In this study, the 99-residue C-terminal domain of APP is successfully reconstituted into polymer nanodiscs and characterized using size-exclusion chromatography, mass spectrometry, solution NMR, and magic-angle spinning solid-state NMR. In addition, the feasibility of using lipid-solubilizing polymers for isolating and characterizing APP in native E. coli membrane environment is demonstrated.
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Affiliation(s)
- Bankala Krishnarjuna
- Biophysics Program, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI 48109, United States
| | - Gaurav Sharma
- Biophysics Program, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI 48109, United States
| | - Volodymyr M Hiiuk
- Biophysics Program, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jochem Struppe
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, Massachusetts 01821, United States
| | - Pavel Nagorny
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Magdalena I Ivanova
- Biophysics Program, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Neurology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Ayyalusamy Ramamoorthy
- Biophysics Program, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Chemical and Biomedical Engineering, FAMU-FSU College of Engineering, Florida State University, Tallahassee, FL 32310, United States
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, United States
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8
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Fu R, Ramamoorthy A. 17O Solid-State NMR Spectroscopy of Lipid Membranes. J Phys Chem B 2024; 128:3527-3537. [PMID: 38568422 DOI: 10.1021/acs.jpcb.4c01016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
Despite the limitations posed by poor sensitivity, studies have reported the unique advantages of 17O based NMR spectroscopy to study systems existing in liquid, solid, or semisolid states. 17O NMR studies have exploited the remarkable sensitivity of quadrupole coupling and chemical shift anisotropy tensors to the local environment in the characterization of a variety of intra- and intermolecular interactions and motion. Recent studies have considerably expanded the use of 17O NMR to study dynamic intermolecular interactions associated with some of the challenging biological systems under magic angle spinning (MAS) and aligned conditions. The very fast relaxing nature of 17O has been well utilized in cellular and in vivo MRS (magnetic resonance spectroscopy) and MRI (magnetic resonance imaging) applications. The main focus of this Review is to highlight the new developments in the biological solids with a detailed discussion for a few selected examples including membrane proteins and nanodiscs. In addition to the unique benefits and limitations, the remaining challenges to overcome, and the impacts of higher magnetic fields and sensitivity enhancement techniques are discussed.
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Affiliation(s)
- Riqiang Fu
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
| | - Ayyalusamy Ramamoorthy
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
- Department of Chemical and Biomedical Engineering, Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32310, United States
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9
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Sahu AK, Reddy UC, Kannoth Manheri M, Mishra AK. Exploring the Physical Properties of Lipid Membranes with Polyhydroxy Oxanorbornane Head Group Using NBD-Conjugated and DPH Fluorescent Probes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:5106-5120. [PMID: 38427698 DOI: 10.1021/acs.langmuir.3c02941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/03/2024]
Abstract
The present study focuses on exploring the physical properties of lipid membranes based on the polyhydroxy oxanorbornane (PH-ONB) headgroup, designed as synthetic analogues of naturally occurring archaeal lipid membranes. Specifically, we study two variants of PH-ONB headgroup-based lipids differing in the number of hydroxy groups present in the headgroup, with one having two hydroxy groups (ONB-2OH) and the other having three (ONB-3OH). These lipids form stable bilayer membranes. The study begins with a comprehensive analysis of the fluorescence characteristics of nitrobenzoxadiazole (NBD)-tagged ONB-based lipids in different solvent environments and within a model lipid membrane 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC). Subsequently, the physical properties of the ONB-based membranes were examined by using an NBD-tagged ONB-based probe and a commonly used extrinsic 1,6-diphenyl-1,3,5-hexatriene (DPH) fluorescent probe. The steady-state and time-resolved fluorescence properties of the NBD-tagged ONB-based probe and DPH were used to compare the physical properties of the ONB-based membranes, including polarity, fluidity, phase transition, order, hydration, location, heterogeneity, and rotational diffusion. The solid gel to liquid crystalline phase transition temperatures of ONB-2OH and ONB-3OH lipid membranes are found to be (68 ± 1) °C and (74 ± 1) °C, respectively. The variation in organization (size), fluidity, and phase transition temperature of ONB-based lipid membranes is explained by the extent of hydrogen bonding interactions between lipid head groups. ONB-based membranes exhibit characteristics similar to those of phospholipid membranes and possess a notably high phase transition temperature. These properties make them a promising and cost-effective synthetic alternative to archaeal lipid membranes with a wide range of potential applications.
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Affiliation(s)
- Anand Kumar Sahu
- Department of Chemistry, Indian Institute of Technology Madras, Chennai 600036, India
| | - U Chandrasekhar Reddy
- Department of Chemistry, Indian Institute of Technology Madras, Chennai 600036, India
| | | | - Ashok Kumar Mishra
- Department of Chemistry, Indian Institute of Technology Madras, Chennai 600036, India
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10
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Thakur GCN, Uday A, Jurkiewicz P. FRET-GP - A Local Measure of the Impact of Transmembrane Peptide on Lipids. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:18390-18402. [PMID: 38048524 DOI: 10.1021/acs.langmuir.3c02505] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/06/2023]
Abstract
Reconstitution of a transmembrane protein in model lipid systems allows studying its structure and dynamics in isolation from the complexity of the natural environment. This approach also provides a well-defined environment for studying the interactions of proteins with lipids. In this work, we describe the FRET-GP method, which utilizes Förster resonance energy transfer (FRET) to specifically probe the nanoenvironment of a transmembrane domain. The tryptophan residues flanking this domain act as efficient FRET donors, while Laurdan acts as acceptor. The fluorescence of this solvatochromic probe is quantified using generalized polarization (GP) to report on lipid mobility in the vicinity of the transmembrane domain. We applied FRET-GP to study the transmembrane peptide WALP incorporated in liposomes. We found that the direct excitation of Laurdan to its second singlet state strongly contributes to GP values measured in FRET conditions. Removal of this parasitic contribution was essential for proper determination of GPFRET - the local analogue of classical GP parameter. The presence of WALP significantly increased both parameters but the local effects were considerably stronger (GPFRET ≫ GP). We conclude that WALP restricts lipid movement in its vicinity, inducing lateral inhomogeneity in membrane fluidity. WALP was also found to influence lipid phase transition. Our findings demonstrated that FRET-GP simultaneously provides local and global results, thereby enhancing the depth of information obtained from the measurement. We highlight the simplicity and sensitivity of the method, but also discuss its potential and limitations in studying protein-lipid interactions.
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Affiliation(s)
- Garima C N Thakur
- J. Heyrovský Institute of Physical Chemistry of the Academy of Sciences of the Czech Republic, v.v.i., Prague 182 00, Czech Republic
| | - Arunima Uday
- J. Heyrovský Institute of Physical Chemistry of the Academy of Sciences of the Czech Republic, v.v.i., Prague 182 00, Czech Republic
| | - Piotr Jurkiewicz
- J. Heyrovský Institute of Physical Chemistry of the Academy of Sciences of the Czech Republic, v.v.i., Prague 182 00, Czech Republic
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11
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Steffes VM, Zhang Z, Ewert KK, Safinya CR. Cryo-TEM Reveals the Influence of Multivalent Charge and PEGylation on Shape Transitions in Fluid Lipid Assemblies: From Vesicles to Discs, Rods, and Spheres. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:18424-18436. [PMID: 38051205 PMCID: PMC10799670 DOI: 10.1021/acs.langmuir.3c02664] [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] [Indexed: 12/07/2023]
Abstract
Lipids, and cationic lipids in particular are of interest as delivery vectors for hydrophobic drugs such as the cancer therapeutic paclitaxel, and the structures of lipid assemblies affect their efficacy. We investigated the effect of incorporating the multivalent cationic lipid MVL5 (+5e) and poly(ethylene glycol)-lipids (PEG-lipids), alone and in combination, on the structure of fluid-phase lipid assemblies of the charge-neutral lipid 1,2-dioleoyl-sn-glycero-phosphocholine (DOPC). This allowed us to elucidate lipid-assembly structure correlations in sonicated formulations with high charge density, which are not accessible with univalent lipids such as the well-studied DOTAP (+1e). Cryogenic transmission electron microscopy (cryo-TEM) allowed us to determine the structure of the lipid assemblies, revealing diverse combinations of vesicles and disc-shaped, worm-like, and spherical micelles. Remarkably, MVL5 forms an essentially pure phase of disc micelles at 50 mol % MVL5. At a higher (75 mol %) content of MVL5, short- and intermediate-length worm-like micellar rods were observed, and in ternary mixtures with PEG-lipid, longer and highly flexible worm-like micelles formed. Independent of their length, the worm-like micelles coexisted with spherical micelles. In stark contrast, DOTAP forms mixtures of vesicles, disc micelles, and spherical micelles at all studied compositions, even when combined with PEG-lipids. The observed similarities and differences in the effects of charge (multivalent versus univalent) and high curvature (multivalent charge versus PEG-lipid) on the assembly structure provide insights into parameters that control the size of fluid lipid nanodiscs, relevant for future applications.
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Affiliation(s)
- Victoria M. Steffes
- Materials Department, University of California, Santa Barbara, California 93106, USA
- Chemistry and Biochemistry Department, University of California, Santa Barbara, California 93106, USA
| | - Zhening Zhang
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA
- Present Address: Biochemistry and Molecular Biophysics Department, Columbia University Medical Center, New York, NY 10032, USA
| | - Kai K. Ewert
- Materials Department, University of California, Santa Barbara, California 93106, USA
| | - Cyrus R. Safinya
- Materials Department, University of California, Santa Barbara, California 93106, USA
- Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, California 93106, USA
- Physics Department, University of California, Santa Barbara, California 93106, USA
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12
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Iwamoto M, Morito M, Oiki S, Nishitani Y, Yamamoto D, Matsumori N. Cardiolipin binding enhances KcsA channel gating via both its specific and dianion-monoanion interchangeable sites. iScience 2023; 26:108471. [PMID: 38077151 PMCID: PMC10709135 DOI: 10.1016/j.isci.2023.108471] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 10/29/2023] [Accepted: 11/13/2023] [Indexed: 01/17/2024] Open
Abstract
KcsA is a potassium channel with a plethora of structural and functional information, but its activity in the KcsA-producing actinomycete membranes remains elusive. To determine lipid species involved in channel-modulation, a surface plasmon resonance (SPR)-based methodology, characterized by immobilization of membrane proteins under a membrane environment, was applied. Dianionic cardiolipin (CL) showed extremely higher affinity for KcsA than monoanionic lipids. The SPR experiments further demonstrated that CL bound not only to the N-terminal M0 helix, a lipid-sensor domain, but to the M0 helix-deleted mutant. In contrast, monoanionic lipids interacted primarily with the M0 helix. This indicates the presence of an alternative CL-binding site, plausibly in the transmembrane domain. Single-channel recordings demonstrated that CL enhanced channel opening in an M0-independent manner. Taken together, the action of monoanionic lipids is exclusively mediated by the M0 helix, while CL binds both the M0 helix and its specific site, further enhancing the channel activity.
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Affiliation(s)
- Masayuki Iwamoto
- Department of Molecular Neuroscience, Faculty of Medical Sciences, University of Fukui, Fukui 910-1193, Japan
| | - Masayuki Morito
- Department of Chemistry, Graduate School of Science, Kyushu University, Fukuoka 819-0395 Japan
| | - Shigetoshi Oiki
- Biomedial Imaging Research Center, University of Fukui, Fukui 910-1193, Japan
| | - Yudai Nishitani
- Department of Applied Physics, Faculty of Science, Fukuoka University, Fukuoka 814-0180, Japan
| | - Daisuke Yamamoto
- Department of Applied Physics, Faculty of Science, Fukuoka University, Fukuoka 814-0180, Japan
| | - Nobuaki Matsumori
- Department of Chemistry, Graduate School of Science, Kyushu University, Fukuoka 819-0395 Japan
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13
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Sutinen A, Jones NC, Hoffmann SV, Ruskamo S, Kursula P. Conformational analysis of membrane-proximal segments of GDAP1 in a lipidic environment using synchrotron radiation suggests a mode of assembly at the mitochondrial outer membrane. Biophys Chem 2023; 303:107113. [PMID: 37778197 DOI: 10.1016/j.bpc.2023.107113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/19/2023] [Accepted: 09/24/2023] [Indexed: 10/03/2023]
Abstract
The mitochondrial outer membrane creates a diffusion barrier between the cytosol and the mitochondrial intermembrane space, allowing the exchange of metabolic products, important for efficient mitochondrial function in neurons. The ganglioside-induced differentiation-associated protein 1 (GDAP1) is a mitochondrial outer membrane protein with a critical role in mitochondrial dynamics and metabolic balance in neurons. Missense mutations in the GDAP1 gene are linked to the most common human peripheral neuropathy, Charcot-Marie-Tooth disease (CMT). GDAP1 is a distant member of the glutathione-S-transferase (GST) superfamily, with unknown enzymatic properties or functions at the molecular level. The structure of the cytosol-facing GST-like domain has been described, but there is no consensus on how the protein interacts with the mitochondrial outer membrane. Here, we describe a model for GDAP1 assembly on the membrane using peptides vicinal to the GDAP1 transmembrane domain. We used oriented circular dichroism spectroscopy (OCD) with synchrotron radiation to study the secondary structure and orientation of GDAP1 segments at the outer and inner surfaces of the outer mitochondrial membrane. These experiments were complemented by small-angle X-ray scattering, providing the first experimental structural models for full-length human GDAP1. The results indicate that GDAP1 is bound into the membrane via a single transmembrane helix, flanked by two peripheral helices interacting with the outer and inner leaflets of the mitochondrial outer membrane in different orientations. Impairment of these interactions could be a mechanism for CMT in the case of missense mutations affecting these segments instead of the GST-like domain.
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Affiliation(s)
- Aleksi Sutinen
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Nykola C Jones
- ISA, Department of Physics and Astronomy, Aarhus University, Aarhus, Denmark
| | | | - Salla Ruskamo
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Petri Kursula
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland; Department of Biomedicine, University of Bergen, Bergen, Norway.
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14
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Zhao P, Zhao Z, Yu Z, Chen L, Jin Y, Wu J, Ren Z. Application of synthetic lipid droplets in metabolic diseases. Clin Transl Med 2023; 13:e1441. [PMID: 37997538 PMCID: PMC10668006 DOI: 10.1002/ctm2.1441] [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: 05/15/2023] [Revised: 09/16/2023] [Accepted: 10/01/2023] [Indexed: 11/25/2023] Open
Abstract
BACKGROUND The study and synthesis of membrane organelles are becoming increasingly important, not only as simplified cellular models for corresponding molecular and metabolic studies but also for applications in synthetic biology of artificial cells and drug delivery vehicles. Lipid droplets (LDs) are central organelles in cellular lipid metabolism and are involved in almost all metabolic processes. Multiple studies have also demonstrated a high correlation between LDs and metabolic diseases. During these processes, LDs reveal a highly dynamic character, with their lipid fraction, protein composition and subcellular localisation constantly changing in response to metabolic demands. However, the molecular mechanisms underlying these functions have not been fully understood due to the limitations of cell biology approaches. Fortunately, developments in synthetic biology have provided a huge breakthrough for metabolism research, and methods for in vitro synthesis of LDs have been successfully established, with great advances in protein binding, lipid function, membrane dynamics and enzymatic reactions. AIMS AND METHODS In this review, we provide a comprehensive overview of the assembly and function of endogenous LDs, from the generation of lipid molecules to how they are assembled into LDs in the endoplasmic reticulum. In particular, we highlight two major classes of synthetic LD models for fabrication techniques and their recent advances in biology and explore their roles and challenges in achieving real applications of artificial LDs in the future.
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Affiliation(s)
- Pengxiang Zhao
- Key Laboratory of Agriculture Animal GeneticsBreeding and Reproduction of the Ministry of Education, College of Animal ScienceHuazhong Agricultural UniversityWuhanHubeiP. R. China
- College of Animal Science and TechnologyShandong Agricultural UniversityTaianShandongP. R. China
| | - Zichen Zhao
- Key Laboratory of Agriculture Animal GeneticsBreeding and Reproduction of the Ministry of Education, College of Animal ScienceHuazhong Agricultural UniversityWuhanHubeiP. R. China
| | - Ziwei Yu
- Key Laboratory of Agriculture Animal GeneticsBreeding and Reproduction of the Ministry of Education, College of Animal ScienceHuazhong Agricultural UniversityWuhanHubeiP. R. China
| | - Lupeng Chen
- Key Laboratory of Agriculture Animal GeneticsBreeding and Reproduction of the Ministry of Education, College of Animal ScienceHuazhong Agricultural UniversityWuhanHubeiP. R. China
| | - Yi Jin
- Key Laboratory of Agriculture Animal GeneticsBreeding and Reproduction of the Ministry of Education, College of Animal ScienceHuazhong Agricultural UniversityWuhanHubeiP. R. China
| | - Jian Wu
- Key Laboratory of Agriculture Animal GeneticsBreeding and Reproduction of the Ministry of Education, College of Animal ScienceHuazhong Agricultural UniversityWuhanHubeiP. R. China
- Frontiers Science Center for Animal Breeding and Sustainable ProductionWuhanHubeiP. R. China
| | - Zhuqing Ren
- Key Laboratory of Agriculture Animal GeneticsBreeding and Reproduction of the Ministry of Education, College of Animal ScienceHuazhong Agricultural UniversityWuhanHubeiP. R. China
- Frontiers Science Center for Animal Breeding and Sustainable ProductionWuhanHubeiP. R. China
- Hubei Hongshan LaboratoryWuhanHubeiP. R. China
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15
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Amengual J, Notaro-Roberts L, Nieh MP. Morphological control and modern applications of bicelles. Biophys Chem 2023; 302:107094. [PMID: 37659154 DOI: 10.1016/j.bpc.2023.107094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 08/10/2023] [Accepted: 08/13/2023] [Indexed: 09/04/2023]
Abstract
Bicellar systems have become popularized as their rich morphology can be applied in biochemistry, physical chemistry, and drug delivery technology. To the biochemical field, bicelles are powerful model membranes for the study of transmembrane protein behavior, membrane transport, and environmental interactions with the cell. Their morphological responses to environmental changes reveal a profound fundamental understanding of physical chemistry related to the principle of self-assembly. Recently, they have also drawn significant attention as theranostic nanocarriers in biopharmaceutical and diagnostic research due to their superior cellular uptake compared to liposomes. It is evident that applications are becoming broader, demanding to understand how the bicelle will form and behave in various environments. To consolidate current works on the bicelle's modern applications, this review will discuss various effects of composition and environmental conditions on the morphology, phase behavior, and stability. Furthermore, various applications such as payload entrapment and polymerization templating are presented to demonstrate their versatility and chemical nature.
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Affiliation(s)
- Justin Amengual
- Polymer Program, Institute of Materials Science, University of Connecticut, Storrs, CT 06269, United States
| | - Luke Notaro-Roberts
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, CT 06269, United States
| | - Mu-Ping Nieh
- Polymer Program, Institute of Materials Science, University of Connecticut, Storrs, CT 06269, United States; Department of Chemical and Biomolecular Engineering, University of Connecticut, Storrs, CT 06269, United States.
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16
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Scheyer MW, Campbell C, William PL, Hussain M, Begum A, Fonseca SE, Asare IK, Dabney P, Dabney-Smith C, Lorigan GA, Sahu ID. Electron paramagnetic resonance spectroscopic characterization of the human KCNE3 protein in lipodisq nanoparticles for structural dynamics of membrane proteins. Biophys Chem 2023; 301:107080. [PMID: 37531799 DOI: 10.1016/j.bpc.2023.107080] [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: 05/25/2023] [Revised: 07/07/2023] [Accepted: 07/24/2023] [Indexed: 08/04/2023]
Abstract
One of the major challenges in solubilization of membrane proteins is to find the optimal physiological environment for their biophysical studies. EPR spectroscopy is a powerful biophysical technique for studying the structural and dynamic properties of macromolecules. However, the challenges in the membrane protein sample preparation and flexible motion of the spin label limit the utilization of EPR spectroscopy to a majority of membrane protein systems in a physiological membrane-bound state. Recently, lipodisq nanoparticles or styrene-maleic acid copolymer-lipid nanoparticles (SMALPs) have emerged as a membrane mimetic system for investigating the structural studies of membrane proteins. However, its detail characterization for membrane protein studies is still poorly understood. Recently, we characterized the potassium channel membrane protein KCNQ1 voltage sensing domain (KCNQ1-VSD) and KCNE1 reconstituted into lipodisq nanoparticles using EPR spectroscopy. In this study, the potassium channel accessory protein KCNE3 containing flexible N- and C-termini was encapsulated into proteoliposomes and lipodisq nanoparticles and characterized for studying its structural and dynamic properties using nitroxide based site-directed spin labeling EPR spectroscopy. CW-EPR lineshape analysis data indicated an increase in spectral line broadenings with the addition of the styrene-maleic acid (SMA) polymer which approaches close to the rigid limit providing a homogeneous stabilization of the protein-lipid complex. Similarly, EPR DEER measurements indicated an enhanced quality of distance measurements with an increase in the phase memory time (Tm) values upon incorporation of the sample into lipodisq nanoparticles, when compared to proteoliposomes. These results agree with the solution NMR structural structure of the KCNE3 and EPR studies of other membrane proteins in lipodisq nanoparticles. This study along with our earlier studies will provide the reference characterization data that will provide benefit to the membrane protein researchers for studying structural dynamics of challenging membrane proteins.
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Affiliation(s)
- Matthew W Scheyer
- Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA
| | - Conner Campbell
- Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA
| | - Patrick L William
- Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA
| | - Mustakim Hussain
- Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA
| | - Afsana Begum
- Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA
| | | | - Isaac K Asare
- Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA
| | - Peyton Dabney
- Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA
| | - Carole Dabney-Smith
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Gary A Lorigan
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Indra D Sahu
- Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA; Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA.
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17
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Wijesinghe WCB, Min D. Single-Molecule Force Spectroscopy of Membrane Protein Folding. J Mol Biol 2023; 435:167975. [PMID: 37330286 DOI: 10.1016/j.jmb.2023.167975] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 01/13/2023] [Accepted: 01/17/2023] [Indexed: 06/19/2023]
Abstract
Single-molecule force spectroscopy is a unique method that can probe the structural changes of single proteins at a high spatiotemporal resolution while mechanically manipulating them over a wide force range. Here, we review the current understanding of membrane protein folding learned by using the force spectroscopy approach. Membrane protein folding in lipid bilayers is one of the most complex biological processes in which diverse lipid molecules and chaperone proteins are intricately involved. The approach of single protein forced unfolding in lipid bilayers has produced important findings and insights into membrane protein folding. This review provides an overview of the forced unfolding approach, including recent achievements and technical advances. Progress in the methods can reveal more interesting cases of membrane protein folding and clarify general mechanisms and principles.
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Affiliation(s)
- W C Bhashini Wijesinghe
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Duyoung Min
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea; Center for Wave Energy Materials, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea.
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18
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Yu T, Flores-Solis D, Eastep GN, Becker S, Zweckstetter M. Phosphatidylserine-dependent structure of synaptogyrin remodels the synaptic vesicle membrane. Nat Struct Mol Biol 2023:10.1038/s41594-023-01004-9. [PMID: 37217654 DOI: 10.1038/s41594-023-01004-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 04/21/2023] [Indexed: 05/24/2023]
Abstract
Synaptic vesicles are small membrane-enclosed organelles that store neurotransmitters at presynaptic terminals. The uniform morphology of synaptic vesicles is important for brain function, because it enables the storage of well-defined amounts of neurotransmitters and thus reliable synaptic transmission. Here, we show that the synaptic vesicle membrane protein synaptogyrin cooperates with the lipid phosphatidylserine to remodel the synaptic vesicle membrane. Using NMR spectroscopy, we determine the high-resolution structure of synaptogyrin and identify specific binding sites for phosphatidylserine. We further show that phosphatidylserine binding changes the transmembrane structure of synaptogyrin and is critical for membrane bending and the formation of small vesicles. Cooperative binding of phosphatidylserine to both a cytoplasmic and intravesicular lysine-arginine cluster in synaptogyrin is required for the formation of small vesicles. Together with other synaptic vesicle proteins, synaptogyrin thus can sculpt the membrane of synaptic vesicles.
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Affiliation(s)
- Taekyung Yu
- German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | | | - Gunnar N Eastep
- German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Stefan Becker
- Department for NMR-based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Markus Zweckstetter
- German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany.
- Department for NMR-based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
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19
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Uchida N. Design of supramolecular nanosheets for drug delivery applications. Polym J 2023; 55:1-8. [PMID: 37359988 PMCID: PMC10169173 DOI: 10.1038/s41428-023-00788-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 03/29/2023] [Accepted: 03/31/2023] [Indexed: 06/28/2023]
Abstract
Two specific concepts have emerged in the field of materials science over the last several decades: nanosheets and supramolecular polymers. More recently, supramolecular nanosheets, in which these two concepts are integrated, have attracted particular attention, and they exhibit many fascinating characteristics. This review focuses on the design and applications of supramolecular nanosheets consisting of tubulin proteins and phospholipid membranes.
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Affiliation(s)
- Noriyuki Uchida
- Department of Applied Chemistry, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588 Japan
- RIKEN Center for Emergent Matter Science, 2-1 Hirosawa, Wako, Saitama, 351-0198 Japan
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20
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Pulido S, Rückert H, Falsone SF, Göbl C, Meyer NH, Zangger K. The membrane-binding bacterial toxin long direct repeat D inhibits protein translation. Biophys Chem 2023; 298:107040. [PMID: 37229877 DOI: 10.1016/j.bpc.2023.107040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 05/08/2023] [Accepted: 05/08/2023] [Indexed: 05/27/2023]
Abstract
Bacterial plasmids and chromosomes widely contain toxin-antitoxin (TA) loci, which are implicated in stress response, growth regulation and even tolerance to antibiotics and environmental stress. Type I TA systems consist of a stable toxin-expressing mRNA, which is counteracted by an unstable RNA antitoxin. The Long Direct Repeat (LDR-) D locus, a type I TA system of Escherichia Coli (E. coli) K12, encodes a 35 amino acid toxic peptide, LdrD. Despite being characterized as a bacterial toxin, causing rapid killing and nucleoid condensation, little was known about its function and its mechanism of toxicity. Here, we show that LdrD specifically interacts with ribosomes which potentially blocks translation. Indeed, in vitro translation of LdrD-coding mRNA greatly reduces translation efficiency. The structure of LdrD in a hydrophobic environment, similar to the one found in the interior of ribosomes was determined by NMR spectroscopy in 100% trifluoroethanol solution. A single compact α-helix was found which would fit nicely into the ribosomal exit tunnel. Therefore, we conclude that rather than destroying bacterial membranes, LdrD exerts its toxic activity by inhibiting protein synthesis through binding to the ribosomes.
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Affiliation(s)
- Sergio Pulido
- Institute of Chemistry, University of Graz, Graz, Austria; LifeFactors ZF S.A.S., Zona France Rionegro, Rionegro, Colombia
| | - Hanna Rückert
- Institute of Chemistry, University of Graz, Graz, Austria
| | - S Fabio Falsone
- Institute of Pharmaceutical Sciences, University of Graz, Graz, Austria
| | - Christoph Göbl
- Dept. of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - N Helge Meyer
- Institute of Chemistry, University of Graz, Graz, Austria; Division of General and Visceral Surgery, Department of Human Medicine, University of Oldenburg, Germany.
| | - Klaus Zangger
- Institute of Chemistry, University of Graz, Graz, Austria.
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21
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Petrovskaya LE, Lukashev EP, Mamedov MD, Kryukova EA, Balashov SP, Dolgikh DA, Rubin AB, Kirpichnikov MP, Siletsky SA. Oriented Insertion of ESR-Containing Hybrid Proteins in Proteoliposomes. Int J Mol Sci 2023; 24:ijms24087369. [PMID: 37108532 PMCID: PMC10138546 DOI: 10.3390/ijms24087369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/13/2023] [Accepted: 04/15/2023] [Indexed: 04/29/2023] Open
Abstract
Microbial rhodopsins comprise a diverse family of retinal-containing membrane proteins that convert absorbed light energy to transmembrane ion transport or sensory signals. Incorporation of these proteins in proteoliposomes allows their properties to be studied in a native-like environment; however, unidirectional protein orientation in the artificial membranes is rarely observed. We aimed to obtain proteoliposomes with unidirectional orientation using a proton-pumping retinal protein from Exiguobacterium sibiricum, ESR, as a model. Three ESR hybrids with soluble protein domains (mCherry or thioredoxin at the C-terminus and Caf1M chaperone at the N-terminus) were obtained and characterized. The photocycle of the hybrid proteins incorporated in proteoliposomes demonstrated a higher pKa of the M state accumulation compared to that of the wild-type ESR. Large negative electrogenic phases and an increase in the relative amplitude of kinetic components in the microsecond time range in the kinetics of membrane potential generation of ESR-Cherry and ESR-Trx indicate a decrease in the efficiency of transmembrane proton transport. On the contrary, Caf-ESR demonstrates a native-like kinetics of membrane potential generation and the corresponding electrogenic stages. Our experiments show that the hybrid with Caf1M promotes the unidirectional orientation of ESR in proteoliposomes.
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Affiliation(s)
- Lada E Petrovskaya
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul. Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
| | - Evgeniy P Lukashev
- Department of Biology, Lomonosov Moscow State University, Leninskie Gory, 1, 119234 Moscow, Russia
| | - Mahir D Mamedov
- Belozersky Institute of Physical-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Elena A Kryukova
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul. Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
| | - Sergei P Balashov
- Department of Physiology and Biophysics, University of California, Irvine, CA 92697, USA
| | - Dmitry A Dolgikh
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul. Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
- Department of Biology, Lomonosov Moscow State University, Leninskie Gory, 1, 119234 Moscow, Russia
| | - Andrei B Rubin
- Department of Biology, Lomonosov Moscow State University, Leninskie Gory, 1, 119234 Moscow, Russia
| | - Mikhail P Kirpichnikov
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul. Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
- Department of Biology, Lomonosov Moscow State University, Leninskie Gory, 1, 119234 Moscow, Russia
| | - Sergey A Siletsky
- Belozersky Institute of Physical-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
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22
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Tosaka T, Kamiya K. Function Investigations and Applications of Membrane Proteins on Artificial Lipid Membranes. Int J Mol Sci 2023; 24:ijms24087231. [PMID: 37108393 PMCID: PMC10138308 DOI: 10.3390/ijms24087231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/05/2023] [Accepted: 04/11/2023] [Indexed: 04/29/2023] Open
Abstract
Membrane proteins play an important role in key cellular functions, such as signal transduction, apoptosis, and metabolism. Therefore, structural and functional studies of these proteins are essential in fields such as fundamental biology, medical science, pharmacology, biotechnology, and bioengineering. However, observing the precise elemental reactions and structures of membrane proteins is difficult, despite their functioning through interactions with various biomolecules in living cells. To investigate these properties, methodologies have been developed to study the functions of membrane proteins that have been purified from biological cells. In this paper, we introduce various methods for creating liposomes or lipid vesicles, from conventional to recent approaches, as well as techniques for reconstituting membrane proteins into artificial membranes. We also cover the different types of artificial membranes that can be used to observe the functions of reconstituted membrane proteins, including their structure, number of transmembrane domains, and functional type. Finally, we discuss the reconstitution of membrane proteins using a cell-free synthesis system and the reconstitution and function of multiple membrane proteins.
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Affiliation(s)
- Toshiyuki Tosaka
- Division of Molecular Science, Graduate School of Science and Technology, Gunma University, Gunma 376-8515, Japan
| | - Koki Kamiya
- Division of Molecular Science, Graduate School of Science and Technology, Gunma University, Gunma 376-8515, Japan
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23
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Krishnarjuna B, Marte J, Ravula T, Ramamoorthy A. Enhancing the stability and homogeneity of non-ionic polymer nanodiscs by tuning electrostatic interactions. J Colloid Interface Sci 2023; 634:887-896. [PMID: 36566634 PMCID: PMC10838601 DOI: 10.1016/j.jcis.2022.12.112] [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: 08/26/2022] [Revised: 12/14/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022]
Abstract
The nanodisc technology is increasingly used for structural studies on membrane proteins and drug delivery. The development of synthetic polymer nanodiscs and the recent discovery of non-ionic inulin-based polymers have significantly broadened the scope of nanodiscs. While the lipid exchange and size flexibility properties of the self-assembled polymer-based nanodiscs are valuable for various applications, the non-ionic polymer nanodiscs are remarkably unique in that they enable the reconstitution of any protein, protein-protein complexes, or drugs irrespective of their charge. However, the non-ionic nature of the belt could influence the stability and size homogeneity of inulin-based polymer nanodiscs. In this study, we investigate the size stability and homogeneity of nanodiscs formed by non-ionic lipid-solubilizing polymers using different biophysical methods. Polymer nanodiscs containing zwitterionic DMPC and different ratios of DMPC:DMPG lipids were made using anionic SMA-EA or non-ionic pentyl-inulin polymers. Non-ionic polymer nanodiscs made using zwitterionic DMPC lipids produced a very broad elution profile on SEC due to their instability in the column, thus affecting sample monodispersity which was confirmed by DLS experiments that showed multiple peaks. However, the inclusion of anionic DMPG lipids improved the stability as observed from SEC and DLS profiles, which was further confirmed by TEM images. Whereas, anionic SMA-EA-based DMPC-nanodiscs showed excellent stability and size homogeneity when solubilizing zwitterionic lipids. The stability of DMPC:DMPG non-ionic polymer nanodiscs is attributed to the inter-nanodisc repulsion by the anionic-DMPG that prevents the uncontrolled collision and fusion of nanodiscs. Thus, the reported results demonstrate the use of electrostatic interactions to tune the solubility, stability, and size homogeneity of non-ionic polymer nanodiscs which are important features for enabling functional and atomic-resolution structural studies of membrane proteins, other lipid-binding molecules, and water-soluble biomolecules including cytosolic proteins, nucleic acids and metabolites.
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Affiliation(s)
- Bankala Krishnarjuna
- Biophysics Program, Department of Chemistry, Macromolecular Science and Engineering, Biomedical Engineering, Michigan Neuroscience Institute, The University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Joseph Marte
- Biophysics Program, Department of Chemistry, Macromolecular Science and Engineering, Biomedical Engineering, Michigan Neuroscience Institute, The University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Thirupathi Ravula
- Biophysics Program, Department of Chemistry, Macromolecular Science and Engineering, Biomedical Engineering, Michigan Neuroscience Institute, The University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Ayyalusamy Ramamoorthy
- Biophysics Program, Department of Chemistry, Macromolecular Science and Engineering, Biomedical Engineering, Michigan Neuroscience Institute, The University of Michigan, Ann Arbor, MI 48109-1055, USA.
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24
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Johansen NT, Tidemand FG, Pedersen MC, Arleth L. Travel light: Essential packing for membrane proteins with an active lifestyle. Biochimie 2023; 205:3-26. [PMID: 35963461 DOI: 10.1016/j.biochi.2022.07.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/29/2022] [Accepted: 07/23/2022] [Indexed: 11/02/2022]
Abstract
We review the considerable progress during the recent decade in the endeavours of designing, optimising, and utilising carrier particle systems for structural and functional studies of membrane proteins in near-native environments. New and improved systems are constantly emerging, novel studies push the perceived limits of a given carrier system, and specific carrier systems consolidate and entrench themselves as the system of choice for particular classes of target membrane protein systems. This review covers the most frequently used carrier systems for such studies and emphasises similarities and differences between these systems as well as current trends and future directions for the field. Particular interest is devoted to the biophysical properties and membrane mimicking ability of each system and the manner in which this may impact an embedded membrane protein and an eventual structural or functional study.
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Affiliation(s)
- Nicolai Tidemand Johansen
- Section for Transport Biology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, 1871, Denmark.
| | - Frederik Grønbæk Tidemand
- Section for Transport Biology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, 1871, Denmark
| | - Martin Cramer Pedersen
- Condensed Matter Physics, Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, Copenhagen E, 2100, Denmark
| | - Lise Arleth
- Condensed Matter Physics, Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, Copenhagen E, 2100, Denmark
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25
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Ma S, Zhang Y, Zhang X, Xie H, Tong Q, Yu K, Yang J. Dynamic Interactions Between Brilliant Green and MscL Investigated by Solid-State NMR Spectroscopy and Molecular Dynamics Simulations. Chemistry 2023; 29:e202202106. [PMID: 36251739 DOI: 10.1002/chem.202202106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Indexed: 11/22/2022]
Abstract
The mechanosensitive ion channel of large conductance (MscL) is a promising template for the development of new antibiotics due to its high conservation and uniqueness to microbes. Brilliant green (BG), a triarylmethane dye, has been identified as a new antibiotic targeted MscL. However, the detailed binding sites to MscL and the dynamic pathway of BG through the MscL channel remain unknown. Here, the dynamic interactions between BG and MscL were investigated using solid-state NMR spectroscopy and molecule dynamics (MD) simulations. Residue site-specific binding sites of BG to the MscL channel were identified by solid-state NMR. In addition, MD simulations revealed that BG conducts through the MscL channel via residues along the inner surface of the pore sequentially, in which the strong hydrophobic interactions between BG and hydrophobic residues F23 and I27 in the hydrophobic gate region of the MscL channel are major restrictions. Particularly, it was demonstrated that BG activates the MscL channel by reducing the hydrophobicity of the F23 in the gate region by water molecules that are bound to BG. Taken together, these simulations and experimental data provide novel insights into the dynamic interactions between BG and MscL, based on which new hydrophobic antibiotics and adjuvants targeting MscL can be developed.
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Affiliation(s)
- Shaojie Ma
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, P. R. China.,Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, P.R. China.,Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology and the Collaborative Innovation Center for Brain Science, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, P.R. China
| | - Yan Zhang
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Xuning Zhang
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, P. R. China.,Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology and the Collaborative Innovation Center for Brain Science, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, P.R. China
| | - Huayong Xie
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, P. R. China
| | - Qiong Tong
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, P. R. China
| | - Kunqian Yu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, P.R. China
| | - Jun Yang
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, P. R. China.,Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology and the Collaborative Innovation Center for Brain Science, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, P.R. China.,Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
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26
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Dmitrieva DA, Kotova TV, Safronova NA, Sadova AA, Dashevskii DE, Mishin AV. Protein Design Strategies for the Structural–Functional Studies of G Protein-Coupled Receptors. BIOCHEMISTRY (MOSCOW) 2023; 88:S192-S226. [PMID: 37069121 DOI: 10.1134/s0006297923140110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
G protein-coupled receptors (GPCRs) are an important family of membrane proteins responsible for many physiological functions in human body. High resolution GPCR structures are required to understand their molecular mechanisms and perform rational drug design, as GPCRs play a crucial role in a variety of diseases. That is difficult to obtain for the wild-type proteins because of their low stability. In this review, we discuss how this problem can be solved by using protein design strategies developed to obtain homogeneous stabilized GPCR samples for crystallization and cryoelectron microscopy.
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Affiliation(s)
- Daria A Dmitrieva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Tatiana V Kotova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Nadezda A Safronova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Alexandra A Sadova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Dmitrii E Dashevskii
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Alexey V Mishin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia.
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27
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Krishnarjuna B, Ravula T, Faison EM, Tonelli M, Zhang Q, Ramamoorthy A. Polymer-Nanodiscs as a Novel Alignment Medium for High-Resolution NMR-Based Structural Studies of Nucleic Acids. Biomolecules 2022; 12:1628. [PMID: 36358983 PMCID: PMC9687133 DOI: 10.3390/biom12111628] [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: 09/29/2022] [Revised: 10/28/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022] Open
Abstract
Residual dipolar couplings (RDCs) are increasingly used for high-throughput NMR-based structural studies and to provide long-range angular constraints to validate and refine structures of various molecules determined by X-ray crystallography and NMR spectroscopy. RDCs of a given molecule can be measured in an anisotropic environment that aligns in an external magnetic field. Here, we demonstrate the first application of polymer-based nanodiscs for the measurement of RDCs from nucleic acids. Polymer-based nanodiscs prepared using negatively charged SMA-EA polymer and zwitterionic DMPC lipids were characterized by size-exclusion chromatography, 1H NMR, dynamic light-scattering, and 2H NMR. The magnetically aligned polymer-nanodiscs were used as an alignment medium to measure RDCs from a 13C/15N-labeled fluoride riboswitch aptamer using 2D ARTSY-HSQC NMR experiments. The results showed that the alignment of nanodiscs is stable for nucleic acids and nanodisc-induced RDCs fit well with the previously determined solution structure of the riboswitch. These results demonstrate that SMA-EA-based lipid-nanodiscs can be used as a stable alignment medium for high-resolution structural and dynamical studies of nucleic acids, and they can also be applicable to study various other biomolecules and small molecules in general.
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Affiliation(s)
- Bankala Krishnarjuna
- Biophysics Program, Department of Chemistry, Biomedical Engineering, and Macromolecular Science and Engineering, Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Thirupathi Ravula
- Biophysics Program, Department of Chemistry, Biomedical Engineering, and Macromolecular Science and Engineering, Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI 48109, USA
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Edgar M. Faison
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Qi Zhang
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ayyalusamy Ramamoorthy
- Biophysics Program, Department of Chemistry, Biomedical Engineering, and Macromolecular Science and Engineering, Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI 48109, USA
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28
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Yildirim B, Beşer BM, Çolak NU, Altay A, Yaşar A. Fluorescence interactions of a novel chalcone derivative with membrane model systems and human serum albumin. Biophys Chem 2022; 290:106879. [DOI: 10.1016/j.bpc.2022.106879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 08/23/2022] [Accepted: 08/24/2022] [Indexed: 11/15/2022]
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29
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Meikle TG, Keizer DW, Separovic F, Yao S. A solution NMR view of Lipidic Cubic Phases: Structure, dynamics, and beyond. BBA ADVANCES 2022; 2:100062. [PMID: 37082598 PMCID: PMC10074910 DOI: 10.1016/j.bbadva.2022.100062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 10/30/2022] [Accepted: 11/02/2022] [Indexed: 11/06/2022] Open
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is well-established nowadays for the elucidation of the 3D structures of proteins and protein complexes, the evaluation of biomolecular dynamics with atomistic resolution across a range of time scales, the screening of drug candidates with site specificity, and for the quantitation of molecular translational diffusion. Lyotropic lipidic cubic phases (LCPs) are lipid bilayer-based materials with a complex geometry, formed via the spontaneous self-assembly of certain lipids in an aqueous environment at specific temperature ranges. LCPs have been successfully applied to the in meso crystallization of membrane proteins for structural studies by X-ray crystallography, and have also shown promising potential for serving as matrices for drug and nutrient delivery/release in vivo. The characterization of the structural and dynamics properties of LCPs is of significant interest for the application of these materials. Here we present a systematic review detailing the characterization of LCPs by solution NMR. Using LCPs formed by monoolein (MO) as an example, various aspects of LCPs readily accessible by solution NMR are covered, including spectral perturbation in the presence of additives, quantification of hydration levels, 13C relaxation-based measurements for studying atom-specific dynamics along the MO hydrocarbon chain, PGSE NMR measurement of translational diffusion and its correlation with release profiles, and the encapsulation of soluble proteins in LCPs. A brief discussion of future perspectives for the characterization of LCPs by solution NMR is also presented.
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30
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Salnikov E, Bechinger B. Effect of lipid saturation on the topology and oligomeric state of helical membrane polypeptides. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:184001. [PMID: 35817122 DOI: 10.1016/j.bbamem.2022.184001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/27/2022] [Accepted: 06/28/2022] [Indexed: 06/15/2023]
Abstract
Natural liquid crystalline membranes are made up of many different lipids carrying a mixture of saturated and unsaturated fatty acyl chains. Whereas in the past considerable attention has been paid to cholesterol content, the phospholipid head groups and the membrane surface charge the detailed fatty acyl composition was often considered less important. However, recent investigations indicate that the detailed fatty acyl chain composition has pronounced effects on the oligomerization of the transmembrane helical anchoring domains of the MHC II receptor or the membrane alignment of the cationic antimicrobial peptide PGLa. In contrast the antimicrobial peptides magainin 2 and alamethicin are less susceptible to lipid saturation. Using histidine-rich LAH4 designer peptides the high energetic contributions of lipid saturation in stabilizing transmembrane helical alignments are quantitatively evaluated. These observations can have important implications for the biological regulation of membrane proteins and should be taken into considerations during biophysical or structural experiments.
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Affiliation(s)
- Evgeniy Salnikov
- University of Strasbourg/CNRS, UMR7177 Chemistry Institute, Membrane Biophysics and NMR, Strasbourg, France
| | - Burkhard Bechinger
- University of Strasbourg/CNRS, UMR7177 Chemistry Institute, Membrane Biophysics and NMR, Strasbourg, France; Institut Universitaire de France, France.
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31
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Taguchi S, Okamoto Y, Suga K, Jung HS, Umakoshi H. Preparation of Planar Lipid Bilayer Membrane by Utilizing Bicelles and Its Characterization. KAGAKU KOGAKU RONBUN 2022. [DOI: 10.1252/kakoronbunshu.48.175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Shogo Taguchi
- Department of Chemical Engineering and Materials Science, Graduate School of Engineering, University of Hyogo
| | - Yukihiro Okamoto
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University
| | - Keishi Suga
- Department of Chemical Engineering, Tohoku University
| | - Ho-Sup Jung
- Center for Food and Bioconvergence, Department of Food Science and Biotechnology, Seoul National University
| | - Hiroshi Umakoshi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University
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32
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Galiakhmetov AR, Davern CM, Esteves RJA, Awosanya EO, Guthrie QAE, Proulx C, Nevzorov AA. Aligned peptoid-based macrodiscs for structural studies of membrane proteins by oriented-sample NMR. Biophys J 2022; 121:3263-3270. [PMID: 35918898 PMCID: PMC9463639 DOI: 10.1016/j.bpj.2022.07.024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 07/01/2022] [Accepted: 07/17/2022] [Indexed: 11/21/2022] Open
Abstract
Development of a robust, uniform, and magnetically orientable lipid mimetic will undoubtedly advance solid-state NMR of macroscopically aligned membrane proteins. Here, we report on a novel lipid membrane mimetic based on peptoid belts. The peptoids, composed of 15 residues, were synthesized by alternating N-(2-phenethyl)glycine with N-(2-carboxyethyl)glycine residues at a 2:1 molar ratio. The chemically synthesized peptoids possess a much lower degree of polydispersity versus styrene-maleic acid polymers, thus yielding uniform discs. Moreover, the peptoid oligomers are more flexible and do not require a specific folding, unlike lipoproteins, in order to wrap around the hydrophobic membrane core. The NMR spectra measured for the membrane-bound form of Pf1 coat protein incorporated in this new lipid mimetics demonstrate a higher order parameter and uniform linewidths compared with the conventional bicelles and peptide-based macrodiscs. Importantly, unlike bicelles, the peptoid-based macrodiscs are detergent free.
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Affiliation(s)
| | - Carolynn M Davern
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina
| | - Richard J A Esteves
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina
| | - Emmanuel O Awosanya
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina
| | - Quibria A E Guthrie
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina
| | - Caroline Proulx
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina
| | - Alexander A Nevzorov
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina.
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33
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Krishnarjuna B, Im SC, Ravula T, Marte J, Auchus RJ, Ramamoorthy A. Non-Ionic Inulin-Based Polymer Nanodiscs Enable Functional Reconstitution of a Redox Complex Composed of Oppositely Charged CYP450 and CPR in a Lipid Bilayer Membrane. Anal Chem 2022; 94:11908-11915. [PMID: 35977417 PMCID: PMC10851674 DOI: 10.1021/acs.analchem.2c02489] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Although polymer-based lipid nanodiscs are increasingly used in the structural studies of membrane proteins, the charge of the belt-forming polymer is a major limitation for functional reconstitution of membrane proteins possessing an opposite net charge to that of the polymer. This limitation also rules out the reconstitution of a protein-protein complex composed of oppositely charged membrane proteins. In this study, we report the first successful functional reconstitution of a membrane-bound redox complex constituting a cationic cytochrome P450 (CYP450) and an anionic cytochrome P450 reductase (CPR) in non-ionic inulin-based lipid nanodiscs. The gel-to-liquid-crystalline phase-transition temperature (Tm) of DMPC:DMPG (7:3 w/w) lipids in polymer nanodiscs was determined by differential scanning calorimetry (DSC) and 31P NMR experiments. The CYP450-CPR redox complex reconstitution in polymer nanodiscs was characterized by size-exclusion chromatography (SEC), and the electron transfer kinetics was carried out using the stopped-flow technique under anaerobic conditions. The Tm of DMPC:DMPG (7:3 w/w) in polymer nanodiscs measured from 31P NMR agrees with that obtained from DSC and was found to be higher than that for liposomes due to the decreased cooperativity of lipids present in the nanodiscs. The stopped-flow measurements revealed the CYP450-CPR redox complex reconstituted in nanodiscs to be functional, and the electron transfer kinetics was found to be temperature-dependent. Based on the successful demonstration of the use of non-ionic inulin-based polymer nanodiscs reported in this study, we expect them to be useful in studying the function and structures of a variety of membrane proteins/complexes irrespective of the charge of the molecular components. Since the polymer nanodiscs were shown to align in an externally applied magnetic field, they can also be used to measure residual dipolar couplings (RDCs) and residual quadrupolar couplings (RQCs) for various molecules ranging from small molecules to soluble proteins and nucleic acids.
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Affiliation(s)
- Bankala Krishnarjuna
- Biophysics Program, Department of Chemistry, Macromolecular Science and Engineering, Biomedical Engineering, Michigan Neuroscience Institute, The University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Sang-Choul Im
- Department of Pharmacology and Internal Medicine, Division of Metabolism, Endocrinology, & Diabetes, University of Michigan, Ann Arbor, MI 48109
| | - Thirupathi Ravula
- Biophysics Program, Department of Chemistry, Macromolecular Science and Engineering, Biomedical Engineering, Michigan Neuroscience Institute, The University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Joseph Marte
- Biophysics Program, Department of Chemistry, Macromolecular Science and Engineering, Biomedical Engineering, Michigan Neuroscience Institute, The University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Richard J. Auchus
- Department of Pharmacology and Internal Medicine, Division of Metabolism, Endocrinology, & Diabetes, University of Michigan, Ann Arbor, MI 48109
| | - Ayyalusamy Ramamoorthy
- Biophysics Program, Department of Chemistry, Macromolecular Science and Engineering, Biomedical Engineering, Michigan Neuroscience Institute, The University of Michigan, Ann Arbor, MI 48109-1055, USA
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34
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Krishnarjuna B, Ramamoorthy A. Detergent-Free Isolation of Membrane Proteins and Strategies to Study Them in a Near-Native Membrane Environment. Biomolecules 2022; 12:1076. [PMID: 36008970 PMCID: PMC9406181 DOI: 10.3390/biom12081076] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 07/31/2022] [Accepted: 08/02/2022] [Indexed: 02/06/2023] Open
Abstract
Atomic-resolution structural studies of membrane-associated proteins and peptides in a membrane environment are important to fully understand their biological function and the roles played by them in the pathology of many diseases. However, the complexity of the cell membrane has severely limited the application of commonly used biophysical and biochemical techniques. Recent advancements in NMR spectroscopy and cryoEM approaches and the development of novel membrane mimetics have overcome some of the major challenges in this area. For example, the development of a variety of lipid-nanodiscs has enabled stable reconstitution and structural and functional studies of membrane proteins. In particular, the ability of synthetic amphipathic polymers to isolate membrane proteins directly from the cell membrane, along with the associated membrane components such as lipids, without the use of a detergent, has opened new avenues to study the structure and function of membrane proteins using a variety of biophysical and biological approaches. This review article is focused on covering the various polymers and approaches developed and their applications for the functional reconstitution and structural investigation of membrane proteins. The unique advantages and limitations of the use of synthetic polymers are also discussed.
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Affiliation(s)
- Bankala Krishnarjuna
- Department of Chemistry and Biophysics, Biomedical Engineering, Macromolecular Science and Engineering, Michigan Neuroscience Institute, The University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Ayyalusamy Ramamoorthy
- Department of Chemistry and Biophysics, Biomedical Engineering, Macromolecular Science and Engineering, Michigan Neuroscience Institute, The University of Michigan, Ann Arbor, MI 48109-1055, USA
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35
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Zhao F, Zhu Z, Xie L, Luo F, Wang H, Qiu Y, Luo W, Zhou F, Xue D, Zhang Z, Hua T, Wu D, Liu Z, Le Z, Tao H. Two‐Dimensional Detergent Expansion Strategy for Membrane Protein Studies. Chemistry 2022; 28:e202201388. [DOI: 10.1002/chem.202201388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Fei Zhao
- iHuman Institute ShanghaiTech University Shanghai 201210 China
| | - Zhihao Zhu
- College of Chemistry Nanchang University Nanchang, Jiangxi Province 330031 China
| | - Linshan Xie
- iHuman Institute ShanghaiTech University Shanghai 201210 China
- School of Life Science and Technology ShanghaiTech University Shanghai 201210 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Feng Luo
- iHuman Institute ShanghaiTech University Shanghai 201210 China
| | - Huixia Wang
- iHuman Institute ShanghaiTech University Shanghai 201210 China
| | - Yanli Qiu
- iHuman Institute ShanghaiTech University Shanghai 201210 China
- School of Life Science and Technology ShanghaiTech University Shanghai 201210 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Weiling Luo
- iHuman Institute ShanghaiTech University Shanghai 201210 China
- School of Life Science and Technology ShanghaiTech University Shanghai 201210 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Fang Zhou
- iHuman Institute ShanghaiTech University Shanghai 201210 China
| | - Dongxiang Xue
- iHuman Institute ShanghaiTech University Shanghai 201210 China
| | - Zhihui Zhang
- iHuman Institute ShanghaiTech University Shanghai 201210 China
| | - Tian Hua
- iHuman Institute ShanghaiTech University Shanghai 201210 China
- School of Life Science and Technology ShanghaiTech University Shanghai 201210 China
| | - Dong Wu
- iHuman Institute ShanghaiTech University Shanghai 201210 China
| | - Zhi‐Jie Liu
- iHuman Institute ShanghaiTech University Shanghai 201210 China
- School of Life Science and Technology ShanghaiTech University Shanghai 201210 China
| | - Zhiping Le
- College of Chemistry Nanchang University Nanchang, Jiangxi Province 330031 China
| | - Houchao Tao
- iHuman Institute ShanghaiTech University Shanghai 201210 China
- Shanghai Frontiers Science Center of TCM Chemical Biology Innovation Research Institute of Traditional Chinese Medicine Shanghai University of Traditional Chinese Medicine Shanghai 201203 China
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36
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Yang M, Luo W, Zhang W, Wang H, Xue D, Wu Y, Zhao S, Zhao F, Zheng X, Tao H. Ugi Reaction Mediated Detergent Assembly for Membrane Protein Studies. Chem Asian J 2022; 17:e202200372. [PMID: 35575910 DOI: 10.1002/asia.202200372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/16/2022] [Indexed: 11/11/2022]
Abstract
Despite the continuous efforts, the current repertoire of detergents is still far from sufficient for the biophysics studies of membrane proteins (MPs). Toward the rapid expansion of detergent diversity, we herein report a new strategy based on Ugi reaction mediated modular assembly. Structural varieties, including hydrophobic tails and hydrophilic heads, could be conveniently introduced from the multiple reaction components. New detergents then were comprehensively evaluated in the physical properties and preliminarily screened by the thermal stabilization for a transporter MsbA and a spectrum of G protein-coupled receptors (GPCRs). For the glucagon-like peptide-1 receptor (GLP-1R), a class B GPCR, detergent M-23-M finally stood out in a second evaluation for the maintenance of homogeneity and was further illustrated its application in the improvement of NMR study. Besides the promising utility in the MP study, the current results exhibit intriguing structural-physical relationship that would allow the guidance in the tuning of detergent properties in the future.
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Affiliation(s)
- Meifang Yang
- University of South China, Department of Pharmacy, CHINA
| | - Weiling Luo
- ShanghaiTech University, iHuman Institute, CHINA
| | - Wei Zhang
- ShanghaiTech University, iHuman Institute, CHINA
| | - Huixia Wang
- ShanghaiTech University, iHuman Institute, CHINA
| | | | - Yiran Wu
- ShanghaiTech University, iHuman Institute, CHINA
| | - Suwen Zhao
- ShanghaiTech University, iHuman Institute, CHINA
| | - Fei Zhao
- ShanghaiTech University, iHuman Institute, 230 Haike Road, 201210, Shanghai, CHINA
| | - Xing Zheng
- University of South China, Department of Pharmacy, CHINA
| | - Houchao Tao
- Shanghai University of Traditional Chinese Medicine, Shanghai Frontiers Science Center of TCM Chemical Biology, Room 2421, Building 2, 1200 Cailun Road, 230032, Shanghai, CHINA
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37
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Nishimura T, Hatatani Y, Ando M, Sasaki Y, Akiyoshi K. Single-component nanodiscs via the thermal folding of amphiphilic graft copolymers with the adjusted flexibility of the main chain. Chem Sci 2022; 13:5243-5251. [PMID: 35655565 PMCID: PMC9093194 DOI: 10.1039/d2sc01674e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 04/12/2022] [Indexed: 12/26/2022] Open
Abstract
Nanodiscs have attracted considerable attention as structural scaffolds for membrane-protein research and as biomaterials in e.g. drug-delivery systems. However, conventional disc-fabrication methods are usually laborious, and disc fabrication via the self-assembly of amphiphiles is difficult. Herein, we report the formation of polymer nanodiscs based on the self-assembly of amphiphilic graft copolymers by adjusting the persistence length of the main chain. Amphiphilic graft copolymers with a series of different main-chain persistence lengths were prepared and these formed, depending on the persistence length, either rods, discs, or vesicles. Notably, polymer nanodiscs were formed upon heating a chilled polymer solution without the need for any additives, and the thus obtained nanodiscs were used to solubilize a membrane protein during cell-free protein synthesis. Given the simplicity of this disc-fabrication method and the ability of these discs to solubilize membrane proteins, this study considerably expands the fundamental and practical scope of graft-copolymer nanodiscs and demonstrates their utility as tools for studying the structure and function of membrane proteins.
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Affiliation(s)
- Tomoki Nishimura
- Department of Chemistry and Materials, Faculty of Textile Science and Technology, Shinshu University 3-15-1, Tokida Ueda Nagano 386-8567 Japan
| | - Yusuke Hatatani
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University Katsura, Nishikyo-ku Kyoto 615-8510 Japan
| | - Mitsuru Ando
- Department of Regeneration Science and Engineering, Institute for Frontier Life and Medical Sciences, Kyoto University Shogoin Kawahara-cho, Sakyo-ku Kyoto 606-8507 Japan
| | - Yoshihiro Sasaki
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University Katsura, Nishikyo-ku Kyoto 615-8510 Japan
| | - Kazunari Akiyoshi
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University Katsura, Nishikyo-ku Kyoto 615-8510 Japan
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38
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Takagi Y, Uchida N, Anraku Y, Muraoka T. Stabilization of bicelles using metal-binding peptide for extended blood circulation. Chem Commun (Camb) 2022; 58:5164-5167. [PMID: 35388392 DOI: 10.1039/d2cc01058e] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A metal-binding peptide appending cholic acid, Chol-MBP, formed bicelles by mixing with 1,2-dipalmitoyl-sn-glycero-3-phosphorylcholine (DPPC). Coordination of Chol-MBP with Cu2+ stabilized DPPC bicelles against dilution and contamination of serum proteins, enabling extended blood circulation. This study demonstrates an effective supramolecular design of phospholipid bicelles with enhanced stability useful for membrane-based biomaterials.
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Affiliation(s)
- Yuichiro Takagi
- Department of Applied Chemistry, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.
| | - Noriyuki Uchida
- Department of Applied Chemistry, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.
| | - Yasutaka Anraku
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.,Innovation Center of NanoMedicine, Kawasaki Institute of Industrial Promotion, 3-25-14, Tonomachi, Kawasaki-ku, Kawasaki 210-0821, Japan
| | - Takahiro Muraoka
- Department of Applied Chemistry, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan. .,Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, 3-8-1 Harumi-cho, Fuchu-Shi, Tokyo 183-8538, Japan.,Kanagawa Institute of Industrial Science and Technology (KISTEC), 705-1 Shimoimaizumi, Ebina, Kanagawa 243-0435, Japan
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39
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Uchida N, Yanagi M, Hamada H. Bicelle Composed of 1,2-Dipalmitoyl- sn-Glycero-3-Phosphatidylcholine and Sodium Cholate. Nat Prod Commun 2022. [DOI: 10.1177/1934578x221092702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
A mixture of 1,2-dipalmitoyl- sn-glycero-3-phosphatidylcholine (DPPC) phospholipid and sodium chelate (SC) formed bicelles (DPPC–SC bicelle) at around 50 °C. In 2H nuclear magnetic resonance (NMR) measurement of the dispersion of DPPC–SC bicelle, quadrupole splitting of D2O, an index of the ability to orient molecules, was observed.
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Affiliation(s)
- Noriyuki Uchida
- RIKEN Center for Emergent Matter Science, Wako, Saitama, Japan
| | - Masayoshi Yanagi
- Department of Life Science, Faculty of Science, Okayama University of Science, Kita-ku, Okayama, Japan
| | - Hiroki Hamada
- Department of Life Science, Faculty of Science, Okayama University of Science, Kita-ku, Okayama, Japan
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40
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Vallejo DD, Rojas Ramírez C, Parson KF, Han Y, Gadkari VV, Ruotolo BT. Mass Spectrometry Methods for Measuring Protein Stability. Chem Rev 2022; 122:7690-7719. [PMID: 35316030 DOI: 10.1021/acs.chemrev.1c00857] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Mass spectrometry is a central technology in the life sciences, providing our most comprehensive account of the molecular inventory of the cell. In parallel with developments in mass spectrometry technologies targeting such assessments of cellular composition, mass spectrometry tools have emerged as versatile probes of biomolecular stability. In this review, we cover recent advancements in this branch of mass spectrometry that target proteins, a centrally important class of macromolecules that accounts for most biochemical functions and drug targets. Our efforts cover tools such as hydrogen-deuterium exchange, chemical cross-linking, ion mobility, collision induced unfolding, and other techniques capable of stability assessments on a proteomic scale. In addition, we focus on a range of application areas where mass spectrometry-driven protein stability measurements have made notable impacts, including studies of membrane proteins, heat shock proteins, amyloidogenic proteins, and biotherapeutics. We conclude by briefly discussing the future of this vibrant and fast-moving area of research.
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Affiliation(s)
- Daniel D Vallejo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Carolina Rojas Ramírez
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Kristine F Parson
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Yilin Han
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Varun V Gadkari
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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41
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Taguchi S, Kimura Y, Akiyama Y, Tachibana Y, Yamamoto T. Fluorescent Anisotropy Evaluation of Bicelle Formation Employing Carboxyl BODIPY and Pyrromethene. J Oleo Sci 2022; 71:353-362. [PMID: 35236795 DOI: 10.5650/jos.ess21295] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Bicelles are extensively used as the parent assemblies of functional membrane materials. This study characterizes membrane fluidity in fatty acid/detergent bicelles containing carboxyl boron-dipyrromethene (BODIPY C12) and pyrromethene as fluorescent probe molecules. The anisotropy value of BODIPY C12 and pyrromethene in the phospholipid vesicles depended on the phase state of the vesicles. The anisotropy of the fluorescent probe molecules in bicelles of oleic acid/3-[(3-cholamidopropyl) dimethylammonio]-2-hydroxypropane sulfonate (OA/CHAPSO) was then evaluated. The OA/CHAPSO bicelles were prepared by mixing CHAPSO detergent solution with OA vesicles at different molar ratios, X OA (= [OA]/([OA]+[CHAPSO])). The anisotropies of the probes in the OA/CHAPSO bicelles increased with decreasing X OA. BODIPY C12 in the range 0.30 ≤ X OA ≤ 0.70 exhibited a distinctly larger anisotropy than pyrromethene. This result agreed with the increase in packing density associated with the adsorption of CHAPSO molecules on the OA bilayer membrane in the OA/CHAPSO bicelle, revealing that the anisotropy of BODIPY C12 molecule enables membrane-fluidity evaluation in OA/CHAPSO bicelles.
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Affiliation(s)
- Shogo Taguchi
- Department of Chemical Engineering and Materials Science, Grad. Sch. of Engineering, University of Hyogo
| | - Yuta Kimura
- Department of Chemical Engineering and Materials Science, Grad. Sch. of Engineering, University of Hyogo
| | - Yuka Akiyama
- Department of Chemical Engineering and Materials Science, Grad. Sch. of Engineering, University of Hyogo
| | - Yasuaki Tachibana
- Department of Chemical Engineering and Materials Science, Grad. Sch. of Engineering, University of Hyogo
| | - Takuji Yamamoto
- Department of Chemical Engineering and Materials Science, Grad. Sch. of Engineering, University of Hyogo
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42
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Ephrem E, Najjar A, Charcosset C, Greige-Gerges H. Bicelles as a carrier for bioactive compounds in beverages: application to nerolidol, an active sesquiterpene alcohol. JOURNAL OF FOOD SCIENCE AND TECHNOLOGY 2022; 59:1030-1039. [PMID: 35185207 PMCID: PMC8814254 DOI: 10.1007/s13197-021-05107-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 03/25/2021] [Accepted: 04/13/2021] [Indexed: 11/29/2022]
Abstract
ABSTRACT Nerolidol is a natural sesquiterpene alcohol with promising but limited application in food and pharmaceutical fields due to several factors including low photostability and low aqueous solubility. Recently, several carriers loading nerolidol were prepared and tested in fresh orange juice. Lipid vesicles loading nerolidol did not exhibit satisfactory organoleptic properties in this beverage. Hence, DMPC/DHPC bicelles were prepared as a new phospholipid-based carrier for nerolidol at different molar ratios. The bicelle suspensions were characterized in terms of homogeneity, particles size, and morphology. The optimal formulation (phospholipid:nerolidol molar ratio 100:1) was selected based on transparent appearance, homogeneity, and particle size (~ 45 nm). Besides, it showed a high encapsulation efficiency of nerolidol and a high incorporation rate of phospholipids. Transmission electron microscopy analysis demonstrated the formation of bicelles. The bicelles membrane fluidity was assessed by 1,6-diphenyl-1,3,5-hexatriene fluorescence anisotropy and differential scanning calorimetry analysis. The membrane fluidity of bicelles appeared to increase in the presence of nerolidol in a concentration dependent manner. To our knowledge this is the first study dealing with the encapsulation of an essential oil component in bicelles. GRAPHIC ABSTRACT
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Affiliation(s)
- Elissa Ephrem
- Bioactive Molecules Research Laboratory, Faculty of Sciences, Section II, Lebanese University, Jdaidet El-Matn, B.P. 90656, Beirut, Lebanon ,LAGEP UMR 5007, CNRS, Univ Lyon, Université Claude Bernard Lyon 1, 43 Boulevard du 11 novembre 1918, 69100 Villeurbanne, France
| | - Amal Najjar
- Bioactive Molecules Research Laboratory, Faculty of Sciences, Section II, Lebanese University, Jdaidet El-Matn, B.P. 90656, Beirut, Lebanon
| | - Catherine Charcosset
- LAGEP UMR 5007, CNRS, Univ Lyon, Université Claude Bernard Lyon 1, 43 Boulevard du 11 novembre 1918, 69100 Villeurbanne, France
| | - Hélène Greige-Gerges
- Bioactive Molecules Research Laboratory, Faculty of Sciences, Section II, Lebanese University, Jdaidet El-Matn, B.P. 90656, Beirut, Lebanon
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43
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Ravula T, Ramamoorthy A. Measurement of Residual Dipolar Couplings Using Magnetically Aligned and Flipped Nanodiscs. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:244-252. [PMID: 34965145 PMCID: PMC9575995 DOI: 10.1021/acs.langmuir.1c02449] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Recent developments in lipid nanodisc technology have successfully overcome the major challenges in the structural and functional studies of membrane proteins and drug delivery. Among the different types of nanodiscs, the use of synthetic amphiphilic polymers created new directions including the applications of solution and solid-state NMR spectroscopy. The ability to magnetically align large-size (>20 nm diameter) polymer nanodiscs and flip them using paramagnetic lanthanide ions has enabled high-resolution studies on membrane proteins using solid-state NMR techniques. The use of polymer-based macro-nanodiscs (>20 nm diameter) as an alignment medium to measure residual dipolar couplings (RDCs) and residual quadrupole couplings by NMR experiments has also been demonstrated. In this study, we demonstrate the use of magnetically aligned and 90°-flipped polymer nanodiscs as alignment media for structural studies on proteins by solution NMR spectroscopy. These macro-nanodiscs, composed of negatively charged SMA-EA polymers and 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) lipids, were used to measure residual 1H-15N dipolar couplings (RDCs) from the water-soluble ∼21 kDa uniformly 15N-labeled flavin mononucleotide binding domain (FBD) of cytochrome-P450 reductase. The experimentally measured 1H-15N RDC values are compared with the values calculated from the crystal structures of cytochrome-P450 reductase that lacks the transmembrane domain. The N-H RDCs measured using aligned and 90°-flipped nanodiscs show a modulation by the function (3 cos2 θ - 1), where θ is the angle between the N-H bond vector and the applied magnetic field direction. This successful demonstration of the use of two orthogonally oriented alignment media should enable structural studies on a variety of systems including small molecules, DNA, and RNA.
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Affiliation(s)
- Thirupathi Ravula
- Biophysics and Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, The University of Michigan, Ann Arbor, MI 48109-1055, USA
- National Magnetic Resonance Facility at Madison, Department of Biochemistry, University of Wisconsin, Madison, WI 53706-1544, USA
| | - Ayyalusamy Ramamoorthy
- Biophysics and Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, The University of Michigan, Ann Arbor, MI 48109-1055, USA
- Corresponding author’s
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44
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Taguchi S, Kimura Y, Akiyama Y, Tachibana Y, Yamamoto T. Characterization of Oleic Acid/CHAPSO Bicellar Mixture Formation via Lipid Transfer. J Oleo Sci 2022; 71:1445-1452. [DOI: 10.5650/jos.ess22147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Shogo Taguchi
- Department of Chemical Engineering and Materials Science, Grad. Sch. of Engineering, University of Hyogo
| | - Yuta Kimura
- Department of Chemical Engineering and Materials Science, Grad. Sch. of Engineering, University of Hyogo
| | - Yuka Akiyama
- Department of Chemical Engineering and Materials Science, Grad. Sch. of Engineering, University of Hyogo
| | - Yasuaki Tachibana
- Department of Chemical Engineering and Materials Science, Grad. Sch. of Engineering, University of Hyogo
| | - Takuji Yamamoto
- Department of Chemical Engineering and Materials Science, Grad. Sch. of Engineering, University of Hyogo
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45
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Banerjee S, Lyubchenko YL. Topographically smooth and stable supported lipid bilayer for high-resolution AFM studies. Methods 2022; 197:13-19. [PMID: 33609699 PMCID: PMC8371085 DOI: 10.1016/j.ymeth.2021.02.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 02/04/2021] [Accepted: 02/10/2021] [Indexed: 01/03/2023] Open
Abstract
The cellular membrane has been identified to play a critical role in various biological processes including the assembly of biological systems. Membranes are complex, primarily two-dimensional assemblies with varied lipid compositions depending on the particular region of the cell. Supported lipid bilayers are considered as appropriate models for physio-chemical studies of membranes including numerous single molecule techniques. Atomic force microscopy (AFM) as a topographic technique is a fully appropriate single molecule technique capable of direct observation of molecular processes on membranes. However, reliable experimental AFM studies require the preparation of the bilayer with a sub-nanometer smooth morphology, which remains stable over long-time observation. Here we present the methodology, which allows one to prepare a smooth, stable, structurally homogeneous lipid bilayer without the presence of any trapped vesicles. We described the application of such lipid bilayers to probe time-dependent early stages of aggregation of monomeric amyloid proteins. Importantly, the proposed methodology can be extended to bilayers with various compositions, by incorporating different lipids for on-membrane aggregation study including cholesterol. Furthermore, this methodology development allowed us to monitor the aggregation of amyloid protein at its physiologically relevant low protein concentration. The flexibility of altering the membrane composition allows to identify the specific role of a particular lipid towards the aggregation kinetics, revealing the plausible mechanism of disease development.
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46
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Mahmoud DB, Bakr MM, Al-karmalawy AA, Moatasim Y, El Taweel A, Mostafa A. Scrutinizing the Feasibility of Nonionic Surfactants to Form Isotropic Bicelles of Curcumin: a Potential Antiviral Candidate Against COVID-19. AAPS PharmSciTech 2021; 23:44. [PMID: 34966978 PMCID: PMC8716085 DOI: 10.1208/s12249-021-02197-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 12/08/2021] [Indexed: 02/07/2023] Open
Abstract
Investigating bicelles as an oral drug delivery system and exploiting their structural benefits can pave the way to formulate hydrophobic drugs and potentiate their activity. Herein, the ability of non-ionic surfactants (labrasol®, tween 80, cremophore EL and pluronic F127) to form curcumin loaded bicelles with phosphatidylcholine, utilizing a simple method, was investigated. Molecular docking was used to understand the mechanism of bicelles formation. The % transmittance and TEM exhibited bicelles formation with labrasol® and tween 80, while cremophor EL and pluronic F127 tended to form mixed micelles. The surfactant-based nanostructures significantly improved curcumin dissolution (99.2 ± 2.6% within 10 min in case of tween 80-based bicelles) compared to liposomes and curcumin suspension in non-sink conditions. The prepared formulations improved curcumin ex vivo permeation over liposomes and drug suspension. Further, the therapeutic antiviral activity of the formulated curcumin against SARS-CoV-2 was potentiated over drug suspension. Although both Labrasol® and tween 80 bicelles could form bicelles and enhance the oral delivery of curcumin when compared to liposomes and drug suspension, the mixed micelles formulations depicted superiority than bicelles formulations. Our findings provide promising formulations that can be utilized for further preclinical and clinical studies of curcumin as an antiviral therapy for COVID-19 patients. Graphical Abstract ![]()
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47
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Abisoye-Ogunniyan A, Carrano IM, Weilhammer DR, Gilmore SF, Fischer NO, Pal S, de la Maza LM, Coleman MA, Rasley A. A Survey of Preclinical Studies Evaluating Nanoparticle-Based Vaccines Against Non-Viral Sexually Transmitted Infections. Front Pharmacol 2021; 12:768461. [PMID: 34899322 PMCID: PMC8662999 DOI: 10.3389/fphar.2021.768461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 11/01/2021] [Indexed: 11/13/2022] Open
Abstract
A worldwide estimate of over one million STIs are acquired daily and there is a desperate need for effective preventive as well as therapeutic measures to curtail this global health burden. Vaccines have been the most effective means for the control and potential eradication of infectious diseases; however, the development of vaccines against STIs has been a daunting task requiring extensive research for the development of safe and efficacious formulations. Nanoparticle-based vaccines represent a promising platform as they offer benefits such as targeted antigen presentation and delivery, co-localized antigen-adjuvant combinations for enhanced immunogenicity, and can be designed to be biologically inert. Here we discuss promising types of nanoparticles along with outcomes from nanoparticle-based vaccine preclinical studies against non-viral STIs including chlamydia, syphilis, gonorrhea, and recommendations for future nanoparticle-based vaccines against STIs.
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Affiliation(s)
- Abisola Abisoye-Ogunniyan
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Isabella M Carrano
- Department of Plant and Microbial Biology, Rausser College of Natural Resources, University of California, Berkeley, Berkeley, CA, United States
| | - Dina R Weilhammer
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Sean F Gilmore
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Nicholas O Fischer
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Sukumar Pal
- Department of Pathology and Laboratory Medicine, University of California, Irvine, Irvine, CA, United States
| | - Luis M de la Maza
- Department of Pathology and Laboratory Medicine, University of California, Irvine, Irvine, CA, United States
| | - Matthew A Coleman
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Amy Rasley
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, United States
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48
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Wang S, Gopinath T, Larsen EK, Weber DK, Walker C, Uddigiri VR, Mote KR, Sahoo SK, Periasamy M, Veglia G. Structural basis for sarcolipin's regulation of muscle thermogenesis by the sarcoplasmic reticulum Ca 2+-ATPase. SCIENCE ADVANCES 2021; 7:eabi7154. [PMID: 34826239 PMCID: PMC8626070 DOI: 10.1126/sciadv.abi7154] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 10/06/2021] [Indexed: 06/10/2023]
Abstract
The sarcoplasmic reticulum (SR) Ca2+-ATPase (SERCA) plays a central role in muscle contractility and nonshivering thermogenesis. SERCA is regulated by sarcolipin (SLN), a single-pass membrane protein that uncouples Ca2+ transport from ATP hydrolysis, promoting futile enzymatic cycles and heat generation. The molecular determinants for regulating heat release by the SERCA/SLN complex are unclear. Using thermocalorimetry, chemical cross-linking, and solid-state NMR spectroscopy in oriented phospholipid bicelles, we show that SERCA’s functional uncoupling and heat release rate are dictated by specific SERCA/SLN intramembrane interactions, with the carboxyl-terminal residues anchoring SLN to the SR membrane in an inhibitory topology. Systematic deletion of the carboxyl terminus does not prevent the SERCA/SLN complex formation but reduces uncoupling in a graded manner. These studies emphasize the critical role of lipids in defining the active topology of SLN and modulating the heat release rate by the SERCA/SLN complex, with implications in fat metabolism and basal metabolic rate.
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Affiliation(s)
- Songlin Wang
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Tata Gopinath
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Erik K. Larsen
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Daniel K. Weber
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Caitlin Walker
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Venkateswara Reddy Uddigiri
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Kaustubh R. Mote
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad, Telangana 500046, India
| | - Sanjaya K. Sahoo
- Department of Physiology, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Muthu Periasamy
- Department of Physiology, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
- Department of Internal Medicine, College of Medicine, University of Central Florida, Orlando, FL 32827, USA
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
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Zong W, Shao X, Chai Y, Wang X, Han S, Chu H, Zhu C, Zhang X. Liposomes encapsulating artificial cytosol as drug delivery system. Biophys Chem 2021; 281:106728. [PMID: 34864227 DOI: 10.1016/j.bpc.2021.106728] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 11/14/2021] [Accepted: 11/15/2021] [Indexed: 02/06/2023]
Abstract
The fabrication of cell models containing artificial cytosol is challenging. Herein we constructed an artificial cytosol contained cell model by electroformation method. Agarose was selected as the main component of the artificial cytosol, and sucrose was added into the agarose to regulate the sol viscosity and the phase transition temperature. The viscosity of the sol with the mass ratio (agarose-sucrose) 1:9 was closest to the natural cytosol. DSPC/20 mol% cholesterol was used to form large unilamellar vesicles (LUVs) as cell model compartment. The rhodamine release experiment confirmed that the unique release profile of agarose-sucrose@LUVs is suitable as a drug carrier. Doxorubicin is loaded in the agarose-sucrose@LUVs, and their half maximum inhibition concentration on HeLa cells is 0.016 μmol L-1, which means 28.7 times increase in inhibition efficiency over free doxorubicin.
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Affiliation(s)
- Wei Zong
- College of Chemistry and Chemical Engineering, Qiqihar University, No.42 Wenhua Street, Qiqihar 161006, China.
| | - Xiaotong Shao
- College of Chemistry and Chemical Engineering, Qiqihar University, No.42 Wenhua Street, Qiqihar 161006, China
| | - Yunhe Chai
- College of Chemistry and Chemical Engineering, Qiqihar University, No.42 Wenhua Street, Qiqihar 161006, China
| | - Xiuwen Wang
- College of Chemistry and Chemical Engineering, Qiqihar University, No.42 Wenhua Street, Qiqihar 161006, China
| | - Shuang Han
- College of Chemistry and Chemical Engineering, Qiqihar University, No.42 Wenhua Street, Qiqihar 161006, China
| | - Hongtao Chu
- College of Chemistry and Chemical Engineering, Qiqihar University, No.42 Wenhua Street, Qiqihar 161006, China
| | - Chuntao Zhu
- School of Chemistry Engineering, Northeast Electric Power University, No.169, ChangChun Road, Jilin 132012, China
| | - Xunan Zhang
- College of Chemistry and Chemical Engineering, Qiqihar University, No.42 Wenhua Street, Qiqihar 161006, China
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Zhang J, Wang K, Xue P, Chen X, Bian L. Molecular recognition and interaction between human plasminogen Kringle 5 and voltage-dependent anion channel-1 by biological specificity technologies and molecular dynamic simulation. Biophys Chem 2021; 280:106710. [PMID: 34741992 DOI: 10.1016/j.bpc.2021.106710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 11/16/2022]
Abstract
Voltage-dependent anion channel-l (VDAC-1) can bind with plasminogen Kringle 5 as the cell surface receptor and induce cell apoptosis, but the detailed information of binding is not clear yet. Thus, the mutual recognition and binding were investigated here utilizing frontal affinity chromatography, surface plasma resonance, mutation analysis combining molecular dynamics simulation. The results showed that Kringle 5 binds with VDAC-1 in equimolar driven mainly by electrostatic force, with 15 amino acid residues participating in Kringle 5 and 21 in VDAC-1. The observed conformational changes indicated the automatic structure regulation providing these two proteins suitable conformations and spatial surroundings for the tighter and stabler binding. Moreover, Glu29 in Kringle 5 was speculated as the key residue maintaining the largest energy contribution. Therefore, this work provided precise information for the recognition and binding of Kringle 5 with VDAC-1 that is valuable for the corresponding treatment of tumours or other angiogenic diseases.
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Affiliation(s)
- Jiaxin Zhang
- College of Life Science, Northwest University, Xi'an 710069, China
| | - Kun Wang
- College of Life Science, Northwest University, Xi'an 710069, China
| | - Pengli Xue
- College of Life Science, Northwest University, Xi'an 710069, China
| | - Xiu Chen
- College of Life Science, Northwest University, Xi'an 710069, China
| | - Liujiao Bian
- College of Life Science, Northwest University, Xi'an 710069, China.
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