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Mu Y, Zhao S, Liu J, Liu Z, He J, Cao H, Zhao H, Wang C, Jin Y, Qi Y, Wang F. Assessment of the Conformation Stability and Glycosylation Heterogeneity of Lactoferrin by Native Mass Spectrometry. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:10089-10096. [PMID: 38626386 DOI: 10.1021/acs.jafc.3c08860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2024]
Abstract
Lactoferrin (LTF) has diverse biological activities and is widely used in functional foods and active additives. Nevertheless, evaluating the proteoform heterogeneity, conformational stability, and activity of LTF remains challenging during its production and storage processes. In this study, we describe the implementation of native mass spectrometry (nMS), glycoproteomics, and an antimicrobial activity assay to assess the quality of LTF. We systematically characterize the purity, glycosylation heterogeneity, conformation, and thermal stability of LTF samples from different sources and transient high-temperature treatments by using nMS and glycoproteomics. Meanwhile, the nMS peak intensity and antimicrobial activity of LTF samples after heat treatment decreased significantly, and the two values were positively correlated. The nMS results provide essential molecular insights into the conformational stability and glycosylation heterogeneity of different LTF samples. Our results underscore the great potential of nMS for LTF quality control and activity evaluation in industrial production.
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Affiliation(s)
- Yu Mu
- College of Food Science and Engineering, Ocean University of Dalian, Dalian 116023, China
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Shan Zhao
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Jing Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- College of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Zheyi Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Jian He
- Inner Mongolia Dairy Technology Research Institute Co., Ltd., Hohhot 010110, China
- Inner Mongolia National Center of Technology Innovation for Dairy Co. Ltd., Hohhot 010110, China
| | - Hongfang Cao
- Inner Mongolia Dairy Technology Research Institute Co., Ltd., Hohhot 010110, China
- Inner Mongolia National Center of Technology Innovation for Dairy Co. Ltd., Hohhot 010110, China
| | - Heng Zhao
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Caiyun Wang
- Inner Mongolia Dairy Technology Research Institute Co., Ltd., Hohhot 010110, China
- Inner Mongolia National Center of Technology Innovation for Dairy Co. Ltd., Hohhot 010110, China
| | - Yan Jin
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Yanxia Qi
- College of Food Science and Engineering, Ocean University of Dalian, Dalian 116023, China
| | - Fangjun Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Inner Mongolia National Center of Technology Innovation for Dairy Co. Ltd., Hohhot 010110, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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2
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Wang T, Ma S, Ji G, Wang G, Liu Y, Zhang L, Zhang Y, Lu H. A chemical proteomics approach for global mapping of functional lysines on cell surface of living cell. Nat Commun 2024; 15:2997. [PMID: 38589397 PMCID: PMC11001985 DOI: 10.1038/s41467-024-47033-w] [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: 06/01/2023] [Accepted: 03/19/2024] [Indexed: 04/10/2024] Open
Abstract
Cell surface proteins are responsible for many crucial physiological roles, and they are also the major category of drug targets as the majority of therapeutics target membrane proteins on the surface of cells to alter cellular signaling. Despite its great significance, ligand discovery against membrane proteins has posed a great challenge mainly due to the special property of their natural habitat. Here, we design a new chemical proteomic probe OPA-S-S-alkyne that can efficiently and selectively target the lysines exposed on the cell surface and develop a chemical proteomics strategy for global analysis of surface functionality (GASF) in living cells. In total, we quantified 2639 cell surface lysines in Hela cell and several hundred residues with high reactivity were discovered, which represents the largest dataset of surface functional lysine sites to date. We discovered and validated that hyper-reactive lysine residues K382 on tyrosine kinase-like orphan receptor 2 (ROR2) and K285 on Endoglin (ENG/CD105) are at the protein interaction interface in co-crystal structures of protein complexes, emphasizing the broad potential functional consequences of cell surface lysines and GASF strategy is highly desirable for discovering new active and ligandable sites that can be functionally interrogated for drug discovery.
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Affiliation(s)
- Ting Wang
- Liver Cancer Institute, Zhongshan Hospital and Department of Chemistry, Fudan University, Shanghai, China
| | - Shiyun Ma
- Liver Cancer Institute, Zhongshan Hospital and Department of Chemistry, Fudan University, Shanghai, China
| | - Guanghui Ji
- Liver Cancer Institute, Zhongshan Hospital and Department of Chemistry, Fudan University, Shanghai, China
| | - Guoli Wang
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Shanghai, China
| | - Yang Liu
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Shanghai, China
| | - Lei Zhang
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Shanghai, China
| | - Ying Zhang
- Liver Cancer Institute, Zhongshan Hospital and Department of Chemistry, Fudan University, Shanghai, China.
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Shanghai, China.
| | - Haojie Lu
- Liver Cancer Institute, Zhongshan Hospital and Department of Chemistry, Fudan University, Shanghai, China.
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Shanghai, China.
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Luo P, Liu Z, Lai C, Jin Z, Wang M, Zhao H, Liu Y, Zhang W, Wang X, Xiao C, Yang X, Wang F. Time-Resolved Ultraviolet Photodissociation Mass Spectrometry Probes the Mutation-Induced Alterations in Protein Stability and Unfolding Dynamics. J Am Chem Soc 2024; 146:8832-8838. [PMID: 38507251 DOI: 10.1021/jacs.4c00316] [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: 03/22/2024]
Abstract
How mutations impact protein stability and structure dynamics is crucial for understanding the pathological process and rational drug design. Herein, we establish a time-resolved native mass spectrometry (TR-nMS) platform via a rapid-mixing capillary apparatus for monitoring the acid-initiated protein unfolding process. The molecular details in protein structure unfolding are further profiled by a 193 nm ultraviolet photodissociation (UVPD) analysis of the structure-informative photofragments. Compared with the wild-type dihydrofolate reductase (WT-DHFR), the M42T/H114R mutant (MT-DHFR) exhibits a significant stability decrease in TR-nMS characterization. UVPD comparisons of the unfolding intermediates and original DHFR forms indicate the special stabilization effect of cofactor NADPH on DHFR structure, and the M42T/H114R mutations lead to a significant decrease in NADPH-DHFR interactions, thus promoting the structure unfolding. Our study paves the way for probing the mutation-induced subtle changes in the stability and structure dynamics of drug targets.
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Affiliation(s)
- Pan Luo
- Institute of Advanced Science Facilities, Shenzhen 518107, China
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China
| | - Zheyi Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Can Lai
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhixiong Jin
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Mengdie Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Heng Zhao
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Yu Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Weiqing Zhang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Xingan Wang
- Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China
| | - Chunlei Xiao
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Xueming Yang
- Institute of Advanced Science Facilities, Shenzhen 518107, China
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Fangjun Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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4
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Chapman EA, Li BH, Krichel B, Chan HJ, Buck KM, Roberts DS, Ge Y. Native Top-Down Mass Spectrometry for Characterizing Sarcomeric Proteins Directly from Cardiac Tissue Lysate. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:738-745. [PMID: 38422011 PMCID: PMC11098619 DOI: 10.1021/jasms.3c00430] [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: 03/02/2024]
Abstract
Native top-down mass spectrometry (nTDMS) has emerged as a powerful structural biology tool that can localize post-translational modifications (PTMs), explore ligand-binding interactions, and elucidate the three-dimensional structure of proteins and protein complexes in the gas-phase. Fourier-transform ion cyclotron resonance (FTICR) MS offers distinct capabilities for nTDMS, owing to its ultrahigh resolving power, mass accuracy, and robust fragmentation techniques. Previous nTDMS studies using FTICR have mainly been applied to overexpressed recombinant proteins and protein complexes. Here, we report the first nTDMS study that directly analyzes human heart tissue lysate by direct infusion FTICR MS without prior chromatographic separation strategies. We have achieved comprehensive nTDMS characterization of cardiac contractile proteins that play critical roles in heart contraction and relaxation. Specifically, our results reveal structural insights into ventricular myosin light chain 2 (MLC-2v), ventricular myosin light chain 1 (MLC-1v), and alpha-tropomyosin (α-Tpm) in the sarcomere, the basic contractile unit of cardiac muscle. Furthermore, we verified the calcium (Ca2+) binding domain in MLC-2v. In summary, our nTDMS platform extends the application of FTICR MS to directly characterize the structure, PTMs, and metal-binding of endogenous proteins from heart tissue lysate without prior separation methods.
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Affiliation(s)
- Emily A. Chapman
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Brad H. Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Boris Krichel
- School of Life Sciences, University of Siegen, 57076, Germany
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA
| | - Hsin-Ju Chan
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Kevin M. Buck
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - David S. Roberts
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA
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5
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Hong JD, Salom D, Choi EH, Du SW, Tworak A, Smidak R, Gao F, Solano YJ, Zhang J, Kiser PD, Palczewski K. Retinylidene chromophore hydrolysis from mammalian visual and non-visual opsins. J Biol Chem 2024; 300:105678. [PMID: 38272218 PMCID: PMC10877631 DOI: 10.1016/j.jbc.2024.105678] [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: 11/30/2023] [Revised: 01/06/2024] [Accepted: 01/13/2024] [Indexed: 01/27/2024] Open
Abstract
Rhodopsin (Rho) and cone opsins are essential for detection of light. They respond via photoisomerization, converting their Schiff-base-adducted 11-cis-retinylidene chromophores to the all-trans configuration, eliciting conformational changes to activate opsin signaling. Subsequent Schiff-base hydrolysis releases all-trans-retinal, initiating two important cycles that maintain continuous vision-the Rho photocycle and visual cycle pathway. Schiff-base hydrolysis has been thoroughly studied with photoactivated Rho but not with cone opsins. Using established methodology, we directly measured the formation of Schiff-base between retinal chromophores with mammalian visual and nonvisual opsins of the eye. Next, we determined the rate of light-induced chromophore hydrolysis. We found that retinal hydrolysis from photoactivated cone opsins was markedly faster than from photoactivated Rho. Bovine retinal G protein-coupled receptor (bRGR) displayed rapid hydrolysis of its 11-cis-retinylidene photoproduct to quickly supply 11-cis-retinal and re-bind all-trans-retinal. Hydrolysis within bRGR in native retinal pigment epithelium microsomal membranes was >6-times faster than that of bRGR purified in detergent micelles. N-terminal-targeted antibodies significantly slowed bRGR hydrolysis, while C-terminal antibodies had no effect. Our study highlights the much faster photocycle of cone opsins relative to Rho and the crucial role of RGR in chromophore recycling in daylight. By contrast, in our experimental conditions, bovine peropsin did not form pigment in the presence of all-trans-retinal nor with any mono-cis retinal isomers, leaving uncertain the role of this opsin as a light sensor.
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Affiliation(s)
- John D Hong
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California Irvine, Irvine, California, USA; Department of Chemistry, University of California Irvine, Irvine, California, USA
| | - David Salom
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California Irvine, Irvine, California, USA.
| | - Elliot H Choi
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California Irvine, Irvine, California, USA
| | - Samuel W Du
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California Irvine, Irvine, California, USA; Department of Physiology and Biophysics, University of California Irvine, Irvine, California, USA
| | - Aleksander Tworak
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California Irvine, Irvine, California, USA
| | - Roman Smidak
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California Irvine, Irvine, California, USA
| | - Fangyuan Gao
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California Irvine, Irvine, California, USA
| | - Yasmeen J Solano
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California Irvine, Irvine, California, USA; Department of Physiology and Biophysics, University of California Irvine, Irvine, California, USA
| | - Jianye Zhang
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California Irvine, Irvine, California, USA
| | - Philip D Kiser
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California Irvine, Irvine, California, USA; Department of Physiology and Biophysics, University of California Irvine, Irvine, California, USA; Department of Clinical Pharmacy Practice, University of California Irvine, Irvine, California, USA; Research Service, VA Long Beach Healthcare System, Long Beach, California, USA
| | - Krzysztof Palczewski
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California Irvine, Irvine, California, USA; Department of Chemistry, University of California Irvine, Irvine, California, USA; Department of Physiology and Biophysics, University of California Irvine, Irvine, California, USA; Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, California, USA.
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6
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Miller WE, O'Connor CM. CMV-encoded GPCRs in infection, disease, and pathogenesis. Adv Virus Res 2024; 118:1-75. [PMID: 38461029 DOI: 10.1016/bs.aivir.2024.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2024]
Abstract
G protein coupled receptors (GPCRs) are seven-transmembrane domain proteins that modulate cellular processes in response to external stimuli. These receptors represent the largest family of membrane proteins, and in mammals, their signaling regulates important physiological functions, such as vision, taste, and olfaction. Many organisms, including yeast, slime molds, and viruses encode GPCRs. Cytomegaloviruses (CMVs) are large, betaherpesviruses, that encode viral GPCRs (vGPCRs). Human CMV (HCMV) encodes four vGPCRs, including UL33, UL78, US27, and US28. Each of these vGPCRs, as well as their rodent and primate orthologues, have been investigated for their contributions to viral infection and disease. Herein, we discuss how the CMV vGPCRs function during lytic and latent infection, as well as our understanding of how they impact viral pathogenesis.
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Affiliation(s)
- William E Miller
- Department of Molecular and Cellular Bioscience, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Christine M O'Connor
- Infection Biology, Sheikha Fatima bint Mubarak Global Center for Pathogen and Human Health Research, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States; Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland Clinic, Cleveland, OH, United States; Case Comprehensive Cancer Center, Cleveland, OH, United States.
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7
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Ariga K. 2D Materials Nanoarchitectonics for 3D Structures/Functions. MATERIALS (BASEL, SWITZERLAND) 2024; 17:936. [PMID: 38399187 PMCID: PMC10890396 DOI: 10.3390/ma17040936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 02/09/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024]
Abstract
It has become clear that superior material functions are derived from precisely controlled nanostructures. This has been greatly accelerated by the development of nanotechnology. The next step is to assemble materials with knowledge of their nano-level structures. This task is assigned to the post-nanotechnology concept of nanoarchitectonics. However, nanoarchitectonics, which creates intricate three-dimensional functional structures, is not always easy. Two-dimensional nanoarchitectonics based on reactions and arrangements at the surface may be an easier target to tackle. A better methodology would be to define a two-dimensional structure and then develop it into a three-dimensional structure and function. According to these backgrounds, this review paper is organized as follows. The introduction is followed by a summary of the three issues; (i) 2D to 3D dynamic structure control: liquid crystal commanded by the surface, (ii) 2D to 3D rational construction: a metal-organic framework (MOF) and a covalent organic framework (COF); (iii) 2D to 3D functional amplification: cells regulated by the surface. In addition, this review summarizes the important aspects of the ultimate three-dimensional nanoarchitectonics as a perspective. The goal of this paper is to establish an integrated concept of functional material creation by reconsidering various reported cases from the viewpoint of nanoarchitectonics, where nanoarchitectonics can be regarded as a method for everything in materials science.
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Affiliation(s)
- Katsuhiko Ariga
- Research Center for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba 305-0044, Ibaraki, Japan;
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa 277-8561, Chiba, Japan
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8
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Marx V. Inside the chase after those elusive proteoforms. Nat Methods 2024; 21:158-163. [PMID: 38308015 DOI: 10.1038/s41592-024-02170-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2024]
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Fu R, Liu H, Zhang Y, Mao L, Zhu L, Jiang H, Zhang L, Liu X. Imidacloprid affects the visual behavior of adult zebrafish (Danio rerio) by mediating the expression of opsin and phototransduction genes and altering the metabolism of neurotransmitters. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 910:168572. [PMID: 37992846 DOI: 10.1016/j.scitotenv.2023.168572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/06/2023] [Accepted: 11/12/2023] [Indexed: 11/24/2023]
Abstract
Imidacloprid poses a significant threat to aquatic ecosystems. In this study, we investigated the visual toxicity of imidacloprid and the underlying molecular mechanisms in adult zebrafish. After exposure to imidacloprid at environmental relevant concentrations (10 and 100μg/L) for 21 days, the detectable contents of imidacloprid were 23.0 ± 0.80 and 121 ± 1.56 ng/mg in eyes of adult zebrafish, respectively. The visual behavior of adult zebrafish was impaired including a reduced ability to track smoothly visual stimuli and visually guided self-motion. The immunofluorescence experiment showed that the content of Rhodopsin (Rho) in the retina of zebrafish was changed significantly. The expression rhythm of genes played key roles in capturing photons in dim (rho) and bright (opn1mw3, opn1lw2 and opn1sw2) light, and in phototransduction (gnb3b, arr3a and rpe65a), was disrupted significantly throughout a 24-h period in adult zebrafish. Targeted metabolomics analysis showed that the content of 16 metabolites associated with neurotransmitter function changed significantly, and were enriched in top three metabolism pathways including Arginine biosynthesis, Alanine, aspartate and glutamate metabolism, and Tryptophan metabolism. These results indicated that imidacloprid exposure at environmentally relevant concentrations could cause optical toxicity through disturbing the expression of opsins and affecting the phototransduction in the retina of zebrafish adults.
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Affiliation(s)
- Ruiqiang Fu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Hongli Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yanning Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Liangang Mao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Lizhen Zhu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Hongyun Jiang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Lan Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Xingang Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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10
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Joseph S, Robbins CB, Haystead A, Hemesath A, Allen A, Kundu A, Ma JP, Scott BL, Moore KPL, Agrawal R, Gunasan V, Stinnett SS, Grewal DS, Fekrat S. Characterizing differences in retinal and choroidal microvasculature and structure in individuals with Huntington's Disease compared to healthy controls: A cross-sectional prospective study. PLoS One 2024; 19:e0296742. [PMID: 38289919 PMCID: PMC10826956 DOI: 10.1371/journal.pone.0296742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 12/18/2023] [Indexed: 02/01/2024] Open
Abstract
OBJECTIVE To characterize retinal and choroidal microvascular and structural changes in patients who are gene positive for mutant huntingtin protein (mHtt) with symptoms of Huntington's Disease (HD). METHODS This study is a cross-sectional comparison of patients who are gene positive for mHtt and exhibit symptoms of HD, either motor manifest or prodromal (HD group), and cognitively normal individuals without a family history of HD (control group). HD patients were diagnosed by Duke movement disorder neurologists based on the Unified Huntington's Disease Rating Scale (UHDRS). Fovea and optic nerve centered OCT and OCTA images were captured using Zeiss Cirrus HD-5000 with AngioPlex. Outcome metrics included central subfield thickness (CST), peripapillary retinal nerve fiber layer (pRNFL) thickness, ganglion cell-inner plexiform layer (GCIPL) thickness, and choroidal vascularity index (CVI) on OCT, and foveal avascular zone (FAZ) area, vessel density (VD), perfusion density (PD), capillary perfusion density (CPD), and capillary flux index (CFI) on OCTA. Generalized estimating equation (GEE) models were used to account for inter-eye correlation. RESULTS Forty-four eyes of 23 patients in the HD group and 77 eyes of 39 patients in the control group were analyzed. Average GCIPL thickness and FAZ area were decreased in the HD group compared to controls (p = 0.001, p < 0.001). No other imaging metrics were significantly different between groups. CONCLUSIONS Patients in the HD group had decreased GCIPL thickness and smaller FAZ area, highlighting the potential use of retinal biomarkers in detecting neurodegenerative changes in HD.
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Affiliation(s)
- Suzanna Joseph
- Department of Ophthalmology, Duke University School of Medicine, Durham, NC, United States of America
- iMIND Research Group, Durham, NC, United States of America
| | - Cason B. Robbins
- Department of Ophthalmology, Duke University School of Medicine, Durham, NC, United States of America
- iMIND Research Group, Durham, NC, United States of America
| | - Alice Haystead
- iMIND Research Group, Durham, NC, United States of America
| | - Angela Hemesath
- Department of Ophthalmology, Duke University School of Medicine, Durham, NC, United States of America
- iMIND Research Group, Durham, NC, United States of America
| | - Ariana Allen
- Department of Ophthalmology, Duke University School of Medicine, Durham, NC, United States of America
- iMIND Research Group, Durham, NC, United States of America
| | - Anita Kundu
- Department of Ophthalmology, Duke University School of Medicine, Durham, NC, United States of America
- iMIND Research Group, Durham, NC, United States of America
| | - Justin P. Ma
- iMIND Research Group, Durham, NC, United States of America
| | - Burton L. Scott
- Department of Neurology, Duke University School of Medicine, Durham, NC, United States of America
| | - Kathryn P. L. Moore
- Department of Neurology, Duke University School of Medicine, Durham, NC, United States of America
| | - Rupesh Agrawal
- National Healthcare Group Eye Institute, Tan Tock Seng Hospital, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Vithiya Gunasan
- National Healthcare Group Eye Institute, Tan Tock Seng Hospital, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Sandra S. Stinnett
- Department of Ophthalmology, Duke University School of Medicine, Durham, NC, United States of America
- iMIND Research Group, Durham, NC, United States of America
| | - Dilraj S. Grewal
- Department of Ophthalmology, Duke University School of Medicine, Durham, NC, United States of America
- iMIND Research Group, Durham, NC, United States of America
| | - Sharon Fekrat
- Department of Ophthalmology, Duke University School of Medicine, Durham, NC, United States of America
- iMIND Research Group, Durham, NC, United States of America
- Department of Neurology, Duke University School of Medicine, Durham, NC, United States of America
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11
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Chapman EA, Roberts DS, Tiambeng TN, Andrews J, Wang MD, Reasoner EA, Melby JA, Li BH, Kim D, Alpert AJ, Jin S, Ge Y. Structure and dynamics of endogenous cardiac troponin complex in human heart tissue captured by native nanoproteomics. Nat Commun 2023; 14:8400. [PMID: 38110393 PMCID: PMC10728164 DOI: 10.1038/s41467-023-43321-z] [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: 07/04/2023] [Accepted: 11/07/2023] [Indexed: 12/20/2023] Open
Abstract
Protein complexes are highly dynamic entities that display substantial diversity in their assembly, post-translational modifications, and non-covalent interactions, allowing them to play critical roles in various biological processes. The heterogeneity, dynamic nature, and low abundance of protein complexes in their native states present challenges to study using conventional structural biology techniques. Here we develop a native nanoproteomics strategy for the enrichment and subsequent native top-down mass spectrometry (nTDMS) analysis of endogenous cardiac troponin (cTn) complex directly from human heart tissue. The cTn complex is enriched and purified using peptide-functionalized superparamagnetic nanoparticles under non-denaturing conditions to enable the isotopic resolution of cTn complex, revealing their complex structure and assembly. Moreover, nTDMS elucidates the stoichiometry and composition of the cTn complex, localizes Ca2+ binding domains, defines cTn-Ca2+ binding dynamics, and provides high-resolution mapping of the proteoform landscape. This native nanoproteomics strategy opens a paradigm for structural characterization of endogenous native protein complexes.
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Affiliation(s)
- Emily A Chapman
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - David S Roberts
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Timothy N Tiambeng
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Jãán Andrews
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Man-Di Wang
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Emily A Reasoner
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Jake A Melby
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Brad H Li
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Donguk Kim
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | | | - Song Jin
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53705, USA.
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53705, USA.
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12
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Zhu Y, Yun SD, Zhang T, Chang JY, Stover L, Laganowsky A. Native mass spectrometry of proteoliposomes containing integral and peripheral membrane proteins. Chem Sci 2023; 14:14243-14255. [PMID: 38098719 PMCID: PMC10718073 DOI: 10.1039/d3sc04938h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 11/18/2023] [Indexed: 12/17/2023] Open
Abstract
Cellular membranes are critical to the function of membrane proteins, whether they are associated (peripheral) or embedded (integral) within the bilayer. While detergents have contributed to our understanding of membrane protein structure and function, there remains challenges in characterizing protein-lipid interactions within the context of an intact membrane. Here, we developed a method to prepare proteoliposomes for native mass spectrometry (MS) studies. We first use native MS to detect the encapsulation of soluble proteins within liposomes. We then find the peripheral Gβ1γ2 complex associated with the membrane can be ejected and analyzed using native MS. Four different integral membrane proteins (AmtB, AqpZ, TRAAK, and TREK2), all of which have previously been characterized in detergent, eject from the proteoliposomes as intact complexes bound to lipids that have been shown to tightly associate in detergent, drawing a correlation between the two approaches. We also show the utility of more complex lipid environments, such as a brain polar lipid extract, and show TRAAK ejects from liposomes of this extract bound to lipids. These findings underscore the capability to eject protein complexes from membranes bound to both lipids and metal ions, and this approach will be instrumental in the identification of key protein-lipid interactions.
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Affiliation(s)
- Yun Zhu
- Department of Chemistry, Texas A&M University College Station TX 77843 USA
| | - Sangho D Yun
- Department of Chemistry, Texas A&M University College Station TX 77843 USA
| | - Tianqi Zhang
- Department of Chemistry, Texas A&M University College Station TX 77843 USA
| | - Jing-Yuan Chang
- Department of Chemistry, Texas A&M University College Station TX 77843 USA
| | - Lauren Stover
- Department of Chemistry, Texas A&M University College Station TX 77843 USA
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University College Station TX 77843 USA
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13
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Levesque I, Juliano BR, Parson KF, Ruotolo BT. A Critical Evaluation of Detergent Exchange Methodologies for Membrane Protein Native Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2662-2671. [PMID: 37956121 DOI: 10.1021/jasms.3c00230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Membrane proteins (MPs) play many critical roles in cellular physiology and constitute the majority of current pharmaceutical targets. However, MPs are comparatively understudied relative to soluble proteins due to the challenges associated with their solubilization in membrane mimetics. Native mass spectrometry (nMS) has emerged as a useful technique to probe the structures of MPs. Typically, nMS studies using MPs have employed detergent micelles to solubilize the MP. Oftentimes, the detergent micelle that the MP was purified in will be exchanged into another detergent prior to analysis by nMS. While methodologies for performing detergent exchange have been extensively described in prior reports, the effectiveness of these protocols remains understudied. Here, we present a critical analysis of detergent exchange efficacy using several model transmembrane proteins and a variety of commonly used detergents, evaluating the completeness of the exchange using a battery of existing protocols. Our data include results for octyl glucoside (OG), octaethylene glycol monododecyl ether (C12E8), and tetraethylene glycol monooctyl ether (C8E4), and these data demonstrate that existing protocols are insufficient and yield incomplete exchange for the proteins under the conditions probed here. In some cases, our data indicate that up to 99% of the measured detergent corresponds to the original pre-exchange detergent rather than the desired post-exchange detergent. We conclude by discussing the need for new detergent exchange methodologies alongside improved exchange yield expectations for studying the potential influence of detergents on MP structures.
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Affiliation(s)
- Iliana Levesque
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Brock R Juliano
- 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
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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14
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Panda A, Brown C, Gupta K. Studying Membrane Protein-Lipid Specificity through Direct Native Mass Spectrometric Analysis from Tunable Proteoliposomes. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:1917-1927. [PMID: 37432128 PMCID: PMC10932607 DOI: 10.1021/jasms.3c00110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/12/2023]
Abstract
Native mass spectrometry (nMS) has emerged as a key analytical tool to study the organizational states of proteins and their complexes with both endogenous and exogenous ligands. Specifically, for membrane proteins, it provides a key analytical dimension to determine the identity of bound lipids and to decipher their effects on the observed structural assembly. We recently developed an approach to study membrane proteins directly from intact and tunable lipid membranes where both the biophysical properties of the membrane and its lipid compositions can be customized. Extending this, we use our liposome-nMS platform to decipher the lipid specificity of membrane proteins through their multiorganelle trafficking pathways. To demonstrate this, we used VAMP2 and reconstituted it in the endoplasmic reticulum (ER), Golgi, synaptic vesicle (SV), and plasma membrane (PM) mimicking liposomes. By directly studying VAMP2 from these customized liposomes, we show how the same transmembrane protein can bind to different sets of lipids in different organellar-mimicking membranes. Considering that the cellular trafficking pathway of most eukaryotic integral membrane proteins involves residence in multiple organellar membranes, this study highlights how the lipid-specificity of the same integral membrane protein may change depending on the membrane context. Further, leveraging the capability of the platform to study membrane proteins from liposomes with curated biophysical properties, we show how we can disentangle chemical versus biophysical properties, of individual lipids in regulating membrane protein assembly.
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Affiliation(s)
- Aniruddha Panda
- Nanobiology Institute, Yale University, West Haven, Connecticut 06516, United States
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut 06520, United States
| | - Caroline Brown
- Nanobiology Institute, Yale University, West Haven, Connecticut 06516, United States
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut 06520, United States
| | - Kallol Gupta
- Nanobiology Institute, Yale University, West Haven, Connecticut 06516, United States
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut 06520, United States
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15
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Lutomski CA, El‐Baba TJ, Hinkle JD, Liko I, Bennett JL, Kalmankar NV, Dolan A, Kirschbaum C, Greis K, Urner LH, Kapoor P, Yen H, Pagel K, Mullen C, Syka JEP, Robinson CV. Infrared Multiphoton Dissociation Enables Top-Down Characterization of Membrane Protein Complexes and G Protein-Coupled Receptors. Angew Chem Int Ed Engl 2023; 62:e202305694. [PMID: 37329506 PMCID: PMC7615181 DOI: 10.1002/anie.202305694] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/20/2023] [Accepted: 06/15/2023] [Indexed: 06/19/2023]
Abstract
Membrane proteins are challenging to analyze by native mass spectrometry (MS) as their hydrophobic nature typically requires stabilization in detergent micelles that are removed prior to analysis via collisional activation. There is however a practical limit to the amount of energy which can be applied, which often precludes subsequent characterization by top-down MS. To overcome this barrier, we have applied a modified Orbitrap Eclipse Tribrid mass spectrometer coupled to an infrared laser within a high-pressure linear ion trap. We show how tuning the intensity and time of incident photons enables liberation of membrane proteins from detergent micelles. Specifically, we relate the ease of micelle removal to the infrared absorption of detergents in both condensed and gas phases. Top-down MS via infrared multiphoton dissociation (IRMPD), results in good sequence coverage enabling unambiguous identification of membrane proteins and their complexes. By contrasting and comparing the fragmentation patterns of the ammonia channel with two class A GPCRs, we identify successive cleavage of adjacent amino acids within transmembrane domains. Using gas-phase molecular dynamics simulations, we show that areas prone to fragmentation maintain aspects of protein structure at increasing temperatures. Altogether, we propose a rationale to explain why and where in the protein fragment ions are generated.
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Affiliation(s)
- Corinne A. Lutomski
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordOX1 3QUUK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordOX1 3QUUK
| | - Tarick J. El‐Baba
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordOX1 3QUUK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordOX1 3QUUK
| | | | | | - Jack L. Bennett
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordOX1 3QUUK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordOX1 3QUUK
| | - Neha V. Kalmankar
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordOX1 3QUUK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordOX1 3QUUK
| | - Andrew Dolan
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordOX1 3QUUK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordOX1 3QUUK
| | - Carla Kirschbaum
- Institute of Chemistry and BiochemistryFreie Universität BerlinBerlin14195Germany
- Fritz Haber Institute of the Max Planck SocietyBerlin14195Germany
| | - Kim Greis
- Institute of Chemistry and BiochemistryFreie Universität BerlinBerlin14195Germany
- Fritz Haber Institute of the Max Planck SocietyBerlin14195Germany
| | - Leonhard H. Urner
- Institute of Chemistry and BiochemistryFreie Universität BerlinBerlin14195Germany
- Fritz Haber Institute of the Max Planck SocietyBerlin14195Germany
- Department of Chemistry and Chemical BiologyTU Dortmund UniversityDortmund44227Germany
| | | | - Hsin‐Yung Yen
- OMass TherapeuticsOxfordOX4 2GXUK
- Institute of Biological ChemistryAcademia SinicaTaipei115Taiwan
| | - Kevin Pagel
- Institute of Chemistry and BiochemistryFreie Universität BerlinBerlin14195Germany
- Fritz Haber Institute of the Max Planck SocietyBerlin14195Germany
| | | | | | - Carol V. Robinson
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordOX1 3QUUK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordOX1 3QUUK
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16
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Lutomski CA, El‐Baba TJ, Hinkle JD, Liko I, Bennett JL, Kalmankar NV, Dolan A, Kirschbaum C, Greis K, Urner LH, Kapoor P, Yen H, Pagel K, Mullen C, Syka JEP, Robinson CV. Infrared Multiphoton Dissociation Enables Top-Down Characterization of Membrane Protein Complexes and G Protein-Coupled Receptors. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 135:e202305694. [PMID: 38516403 PMCID: PMC10953453 DOI: 10.1002/ange.202305694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Indexed: 03/23/2024]
Abstract
Membrane proteins are challenging to analyze by native mass spectrometry (MS) as their hydrophobic nature typically requires stabilization in detergent micelles that are removed prior to analysis via collisional activation. There is however a practical limit to the amount of energy which can be applied, which often precludes subsequent characterization by top-down MS. To overcome this barrier, we have applied a modified Orbitrap Eclipse Tribrid mass spectrometer coupled to an infrared laser within a high-pressure linear ion trap. We show how tuning the intensity and time of incident photons enables liberation of membrane proteins from detergent micelles. Specifically, we relate the ease of micelle removal to the infrared absorption of detergents in both condensed and gas phases. Top-down MS via infrared multiphoton dissociation (IRMPD), results in good sequence coverage enabling unambiguous identification of membrane proteins and their complexes. By contrasting and comparing the fragmentation patterns of the ammonia channel with two class A GPCRs, we identify successive cleavage of adjacent amino acids within transmembrane domains. Using gas-phase molecular dynamics simulations, we show that areas prone to fragmentation maintain aspects of protein structure at increasing temperatures. Altogether, we propose a rationale to explain why and where in the protein fragment ions are generated.
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Affiliation(s)
- Corinne A. Lutomski
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordOX1 3QUUK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordOX1 3QUUK
| | - Tarick J. El‐Baba
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordOX1 3QUUK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordOX1 3QUUK
| | | | | | - Jack L. Bennett
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordOX1 3QUUK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordOX1 3QUUK
| | - Neha V. Kalmankar
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordOX1 3QUUK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordOX1 3QUUK
| | - Andrew Dolan
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordOX1 3QUUK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordOX1 3QUUK
| | - Carla Kirschbaum
- Institute of Chemistry and BiochemistryFreie Universität BerlinBerlin14195Germany
- Fritz Haber Institute of the Max Planck SocietyBerlin14195Germany
| | - Kim Greis
- Institute of Chemistry and BiochemistryFreie Universität BerlinBerlin14195Germany
- Fritz Haber Institute of the Max Planck SocietyBerlin14195Germany
| | - Leonhard H. Urner
- Institute of Chemistry and BiochemistryFreie Universität BerlinBerlin14195Germany
- Fritz Haber Institute of the Max Planck SocietyBerlin14195Germany
- Department of Chemistry and Chemical BiologyTU Dortmund UniversityDortmund44227Germany
| | | | - Hsin‐Yung Yen
- OMass TherapeuticsOxfordOX4 2GXUK
- Institute of Biological ChemistryAcademia SinicaTaipei115Taiwan
| | - Kevin Pagel
- Institute of Chemistry and BiochemistryFreie Universität BerlinBerlin14195Germany
- Fritz Haber Institute of the Max Planck SocietyBerlin14195Germany
| | | | | | - Carol V. Robinson
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordOX1 3QUUK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin BuildingUniversity of OxfordOxfordOX1 3QUUK
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17
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Dhillon P, Robinson C. In conversation with Carol Robinson. FEBS J 2023; 290:4376-4381. [PMID: 36892400 DOI: 10.1111/febs.16743] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 01/31/2023] [Indexed: 03/10/2023]
Abstract
Dame Carol Robinson is a professor of chemistry and Director of the Kavli Institute for Nanoscience Discovery at the University of Oxford. Carol's career in science began at the age of 16 as a lab technician at Pfizer (based in Kent), during which time she studied part-time and took evening classes to obtain a degree in chemistry. This was followed by a master's degree at the University of Swansea and a PhD at the University of Cambridge. Carol's postdoctoral training was undertaken in Peter Bennett's lab at the Department of Pathology and Microbiology, University of Bristol. Subsequently, she took a career break of 8 years to spend time with her family but made a strong comeback, taking up a position at the University of Oxford, where she began to explore protein folding. It was here that she first demonstrated, using the GroEL chaperonin-substrate complex as a prototype, that protein secondary structure can be analysed in the gas phase. Carol later made history as the first female professor of chemistry at the University of Cambridge (2001) and again as the first female professor of chemistry at the University of Oxford (2009). In her research, she has also continuously pushed boundaries, pioneering the application of mass spectrometry for the elucidation of the 3D architecture of macromolecular complexes, including membrane-bound assemblies. She has received many awards and honours in recognition of her significant contributions to the field of gas-phase structural biology, including the Royal Society Fellowship, the Davy Medal, the Rosalind Franklin Award and the FEBS/EMBO Women in Science Award. In this interview, she discusses some of her career highlights and ongoing research aspirations and draws on her unique experiences to offer advice to early career scientists.
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Affiliation(s)
| | - Carol Robinson
- Department of Chemistry, University of Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, UK
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18
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Wu A, Salom D, Hong JD, Tworak A, Watanabe K, Pardon E, Steyaert J, Kandori H, Katayama K, Kiser PD, Palczewski K. Structural basis for the allosteric modulation of rhodopsin by nanobody binding to its extracellular domain. Nat Commun 2023; 14:5209. [PMID: 37626045 PMCID: PMC10457330 DOI: 10.1038/s41467-023-40911-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
Rhodopsin is a prototypical G protein-coupled receptor (GPCR) critical for vertebrate vision. Research on GPCR signaling states has been facilitated using llama-derived nanobodies (Nbs), some of which bind to the intracellular surface to allosterically modulate the receptor. Extracellularly binding allosteric nanobodies have also been investigated, but the structural basis for their activity has not been resolved to date. Here, we report a library of Nbs that bind to the extracellular surface of rhodopsin and allosterically modulate the thermodynamics of its activation process. Crystal structures of Nb2 in complex with native rhodopsin reveal a mechanism of allosteric modulation involving extracellular loop 2 and native glycans. Nb2 binding suppresses Schiff base deprotonation and hydrolysis and prevents intracellular outward movement of helices five and six - a universal activation event for GPCRs. Nb2 also mitigates protein misfolding in a disease-associated mutant rhodopsin. Our data show the power of nanobodies to modulate the photoactivation of rhodopsin and potentially serve as therapeutic agents for disease-associated rhodopsin misfolding.
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Affiliation(s)
- Arum Wu
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, CA, 92697, USA
| | - David Salom
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, CA, 92697, USA
| | - John D Hong
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, CA, 92697, USA
- Department of Chemistry, University of California, Irvine, CA, 92697, USA
| | - Aleksander Tworak
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, CA, 92697, USA
| | - Kohei Watanabe
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, 466- 8555, Japan
- PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | - Els Pardon
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Jan Steyaert
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, 466- 8555, Japan
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya, 466-8555, Japan
| | - Kota Katayama
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, 466- 8555, Japan.
- PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan.
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya, 466-8555, Japan.
| | - Philip D Kiser
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, CA, 92697, USA.
- Department of Physiology & Biophysics, University of California, Irvine, CA, USA.
- Department of Clinical Pharmacy Practice, University of California, Irvine, CA, USA.
- Research Service, VA Long Beach Healthcare System, Long Beach, CA, USA.
| | - Krzysztof Palczewski
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, CA, 92697, USA.
- Department of Chemistry, University of California, Irvine, CA, 92697, USA.
- Department of Physiology & Biophysics, University of California, Irvine, CA, USA.
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, 92697, USA.
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19
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Chapman EA, Roberts DS, Tiambeng TN, Andrews J, Wang MD, Reasoner EA, Melby JA, Li BH, Kim D, Alpert AJ, Jin S, Ge Y. Structure and dynamics of endogenous protein complexes in human heart tissue captured by native nanoproteomics. RESEARCH SQUARE 2023:rs.3.rs-3108087. [PMID: 37461709 PMCID: PMC10350235 DOI: 10.21203/rs.3.rs-3108087/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Protein complexes are highly dynamic entities that display substantial diversity in their assembly, post-translational modifications, and non-covalent interactions, allowing them to play critical roles in various biological processes. The heterogeneity, dynamic nature, and low abundance of protein complexes in their native states present tremendous challenges to study using conventional structural biology techniques. Here we develop a "native nanoproteomics" strategy for the native enrichment and subsequent native top-down mass spectrometry (nTDMS) of low-abundance protein complexes. Specifically, we demonstrate the first comprehensive characterization of the structure and dynamics of cardiac troponin (cTn) complexes directly from human heart tissue. The endogenous cTn complex is effectively enriched and purified using peptide-functionalized superparamagnetic nanoparticles under non-denaturing conditions to enable the isotopic resolution of cTn complexes, revealing their complex structure and assembly. Moreover, nTDMS elucidates the stoichiometry and composition of the heterotrimeric cTn complex, localizes Ca2+ binding domains (II-IV), defines cTn-Ca2+ binding dynamics, and provides high-resolution mapping of the proteoform landscape. This native nanoproteomics strategy opens a new paradigm for structural characterization of low-abundance native protein complexes.
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Affiliation(s)
- Emily A. Chapman
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - David S. Roberts
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Timothy N. Tiambeng
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Jãán Andrews
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Man-Di Wang
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Emily A. Reasoner
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Jake A. Melby
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Brad H. Li
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Donguk Kim
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | | | - Song Jin
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA
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20
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Gerhardt MJ, Petersen-Jones SM, Michalakis S. CNG channel-related retinitis pigmentosa. Vision Res 2023; 208:108232. [PMID: 37054604 PMCID: PMC10373105 DOI: 10.1016/j.visres.2023.108232] [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: 02/13/2023] [Revised: 03/27/2023] [Accepted: 03/27/2023] [Indexed: 04/15/2023]
Abstract
The genes CNGA1 and CNGB1 encode the alpha and beta subunits of the rod CNG channel, a ligand-gated cation channel whose activity is controlled by cyclic guanosine monophosphate (cGMP). Autosomal inherited mutations in either of the genes lead to a progressive rod-cone retinopathy known as retinitis pigmentosa (RP). The rod CNG channel is expressed in the plasma membrane of the outer segment and functions as a molecular switch that converts light-mediated changes in cGMP into a voltage and Ca2+ signal. Here, we will first review the molecular properties and physiological role of the rod CNG channel and then discuss the characteristics of CNG-related RP. Finally, we will summarize recent activities in the field of gene therapy aimed at developing therapies for CNG-related RP.
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Affiliation(s)
- Maximilian J Gerhardt
- Department of Ophthalmology, University Hospital, LMU Munich, Mathildenstraße 8, 80336 München, Germany
| | - Simon M Petersen-Jones
- College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824, United States
| | - Stylianos Michalakis
- Department of Ophthalmology, University Hospital, LMU Munich, Mathildenstraße 8, 80336 München, Germany.
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21
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Chapman EA, Roberts DS, Tiambeng TN, Andrews J, Wang MD, Reasoner EA, Melby JA, Li BH, Kim D, Alpert AJ, Jin S, Ge Y. Structure and dynamics of endogenous protein complexes in human heart tissue captured by native nanoproteomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.13.544817. [PMID: 37398031 PMCID: PMC10312745 DOI: 10.1101/2023.06.13.544817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Protein complexes are highly dynamic entities that display substantial diversity in their assembly, post-translational modifications, and non-covalent interactions, allowing them to play critical roles in various biological processes. The heterogeneity, dynamic nature, and low abundance of protein complexes in their native states present tremendous challenges to study using conventional structural biology techniques. Here we develop a "native nanoproteomics" strategy for the native enrichment and subsequent native top-down mass spectrometry (nTDMS) of low-abundance protein complexes. Specifically, we demonstrate the first comprehensive characterization of the structure and dynamics of cardiac troponin (cTn) complexes directly from human heart tissue. The endogenous cTn complex is effectively enriched and purified using peptide-functionalized superparamagnetic nanoparticles under non-denaturing conditions to enable the isotopic resolution of cTn complexes, revealing their complex structure and assembly. Moreover, nTDMS elucidates the stoichiometry and composition of the heterotrimeric cTn complex, localizes Ca2+ binding domains (II-IV), defines cTn-Ca2+ binding dynamics, and provides high-resolution mapping of the proteoform landscape. This native nanoproteomics strategy opens a new paradigm for structural characterization of low-abundance native protein complexes.
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22
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Panda A, Giska F, Duncan AL, Welch AJ, Brown C, McAllister R, Hariharan P, Goder JND, Coleman J, Ramakrishnan S, Pincet F, Guan L, Krishnakumar S, Rothman JE, Gupta K. Direct determination of oligomeric organization of integral membrane proteins and lipids from intact customizable bilayer. Nat Methods 2023; 20:891-897. [PMID: 37106230 PMCID: PMC10932606 DOI: 10.1038/s41592-023-01864-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 03/23/2023] [Indexed: 04/29/2023]
Abstract
Hierarchical organization of integral membrane proteins (IMP) and lipids at the membrane is essential for regulating myriad downstream signaling. A quantitative understanding of these processes requires both detections of oligomeric organization of IMPs and lipids directly from intact membranes and determination of key membrane components and properties that regulate them. Addressing this, we have developed a platform that enables native mass spectrometry (nMS) analysis of IMP-lipid complexes directly from intact and customizable lipid membranes. Both the lipid composition and membrane properties (such as curvature, tension, and fluidity) of these bilayers can be precisely customized to a target membrane. Subsequent direct nMS analysis of these intact proteolipid vesicles can yield the oligomeric states of the embedded IMPs, identify bound lipids, and determine the membrane properties that can regulate the observed IMP-lipid organization. Applying this method, we show how lipid binding regulates neurotransmitter release and how membrane composition regulates the functional oligomeric state of a transporter.
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Affiliation(s)
- Aniruddha Panda
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Fabian Giska
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Anna L Duncan
- Department of Biochemistry, University of Oxford, Oxford, UK
- Department of Chemistry, Aarhus University, Aarhus C, Denmark
| | | | - Caroline Brown
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Rachel McAllister
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Parameswaran Hariharan
- Department of Cell Physiology and Molecular Biophysics, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Jean N D Goder
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Jeff Coleman
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Sathish Ramakrishnan
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Frédéric Pincet
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Laboratoire de Physique de l'Ecole Normale Supérieure, ENS, CNRS, Université PSL, Sorbonne Université, Université Paris-Cité, Paris, France
| | - Lan Guan
- Department of Cell Physiology and Molecular Biophysics, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Shyam Krishnakumar
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Neurology, Yale University School of Medicine, New Haven, CT, USA
| | - James E Rothman
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Kallol Gupta
- Nanobiology Institute, Yale University, West Haven, CT, USA.
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA.
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23
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Bai Y, Liu Z, Li Y, Zhao H, Lai C, Zhao S, Chen K, Luo C, Yang X, Wang F. Structural Mass Spectrometry Probes the Inhibitor-Induced Allosteric Activation of CDK12/CDK13-Cyclin K Dissociation. J Am Chem Soc 2023; 145:11477-11481. [PMID: 37207290 DOI: 10.1021/jacs.3c01697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The rational design and development of effective inhibitors for cyclin-dependent kinases 12 and 13 (CDK12 and CDK13) are largely dependent on the understanding of the dynamic inhibition conformations but are difficult to be achieved by conventional characterization tools. Herein, we integrate the structural mass spectrometry (MS) methods of lysine reactivity profiling (LRP) and native MS (nMS) to systematically interrogate both the dynamic molecular interactions and overall protein assembly of CDK12/CDK13-cyclin K (CycK) complexes under the modulation of small molecule inhibitors. The essential structure insights, including inhibitor binding pocket, binding strength, interfacial molecular details, and dynamic conformation changes, can be derived from the complementary results of LRP and nMS. We find the inhibitor SR-4835 binding can greatly destabilize the CDK12/CDK13-CycK interactions in an unusual allosteric activation way, thereby providing a novel alternative for the kinase activity inhibition. Our results underscore the great potential of LRP combination with nMS for the evaluation and rational design of effective kinase inhibitors at the molecular level.
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Affiliation(s)
- Yu Bai
- School of Pharmacy, China Medical University, Shenyang 110122, China
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Zheyi Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuanqing Li
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
- Drug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Heng Zhao
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Can Lai
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shan Zhao
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Kaixian Chen
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
- Drug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cheng Luo
- Drug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xueming Yang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Fangjun Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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24
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Yang HC, Li W, Sun J, Gross ML. Advances in Mass Spectrometry on Membrane Proteins. MEMBRANES 2023; 13:457. [PMID: 37233518 PMCID: PMC10220746 DOI: 10.3390/membranes13050457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/15/2023] [Accepted: 04/21/2023] [Indexed: 05/27/2023]
Abstract
Understanding the higher-order structure of membrane proteins (MPs), which are vital for numerous biological processes, is crucial for comprehending their function. Although several biophysical approaches have been used to study the structure of MPs, limitations exist owing to the proteins' dynamic nature and heterogeneity. Mass spectrometry (MS) is emerging as a powerful tool for investigating membrane protein structure and dynamics. Studying MPs using MS, however, must meet several challenges including the lack of stability and solubility of MPs, the complexity of the protein-membrane system, and the difficulty of digestion and detection. To meet these challenges, recent advances in MS have engendered opportunities in resolving the dynamics and structures of MP. This article reviews achievements over the past few years that enable the study of MPs by MS. We first introduce recent advances in hydrogen deuterium exchange and native mass spectrometry for MPs and then focus on those footprinting methods that report on protein structure.
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Affiliation(s)
- Hsin-Chieh Yang
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Weikai Li
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA;
| | - Jie Sun
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
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25
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Barret D, Schuster D, Rodrigues M, Leitner A, Picotti P, Schertler G, Kaupp U, Korkhov V, Marino J. Structural basis of calmodulin modulation of the rod cyclic nucleotide-gated channel. Proc Natl Acad Sci U S A 2023; 120:e2300309120. [PMID: 37011209 PMCID: PMC10104587 DOI: 10.1073/pnas.2300309120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 03/06/2023] [Indexed: 04/05/2023] Open
Abstract
Calmodulin (CaM) regulates many ion channels to control calcium entry into cells, and mutations that alter this interaction are linked to fatal diseases. The structural basis of CaM regulation remains largely unexplored. In retinal photoreceptors, CaM binds to the CNGB subunit of cyclic nucleotide-gated (CNG) channels and, thereby, adjusts the channel's Cyclic guanosine monophosphate (cGMP) sensitivity in response to changes in ambient light conditions. Here, we provide the structural characterization for CaM regulation of a CNG channel by using a combination of single-particle cryo-electron microscopy and structural proteomics. CaM connects the CNGA and CNGB subunits, resulting in structural changes both in the cytosolic and transmembrane regions of the channel. Cross-linking and limited proteolysis-coupled mass spectrometry mapped the conformational changes induced by CaM in vitro and in the native membrane. We propose that CaM is a constitutive subunit of the rod channel to ensure high sensitivity in dim light. Our mass spectrometry-based approach is generally relevant for studying the effect of CaM on ion channels in tissues of medical interest, where only minute quantities are available.
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Affiliation(s)
- Diane C. A. Barret
- Laboratory of Biomolecular Research, Paul Scherrer Institute, 5232Villigen, Switzerland
| | - Dina Schuster
- Laboratory of Biomolecular Research, Paul Scherrer Institute, 5232Villigen, Switzerland
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, 8049Zürich, Switzerland
- Institute of Molecular Biology and Biophysics, ETH Zürich, 8049Zurich, Switzerland
| | - Matthew J. Rodrigues
- Laboratory of Biomolecular Research, Paul Scherrer Institute, 5232Villigen, Switzerland
| | - Alexander Leitner
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, 8049Zürich, Switzerland
| | - Paola Picotti
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, 8049Zürich, Switzerland
| | | | - U. Benjamin Kaupp
- Life and Medical Sciences Institute, University of Bonn, 53115Bonn, Germany
- Max Planck Institute for Multidisciplinary Sciences, 37077Göttingen, Germany
| | - Volodymyr M. Korkhov
- Laboratory of Biomolecular Research, Paul Scherrer Institute, 5232Villigen, Switzerland
- Institute of Molecular Biology and Biophysics, ETH Zürich, 8049Zurich, Switzerland
| | - Jacopo Marino
- Laboratory of Biomolecular Research, Paul Scherrer Institute, 5232Villigen, Switzerland
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26
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Fiorentino F, Rotili D, Mai A. Native mass spectrometry-directed drug discovery: Recent advances in investigating protein function and modulation. Drug Discov Today 2023; 28:103548. [PMID: 36871843 DOI: 10.1016/j.drudis.2023.103548] [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: 12/18/2022] [Revised: 02/15/2023] [Accepted: 02/28/2023] [Indexed: 03/07/2023]
Abstract
Native mass spectrometry (nMS) is a biophysical method for studying protein complexes and can provide insights into subunit stoichiometry and composition, protein-ligand, and protein-protein interactions (PPIs). These analyses are made possible by preserving non-covalent interactions in the gas phase, thereby allowing the analysis of proteins in their native state. Consequently, nMS has been increasingly applied in early drug discovery campaigns for the characterization of protein-drug interactions and the evaluation of PPI modulators. Here, we discuss recent developments in nMS-directed drug discovery and provide a timely perspective on the possible applications of this technology in drug discovery.
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Affiliation(s)
- Francesco Fiorentino
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy.
| | - Dante Rotili
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy.
| | - Antonello Mai
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; Pasteur Institute, Cenci-Bolognetti Foundation, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
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27
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Hofmann KP, Lamb TD. Rhodopsin, light-sensor of vision. Prog Retin Eye Res 2023; 93:101116. [PMID: 36273969 DOI: 10.1016/j.preteyeres.2022.101116] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 08/20/2022] [Accepted: 08/22/2022] [Indexed: 11/06/2022]
Abstract
The light sensor of vertebrate scotopic (low-light) vision, rhodopsin, is a G-protein-coupled receptor comprising a polypeptide chain with bound chromophore, 11-cis-retinal, that exhibits remarkable physicochemical properties. This photopigment is extremely stable in the dark, yet its chromophore isomerises upon photon absorption with 70% efficiency, enabling the activation of its G-protein, transducin, with high efficiency. Rhodopsin's photochemical and biochemical activities occur over very different time-scales: the energy of retinaldehyde's excited state is stored in <1 ps in retinal-protein interactions, but it takes milliseconds for the catalytically active state to form, and many tens of minutes for the resting state to be restored. In this review, we describe the properties of rhodopsin and its role in rod phototransduction. We first introduce rhodopsin's gross structural features, its evolution, and the basic mechanisms of its activation. We then discuss light absorption and spectral sensitivity, photoreceptor electrical responses that result from the activity of individual rhodopsin molecules, and recovery of rhodopsin and the visual system from intense bleaching exposures. We then provide a detailed examination of rhodopsin's molecular structure and function, first in its dark state, and then in the active Meta states that govern its interactions with transducin, rhodopsin kinase and arrestin. While it is clear that rhodopsin's molecular properties are exquisitely honed for phototransduction, from starlight to dawn/dusk intensity levels, our understanding of how its molecular interactions determine the properties of scotopic vision remains incomplete. We describe potential future directions of research, and outline several major problems that remain to be solved.
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Affiliation(s)
- Klaus Peter Hofmann
- Institut für Medizinische Physik und Biophysik (CC2), Charité, and, Zentrum für Biophysik und Bioinformatik, Humboldt-Unversität zu Berlin, Berlin, 10117, Germany.
| | - Trevor D Lamb
- Eccles Institute of Neuroscience, John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2600, Australia.
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28
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Reid DJ, Thibert S, Zhou M. Dissecting the structural heterogeneity of proteins by native mass spectrometry. Protein Sci 2023; 32:e4612. [PMID: 36851867 PMCID: PMC10031758 DOI: 10.1002/pro.4612] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 03/01/2023]
Abstract
A single gene yields many forms of proteins via combinations of post-transcriptional/post-translational modifications. Proteins also fold into higher-order structures and interact with other molecules. The combined molecular diversity leads to the heterogeneity of proteins that manifests as distinct phenotypes. Structural biology has generated vast amounts of data, effectively enabling accurate structural prediction by computational methods. However, structures are often obtained heterologously under homogeneous states in vitro. The lack of native heterogeneity under cellular context creates challenges in precisely connecting the structural data to phenotypes. Mass spectrometry (MS) based proteomics methods can profile proteome composition of complex biological samples. Most MS methods follow the "bottom-up" approach, which denatures and digests proteins into short peptide fragments for ease of detection. Coupled with chemical biology approaches, higher-order structures can be probed via incorporation of covalent labels on native proteins that are maintained at the peptide level. Alternatively, native MS follows the "top-down" approach and directly analyzes intact proteins under nondenaturing conditions. Various tandem MS activation methods can dissect the intact proteins for in-depth structural elucidation. Herein, we review recent native MS applications for characterizing heterogeneous samples, including proteins binding to mixtures of ligands, homo/hetero-complexes with varying stoichiometry, intrinsically disordered proteins with dynamic conformations, glycoprotein complexes with mixed modification states, and active membrane protein complexes in near-native membrane environments. We summarize the benefits, challenges, and ongoing developments in native MS, with the hope to demonstrate an emerging technology that complements other tools by filling the knowledge gaps in understanding molecular heterogeneity of proteins. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Deseree J Reid
- Chemical and Biological Signature Sciences, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Stephanie Thibert
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Mowei Zhou
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
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29
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Mass spectrometry of intact membrane proteins: shifting towards a more native-like context. Essays Biochem 2023; 67:201-213. [PMID: 36807530 PMCID: PMC10070488 DOI: 10.1042/ebc20220169] [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: 11/17/2022] [Revised: 01/20/2023] [Accepted: 01/23/2023] [Indexed: 02/23/2023]
Abstract
Integral membrane proteins are involved in a plethora of biological processes including cellular signalling, molecular transport, and catalysis. Many of these functions are mediated by non-covalent interactions with other proteins, substrates, metabolites, and surrounding lipids. Uncovering such interactions and deciphering their effect on protein activity is essential for understanding the regulatory mechanisms underlying integral membrane protein function. However, the detection of such dynamic complexes has proven to be challenging using traditional approaches in structural biology. Native mass spectrometry has emerged as a powerful technique for the structural characterisation of membrane proteins and their complexes, enabling the detection and identification of protein-binding partners. In this review, we discuss recent native mass spectrometry-based studies that have characterised non-covalent interactions of membrane proteins in the presence of detergents or membrane mimetics. We additionally highlight recent progress towards the study of membrane proteins within native membranes and provide our perspective on how these could be combined with recent developments in instrumentation to investigate increasingly complex biomolecular systems.
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30
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Kojima K, Sudo Y. Convergent evolution of animal and microbial rhodopsins. RSC Adv 2023; 13:5367-5381. [PMID: 36793294 PMCID: PMC9923458 DOI: 10.1039/d2ra07073a] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 02/05/2023] [Indexed: 02/15/2023] Open
Abstract
Rhodopsins, a family of photoreceptive membrane proteins, contain retinal as a chromophore and were firstly identified as reddish pigments from frog retina in 1876. Since then, rhodopsin-like proteins have been identified mainly from animal eyes. In 1971, a rhodopsin-like pigment was discovered from the archaeon Halobacterium salinarum and named bacteriorhodopsin. While it was believed that rhodopsin- and bacteriorhodopsin-like proteins were expressed only in animal eyes and archaea, respectively, before the 1990s, a variety of rhodopsin-like proteins (called animal rhodopsins or opsins) and bacteriorhodopsin-like proteins (called microbial rhodopsins) have been progressively identified from various tissues of animals and microorganisms, respectively. Here, we comprehensively introduce the research conducted on animal and microbial rhodopsins. Recent analysis has revealed that the two rhodopsin families have common molecular properties, such as the protein structure (i.e., 7-transmembrane structure), retinal structure (i.e., binding ability to cis- and trans-retinal), color sensitivity (i.e., UV- and visible-light sensitivities), and photoreaction (i.e., triggering structural changes by light and heat), more than what was expected at the early stages of rhodopsin research. Contrastingly, their molecular functions are distinctively different (e.g., G protein-coupled receptors and photoisomerases for animal rhodopsins and ion transporters and phototaxis sensors for microbial rhodopsins). Therefore, based on their similarities and dissimilarities, we propose that animal and microbial rhodopsins have convergently evolved from their distinctive origins as multi-colored retinal-binding membrane proteins whose activities are regulated by light and heat but independently evolved for different molecular and physiological functions in the cognate organism.
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Affiliation(s)
- Keiichi Kojima
- Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University Japan
| | - Yuki Sudo
- Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University Japan
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31
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Gulati S, Palczewski K. Structural view of G protein-coupled receptor signaling in the retinal rod outer segment. Trends Biochem Sci 2023; 48:172-186. [PMID: 36163145 PMCID: PMC9868064 DOI: 10.1016/j.tibs.2022.08.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 08/26/2022] [Accepted: 08/29/2022] [Indexed: 01/26/2023]
Abstract
Visual phototransduction is the most extensively studied G protein-coupled receptor (GPCR) signaling pathway because of its quantifiable stimulus, non-redundancy of genes, and immense importance in vision. We summarize recent discoveries that have advanced our understanding of rod outer segment (ROS) morphology and the pathological basis of retinal diseases. We have combined recently published cryo-electron tomography (cryo-ET) data on the ROS with structural knowledge on individual proteins to define the precise spatial limitations under which phototransduction occurs. Although hypothetical, the reconstruction of the rod phototransduction system highlights the potential roles of phosphodiesterase 6 (PDE6) and guanylate cyclases (GCs) in maintaining the spacing between ROS discs, suggesting a plausible mechanism by which intrinsic optical signals are generated in the retina.
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Affiliation(s)
| | - Krzysztof Palczewski
- Gavin Herbert Eye Institute and the Department of Ophthalmology, Center for Translational Vision Research, Department of Physiology and Biophysics, Department of Chemistry, Molecular Biology, and Biochemistry, University of California Irvine, 850 Health Sciences Road, Irvine, CA 92697-4375, USA.
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32
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Biology, Pathobiology and Gene Therapy of CNG Channel-Related Retinopathies. Biomedicines 2023; 11:biomedicines11020269. [PMID: 36830806 PMCID: PMC9953513 DOI: 10.3390/biomedicines11020269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 01/21/2023] Open
Abstract
The visual process begins with the absorption of photons by photopigments of cone and rod photoreceptors in the retina. In this process, the signal is first amplified by a cyclic guanosine monophosphate (cGMP)-based signaling cascade and then converted into an electrical signal by cyclic nucleotide-gated (CNG) channels. CNG channels are purely ligand-gated channels whose activity can be controlled by cGMP, which induces a depolarizing Na+/Ca2+ current upon binding to the channel. Structurally, CNG channels belong to the superfamily of pore-loop cation channels and share structural similarities with hyperpolarization-activated cyclic nucleotide (HCN) and voltage-gated potassium (KCN) channels. Cone and rod photoreceptors express distinct CNG channels encoded by homologous genes. Mutations in the genes encoding the rod CNG channel (CNGA1 and CNGB1) result in retinitis-pigmentosa-type blindness. Mutations in the genes encoding the cone CNG channel (CNGA3 and CNGB3) lead to achromatopsia. Here, we review the molecular properties of CNG channels and describe their physiological and pathophysiological roles in the retina. Moreover, we summarize recent activities in the field of gene therapy aimed at developing the first gene therapies for CNG channelopathies.
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33
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Yee C, Görtemaker K, Wellpott R, Koch KW. Kinetics of cone specific G-protein signaling in avian photoreceptor cells. Front Mol Neurosci 2023; 16:1107025. [PMID: 36733826 PMCID: PMC9887155 DOI: 10.3389/fnmol.2023.1107025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 01/03/2023] [Indexed: 01/19/2023] Open
Abstract
Cone photoreceptor cells of night-migratory songbirds seem to process the primary steps of two different senses, vision and magnetoreception. The molecular basis of phototransduction is a prototypical G protein-coupled receptor pathway starting with the photoexcitation of rhodopsin or cone opsin thereby activating a heterotrimeric G protein named transducin. This interaction is well understood in vertebrate rod cells, but parameter describing protein-protein interactions of cone specific proteins are rare and not available for migratory birds. European robin is a model organism for studying the orientation of birds in the earth magnetic field. Recent findings showed a link between the putative magnetoreceptor cryptochrome 4a and the cone specific G-protein of European robin. In the present work, we investigated the interaction of European robin cone specific G protein and cytoplasmic regions of long wavelength opsin. We identified the second loop in opsin connecting transmembrane regions three and four as a critical binding interface. Surface plasmon resonance studies using a synthetic peptide representing the second cytoplasmic loop and purified G protein α-subunit showed a high affinity interaction with a K D value of 21 nM. Truncation of the G protein α-subunit at the C-terminus by six amino acids slightly decreased the affinity. Our results suggest that binding of the G protein to cryptochrome can compete with the interaction of G protein and non-photoexcited long wavelength opsin. Thus, the parallel presence of two different sensory pathways in bird cone photoreceptors is reasonable under dark-adapted conditions or during illumination with short wavelengths.
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Affiliation(s)
- Chad Yee
- Division of Biochemistry, Department of Neuroscience, University of Oldenburg, Oldenburg, Germany
| | - Katharina Görtemaker
- Division of Biochemistry, Department of Neuroscience, University of Oldenburg, Oldenburg, Germany
| | - Rieke Wellpott
- Division of Biochemistry, Department of Neuroscience, University of Oldenburg, Oldenburg, Germany
| | - Karl-Wilhelm Koch
- Division of Biochemistry, Department of Neuroscience, University of Oldenburg, Oldenburg, Germany,Research Center Neurosensory Sciences, University of Oldenburg, Oldenburg, Germany,*Correspondence: Karl-Wilhelm Koch, ✉
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Dallo S, Shin J, Zhang S, Ren Q, Bao H. Designer Nanodiscs to Probe and Reprogram Membrane Biology in Synapses. J Mol Biol 2023; 435:167757. [PMID: 35872069 PMCID: PMC9805492 DOI: 10.1016/j.jmb.2022.167757] [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: 06/01/2022] [Revised: 07/17/2022] [Accepted: 07/18/2022] [Indexed: 02/04/2023]
Abstract
Signal transduction at the synapse is mediated by a variety of protein-lipid interactions, which are vital for the spatial and temporal regulation of synaptic vesicle biogenesis, neurotransmitter release, and postsynaptic receptor activation. Therefore, our understanding of synaptic transmission cannot be completed until the elucidation of these critical protein-lipid interactions. On this front, recent advances in nanodiscs have vastly expanded our ability to probe and reprogram membrane biology in synapses. Here, we summarize the progress of the nanodisc toolbox and discuss future directions in this exciting field.
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Affiliation(s)
- Sarah Dallo
- Department of Molecular Medicine, UF Scripps Biomedical Research, 130 Scripps Way, Jupiter 33458, FL, USA
| | - Jeehae Shin
- Department of Molecular Medicine, UF Scripps Biomedical Research, 130 Scripps Way, Jupiter 33458, FL, USA
| | - Shanwen Zhang
- Department of Molecular Medicine, UF Scripps Biomedical Research, 130 Scripps Way, Jupiter 33458, FL, USA
| | - Qian Ren
- Department of Molecular Medicine, UF Scripps Biomedical Research, 130 Scripps Way, Jupiter 33458, FL, USA
| | - Huan Bao
- Department of Molecular Medicine, UF Scripps Biomedical Research, 130 Scripps Way, Jupiter 33458, FL, USA.
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Chromophore hydrolysis and release from photoactivated rhodopsin in native membranes. Proc Natl Acad Sci U S A 2022; 119:e2213911119. [PMID: 36322748 PMCID: PMC9659404 DOI: 10.1073/pnas.2213911119] [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] [Indexed: 01/16/2023] Open
Abstract
For sustained vision, photoactivated rhodopsin (Rho*) must undergo hydrolysis and release of all-trans-retinal, producing substrate for the visual cycle and apo-opsin available for regeneration with 11-cis-retinal. The kinetics of this hydrolysis has yet to be described for rhodopsin in its native membrane environment. We developed a method consisting of simultaneous denaturation and chromophore trapping by isopropanol/borohydride, followed by exhaustive protein digestion, complete extraction, and liquid chromatography-mass spectrometry. Using our method, we tracked Rho* hydrolysis, the subsequent formation of N-retinylidene-phosphatidylethanolamine (N-ret-PE) adducts with the released all-trans-retinal, and the reduction of all-trans-retinal to all-trans-retinol. We found that hydrolysis occurred faster in native membranes than in detergent micelles typically used to study membrane proteins. The activation energy of the hydrolysis in native membranes was determined to be 17.7 ± 2.4 kcal/mol. Our data support the interpretation that metarhodopsin II, the signaling state of rhodopsin, is the primary species undergoing hydrolysis and release of its all-trans-retinal. In the absence of NADPH, free all-trans-retinal reacts with phosphatidylethanolamine (PE), forming a substantial amount of N-ret-PE (∼40% of total all-trans-retinal at physiological pH), at a rate that is an order of magnitude faster than Rho* hydrolysis. However, N-ret-PE formation was highly attenuated by NADPH-dependent reduction of all-trans-retinal to all-trans-retinol. Neither N-ret-PE formation nor all-trans-retinal reduction affected the rate of hydrolysis of Rho*. Our study provides a comprehensive picture of the hydrolysis of Rho* and the release of all-trans-retinal and its reentry into the visual cycle, a process in which alteration can lead to severe retinopathies.
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Foley JF. Shining a light on rhodopsin signaling. Sci Signal 2022; 15:eabq5583. [PMID: 35439024 DOI: 10.1126/scisignal.abq5583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Monitoring rhodopsin signaling in real time reveals the role of native lipids in modulating GPCR interactions.
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Affiliation(s)
- John F Foley
- Science Signaling, AAAS, Washington, DC 20005, USA.
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