Article
Chemistry, Multidisciplinary
Melissa Frick, Christian Schwieger, Carla Schmidt
Summary: Membrane proteins, crucial for cell function, can be effectively studied using liposomes as membrane mimetics for mass spectrometric analysis. Liposomes, advantageous for their ease of preparation and ability to vary in size and composition, have been shown to dissociate into lipid clusters in the gas phase of a mass spectrometer while retaining intact protein and protein-lipid complexes. This approach opens the door for the widespread application of liposomes in mass spectrometric analysis of membrane-associated proteins.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Analytical
Yang Zhou, Xingrui Song, Xiaowen Yan, Limin Yang, Shi Chen, Qiuquan Wang
Summary: The chromatography-mass spectrometry hyphenated technique is widely used for quantifying trace analytes in complex biosamples. However, the broadening and remixing of separated analyte-containing chromatographic peaks prior to mass spectrometric quantification is a common issue due to molecular diffusion. We developed a zero-interfacing approach that successfully couples microbore HPLC with ICPMS, maintaining the molecular resolution obtained on HPLC and the limit of detection of ICPMS.
ANALYTICAL CHEMISTRY
(2022)
Article
Thermodynamics
Gage P. Ashton, Lindsay P. Harding, Gareth M. B. Parkes
Summary: Thermomicroscopy is an excellent complimentary tool to other analytical techniques, providing optical data to elucidate complex events in thermal profiles. The combination of hot-stage microscopy and real-time mass spectrometry allows for simultaneous detection of physical and chemical properties of materials during heating.
JOURNAL OF THERMAL ANALYSIS AND CALORIMETRY
(2022)
Article
Chemistry, Multidisciplinary
Oliver J. Hale, Helen J. Cooper
Summary: This study demonstrates a mass spectrometry analysis method for the direct analysis of intact oligomeric membrane proteins from tissue. By characterizing protein assembly directly from sheep eye lens sections without sample pre-treatment, our approach allows for simultaneous analysis of soluble protein assemblies.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Multidisciplinary
Corinne A. Lutomski, Tarick J. El-Baba, Joshua D. Hinkle, Idlir Liko, Jack L. Bennett, Neha V. Kalmankar, Andrew Dolan, Carla Kirschbaum, Kim Greis, Leonhard H. Urner, Parth Kapoor, Hsin-Yung Yen, Kevin Pagel, Christopher Mullen, John E. P. Syka, Carol V. Robinson
Summary: By using an infrared laser in a high-pressure linear ion trap, researchers were able to remove detergent micelles and obtain good sequence coverage for membrane proteins and their complexes through top-down mass spectrometry.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biochemical Research Methods
Yongli Chen, Yikun Yang, Xiliu Zeng, Jing Long Feng, Ken Oakes, Xu Zhang, Shufen Cui
Summary: Although liposomes have shown significant success in clinical drug delivery, studying the pharmacokinetics of liposomal nanomedicines remains challenging due to the difficulty in accurately measuring low concentrations of free drug. This study presents a microdialysis-based microfluidic chip interfaced with mass spectrometry to address this issue. By incorporating an effective anti-foulant, PEG 20,0 0 0, the microfluidic chip demonstrated excellent drug extraction and desalting efficiency, providing a promising approach for real-time monitoring of nanomedicine pharmacokinetic profiles.
JOURNAL OF CHROMATOGRAPHY A
(2022)
Article
Chemistry, Multidisciplinary
Beibei Wang, D. Peter Tieleman
Summary: Electrospray ionization (ESI) is essential for mass spectrometry in biological systems, but the mechanism of ESI is not well understood, leading to ambiguity in mass spectra interpretation. This study focuses on lipid nanodiscs in complex biological systems and uses molecular dynamics simulations to investigate the release of nanodiscs in ESI. Two major scenarios were observed, providing insights into the diversity of gaseous product ions and improving the interpretation of mass spectra in lipid-protein systems.
COMMUNICATIONS CHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Sarah M. Fantin, Kristine F. Parson, Pramod Yadav, Brock Juliano, Geoffrey C. Li, Charles R. Sanders, Melanie D. Ohi, Brandon T. Ruotolo
Summary: Peripheral myelin protein (PMP22) misfolding is identified as a key factor in various peripheral neuropathies. Mutant forms of PMP22 exhibit differences in stability and propensity to form homodimeric complexes compared to wild-type protein. The formation of PMP22 dimers from destabilized monomers is proposed as a key element in PMP22 mistrafficking, based on combined findings from native ion mobility-mass spectrometry and cellular data.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Chemistry, Analytical
Noortje de Haan, Ming Song, Oliver C. Grant, Zilu Ye, Fawzi Khoder Agha, Mikkel Koed Moller Aasted, Robert J. Woods, Sergey Y. Vakhrushev, Hans H. Wandall
Summary: Cell surface glycans play a crucial role in cell communication, adhesion, and migration. However, obtaining specific information about the structures of glycoproteins on the cell surface remains a challenge. In this study, we developed a new method to analyze the N-glycoprotein forms expressed on the cell surface, allowing us to study their functional role in cell processes.
ANALYTICAL CHEMISTRY
(2023)
Review
Biochemical Research Methods
Jan-Simon Behnke, Leonhard H. Urner
Summary: This article reviews the role of detergents in mass spectrometry for studying membrane proteins and highlights the importance of optimizing detergent chemistry and handling. It also introduces a new research direction: the optimization of mass spectrometry detergents for different applications in mass spectrometry-based membrane proteomics. The review focuses on qualitative design aspects, including their relevance in bottom-up proteomics, top-down proteomics, native mass spectrometry, and Nativeomics. In addition to established design aspects, such as charge, concentration, degradability, detergent removal, and exchange, detergent heterogeneity is identified as a promising driver for innovation. Rationalizing the role of detergent structures in membrane proteomics is expected to enable the analysis of challenging biological systems.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2023)
Review
Chemistry, Analytical
Veronica Termopoli, Maurizio Piergiovanni, Davide Ballabio, Viviana Consonni, Emmanuel Cruz Munoz, Fabio Gosetti
Summary: Membrane introduction mass spectrometry (MIMS) is a direct mass spectrometry technique that allows online monitoring and rapid quantification of trace levels of compounds in complex matrices without extensive sample preparation steps and chromatographic separation. It uses a thin, semi-permeable, and selective membrane to pre-concentrate analytes based on their physicochemical properties, and transfers them directly to the mass spectrometer using different acceptor phases.
Article
Biochemical Research Methods
Julia A. Townsend, Michael T. Marty
Summary: Membrane proteins often form functional complexes in lipid bilayers, making it difficult to characterize their oligomerization. However, using native mass spectrometry combined with lipid nanodiscs, it is possible to study the oligomeric state distribution and lipid preferences of these complexes. This study presents a novel data analysis method using macromolecular mass defect analysis to interpret complex spectra. It also discusses the limitations and strategies to resolve ambiguities, along with recent research on antimicrobial peptides, amyloid proteins, and viroporins in lipid membranes.
Article
Chemistry, Analytical
Kyle A. Brown, Morgan K. Gugger, Zhen Yu, David Moreno, Song Jin, Ying Ge
Summary: Nonionic surfactants are commonly used reagents for cell lysis and protein extraction in structural biology. However, their presence often interferes with protein analysis by electrospray ionization-mass spectrometry (ESI-MS). This study introduces a cleavable surfactant, DSSM, which is compatible with ESI-MS analysis and enables top-down proteomics characterization. DSSM can replace DDM in proteomic experiments and structural biology studies.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Xiaoxuan Lin, Adam M. Zmyslowski, Isabelle A. Gagnon, Robert K. Nakamoto, Tobin R. Sosnick
Summary: This study presents a protocol for conducting in vivo HDX-MS, focusing on BtuB. The in vivo HDX-MS data support the conclusions from previous in vitro studies, providing further evidence for the potential of HDX-MS studies in a native cellular environment.
Article
Orthopedics
B. Rocha, B. Cillero-Pastor, C. Ruiz-Romero, M. R. L. Paine, J. D. Canete, R. M. A. Heeren, F. J. Blanco
Summary: This study examined the abundance and distribution of lipids in the synovial membrane of human joints, revealing differential profiles in Osteoarthritis (OA) compared to control samples. Elevated levels of phosphatidylcholines, fatty acids, and lysophosphatidic acids were found in OA synovium, along with lower levels of lysophosphatidylcholines. Spatial distribution of specific glycerophospholipids was correlated with hypertrophic, inflamed, or vascularized synovial areas. Compared to other inflammatory arthropathies, OA tissue showed lower amounts of phosphatidylethanolamine-based plasmalogens.
OSTEOARTHRITIS AND CARTILAGE
(2021)
Article
Chemistry, Multidisciplinary
Di Wu, Manman Guo, Carol V. Robinson
Summary: Understanding the impact of genetic variations and post-translational modifications on protein interactions is made possible by using native mass spectrometry (MS). In this study, we characterized the proteoforms of plasma serine protease inhibitors and found that different fucosylation linkages have opposing effects on protein interactions.
Article
Chemistry, Analytical
Deseree J. Reid, Tapasyatanu Dash, Zhihan Wang, Craig A. Aspinwall, Michael T. Marty
Summary: Daptomycin is a cyclic lipopeptide antibiotic that interacts with lipid membranes in a non-specific manner. The interaction strength depends on membrane rigidity, with more rigid membranes showing stronger interactions. More fluid membranes may undergo pore formation to expose daptomycin to oxidation. These findings highlight the complementary use of native mass spectrometry, fast photochemical oxidation of peptides, and membrane conductance experiments in studying antibiotic-membrane interactions.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Tarick J. El-Baba, Corinne A. Lutomski, Sean A. Burnap, Jani R. Bolla, Lindsay A. Baker, Andrew J. Baldwin, Weston B. Struwe, Carol V. Robinson
Summary: In this study, the impact of glycans on mediating ACE2 dimerization and interactions with Spike was investigated. The researchers found that glycans play a regulatory role in ACE2 dimerization and that positive cooperativity drives ACE2 to complex with multiple Spike trimers. These findings are important for developing strategies to neutralize the virus.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Biochemical Research Methods
Henry M. Sanders, Farzaneh Chalyavi, Caitlyn R. Fields, Marius M. Kostelic, Ming-Hao Li, Daniel P. Raleigh, Martin T. Zanni, Michael T. Marty
Summary: The aggregation of islet amyloid polypeptide (IAPP) is associated with beta-cell dysfunction in type 2 diabetes (T2D) in humans. The interaction of IAPP oligomers with lipid membranes can disrupt the bilayer integrity and/or homeostasis of the cell. Amino acid sequence variations of IAPPs between species can greatly decrease their propensity for aggregation.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Correction
Biochemistry & Molecular Biology
Rei Matsuoka, Roman Fudim, Sukkyeong Jung, Chenou Zhang, Andre Bazzone, Yurie Chatzikyriakidou, Carol V. Robinson, Norimichi Nomura, So Iwata, Michael Landreh, Laura Orellana, Oliver Beckstein, David Drew
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2023)
Review
Pharmacology & Pharmacy
Hsin-Yung Yen, Ali Jazayeri, Carol Robinson
Summary: GPCRs are important drug targets due to their involvement in physiological processes. Mass spectrometry techniques, such as HDX-MS and native-MS, provide opportunities to investigate GPCR pharmacology and discover new drugs. This review highlights the potential of MS techniques for in-depth investigations of GPCR biology.
PHARMACOLOGICAL REVIEWS
(2023)
Article
Multidisciplinary Sciences
Gabriela Dias Noske, Yun Song, Rafaela Sachetto Fernandes, Rod Chalk, Haitem Elmassoudi, Lizbe Koekemoer, C. David J. Owen, Tarick V. El-Baba, Carol Robinson, Glaucius Oliva, Andre Schutzer Godoy
Summary: The main protease of SARS-CoV-2, M-pro, is responsible for cleaving the viral polyprotein and is crucial for enzyme dimerization and activity. N-terminal cleavage is not critical for dimerization, and different types of inhibitors can affect the oligomeric states. This study provides insights into the maturation process of M-pro and how it can be targeted by inhibitors.
NATURE COMMUNICATIONS
(2023)
Article
Biochemical Research Methods
Kenneth R. R. Durbin, Matthew T. T. Robey, Lilien N. N. Voong, Ryan T. T. Fellers, Corinne A. A. Lutomski, Tarick J. J. El-Baba, Carol V. V. Robinson, Neil L. L. Kelleher
Summary: Native mass spectrometry has become an important technique for determining the composition of protein complexes. However, there is a lack of software tools for comprehensive analysis of native mass spectrometry data. In this study, we introduce ProSight Native as an informatics platform that can determine the complete composition of protein complexes. We demonstrated its features by successfully determining the composition of a homotetrameric membrane complex and a heterodimer complex with associated ligands.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemical Research Methods
Melanie T. Odenkirk, Guozhi Zhang, Michael T. Marty
Summary: Lipids play important roles in membrane protein structure, interactions, and activity. Nanodiscs are a suitable model for studying protein-lipid interactions in a lipid bilayer. This study investigated how nanodisc assembly conditions affect the lipid profile. The results suggest that while most lipids are unaffected, some changes occurred in specific lipid classes under certain assembly conditions.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Article
Biochemical Research Methods
Julia A. Townsend, Michael T. Marty
Summary: Membrane proteins often form functional complexes in lipid bilayers, making it difficult to characterize their oligomerization. However, using native mass spectrometry combined with lipid nanodiscs, it is possible to study the oligomeric state distribution and lipid preferences of these complexes. This study presents a novel data analysis method using macromolecular mass defect analysis to interpret complex spectra. It also discusses the limitations and strategies to resolve ambiguities, along with recent research on antimicrobial peptides, amyloid proteins, and viroporins in lipid membranes.
Article
Multidisciplinary Sciences
Hongmiao Hu, Anne-Marie M. van Roon, George E. Ghanim, Bilal Ahsan, Abraham O. Oluwole, Sew-Yeu Peak-Chew, Carol V. Robinson, Thi Hoang Duong Nguyen
Summary: Shelterin and nucleosomes interact at mammalian telomeres, but the mechanism is not yet understood. Cryo-electron microscopy was used to study the structure of a human telomeric nucleosome bound to the shelterin factor TRF1. The study revealed that TRF1 binds to unwrapped nucleosomal DNA ends by engaging both the DNA and the histone octamer, resulting in a shift in the nucleosomal DNA. Phosphorylation of TRF1 and a noncanonical DNA binding surface on TRF1 were found to be crucial for its association with telomeric nucleosomes. These findings provide important insights into shelterin-chromatin interactions and its roles at telomeres.
Article
Multidisciplinary Sciences
Luke Smithers, Oksana Degtjarik, Dietmar Weichert, Chia-Ying Huang, Coilin Boland, Katherine Bowen, Abraham Oluwole, Corinne Lutomski, Carol V. Robinson, Eoin M. Scanlan, Meitian Wang, Vincent Olieric, Moran Shalev-Benami, Martin Caffrey
Summary: This study investigates the structural changes of the enzyme apolipoprotein N-acyltransferase (Lnt) during its reaction. The study confirms the ping-pong mechanism of Lnt and explains the molecular basis for its ability to bind different substrates.
Article
Chemistry, Multidisciplinary
Yun Zhu, Melanie T. Odenkirk, Pei Qiao, Tianqi Zhang, Samantha Schrecke, Ming Zhou, Michael T. Marty, Erin S. Baker, Arthur Laganowsky
Summary: By combining native mass spectrometry (MS) and lipidomics, we have developed an innovative approach to identify the lipids retained by membrane proteins from natural lipid extracts. Our findings indicate that the bacterial ammonia channel (AmtB) selectively retains specific cardiolipin (CDL) and phosphatidylethanolamine (PE) from these extracts. This research provides a new avenue to explore the important lipid-protein interactions in membrane protein structure and function.
Article
Biochemical Research Methods
Jack P. Ryan, Marius M. Kostelic, Chih-Chieh Hsieh, Joshua Powers, Craig Aspinwall, James N. Dodds, John E. Schiel, Michael T. Marty, Erin S. Baker
Summary: This article introduces a method that combines different analytical workflows to evaluate the composition and ratio of AAV capsids. The method includes two steps, each for evaluating the intact capsids and viral protein subunits. By applying this method, a better understanding of the characteristics and functions of AAV capsids can be achieved.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Article
Chemistry, Analytical
Weijing Liu, Hiruni S. Jayasekera, James D. Sanders, Guozhi Zhang, Rosa Viner, Michael T. Marty
Summary: In this study, an online buffer exchange coupled to native mass spectrometry (OBE-nMS) technique was developed for analyzing membrane proteins in different membrane mimetics. The results showed that mobile phases containing ammonium acetate and lauryl-dimethylamine oxide were most universal for characterizing both bacterial and mammalian membrane proteins in detergent micelles. For membrane proteins in nanodiscs, ammonium acetate was sufficient as the mobile phase. This technique enables rapid measurement of each membrane protein and facilitates the assessment of their integrity prior to structural elucidation.
ANALYTICAL CHEMISTRY
(2023)