Article
Multidisciplinary Sciences
Siyun Chen, Tamar Getter, David Salom, Di Wu, Daniel Quetschlich, Dror S. Chorev, Krzysztof Palczewski, Carol V. Robinson
Summary: This study investigated the signalling events of G protein-coupled receptors (GPCRs) using mass spectrometry in native membranes. The findings revealed the role of native lipids in rhodopsin signalling and regeneration, and proposed a paradigm for GPCR drug discovery in native membrane environments.
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, Analytical
Kevin Jooss, Luis F. Schachner, Rachel Watson, Zachary B. Gillespie, Sarah A. Howard, Marcus A. Cheek, Matthew J. Meiners, Amin Sobh, Jonathan D. Licht, Michael-Christopher Keogh, Neil L. Kelleher
Summary: The study introduces a new platform for separating and characterizing whole nucleosomes and their modifications, aiding in understanding epigenetic regulatory mechanisms. The platform offers low sample requirements and costs, with high detection sensitivity.
ANALYTICAL CHEMISTRY
(2021)
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)
Review
Biochemistry & Molecular Biology
Deseree J. J. Reid, Stephanie Thibert, Mowei Zhou
Summary: A single gene can generate multiple forms of proteins through posttranscriptional/posttranslational modifications, which results in the heterogeneity of proteins and distinct phenotypes. Structural biology has provided abundant data for accurate structural prediction, but the lack of native heterogeneity in in vitro conditions makes it difficult to connect the structural data with phenotypes. Mass spectrometry (MS) based proteomics methods can profile proteome composition and allow for the analysis of intact proteins under non-denaturing conditions, providing insights into the molecular heterogeneity of proteins.
Article
Chemistry, Analytical
Elise Daems, Debbie Dewaele, Konstantin Barylyuk, Karolien De Wael, Frank Sobott
Summary: The applications of aptamers, small oligonucleotide-based receptors with high specificity and affinity for their targets, are expanding. However, our understanding of the mechanisms governing aptamer-ligand recognition and binding is lacking, hindering the rational design of new aptamers and optimization of known ones. Using native ion mobility-mass spectrometry, the capabilities and limitations for analyzing the higher-order structure and non-covalent interactions of aptamers were demonstrated.
Article
Biochemistry & Molecular Biology
Michiko Tajiri, Hiroto Aoki, Atsuko Shintani, Kaori Sue, Satoko Akashi, Yoshiaki Furukawa
Summary: Cu/Zn-superoxide dismutase (SOD1) can bind a non-stoichiometric amount of copper and zinc ions, forming a homodimer with a stochastic combination of subunits. Correct metallation of SOD1 is important for amyotrophic lateral sclerosis.
FREE RADICAL BIOLOGY AND MEDICINE
(2022)
Article
Astronomy & Astrophysics
James G. G. Rogers, Hilke E. E. Schlichting, James E. E. Owen
Summary: The population of small, close-in exoplanets consists of super-Earths and sub-Neptunes. We have calculated the mass-radius relations for sub-Neptunes, taking into account their thermal evolution, irradiation, and mass loss. Our results show that the mass-radius relations for sub-Neptunes can be similar to those for water worlds with a silicate-to-ice composition ratio of 1:1. We also highlight the importance of considering thermally driven atmospheric escape processes when determining the composition of sub-Neptunes based on their mass and radii.
ASTROPHYSICAL JOURNAL LETTERS
(2023)
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, Analytical
Deseree J. Reid, Tapasyatanu Dash, Zhihan Wang, Craig A. Aspinwall, Michael T. Marty
Summary: In this study, native mass spectrometry (MS) and fast photochemical oxidation of peptides (FPOP) were used to investigate the interactions between the antibiotic daptomycin and different lipid bilayer nanodiscs. The results showed that daptomycin incorporates randomly into bilayers and has stronger interactions with rigid membranes. Pore formation may occur in fluid membranes, exposing daptomycin to oxidation. These findings demonstrate the complementarity of native MS, FPOP, and membrane conductance experiments in understanding antibiotic peptide-membrane interactions.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Blake E. Szkoda, Angela Di Capua, Joy Shaffer, Edward J. Behrman, Vicki H. Wysocki, Venkat Gopalan
Summary: In this study, the DNA binding affinity and inducer impact of the transcriptional repressor FraR were investigated using OBE-nMS and EMSA techniques. The results provided insights into the regulation of F-Asn metabolism by FraR.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Biochemical Research Methods
Brandon T. Ruotolo
Summary: Recent advancements have made it possible to comprehensively understand protein structure, oligomeric state, sequence, and modification status, providing new possibilities for treating human diseases. Mass spectrometry (MS) tools, especially those associated with ion mobility (IM) separation, have played a crucial role in this progress. However, the application of collision cross section (CCS) values in native proteomics still has limitations.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Biochemical Research Methods
Ilya I. Pikovskoi, Dmitry S. Kosyakov
Summary: In this study, Kendrick mass defect (KMD) analysis was used to identify oligomer series with different polymerization degrees and structurally related compounds in the Orbitrap mass spectra of Siberian pine dioxane lignin preparation. It was shown that KMD analysis can effectively determine the elemental compositions and structures of oligomers with high molecular weights (> 1 kDa), and was also applied to interpret complex tandem mass spectra and establish main collision-induced dissociation pathways.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Adam J. Anthony, Amit K. S. Gautam, Lohra M. Miller, Yiran Ma, Anya G. Hardwick, Anu Sharma, Subhadip Ghatak, Andreas Matouschek, Martin F. Jarrold, David E. Clemmer
Summary: Charge detection mass spectrometry (CDMS) was used to study proteasomes and their oligomers. Mass measurements of 20S, 19S, 26S, and 30S proteasomes from Saccharomyces cerevisiae were conducted, and larger assemblies (20S)(x) and (19S)(x) were observed under certain conditions. The findings contribute to a better understanding of proteasomes and their oligomeric states.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Adam J. Anthony, Amit K. S. Gautam, Lohra M. Miller, Yiran Ma, Anya G. Hardwick, Anu Sharma, Subhadip Ghatak, Andreas Matouschek, Martin F. Jarrold, David E. Clemmer
Summary: This study examined the use of Charge Detection Mass Spectrometry (CDMS) to study proteasomes. The masses of different proteasomes were measured and larger assemblies were observed under certain conditions. The study also discussed possible structures for the formation of these assemblies and the utility of CDMS in characterizing proteasomes and related oligomers.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Serina Fukui, Eiji Sugiyama, Hajime Mizuno, Iwao Sakane, Daiki Asakawa, Kazumi Saikusa, Yuki Nishiya, Yuri Amano, Kentaro Takahara, Daisuke Higo, Toshimasa Toyo'oka, Kenichiro Todoroki
Summary: A rapid method for separating dl-2-hydroxyglutaric acid using a single analytical instrument was presented, demonstrating potential for clinical analysis. This method is more efficient and effective compared to traditional methods, showing promise for future applications in clinical settings.
JOURNAL OF SEPARATION SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Masahiko Okuda, Tetsufumi Suwa, Hidefumi Suzuki, Yuki Yamaguchi, Yoshifumi Nishimura
Summary: This study reveals that the shared N-terminal tail (NTT) of the common subunit RPB6 in all three eukaryotic RNA polymerases interacts with the PH domain (PH-D) of the p62 subunit of TFIIH, playing crucial roles in transcription and nucleotide excision repair.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemical Research Methods
Daiki Asakawa, Kazumi Saikusa
Summary: Small molecules with polar functional groups, like substituted phenethylamines, are commonly analyzed using liquid chromatography-mass spectrometry (LC-MS) with electrospray ionization (ESI). However, the ESI of substituted phenethylamines often results in intense fragment ion signals, making it difficult to identify these compounds. By using computational methods and suitable functionals, the dissociation efficiency of substituted phenethylamines can be evaluated, providing reliable results.
JOURNAL OF MASS SPECTROMETRY
(2022)
Article
Multidisciplinary Sciences
Ayako Furukawa, Masatoshi Wakamori, Yasuhiro Arimura, Hideaki Ohtomo, Yasuo Tsunaka, Hitoshi Kurumizaka, Takashi Umehara, Yoshifumi Nishimura
Summary: Linker DNA and linker histone both regulate the dynamics and acetylation of H3 N-tail. H3 N-tail acetylation and dynamics are greatly suppressed in the nucleosome core particle (NCP) compared to the nucleosome. In the chromatosome, H3 N-tail adopts two different conformations, and its acetylation rate is similar to that in the nucleosome.
Article
Biochemistry & Molecular Biology
Yasuo Tsunaka, Ayako Furukawa, Yoshifumi Nishimura
Summary: The eukaryotic chromatin is made up of nucleosomes, which consists of histones and DNA. Posttranslational modifications of histone tails play important roles in various epigenetic functions. Recent studies have revealed the existence of a network of histone tails within the nucleosome.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2022)
Article
Biochemical Research Methods
Daiki Asakawa, Kazumi Saikusa
Summary: We propose using substituted benzyl ammonium species as thermometer ions to characterize the internal energy distribution of ions produced by electrospray ionization. Experimental results show that the activation of benzyl ammonium species preferentially generates benzyl cations. Calculations reveal that the threshold energies of fragmentation for the tested model ions are significantly lower than those of conventional 4-substituted benzylpyridinium thermometer ions. Furthermore, the internal energies of the ions depend on the radiofrequency voltage of the ion funnel.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2022)
Article
Biochemistry & Molecular Biology
Tomoya Kinumi, Kazumi Saikusa, Megumi Kato, Reiko Kojima, Chieko Igarashi, Naohiro Noda, Shinya Honda
Summary: Monoclonal antibodies are the largest class of biopharmaceuticals. A reference material for monoclonal antibodies, RM 6208-a, AIST-MAB, has been established to aid in the development and quality control of these antibodies. This reference material can be used for validation of analytical procedures, comparison of results, and evaluation of antibody analyses.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Biology
Yasuo Tsunaka, Hideaki Ohtomo, Yoshifumi Nishimura
Summary: The histone chaperone FACT regulates the conformation of the H2A and H2B tails in the asymmetrically unwrapped nucleosome both proximally and distally.
COMMUNICATIONS BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Kayo Nozawa, Yoshimasa Takizawa, Leonidas Pierrakeas, Chizuru Sogawa-Fujiwara, Kazumi Saikusa, Satoko Akashi, Ed Luk, Hitoshi Kurumizaka
Summary: The canonical nucleosome is the major packaging unit of eukaryotic chromatin, and the H3-H4 octasome is a nucleosome-like particle with alternative histone stoichiometry. The structure of the H3-H4 octasome is flexible.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemical Research Methods
Kazumi Saikusa, Tomoya Kinumi, Megumi Kato
Summary: We established an online SEC/nanoESI system that allows for the analysis of various proteins. The system showed high structural stability and resolution, and can automatically obtain mass spectra of different proteins.
RAPID COMMUNICATIONS IN MASS SPECTROMETRY
(2022)
Article
Biochemistry & Molecular Biology
Hideaki Ohtomo, Shinsuke Ito, Nicholas J. McKenzie, Michael Uckelmann, Masatoshi Wakamori, Haruhiko Ehara, Ayako Furukawa, Yasuo Tsunaka, Marika Shibata, Shun-ichi Sekine, Takashi Umehara, Chen Davidovich, Haruhiko Koseki, Yoshifum Nishimura
Summary: PRC1 and PRC2 play important roles in epigenetic gene regulation. H2A ubiquitination by PRC1 promotes H3K27 methylation by PRC2 through altering the dynamics of H3-tail and its contacts with DNA, with the linker-DNA being crucial for this process.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Review
Biophysics
Masahiko Okuda, Yasuo Tsunaka, Yoshifumi Nishimura
Summary: Recent studies using NMR and MD simulations are revealing the dynamic structures of target proteins complexed with TFIIH, including TFIIE, p53, DP1, XPC, UVSSA, and three RNA polymerases. Dynamic conformations of histone tails in nucleosomes and histone chaperones are also being uncovered.
BIOPHYSICAL REVIEWS
(2022)
Article
Biochemistry & Molecular Biology
Masahiko Okuda, Yoshifumi Nishimura
Summary: The general transcription factor TFIIH plays multiple roles in eukaryotes, including transcription, DNA repair, and cell cycle regulation. It contains a pleckstrin homology (PH) domain that recruits TFIIH to specific sites through interactions with other factors. The PH domain in fission yeast Schizosaccharomyces pombe (spPH) has a structure more similar to the human p62 subunit (hPH) than to the budding yeast Saccharomyces cerevisiae Tfb1 subunit (scPH), despite having higher sequence similarity to scPH. Additionally, spPH interacts with its target proteins spTfa1 and spRhp41 in a different manner than hPH and scPH, suggesting a polymorphic mode of interaction between the PH domain and target proteins in different organisms.
BIOSCIENCE REPORTS
(2023)
Review
Cell Biology
Tomoya Kujirai, Haruhiko Ehara, Shun-ichi Sekine, Hitoshi Kurumizaka
Summary: In eukaryotes, genomic DNA is packaged into chromatin and the nucleosome acts as a barrier to transcription. The RNA polymerase II elongation complex disassembles the nucleosome during transcription to allow passage. After transcription, the nucleosome is rebuilt by transcription-coupled nucleosome reassembly, which plays a crucial role in preserving epigenetic information. The histone chaperone FACT is involved in nucleosome disassembly, maintenance, and reassembly during transcription in chromatin. Recent structural studies have provided insights into the structural transitions of the nucleosome during transcription.
Article
Biochemistry & Molecular Biology
Hideaki Ohtomo, Tsutomu Yamane, Takashi Oda, Noriyuki Kodera, Jun-ichi Kurita, Yasuo Tsunaka, Romain Amyot, Mitsunori Ikeguchi, Yoshifumi Nishimura
Summary: Nucleosome assembly protein 1 (NAP1) binds to histone H2A-H2B heterodimers and mediates their deposition on and eviction from the nucleosome. Through integrative methods, the dynamic structures of the full-length hNAP1 dimer bound to one and two H2A-H2B heterodimers have been examined. The first H2A-H2B dimer primarily binds to the core domain of hNAP1, while the second H2A-H2B dimer dynamically binds to both CTADs. Based on these findings, a model of H2A-H2B eviction by NAP1 from nucleosomes is proposed.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
