Porin Associates with Tom22 to Regulate the Mitochondrial Protein Gate Assembly.

Mitochondria import nearly all of their resident proteins from the cytosol, and the TOM complex functions as their entry gate. The TOM complex undergoes a dynamic conversion between the majority population of a three-channel gateway ("trimer") and the minor population that lacks Tom22 and has only two Tom40 channels ("dimer"). Here, we found that the porin Por1 acts as a sink to bind newly imported Tom22. This Por1 association thereby modulates Tom22 integration into the TOM complex, guaranteeing formation of the functional trimeric TOM complex. Por1 sequestration of Tom22 dissociated from the trimeric TOM complex also enhances the dimeric TOM complex, which is preferable for the import of TIM40/MIA-dependent proteins into mitochondria. Furthermore, Por1 appears to contribute to cell-cycle-dependent variation of the functional trimeric TOM complex by chaperoning monomeric Tom22, which arises from the cell-cycle-controlled variation of phosphorylated Tom6.

Structure of the mitochondrial import gate reveals distinct preprotein paths.

The translocase of the outer mitochondrial membrane (TOM) is the main entry gate for proteins1-4. Here we use cryo-electron microscopy to report the structure of the yeast TOM core complex5-9 at 3.8-Å resolution. The structure reveals the high-resolution architecture of the translocator consisting of two Tom40 ß-barrel channels and α-helical transmembrane subunits, providing insight into critical features that are conserved in all eukaryotes1-3. Each Tom40 ß-barrel is surrounded by small TOM subunits, and tethered by two Tom22 subunits and one phospholipid. The N-terminal extension of Tom40 forms a helix inside the channel; mutational analysis reveals its dual role in early and late steps in the biogenesis of intermembrane-space proteins in cooperation with Tom5. Each Tom40 channel possesses two precursor exit sites. Tom22, Tom40 and Tom7 guide presequence-containing preproteins to the exit in the middle of the dimer, whereas Tom5 and the Tom40 N extension guide preproteins lacking a presequence to the exit at the periphery of the dimer.

The ProteomeXchange consortium at 10 years: 2023 update.

Mass spectrometry (MS) is by far the most used experimental approach in high-throughput proteomics. The ProteomeXchange (PX) consortium of proteomics resources (http://www.proteomexchange.org) was originally set up to standardize data submission and dissemination of public MS proteomics data. It is now 10 years since the initial data workflow was implemented. In this manuscript, we describe the main developments in PX since the previous update manuscript in Nucleic Acids Research was published in 2020. The six members of the Consortium are PRIDE, PeptideAtlas (including PASSEL), MassIVE, jPOST, iProX and Panorama Public. We report the current data submission statistics, showcasing that the number of datasets submitted to PX resources has continued to increase every year. As of June 2022, more than 34 233 datasets had been submitted to PX resources, and from those, 20 062 (58.6%) just in the last three years. We also report the development of the Universal Spectrum Identifiers and the improvements in capturing the experimental metadata annotations. In parallel, we highlight that data re-use activities of public datasets continue to increase, enabling connections between PX resources and other popular bioinformatics resources, novel research and also new data resources. Finally, we summarise the current state-of-the-art in data management practices for sensitive human (clinical) proteomics data.

Universal Spectrum Identifier for mass spectra.

Mass spectra provide the ultimate evidence to support the findings of mass spectrometry proteomics studies in publications, and it is therefore crucial to be able to trace the conclusions back to the spectra. The Universal Spectrum Identifier (USI) provides a standardized mechanism for encoding a virtual path to any mass spectrum contained in datasets deposited to public proteomics repositories. USI enables greater transparency of spectral evidence, with more than 1 billion USI identifications from over 3 billion spectra already available through ProteomeXchange repositories.

Continuous Nanospace in Nanoporous Liquid Crystal Investigated by 129 Xe NMR Spectroscopy.

Continuous nanopores within fluid materials could be used for novel chemical events such as the accommodation of guest molecules, unique arrays of the entrapped molecules, and chemical reactions in a dynamic molecular assembly. Columnar liquid crystals composed of a one-dimensionally stacked assembly of shape-persistent macrocycles form nanochannels owing to the intrinsic nanospace in the column. However, the existence of substantial nanoporosity has not been confirmed experimentally thus far. In this study, for the first time in the literature, we confirmed the presence of discrete and spatiotemporally continuous voids in a liquid-crystalline material. In 129 Xe NMR spectroscopy of liquid crystalline columnar assembly of imine-bridged shape-persistent macrocycles under Xe atmosphere, the NMR signals of the Xe atoms entrapped in the liquid-crystalline macrocycle depended on the gas pressure and phase-transition temperatures. These results indicate that the encapsulation of Xe gas molecules within the discrete and oriented nanospaces of nanoporous liquid crystals is different from the homogeneous dissolution of the solute in an ordinary solution.

Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work.

The Human Proteome Organization (HUPO) Proteomics Standards Initiative (PSI) has been successfully developing guidelines, data formats, and controlled vocabularies (CVs) for the proteomics community and other fields supported by mass spectrometry since its inception 20 years ago. Here we describe the general operation of the PSI, including its leadership, working groups, yearly workshops, and the document process by which proposals are thoroughly and publicly reviewed in order to be ratified as PSI standards. We briefly describe the current state of the many existing PSI standards, some of which remain the same as when originally developed, some of which have undergone subsequent revisions, and some of which have become obsolete. Then the set of proposals currently being developed are described, with an open call to the community for participation in the forging of the next generation of standards. Finally, we describe some synergies and collaborations with other organizations and look to the future in how the PSI will continue to promote the open sharing of data and thus accelerate the progress of the field of proteomics.

Denosumab effect on bone mineral density and urinary-NTX in breast cancer patients receiving aromatase inhibitors.

INTRODUCTION: Aromatase inhibitors are used post-surgical intervention in postmenopausal patients with breast cancer. However, these drugs accelerate decline in bone mineral density (BMD), which is countered by use of denosumab, and the efficacy of the drug can be assessed by bone turnover markers. We investigated the effects of denosumab administration for 2 years on BMD and urinary N-telopeptide of type I collagen (u-NTX) levels in breast cancer patients treated with aromatase inhibitors. MATERIALS AND METHODS: This was a single-center retrospective study. Postoperative hormone receptor-positive breast cancer patients with low T-scores biannually received denosumab from the time of initiation of aromatase inhibitor therapy for 2 years. BMD was measured every 6 months, and u-NTX levels were assessed after 1 month and thereby every 3 months. RESULTS: The median patient age of the 55 patients included in this study was 69 (range: 51-90) years. BMD gradually increased in the lumbar spine and femoral neck and u-NTX levels were lowest at 3 months post-initiation of therapy. Patients were divided into two groups based on the change ratio of u-NTX 3 months post-denosumab administration. Of these, the group with higher change ratio showed a higher degree of BMD restoration in the lumbar spine and femoral neck 6 months post-denosumab treatment. CONCLUSION: Denosumab increased BMD in patients treated with aromatase inhibitors. The u-NTX level decreased soon after start of denosumab treatment, and its change ratio is predictive of improvement in BMD.

Proteomics Standards Initiative's ProForma 2.0: Unifying the Encoding of Proteoforms and Peptidoforms.

It is important for the proteomics community to have a standardized manner to represent all possible variations of a protein or peptide primary sequence, including natural, chemically induced, and artifactual modifications. The Human Proteome Organization Proteomics Standards Initiative in collaboration with several members of the Consortium for Top-Down Proteomics (CTDP) has developed a standard notation called ProForma 2.0, which is a substantial extension of the original ProForma notation developed by the CTDP. ProForma 2.0 aims to unify the representation of proteoforms and peptidoforms. ProForma 2.0 supports use cases needed for bottom-up and middle-/top-down proteomics approaches and allows the encoding of highly modified proteins and peptides using a human- and machine-readable string. ProForma 2.0 can be used to represent protein modifications in a specified or ambiguous location, designated by mass shifts, chemical formulas, or controlled vocabulary terms, including cross-links (natural and chemical) and atomic isotopes. Notational conventions are based on public controlled vocabularies and ontologies. The most up-to-date full specification document and information about software implementations are available at http://psidev.info/proforma.

Thermally Stable Array of Discrete C60s on a Two-Dimensional Crystalline Adlayer of Macrocycles both in Vacuo and under Ambient Pressure.

A periodic monolayer array of discrete C60s was generated on an atomically flat Au(111) surface with the aid of a template adlayer. The template was a two-dimensional (2D) array of molecular pits prepared on an Au(111) surface through 2D crystallization of shape-persistent macrocycles composed of four carbazole and four salphens/Ni-salphens with a 1 nm hollow. Scanning tunneling microscopy imaging under ultra-high vacuum revealed that the square-shaped macrocycles, with 1.5 nm sides, were arranged with a periodic spacing of approximately 4.0 nm on the Au(111) surface, where the orientation and periodicity of the macrocycles were dependent on their chemical structures. After sublimation of C60s onto the adlayer, a single C60 molecule was entrapped in each pit, and an ordered molecular array of C60s was attained with a pattern similar to that of the macrocycles. The periodic pattern of C60s on the surface was thermally stable up to approximately 200 °C, even under ambient pressure. Scanning tunneling spectroscopy suggested the existence of an electronic interaction between the C60s and the Au(111) surface that was influenced by the macrocycle template on the surface.

Organelle membrane-specific chemical labeling and dynamic imaging in living cells.

Lipids play crucial roles as structural elements, signaling molecules and material transporters in cells. However, the functions and dynamics of lipids within cells remain unclear because of a lack of methods to selectively label lipids in specific organelles and trace their movement by live-cell imaging. We describe here a technology for the selective labeling and fluorescence imaging (microscopic or nanoscopic) of phosphatidylcholine in target organelles. This approach involves the metabolic incorporation of azido-choline, followed by a spatially limited bioorthogonal reaction that enables the visualization and quantitative analysis of interorganelle lipid transport in live cells. More importantly, with live-cell imaging, we obtained direct evidence that the autophagosomal membrane originates from the endoplasmic reticulum. This method is simple and robust and is thus powerful for real-time tracing of interorganelle lipid trafficking.

The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics.

The ProteomeXchange (PX) consortium of proteomics resources (http://www.proteomexchange.org) has standardized data submission and dissemination of mass spectrometry proteomics data worldwide since 2012. In this paper, we describe the main developments since the previous update manuscript was published in Nucleic Acids Research in 2017. Since then, in addition to the four PX existing members at the time (PRIDE, PeptideAtlas including the PASSEL resource, MassIVE and jPOST), two new resources have joined PX: iProX (China) and Panorama Public (USA). We first describe the updated submission guidelines, now expanded to include six members. Next, with current data submission statistics, we demonstrate that the proteomics field is now actively embracing public open data policies. At the end of June 2019, more than 14 100 datasets had been submitted to PX resources since 2012, and from those, more than 9 500 in just the last three years. In parallel, an unprecedented increase of data re-use activities in the field, including 'big data' approaches, is enabling novel research and new data resources. At last, we also outline some of our future plans for the coming years.

A Light-Harvesting/Charge-Separation Model with Energy Gradient Made of Assemblies of meta-Pyridyl Zinc Porphyrins.

Self-assembly of porphyrins is a fascinating topic, not only for mimicking chlorophyll assemblies in photosynthetic organisms, but also for the potential of creating molecular-level devices. Herein, zinc porphyrin derivatives bearing a meta-pyridyl group at the meso position were prepared and their assemblies studied in chloroform. Among the porphyrins studied, one with a carbamoylpyridyl moiety gave a distinct 1 H NMR spectrum in CDCl3 , which allowed the supramolecular structure in solution to be probed in detail. Ring-current-induced chemical-shift changes in the 1 H NMR spectrum, together with vapor-pressure osmometry and diffusion-ordered NMR spectroscopy, among other evidence, suggested that the porphyrin molecules form a trimer with a triangular cone structure. Incorporation of a directly linked porphyrin-ferrocene dyad with the same assembling properties in the assemblies led to a rare example of a light-harvesting/charge-separation system in which an energy gradient is incorporated and reductive quenching occurs.

The jPOST environment: an integrated proteomics data repository and database.

Rapid progress is being made in mass spectrometry (MS)-based proteomics, yielding an increasing number of larger datasets with higher quality and higher throughput. To integrate proteomics datasets generated from various projects and institutions, we launched a project named jPOST (Japan ProteOme STandard Repository/Database, https://jpostdb.org/) in 2015. Its proteomics data repository, jPOSTrepo, began operations in 2016 and has accepted more than 10 TB of MS-based proteomics datasets in the past two years. In addition, we have developed a new proteomics database named jPOSTdb in which the published raw datasets in jPOSTrepo are reanalyzed using standardized protocol. jPOSTdb provides viewers showing the frequency of detected post-translational modifications, the co-occurrence of phosphorylation sites on a peptide and peptide sharing among proteoforms. jPOSTdb also provides basic statistical analysis tools to compare proteomics datasets.

Lipid homeostasis in mitochondria.

Mitochondria are surrounded by the two membranes, the outer and inner membranes, whose lipid compositions are optimized for proper functions and structural organizations of mitochondria. Although a part of mitochondrial lipids including their characteristic lipids, phosphatidylethanolamine and cardiolipin, are synthesized within mitochondria, their precursor lipids and other lipids are transported from other organelles, mainly the ER. Mitochondrially synthesized lipids are re-distributed within mitochondria and to other organelles, as well. Recent studies pointed to the important roles of inter-organelle contact sites in lipid trafficking between different organelle membranes. Identification of Ups/PRELI proteins as lipid transfer proteins shuttling between the mitochondrial outer and inner membranes established a part of the molecular and structural basis of the still elusive intra-mitochondrial lipid trafficking.

DBTSS/DBKERO for integrated analysis of transcriptional regulation.

DBTSS (Database of Transcriptional Start Sites)/DBKERO (Database of Kashiwa Encyclopedia for human genome mutations in Regulatory regions and their Omics contexts) is the database originally initiated with the information of transcriptional start sites and their upstream transcriptional regulatory regions. In recent years, we updated the database to assist users to elucidate biological relevance of the human genome variations or somatic mutations in cancers which may affect the transcriptional regulation. In this update, we facilitate interpretations of disease associated genomic variation, using the Japanese population as a model case. We enriched the genomic variation dataset consisting of the 13,368 individuals collected for various genome-wide association studies and the reference epigenome information in the surrounding regions using a total of 455 epigenome datasets (four tissue types from 67 healthy individuals) collected for the International Human Epigenome Consortium (IHEC). The data directly obtained from the clinical samples was associated with that obtained from various model systems, such as the drug perturbation datasets using cultured cancer cells. Furthermore, we incorporated the results obtained using the newly developed analytical methods, Nanopore/10x Genomics long-read sequencing of the human genome and single cell analyses. The database is made publicly accessible at the URL (http://dbtss.hgc.jp/).

jPOSTrepo: an international standard data repository for proteomes.

Major advancements have recently been made in mass spectrometry-based proteomics, yielding an increasing number of datasets from various proteomics projects worldwide. In order to facilitate the sharing and reuse of promising datasets, it is important to construct appropriate, high-quality public data repositories. jPOSTrepo (https://repository.jpostdb.org/) has successfully implemented several unique features, including high-speed file uploading, flexible file management and easy-to-use interfaces. This repository has been launched as a public repository containing various proteomic datasets and is available for researchers worldwide. In addition, our repository has joined the ProteomeXchange consortium, which includes the most popular public repositories such as PRIDE in Europe for MS/MS datasets and PASSEL for SRM datasets in the USA. Later MassIVE was introduced in the USA and accepted into the ProteomeXchange, as was our repository in July 2016, providing important datasets from Asia/Oceania. Accordingly, this repository thus contributes to a global alliance to share and store all datasets from a wide variety of proteomics experiments. Thus, the repository is expected to become a major repository, particularly for data collected in the Asia/Oceania region.

The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition.

The ProteomeXchange (PX) Consortium of proteomics resources (http://www.proteomexchange.org) was formally started in 2011 to standardize data submission and dissemination of mass spectrometry proteomics data worldwide. We give an overview of the current consortium activities and describe the advances of the past few years. Augmenting the PX founding members (PRIDE and PeptideAtlas, including the PASSEL resource), two new members have joined the consortium: MassIVE and jPOST. ProteomeCentral remains as the common data access portal, providing the ability to search for data sets in all participating PX resources, now with enhanced data visualization components.We describe the updated submission guidelines, now expanded to include four members instead of two. As demonstrated by data submission statistics, PX is supporting a change in culture of the proteomics field: public data sharing is now an accepted standard, supported by requirements for journal submissions resulting in public data release becoming the norm. More than 4500 data sets have been submitted to the various PX resources since 2012. Human is the most represented species with approximately half of the data sets, followed by some of the main model organisms and a growing list of more than 900 diverse species. Data reprocessing activities are becoming more prominent, with both MassIVE and PeptideAtlas releasing the results of reprocessed data sets. Finally, we outline the upcoming advances for ProteomeXchange.

Adsorption of Pluronic Surfactants in Alkylene Carbonates on Silica.

Adsorption of triblock Pluronic surfactants bearing poly(ethylene oxide) (PEO) chains of different lengths, L-62 (5 EO groups on each end), L-64 (13 EO groups on each end), and F-68 (79 EO groups on each end), on silica has been characterized using atomic force microscopy (AFM). The solvent used herein was a mixture of ethylene carbonate (EC) and propylene carbonate (PC). The three Pluronic surfactants were dissolved in the mixed solvent, with the PEO chain acting as a solvophilic group and the poly(propylene oxide) (PPO) chain acting as a solvophobic group. The approaching force curve measurements for the three Pluronics (at 10 mmol dm-3) revealed repulsive forces from an apparent separation of 20-30 nm. The most solvophilic Pluronic surfactant with the longest PEO chain (F-68) showed continuously increasing repulsive interaction with decreasing separation. The Milner-Witten-Cates (MWC) theory described the repulsive force curve data of F-68, suggesting that F-68 forms a polymer brush on the silica surface. The retracting force curve measurements detected stretching forces for the three Pluronic systems. These stretching forces were observed more frequently for the L-62 system than for the F-68 system, but the pull-off distance was shorter for L-62 than for F-68.

Columnar Liquid-Crystalline Macrocycles Synthesized via Metal Ion-Assisted Self-Assembly.

Columnar assemblies of liquid-crystalline (LC) macrocycles hold promise for the construction of nanochannels in fluid materials. Metal-assisted self-assembly is an efficient way to prepare LC macrocycles. A large π-conjugated ligand, 9,10-diphenylanthracene (DPA) bearing two ß-diketones, was prepared as a building unit for the macrocycle, and a series of side chains were incorporated into the DPA to yield LC materials. The bis(ß-diketone) ligands on DPA allow for the efficient formation of triangular 3:3 metallomacrocycles in the presence of square-planar Cu2+ ions. The copper-containing 3:3 metallomacrocycle with the appropriate side chains exhibited thermotropic columnar LC phases in which the columns were arranged in rectangular arrays over a wide temperature range, and well-ordered birefringent textures were observed under a polarized microscope.

Specific and Oriented Encapsulation of Fullerene C70 into a Supramolecular Double-Decker Cage Composed of Shape-Persistent Macrocycles.

An efficient strategy for the specific recognition of ellipsoidal fullerenes uses molecular containers with well-designed three-dimensional (3D) nanospaces. We describe the synthesis of a supramolecular double-decker cage composed of shape-persistent metallomacrocycles and pillar ligands. A discrete 3D nanospace was built within the molecular framework of the shape-persistent-macrocycle/bidentate-pillar molecule. The single-crystal structure of the supramolecular cage reveals a uniquely shaped inner cavity with a size and net volume (>670 Å3 ) that are well matched to the shape and size of C70 . The cage exhibited higher selectivity for C70 over C60 , the smaller carbon allotrope. We suggest that such C70 -selective recognition is derived from multiple CH-π interactions between hydrogen atoms inside the cage and C70 .