Article
Chemistry, Physical
A. O. Hernandez-Castillo, Johannes Bischoff, Ju Hyeon Lee, Jennifer Langenhan, Mallikarjun Karra, Gerard Meijer, Sandra Eibenberger-Arias
Summary: This study presents rotational and vibrational resolved spectroscopy of the chiral molecule 1-indanol, focusing on the electronic transition between the S-1 and S-0 states. By analyzing the spectral features of different conformers and the Ne-eq1 complex, insights into their behavior in various energy levels and conformations are revealed.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
Article
Biochemistry & Molecular Biology
Heng Zhang, Daniel S. Zhu, Jieqing Zhu
Summary: Recent advances in protein structure prediction using AlphaFold2 have allowed for comprehensive analysis of integrin structures, a family of cell surface receptors. By analyzing the single-chain and heterodimer structures of all 24 human integrins, this study provides high-resolution structure insights and a valuable structure database for further studies on integrin structure and function.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Chemistry, Physical
Junkai Chong, Xiang Cheng, Longheng Xiao, Min Guo, Jianming Gao, Fangqin Cheng, Mei Zhang, Xiangtao Huo
Summary: The macromolecular structure of Shanxi low-rank coal is characterized by the special paleogeological structure of Shanxi. Qualitative and quantitative methods revealed that the coal consists of amorphous carbon and ordered aromatic clusters, forming an intermediate turbostratic structure. The molecular and carbon skeleton structure models were established, showing aromatic and aliphatic structures dominated the coal composition. The aromatic carbon content was 75.31%, mainly composed of 1 to 2 benzene rings, while the aliphatic structure consisted of cycloalkyl and alkyl side chains. The carbon skeleton structure analysis provided information on the coal's diameter, interlayer spacing, average flakes per stack, and stacking height, along with other parameters for a comprehensive understanding of the coal structure.
JOURNAL OF MOLECULAR STRUCTURE
(2023)
Article
Biochemistry & Molecular Biology
Shuxia Peng, Robert L. Matts, Junpeng Deng
Summary: The 90-kDa heat shock protein (Hsp90) plays a vital role in cancer, neurodegenerative and infectious diseases. The equilibrium between Hsp90 dimers and oligomers is crucial for its function. In the presence of ATP, Hsp90 dimers act as foldases for client folding. W320 serves as a key switch for regulating Hsp90 self-oligomerization and client protein binding.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Chemistry, Physical
Ida Moszczynska, Andrzej Katrusiak
Summary: High pressure promotes the formation of anagostic bonds CH center dot center dot center dot Ru in the polymorphs of ruthenocene RuCp2. The transition between different phases of ruthenocene under pressure exhibits a wide hysteresis and is accompanied by twinning-like oriented growth of crystals.
JOURNAL OF PHYSICAL CHEMISTRY C
(2022)
Article
Meteorology & Atmospheric Sciences
S. Vishnu, William R. Boos, William D. Collins
Summary: Through simulating an ensemble of global models, we found that the intensity of South Asian monsoon LPS has decreased, while weaker LPS showed no significant trend. In the future, LPS will shift from ocean to land, and precipitation will increase, leading to an increase in seasonal mean and extreme precipitation over central India.
NPJ CLIMATE AND ATMOSPHERIC SCIENCE
(2023)
Article
Geography, Physical
Zhuohong Li, Hongyan Zhang, Fangxiao Lu, Ruoyao Xue, Guangyi Yang, Liangpei Zhang
Summary: Large-scale high-resolution land-cover mapping is crucial for understanding the Earth's surface and addressing ecological and resource challenges. This study proposes a low-to-high network (L2HNet) that can automatically generate high-resolution land-cover maps by using low-resolution land-cover products as training labels. The L2HNet outperforms other methods in creating accurate land-cover maps, making it a valuable tool for large-scale map updating and classification tasks.
ISPRS JOURNAL OF PHOTOGRAMMETRY AND REMOTE SENSING
(2022)
Article
Chemistry, Medicinal
Samuel Cajahuaringa, Daniel L. Z. Caetano, Leandro N. N. Zanotto, Guido Araujo, Munir S. S. Skaf
Summary: Ion mobility mass spectrometry (IM-MS) techniques are valuable for structural characterization of biomolecular systems. However, interpreting IM-MS data is often challenging due to conformational isomerism. To address this, we developed MassCCS, an open-source code that computes the collision cross-section (CCS) of molecules using atomic and molecular buffer gas particles. MassCCS is highly accurate and efficient, especially for large macromolecular assemblies. Extensive tests showed its reliability, scalability, and performance. The code is freely available at https://github.com/cces-cepid/massccs.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Review
Crystallography
Katarzyna Kurpiewska, Joanna Slawek, Agnieszka Klonecka, Maciej Kozak
Summary: Since its introduction in the early 1970s, high pressure crystallography (HPX) has shown great potential for the investigation of different types of matter. This emerging technique has been rapidly implemented, making it available to biologists, and there is immense potential for utilizing this technique in biological systems in the future. The increase in the number of crystal structures of different macromolecules determined under high pressure over the last five decades can be ascribed mainly to the emergence of high-pressure cells with very large, open angles, and the advent of third generation synchrotron sources.
Article
Biochemistry & Molecular Biology
Adam J. Quek, Nathan P. Cowieson, Tom T. Caradoc-Davies, Paul J. Conroy, James C. Whisstock, Ruby H. P. Law
Summary: This study successfully determined the response of Plasminogen (Plg) to various ligand/receptor peptides by measuring the kinetics of its conformational changes. The results showed that the Kopen of & epsilon;-aminocaproic acid (EACA) is approximately three times greater than that of tranexamic acid (TXA), and internal lysine(s) are necessary for the formation of open Plg. Additionally, the closed form of GI, which has an N-linked glycosylation, is less stable.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Kunio Nakata, Naoyuki Miyazaki, Hiroki Yamaguchi, Mika Hirose, Tatsuki Kashiwagi, Nidamarthi H. Kutumbarao, Osamu Miyashita, Florence Tama, Hiroshi Miyano, Toshimi Mizukoshi, Kenji Iwasaki
Summary: The three-dimensional structure of phosphoketolase (PKT) from Bifidobacterium longum was determined using cryo-EM single-particle analysis. The study observed interesting structural features and multiple conformations of amino acid residues, as well as the presence of water molecules. The conformational changes of the QN-loop were found to be related to the enzymatic function of PKT.
JOURNAL OF STRUCTURAL BIOLOGY
(2022)
Article
Biochemical Research Methods
David C. Wych, Phillip C. Aoto, Lily Vu, Alexander M. Wolff, David L. Mobley, James S. Fraser, Susan S. Taylor, Michael E. Wall
Summary: This article investigates the use of molecular-dynamics (MD) simulations to improve macromolecular crystallography (MX) studies. By combining MD simulations with conventional modeling and refinement tools, the authors were able to improve the interpretation of ambiguous density in protein crystals, leading to more accurate protein models and mechanistic insights into enzyme interactions.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2023)
Article
Chemistry, Medicinal
Qiaojing Huang, Luhua Lai, Zhirong Liu
Summary: Dynamic allosteric regulation refers to a type of regulation that does not involve noticeable conformational changes. By developing a unified anisotropic elastic network model, the contribution of pure dynamic allosteric regulation was quantitatively estimated. The study found that pure dynamic allosteric regulation has a generally small contribution, which decays exponentially with the distance between the substrate and the allosteric ligand. Toy models were also used to analyze the factors determining dynamic allosteric regulation in proteins.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Biochemical Research Methods
Tobias Gerling, Neus Godino, Felix Pfisterer, Nina Hupf, Michael Kirschbaum
Summary: Continuous flow cell sorting based on image analysis is a powerful concept that isolates specialized cell types through spatially-resolved features in cells. A new low-complexity microfluidic approach is presented, which provides high-resolution images and allows thorough image analysis. Live T cells were successfully sorted based on subcellular localization of fluorescence signals with high purities and recovery rates.
Article
Chemistry, Multidisciplinary
Thomas R. Berki, Jonathan Martinelli, Lorenzo Tei, Helen Willcock, Stephen J. Butler
Summary: A new synthetic strategy for macromolecular MRI contrast agents was reported, using RAFT polymerization to prepare water-soluble polymeric CAs with enhanced relaxivities compared to clinically used CAs. The study demonstrated significant increases in relaxivities for linear polymers and hyperbranched polymers, showing the potential for more advanced polymeric CAs with multimodal, bioresponsive, or targeting properties.
Article
Multidisciplinary Sciences
Simon Miller, Ashutosh Srivastava, Yoshiko Nagai, Yoshiki Aikawa, Florence Tama, Tsuyoshi Hirota
Summary: Intrinsic structural differences between CRY1 and CRY2, particularly in the FAD pocket and lid loop, can be targeted for isoform-selective regulation using compounds like KL101 and TH301.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Dusan Kolarski, Carla Miro-Vinyals, Akiko Sugiyama, Ashutosh Srivastava, Daisuke Ono, Yoshiko Nagai, Mui Iida, Kenichiro Itami, Florence Tama, Wiktor Szymanski, Tsuyoshi Hirota, Ben L. Feringa
Summary: This study presents the development of a visible light-responsive inhibitor of casein kinase I, enabling precise and reversible control of cellular and tissue circadian rhythms. The inhibitor can switch between CKI isoforms and reveal the importance of CKI delta in period regulation, allowing for long-term regulation of CKI activity and reversible modulation of circadian rhythms through chronophotopharmacology.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Kunio Nakata, Naoyuki Miyazaki, Hiroki Yamaguchi, Mika Hirose, Tatsuki Kashiwagi, Nidamarthi H. Kutumbarao, Osamu Miyashita, Florence Tama, Hiroshi Miyano, Toshimi Mizukoshi, Kenji Iwasaki
Summary: The three-dimensional structure of phosphoketolase (PKT) from Bifidobacterium longum was determined using cryo-EM single-particle analysis. The study observed interesting structural features and multiple conformations of amino acid residues, as well as the presence of water molecules. The conformational changes of the QN-loop were found to be related to the enzymatic function of PKT.
JOURNAL OF STRUCTURAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Maki Kuzuya, Hidemi Hirano, Kenichi Hayashida, Masakatsu Watanabe, Kazumi Kobayashi, Tohru Terada, Md Iqbal Mahmood, Florence Tama, Kazutoshi Tani, Yoshinori Fujiyoshi, Atsunori Oshima
Summary: In this study, the cryo-EM structures of human PANX1 in lipid nanodiscs were analyzed to elucidate the gating mechanism and its regulation by the amino terminus in phospholipids. The results showed that the amino-terminal domain plays an essential role in channel opening and is associated with lipid movement.
Article
Biochemistry & Molecular Biology
Albert M. Schulte, Dusan Kolarski, Vidya Sundaram, Ashutosh Srivastava, Florence Tama, Ben L. Feringa, Wiktor Szymanski
Summary: Protein kinases play a crucial role in cellular processes and signaling pathways, and their dysfunction is associated with various diseases. Photopharmacology, as an unconventional approach, uses light-controlled bioactive molecules to selectively activate drugs for kinase inhibition. This study presents the discovery and optimization of a photoswitchable inhibitor targeting casein kinase 1 delta (CK1 delta), which is involved in important signaling processes such as cell differentiation, circadian rhythm, DNA repair, and apoptosis. The optimized photoswitchable inhibitor showed improved properties, including high photostationary state distributions and solubility, as well as a 10-fold difference in activity between irradiated and thermally adapted samples.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Remi Vuillemot, Osamu Miyashita, Florence Tama, Isabelle Rouiller, Slavica Jonic
Summary: This article presents a new flexible fitting method, NMMD, which combines normal mode analysis (NMA) and molecular dynamics simulation (MD), to obtain atomic models of cryo-EM maps more efficiently and accurately.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Optics
Miki Nakano, Osamu Miyashita, Yasumasa Joti, Akihiro Suzuki, Hideyuki Mitomo, Yoshiya Niida, Ying Yang, Hirokatsu Yumoto, Takahisa Koyama, Kensuke Tono, Haruhiko Ohashi, Makina Yabashi, Tetsuya Ishikawa, Yoshitaka Bessho, Kuniharu Ijiro, Yoshinori Nishino, Florence Tama
Summary: The study demonstrates the reconstruction of the three-dimensional structure of a gold nanoparticle from XFEL diffraction data using microliquid enclosure arrays (MLEAs) sample holders. The quality of the restored structure was significantly improved by background subtraction, achieving a resolution of 5 nm.
Article
Multidisciplinary Sciences
Reika Isoda, Zoltan Palmai, Akira Yoshinari, Li-Qing Chen, Florence Tama, Wolf B. Frommer, Masayoshi Nakamura
Summary: SWEET sucrose transporters play important roles in the allocation of sucrose in plants and have been shown to mediate transport of the plant growth regulator gibberellin (GA). The study reveals a functional connection between sucrose and GA and demonstrates that sucrose is the physiologically relevant substrate. These findings are important for understanding the role of SWEETs in pathogen susceptibility and male fertility.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Simon Miller, Manish Kesherwani, Priscilla Chan, Yoshiko Nagai, Moeri Yagi, Jamie Cope, Florence Tama, Steve A. Kay, Tsuyoshi Hirota
Summary: This study elucidated the selectivity of SHP656 for CRY2 and identified the R form of SHP656 as the active isomer. The findings suggest a direct role of CRY2 in glioblastoma antitumorigenesis and provide a rationale for the selective modulation of CRY isoforms in the therapeutic treatment of glioblastoma and other circadian clock-related diseases.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Remi Vuillemot, Alex Mirzaei, Mohamad Harastani, Ilyes Hamitouche, Leo Frechin, Bruno P. Klaholz, Osamu Miyashita, Florence Tama, Isabelle Rouiller, Slavica Jonic
Summary: This article presents a new method for extracting atomic-resolution landscapes of continuous conformational variability of biomolecular complexes from cryo-EM single particle images. The method, called MDSPACE, uses a 3D-to-2D flexible fitting method based on molecular dynamics simulation and is embedded in an iterative conformational-landscape refinement scheme. The article describes the MDSPACE approach and demonstrates its performance using synthetic and experimental datasets.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Chemistry, Physical
Miki Nakano, Osamu Miyashita, Florence Tama
Summary: Single-particle analysis using x-ray free-electron lasers is a novel method for obtaining structural information of samples. This study evaluates the resolution of three-dimensional structures obtained from XFEL single-particle reconstruction using synthetic data. It is found that larger molecules can be restored with higher detail relative to their size, but achieving high absolute resolution is challenging.
STRUCTURAL DYNAMICS-US
(2023)
Article
Biochemistry & Molecular Biology
Osamu Miyashita, Florence Tama
Summary: Flexible fitting based on molecular dynamics simulation is a technique for structure modeling from cryo-EM data that has been used for nearly two decades. It provides a way to extract atomistic details of conformational changes encoded in cryo-EM data and improve the quality of structural models. Additionally, it enables the characterization of conformational heterogeneity in cryo-EM data. We will summarize the advancements made in these techniques and highlight recent developments in this field.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2023)
Proceedings Paper
Computer Science, Interdisciplinary Applications
Paula Olaya, Silvina Caino-Lores, Vanessa Lama, Ria Patel, Ariel Keller Rorabaugh, Osamu Miyashita, Florence Tama, Michela Taufer
Summary: Capturing the structural information of biological molecules is crucial for understanding their function and mechanism. This research presents a framework, XPSI, which utilizes X-ray Free Electron Lasers to accurately predict the orientation, conformation, and protein type of molecules from their diffraction patterns. Compared to other machine learning methods, XPSI shows low computational cost and high prediction accuracy.
2022 IEEE 18TH INTERNATIONAL CONFERENCE ON E-SCIENCE (ESCIENCE 2022)
(2022)
Proceedings Paper
Computer Science, Interdisciplinary Applications
Ria Patel, Ariel Keller Rorabaugh, Paula Olaya, Silvina Caino-Lores, Georgia Channing, Catherine Schuman, Osamu Miyashita, Florence Tama, Michela Taufer
Summary: Neural networks are crucial for successful management of high-throughput scientific workflows. This study utilizes a multi-objective neural architecture search approach to generate accurate neural networks while optimizing for computational efficiency. By selecting and refining a subset of networks, efficient networks suitable for data analysis are obtained.
2022 IEEE 18TH INTERNATIONAL CONFERENCE ON E-SCIENCE (ESCIENCE 2022)
(2022)
Article
Biochemistry & Molecular Biology
Han Asi, Bhaskar Dasgupta, Tetsuro Nagai, Osamu Miyashita, Florence Tama
Summary: XFEL has huge potential in structural biology, but experimental difficulties and complex data analysis make it challenging to reconstruct 3D structures of biological molecules. In this study, we propose a hybrid approach that combines low-resolution XFEL diffraction pattern with a known conformation to characterize biomolecular conformational transitions. Our algorithm successfully describes the transitions and demonstrates the effect of incident beam orientation on the accuracy of 3D structure modeling.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)