Article
Biochemical Research Methods
Ahmed Bin Zaman, Toki Tahmid Inan, Kenneth De Jong, Amarda Shehu
Summary: Researchers have demonstrated a method using AlphaFold2 that can reveal multiple native structures of proteins, and have provided a benchmark dataset for further research on this problem.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2023)
Article
Multidisciplinary Sciences
Han Ba Bui, Satoshi Watanabe, Norimichi Nomura, Kehong Liu, Tomoko Uemura, Michio Inoue, Akihisa Tsutsumi, Hiroyuki Fujita, Kengo Kinoshita, Yukinari Kato, So Iwata, Masahide Kikkawa, Kenji Inaba
Summary: In this study, the cryo-EM structures of human ZnT7 in Zn2+-bound and unbound forms were presented, providing insights into its mechanism of Zn2+ transport.
NATURE COMMUNICATIONS
(2023)
Article
Food Science & Technology
Haritha Duppeti, Sachindra Nakkarike Manjabhatta, Bettadaiah Bheemanakere Kempaiah
Summary: Processing methods such as microwave drying and boiling have the greatest impact on the structural and functional properties of white shrimp proteins (WSP), affecting their water solubility, emulsifying properties, and foaming properties. Boiling has the highest flavor adsorption potential among all the processing methods, followed by microwave drying.
FOOD RESEARCH INTERNATIONAL
(2023)
Article
Biochemistry & Molecular Biology
Alisa A. Vologzhannikova, Marina P. Shevelyova, Alexey S. Kazakov, Andrey S. Sokolov, Nadezhda Borisova, Eugene A. Permyakov, Nikoleta Kircheva, Valya Nikolova, Todor Dudev, Sergei E. Permyakov
Summary: The study investigated the interaction of Sr2+ with Ca2+ binding sites of a canonical EF-hand protein, alpha-parvalbumin, suggesting that Sr2+ and Ca2+ bind to CD/EF sites of alpha-PA with sequential binding processes. Despite lower affinity to Sr2+, alpha-PA competes with Ca2+ for the same EF-hands, inducing similar structural rearrangements. The presence of a secondary Sr2+ binding site(s) may contribute to Sr2+ impact on the functional activity of proteins.
Article
Multidisciplinary Sciences
Ting-Ting Chu, Xintao Tu, Kun Yang, Jianjun Wu, Joyce J. Repa, Nan Yan
Summary: This study identifies a cGAS- and cGAMP-independent mode of STING activation that affects neuropathology and provides a therapeutic target for the treatment of Niemann-Pick disease type C.
Article
Biochemistry & Molecular Biology
Xuejun Bei, Shaohua Wang, Xia Huang, Xiuli Zhang, Jiayi Zhou, Huiting Zhang, Guoguo Li, Chunzhen Cheng
Summary: This study cloned three duplicated CaBPs from Citrus sinensis and investigated their sequence characteristics, gene expression patterns and promoter activities under calcium, phytohormone and wounding treatments. The results showed that these three genes had high sequence similarity and their expression was induced by calcium, phytohormones and wounding. The study suggested that these three genes were functionally redundant in the phytohormone and wounding responses of C. sinensis.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Biochemistry & Molecular Biology
Honami Osuda, Yui Sunano, Masakazu Hara
Summary: A cryoprotective protein was isolated from a soluble protein fraction in radish taproot, which showed inhibitory effects on LDH cryoinactivation, cryodenaturation, and cryoaggregation. The protein, identified as a radish vacuolar calcium-binding protein, exhibited greater cryoprotective activity than general cryoprotectants. A specific hydrophobic region within the protein, specifically Seg03, was found to be responsible for protecting LDH from freeze-thaw damage.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Materials Science, Multidisciplinary
Lucrecia Iruzubieta-Villagra, Ines Ramos, Susana Cisint, Claudia A. Crespo, Silvia Fernandez
Summary: The intracellular localization of Ca2+, Ca2+-ATPase, Calmodulin, and Calbindin D-28KD in the testes of Leptodactylus chaquensis were studied. Results showed the presence of Ca2+ in the nucleus and mitochondria of germ cells, as well as the activity of Ca2+-ATPase in the nuclear envelope and mitochondrial crests, suggesting the involvement of this transporter in Ca2+ storage. Ca2+ deposits were also found in Sertoli cells and at the subacrosomal space and acrosomal vesicle in spermatozoa. The activity of Ca2+-ATPase in the acrosomal and plasma membranes of sperm suggested the existence of a transport system for maintaining low cytoplasmic Ca2+ levels.
MICROSCOPY AND MICROANALYSIS
(2022)
Article
Biochemistry & Molecular Biology
Steve Zaharias, Talia Fargason, Rory Greer, Yuhua Song, Jun Zhang
Summary: Electronegative clusters (ENCs) composed of acidic residues and/or phosphorylation sites are common in RNA-binding proteins. ENC phosphorylation can increase the RNA-binding affinity of unstructured RNA-binding domains by stabilizing the complex. The allosteric interaction between the phosphorylated ENC and the RNA-binding domain enhances RNA binding.
Article
Chemistry, Multidisciplinary
Daniele Ubbiali, Marta Fratini, Lolita Piersimoni, Christian H. Ihling, Marc Kipping, Ingo Heilmann, Claudio Iacobucci, Andrea Sinz
Summary: The conformational ensemble of alpha-synuclein shifts during liquid-liquid phase separation, and a novel mass spectrometry-based approach is established to solve open questions in LLPS structural biology.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Review
Biochemistry & Molecular Biology
Marco Pedretti, Luca Bombardi, Carolina Conter, Filippo Favretto, Paola Dominici, Alessandra Astegno
Summary: Centrins are a family of small proteins containing EF hands found in all eukaryotes and often complexed with centrosome-related structures, displaying diverse cellular functions and large variance in Ca2+ sensing abilities compared to calmodulin (CaM). Current knowledge on centrins from biophysical and structural perspectives emphasizes centrin-target interactions, providing insight into their different functions and contribution to the complexity of Ca2+ signaling cascade. This understanding can help clarify the functional redundancy of centrins and centrin-binding proteins.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Vinnarasi Saravanan, Ijas Ahammed, Akash Bhattacharya, Swati Bhattacharya
Summary: This study explores the dynamics and allosteric behavior of Sorcin in the context of Ca2+ uptake and Doxorubicin binding using in-silico molecular dynamics simulations. The results show that Ca2+ binding induces reversible conformational changes in Sorcin structure, while Doxorubicin binding disrupts long-range allosteric information transfer. However, the binding does not destabilize the secondary structure.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Chemistry, Multidisciplinary
Sandra Rocha, Ranjeet Kumar, Bengt Norden, Pernilla Wittung-Stafshede
Summary: The study reveals that alpha-synuclein binds to negatively charged vesicles and reorients its helix structure under shear flow, tilting into the vesicle membrane. The presence of flow accelerates the reorientation dynamics of the protein, suggesting a potential flow catalysis mechanism to overcome steric barriers.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Agriculture, Multidisciplinary
Yiyu Chen, Tengchuan Jin, Mengsi Li, Xiao Yun, Fei Huan, Qingmei Liu, Mengjun Hu, Xiaofeng Wei, Peiyi Zheng, Guangming Liu
Summary: The crystal structure of Scy p 4 was obtained with a resolution of 1.60 angstrom by X-ray diffraction, and it revealed the presence of linear and conformational epitopes. Mutation of Asp70 and Asp18/20/70 resulted in loss of calcium-binding capacity and allergenicity. Comparative analysis showed high structural similarity of sarcoplasmic-calcium-binding protein (SCP) in crustaceans, which may contribute to cross-reactivity. The structure of Scy p 4 provides a template for epitope evaluation and localization of SCPs, aiding in the understanding of cross-reactivity among species.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Article
Cardiac & Cardiovascular Systems
Hideaki Inazumi, Koichiro Kuwahara, Yasuaki Nakagawa, Yoshihiro Kuwabara, Takuro Numaga-Tomita, Toshihide Kashihara, Tsutomu Nakada, Nagomi Kurebayashi, Miku Oya, Miki Nonaka, Masami Sugihara, Hideyuki Kinoshita, Kenji Moriuchi, Hiromu Yanagisawa, Toshio Nishikimi, Hirohiko Motoki, Mitsuhiko Yamada, Sachio Morimoto, Kinya Otsu, Richard M. Mortensen, Kazuwa Nakao, Takeshi Kimura
Summary: NRSF is a transcriptional repressor that suppresses the reactivation of fetal cardiac gene program and maintains cardiac integrity. This study reveals that NRSF regulates ventricular function by controlling the expression of G alpha(o) gene, and excessive expression of G alpha(o) leads to cardiac dysfunction. Additionally, G alpha(o) plays a critical role in cardiac Ca2+ homeostasis and systolic function.
CIRCULATION RESEARCH
(2022)
Article
Chemistry, Medicinal
Dominik Budday, Sigrid Leyendecker, Henry van den Bedem
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2018)
Letter
Biochemistry & Molecular Biology
Scott Horowitz, Loic Salmon, Philipp Koldewey, Logan S. Ahlstrom, Raoul Martin, Shu Quan, Pavel V. Afonine, Henry van den Bedem, Lili Wang, Qingping Xu, Raymond C. Trievel, Charles L. Brooks, James C. A. Bardwell
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2018)
Article
Multidisciplinary Sciences
Kaiming Zhang, Huawei Zhang, Shanshan Li, Grigore D. Pintilie, Tung-Chung Mou, Yuanzhu Gao, Qinfen Zhang, Henry van den Bedeme, Michael F. Schmid, Shannon Wing Ngor Au, Wah Chiu
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2019)
Article
Biochemistry & Molecular Biology
Lina Herhaus, Henry van den Bedem, Sean Tang, Innokentiy Maslennikov, Soichi Wakatsuki, Ivan Dikic, Simin Rahighi
JOURNAL OF MOLECULAR BIOLOGY
(2019)
Article
Instruments & Instrumentation
Henry van den Bedem, Mark A. Wilson
JOURNAL OF SYNCHROTRON RADIATION
(2019)
Article
Chemistry, Physical
Po-Nan Li, Jonathan Herrmann, Soichi Wakatsuki, Henry van den Bedem
JOURNAL OF PHYSICAL CHEMISTRY B
(2019)
Article
Multidisciplinary Sciences
Medhanjali Dasgupta, Dominik Budday, Saulo H. P. de Oliveira, Peter Madzelan, Darya Marchany-Rivera, Javier Seravalli, Brandon Hayes, Raymond G. Sierra, Sebastien Boutet, Mark S. Hunter, Roberto Alonso-Mori, Alexander Batyuk, Jennifer Wierman, Artem Lyubimov, Aaron S. Brewster, Nicholas K. Sauter, Gregory A. Applegate, Virendra K. Tiwari, David B. Berkowitz, Michael C. Thompson, Aina E. Cohen, James S. Fraser, Michael E. Wall, Henry van den Bedem, Mark A. Wilson
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2019)
Article
Chemistry, Multidisciplinary
Alexander M. Wolff, Iris D. Young, Raymond G. Sierra, Aaron S. Brewster, Michael W. Martynowycz, Eriko Nango, Michihiro Sugahara, Takanori Nakane, Kazutaka Ito, Andrew Aquila, Asmit Bhowmick, Justin T. Biel, Sergio Carbajo, Aina E. Cohen, Saul Cortez, Ana Gonzalez, Tomoya Hino, Dohyun Im, Jake D. Koralek, Minoru Kubo, Tomas S. Lazarou, Takashi Nomura, Shigeki Owada, Avi J. Samelson, Tomoyuki Tanaka, Rie Tanaka, Erin M. Thompson, Henry van den Bedem, Rahel A. Woldeyes, Fumiaki Yumoto, Wei Zhao, Kensuke Tono, Sebastien Boutet, So Iwata, Tamir Gonen, Nicholas K. Sauter, James S. Fraser, Michael C. Thompson
Article
Biophysics
R. Bryn Fenwick, David Oyen, Henry van den Bedem, H. Jane Dyson, Peter E. Wright
Summary: NMR relaxation dispersion measurements were used to study conformational changes in DHFR on the millisecond-microsecond timescale, generating structural models of alternative conformations using unsigned chemical shift changes. The combination of fragment modeling with sparse chemical shift data successfully characterized a minor conformational state of DHFR sampled on the microsecond-millisecond timescale, showing potential for in silico drug screening and contributing to understanding the role of minor states in biology and molecular evolution.
BIOPHYSICAL JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Blake T. Riley, Stephanie A. Wankowicz, Saulo H. P. de Oliveira, Gydo C. P. van Zundert, Daniel W. Hogan, James S. Fraser, Daniel A. Keedy, Henry van den Bedem
Summary: The new qFit 3 software automates the analysis of dynamic protein structure data by generating a multi-conformer model, providing important insights for biological research. The software has been improved to run efficiently on small servers, desktops, or laptops. qFit 3 is open-source and available at the specified URL.
Article
Chemistry, Physical
Zhen Su, Medhanjali Dasgupta, Frederic Poitevin, Irimpan I. Mathews, Henry van den Bedem, Michael E. Wall, Chun Hong Yoon, Mark A. Wilson
Summary: The reproducibility of diffuse scattering from different protein forms was high, indicating the potential for high-quality data. The liquid-like motions (LLM) model was effective in characterizing atomic mobility and distinguishing between alternative anisotropic atomic displacement parameter (ADP) models. Successful diffuse scattering experiments can benefit from understanding data reproducibility and utilizing LLM analysis.
STRUCTURAL DYNAMICS-US
(2021)
Article
Chemistry, Medicinal
Kate A. Stafford, Brandon M. Anderson, Jon Sorenson, Henry van den Bedem
Summary: This paper introduces a deep learning-based approach, AtomNet PoseRanker (ANPR), to improve the quality of docking poses in virtual high-throughput screening (vHTS). Unlike traditional methods, ANPR can handle the dynamic nature of proteins, thus improving the accuracy of docking results.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Chemistry, Medicinal
Xiyu Chen, Sigrid Leyendecker, Henry van den Bedem
Summary: The conformation of a protein affects its function and interaction with ligands, with entropy playing a crucial role. This study presents a method to estimate the vibrational entropy of proteins using kinematic flexibility analysis, providing insights into protein-ligand binding.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Biology
Stephanie A. Wankowicz, Saulo H. de Oliveira, Daniel W. Hogan, Henry van den Bedem, James S. Fraser
Summary: This study measured conformational heterogeneity in a large number of crystallographic datasets and found that binding site residues become more rigid upon ligand binding, while distant residues become more flexible, especially in non-solvent-exposed regions. Additionally, protein flexibility was observed to increase as the number of hydrogen bonds decreases and relative hydrophobicity increases.
Proceedings Paper
Engineering, Biomedical
Po-Nan Li, Saulo H. P. de Oliveira, Soichi Wakatsuki, Henry van den Bedem
2020 IEEE 20TH INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOENGINEERING (BIBE 2020)
(2020)