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Biochemistry & Molecular Biology
Qiuyan Chen, Ya Zhuo, Pankaj Sharma, Ivette Perez, Derek J. Francis, Srinivas Chakravarthy, Sergey A. Vishnivetskiy, Sandra Berndt, Susan M. Hanson, Xuanzhi Zhan, Evan K. Brooks, Christian Altenbach, Wayne L. Hubbell, Candice S. Klug, T. M. Iverson, Vsevolod V. Gurevich
Summary: Research indicates that non-visual arrestin-2 and arrestin-3 exhibit distinct patterns of oligomerization and conformational changes in response to IP6, likely due to differences in conserved regions between the two isoforms. This suggests potential physiological consequences for arrestin-2/3 trafficking and JNK3 activation, highlighting the importance of understanding the functional differences between these two proteins.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Uttpal Anand, Anna Shteinfer-Kuzmine, Gal Sela, Manikandan Santhanam, Benjamin Gottschalk, Rajaa Boujemaa-Paterski, Ohad Medalia, Wolfgang F. Graier, Varda Shoshan-Barmatz
Summary: The mitochondrial protein VDAC1 plays a crucial role in regulating various cellular processes, including metabolism, apoptosis, and cell signaling. In this study, a short peptide derived from the N-terminal region of VDAC1 was designed to improve cellular stability and activity. The peptide exhibited multiple effects on cancer cells, such as apoptosis induction, autophagy, senescence, and cell adhesion. Furthermore, the peptide altered the expression of proteins associated with cell metabolism and signaling. These findings highlight the importance of VDAC1 in controlling diverse cellular functions through its interaction with other proteins.
Article
Biochemistry & Molecular Biology
Jianfeng Sun, Dmitrij Frishman
Summary: The study introduces a novel deep-learning approach for predicting interaction sites in transmembrane proteins, which outperforms existing methods. Results also show that approximately 10-25% of amino acid sites are predicted to be involved in interactions in the main functional families of human transmembrane proteins.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Linda M. D. Markus, Itai Sharon, Kim Munro, Marcel Grogg, Donald Hilvert, Mike Strauss, T. Martin Schmeing
Summary: Cyanophycin is a natural polymer made up of a poly-aspartate backbone with arginine attached to each of the aspartate side chains. It is produced by various bacteria and has potential industrial applications, mainly as a source of fixed nitrogen.
Review
Cell Biology
Saeko Aoyama-Ishiwatari, Yusuke Hirabayashi
Summary: Recent studies have shown that organelles do not exist in isolation, but form complex cooperative networks. Mitochondria-endoplasmic reticulum contact sites play crucial roles in regulating various biochemical and signaling functions within cells.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Hao Ye, Jiayang Gao, Zizhen Liang, Youshun Lin, Qianyi Yu, Shuxian Huang, Liwen Jiang
Summary: This study identifies and demonstrates the role of Arabidopsis oxysterol-binding protein-related protein 2A (ORP2A) in mediating ER-autophagosomal membrane contacts and autophagosome biogenesis. ORP2A interacts with VAMP-associated protein 27-1 and ATG8e to form membrane contact sites between the ER and autophagosomes. Knockdown of ORP2A leads to impaired autophagy levels and inhibited plant growth. Additionally, ORP2A binds multiple phospholipids and colocalizes with phosphatidylinositol 3-phosphate (PI3P).
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Biochemistry & Molecular Biology
Subash C. Pakhrin, Bikash Shrestha, Badri Adhikari, Dukka B. KC
Summary: The article explores the significant progress in the field of protein structure prediction due to Deep Learning (DL)-based methods, including advancements in protein contact map prediction, protein distogram prediction, protein real-valued distance prediction, and Quality Assessment/refinement steps. It also mentions recent DL-based developments in protein structure determination using Cryo-Electron (Cryo-EM) microscopy, and provides an outlook on possible future research directions for DL-based approaches in the protein structure prediction arena.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Taeyong Park, Hyeonuk Woo, Jinsol Yang, Sohee Kwon, Jonghun Won, Chaok Seok
Summary: Proteins interact with other biomolecules to perform functions, often forming homo- or hetero-oligomers. Computational prediction of oligomer structures is useful when experimentally resolved structures are lacking. The study presented methods for predicting oligomer structures and discussed the challenges in improving predictions using AlphaFold2 models.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2021)
Article
Biochemical Research Methods
Minghua Hou, Chunxiang Peng, Xiaogen Zhou, Biao Zhang, Guijun Zhang
Summary: In this work, a multi-contact-based folding method called MultiCFold is introduced. It utilizes the detailed information from different contact maps to guide protein structure folding, and incorporates non-contact information as a supplement. Experimental results show that MultiCFold performs well in protein structure prediction.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemical Research Methods
Renfei Ma, Shangfu Li, Luca Parisi, Wenshuo Li, Hsien-Da Huang, Tzong-Yi Lee
Summary: Phosphorylation is a crucial mechanism for regulating protein activities, but experimental determination of kinase-specific phosphorylation sites is time-consuming and expensive. This study aims to create predictive models for understudied kinases by leveraging relevant sources of similarities. Results demonstrate that 82 out of 116 understudied kinases were predicted with adequate performance, proving the reliability of web-like predictive networks in capturing patterns in such kinases.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biochemistry & Molecular Biology
Yizhou Yin, Matthew G. Romei, Kannan Sankar, Lipika R. Pal, Kam Hon Hoi, Yanli Yang, Brandon Leonard, Gladys De Leon Boenig, Nikit Kumar, Marissa Matsumoto, Jian Payandeh, Seth F. Harris, John Moult, Greg A. Lazar
Summary: This study analyzed and characterized the structural interactions of the antibody fragment antigen-binding (Fab) regions, leading to the discovery of previously unnoticed interfaces between antibodies. Experimental validation revealed the potential of these interfaces and provided new opportunities for their drug optimization.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Fisheries
Yunting Fan, Jing Xu, Xiaojun Lin, Jiang Zheng, Lixing Huang, Qingpi Yan, Jiangyuan Huang, Ying Tan
Summary: In this study, five aptamers with high affinities for temperature-sensitive Pseudomonas plecoglossicida were selected using SELEX. The binding proteins of these aptamers were identified as ribosomal proteins. The findings provide insights into the temperature-sensitive pathogenic mechanism of P. plecoglossicida in P. crocea.
AQUACULTURE REPORTS
(2023)
Article
Chemistry, Multidisciplinary
Tobias Muehlethaler, Dario Gioia, Andrea E. Prota, May E. Sharpe, Andrea Cavalli, Michel O. Steinmetz
Summary: Using a combined computational and crystallographic approach, researchers identified 27 distinct binding sites in tubulin, including 11 previously unknown sites. They also observed an intricate pocket communication network and identified 56 chemically diverse fragments that bound to 10 distinct tubulin sites. These results provide a structural basis for developing novel small molecules as tubulin modulators and lay down a framework that may aid in discovering new pockets in other pharmaceutically important targets.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Biochemical Research Methods
Bahareh Behkamal, Mahmoud Naghibzadeh, Andrea Pagnani, Mohammad Reza Saberi, Kamal Al Nasr
Summary: This article proposes a linear programming-based topology determination method to solve the secondary structure topology problem in three-dimensional geometrical space. It transforms the secondary structure matching problem into a complete weighted bipartite graph matching problem and uses linear programming algorithm to extract the true topology.
Review
Biochemistry & Molecular Biology
Marco Giampa, Maria J. Amundarain, Maria Georgina Herrera, Nicolo Tonali, Veronica I. Dodero
Summary: The aggregation of proteins into amyloid fibers is associated with various cellular and neurodegenerative diseases. Understanding the molecular mechanism of aggregation is crucial for finding new therapeutic targets. This review explores different approaches and theories for studying amyloid aggregation, with a focus on alpha-syn.
Article
Immunology
Roni Winkler, Ella Gillis, Lior Lasman, Modi Safra, Shay Geula, Clara Soyris, Aharon Nachshon, Julie Tai-Schmiedel, Nehemya Friedman, Vu Thuy Khanh Le-Trilling, Mirko Trilling, Michal Mandelboim, Jacob H. Hanna, Schraga Schwartz, Noam Stern-Ginossar
Article
Cell Biology
Heather Lee, Suying Bao, Yingzhi Qian, Shay Geula, Juliana Leslie, Chaolin Zhang, Jacob H. Hanna, Lei Ding
NATURE CELL BIOLOGY
(2019)
Review
Biochemistry & Molecular Biology
Varda Shoshan-Barmatz, Srinivas Pittala, Dario Mizrachi
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2019)
Article
Biotechnology & Applied Microbiology
Srinivas Pittala, Yakov Krelin, Yael Kuperman, Varda Shoshan-Barmatz
Article
Cell Biology
Tasleem Arif, Oriel Stern, Srinivas Pittala, Vered Chalifa-Caspi, Varda Shoshan-Barmatz
Article
Cell Biology
Srinivas Pittala, Idan Levy, Soumasree De, Swaroop Kumar Pandey, Nataly Melnikov, Tehila Hyman, Varda Shoshan-Barmatz
Article
Oncology
Zohar Amsalem, Tasleem Arif, Anna Shteinfer-Kuzmine, Vered Chalifa-Caspi, Varda Shoshan-Barmatz
Article
Oncology
Erez Zerbib, Tasleem Arif, Anna Shteinfer-Kuzmine, Vered Chalifa-Caspi, Varda Shoshan-Barmatz
Summary: Tumors consist of proliferating cancer cells and their microenvironment, including extracellular matrix, blood vessels, and tissue cells. Understanding molecular interactions between cancer cells and the microenvironment is crucial for developing therapeutic strategies. Depleting VDAC1 in cancer cells leads to metabolic reprogramming, inhibits tumor growth, and disrupts tumor-host interactions, making it a potential therapeutic target for inhibiting cancer progression.
Editorial Material
Oncology
Joao Pessoa, Marta Martins, Sandra Casimiro, Carlos Perez-Plasencia, Varda Shoshan-Barmatz
FRONTIERS IN ONCOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Swaroop Kumar Pandey, Renen Machlof-Cohen, Manikandan Santhanam, Anna Shteinfer-Kuzmine, Varda Shoshan-Barmatz
Summary: This study found that VDAC1 is overexpressed in patients with mesothelioma and its levels increase with disease stage, leading to low survival rates. Silencing VDAC1 expression can inhibit cell proliferation of mesothelioma cancer cells and cause metabolic reprogramming. VDAC1 silencing also has effects on modulating the tumor microenvironment and inflammation, eliminating cancer stem cells, and inducing cell differentiation.
Article
Biochemistry & Molecular Biology
Anna Shteinfer-Kuzmine, Shirel Argueti-Ostrovsky, Marcel F. Leyton-Jaimes, Uttpal Anand, Salah Abu-Hamad, Ran Zalk, Varda Shoshan-Barmatz, Adrian Israelson
Summary: This study suggests that the interaction between VDAC1 and SOD1 is involved in the pathogenesis of ALS. By inhibiting VDAC1 oligomerization, it is possible to reduce cell apoptosis and related processes caused by mutant SOD1, thus improving muscle function in ALS patients.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Uttpal Anand, Anna Shteinfer-Kuzmine, Gal Sela, Manikandan Santhanam, Benjamin Gottschalk, Rajaa Boujemaa-Paterski, Ohad Medalia, Wolfgang F. Graier, Varda Shoshan-Barmatz
Summary: The mitochondrial protein VDAC1 plays a crucial role in regulating various cellular processes, including metabolism, apoptosis, and cell signaling. In this study, a short peptide derived from the N-terminal region of VDAC1 was designed to improve cellular stability and activity. The peptide exhibited multiple effects on cancer cells, such as apoptosis induction, autophagy, senescence, and cell adhesion. Furthermore, the peptide altered the expression of proteins associated with cell metabolism and signaling. These findings highlight the importance of VDAC1 in controlling diverse cellular functions through its interaction with other proteins.
Article
Oncology
Almog Nadir, Anna Shteinfer-Kuzmine, Swaroop Kumar Pandey, Juan Ortas, Daniel Kerekes, Varda Shoshan-Barmatz
Summary: This study identified three different plant extracts that can effectively induce cell death and focused on the most potent extract. The extract kills tumor cells through multiple mechanisms, including impairing cell energy and metabolism, generating reactive oxygen species, increasing intracellular calcium levels, and inducing mitochondria-mediated apoptosis. In a mouse model of glioblastoma, the extract inhibits tumor growth and induces massive tumor cell death, including cancer stem cells, by inhibiting blood supply and modulating the tumor microenvironment. These findings suggest that the plant extract has potential as a cancer therapeutic.
Review
Biochemistry & Molecular Biology
Varda Shoshan-Barmatz, Anna Shteinfer-Kuzmine, Ankit Verma
Article
Cell Biology
Lior Lasman, Vladislav Krupalnik, Sergey Viukov, Nofar Mor, Alejandro Aguilera-Castrejon, Dan Schneir, Jonathan Bayerl, Orel Mizrahi, Shani Peles, Shadi Tawil, Shashank Sathe, Aharon Nachshon, Tom Shani, Mirk Zerbib, Itay Kilimnik, Stefan Aigner, Archana Shankar, Jasmine R. Mueller, Schraga Schwartz, Noam Stern-Ginossar, Gene W. Yeo, Shay Genla, Noa Novershtern, Jacob H. Hanna
GENES & DEVELOPMENT
(2020)