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
Biochemical Research Methods
Yuansong Zeng, Zhuoyi Wei, Qianmu Yuan, Sheng Chen, Weijiang Yu, Yutong Lu, Jianzhao Gao, Yuedong Yang
Summary: Drawing on the breakthrough of AlphaFold2 in protein structure prediction, we propose a novel graph-based model, GraphBepi, for accurate B-cell epitope prediction. By utilizing the predicted structure from AlphaFold2, GraphBepi constructs the protein graph and captures both sequence and spatial information through edge-enhanced deep graph neural networks (EGNN) and bidirectional long short-term memory neural networks (BiLSTM). The combined representations are input into a multilayer perceptron to predict B-cell epitopes. Comprehensive tests demonstrate that GraphBepi outperforms state-of-the-art methods in terms of AUC and AUPR.
Article
Biochemistry & Molecular Biology
Matthew Holcomb, Ya-Ting Chang, David S. Goodsell, Stefano Forli
Summary: AlphaFold2 is a promising tool for predicting protein structures, but its predicted structures may not be suitable for docking. Researchers redocked ligands against experimental and AlphaFold2 structures to evaluate docking performance. The quality measure provided during structure prediction is not a good predictor of docking performance, but removing low-confidence regions and making side chains flexible improves the outcomes. Despite high-quality backbone prediction, fine structural details limit the use of AlphaFold2 models as docking targets.
Review
Biochemistry & Molecular Biology
Patrick Willems, Jingjing Huang, Joris Messens, Frank Van Breusegem
Summary: Deep learning algorithms, such as AlphaFold2, accurately predict the three-dimensional structure of proteins, providing an unparalleled resource for annotating protein function. This study analyzed the function and evolution of cysteine residues in plants using AlphaFold2 predicted structures. The analysis identified metal ligands coordinated by cysteine residues and systematically analyzed cysteine disulfides. The results showed that most of the predicted disulfides were reliable, with high agreement with known protein structures and characteristic features.
FREE RADICAL BIOLOGY AND MEDICINE
(2023)
Article
Biochemistry & Molecular Biology
Gerard Duart, John Lamb, Juan Ortiz-Mateu, Arne Elofsson, Ismael Mingarro
Summary: Salt bridges play a crucial role in protein stabilization, especially in membrane proteins. The study found that potentially salt-bridge forming pairs are statistically over-represented in transmembrane helices. Experimental results showed that salt bridges contribute approximately 0.5 kcal/mol to the membrane insertion process during protein biogenesis.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Review
Chemistry, Multidisciplinary
Xin-heng He, Chong-zhao You, Hua-liang Jiang, Yi Jiang, H. Eric Xu, Xi Cheng
Summary: G protein-coupled receptors (GPCRs) are important drug targets that play crucial roles in various physiological processes. Although extensive efforts have been made in the field of structural biology, a significant number of GPCR structures remain unsolved due to their structural instability. Recently, AlphaFold2 has been developed as a tool to predict the structure models of GPCRs and other functionally important proteins. However, our evaluation reveals several differences between the predicted models and experimental structures, such as the assembly of domains, shape of ligand-binding pockets, and conformation of binding interfaces. These differences hinder the use of predicted structure models in functional studies and structure-based drug design, where reliable high-resolution structural information is required.
ACTA PHARMACOLOGICA SINICA
(2023)
Article
Biochemistry & Molecular Biology
Hedvig Tordai, Erzsebet Suhajda, Ian Sillitoe, Sreenath Nair, Mihaly Varadi, Tamas Hegedus
Summary: In recent years, the number of unique transmembrane protein structures has doubled, thanks to the advancement of cryo-electron microscopy and AlphaFold2. However, collecting structures for specific protein families remains challenging. This study demonstrates the applicability and usability of automatic collection and presentation of protein structures through the ABC protein superfamily.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Eva Smorodina, Igor Diankin, Fei Tao, Rui Qing, Steve Yang, Shuguang Zhang
Summary: Solute carrier transporters play vital roles in cellular nutrient transports and other biological activities. In this study, we used AlphaFold2 to predict the 3D structures of 13 human solute carrier transporters and discovered that hydrophobic amino acid substitutions can make these transporters water-soluble. Our findings have implications in the design of water-soluble transmembrane proteins.
SCIENTIFIC REPORTS
(2022)
Article
Multidisciplinary Sciences
Brian D. D. Adair, Jian-Ping Xiong, Mark Yeager, M. Amin Arnaout
Summary: This study determines the cryoEM structure of full-length platelet integrin αIIbβ3 in both its apo and eptifibatide-bound states, providing insights into its conformational changes in response to intracellular signals and drug binding, and suggesting potential adverse effects on platelet hemostasis.
NATURE COMMUNICATIONS
(2023)
Article
Materials Science, Multidisciplinary
Alena Vishina, Olle Eriksson, Heike C. Herper
Summary: With advancements in crystal structure prediction, databases of new materials are being developed. Through these databases, stable and metastable materials can be discovered and studied for their properties. Using a high-throughput and data-mining approach, four promising candidates for rare-earth-free permanent magnets have been found.
Article
Multidisciplinary Sciences
Daniel Montezano, Rebecca Bernstein, Matthew M. Copeland, Joanna S. G. Slusky
Summary: By utilizing coevolution data, we have created a large and high-quality database of transmembrane proteins. Our method, IsItABarrel, achieves a balanced accuracy of 95.88% in discriminating among protein classes. Compared to previous algorithms, IsItABarrel shows a high rate of false positives. The database contains a significantly larger number of bacterial TMBB proteins compared to previous sets, and we anticipate it will serve as a valuable resource for researchers.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemistry & Molecular Biology
Apolline Bruley, Tristan Bitard-Feildel, Isabelle Callebaut, Elodie Duprat
Summary: Order and disorder play important roles in protein functions, but the diversity of disorder makes it difficult to understand. Researchers developed an analytical tool called pyHCA, which estimates the foldability of a protein segment based on its amino acid sequence and the density of regular secondary structures associated with hydrophobic clusters. They applied pyHCA to protein sequences from various species and compared the results with AlphaFold2, providing guidance for mapping structural innovations at proteome and gene scales.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2023)
Article
Biochemical Research Methods
P. Ramakrishna Reddy, A. Kulandaisamy, M. Michael Gromiha
Summary: In this study, the relationship between sequence and structure-based parameters and the free energy transfer of α-helical membrane proteins (TMPs) was examined. The results showed that several factors such as hydrophobic peptide transfer, relative contact order, total interaction energy, hydrogen bond count, and lipid accessibility of transmembrane regions play important roles in TMPs stability. Additionally, multiple regression models were developed to predict the stability of α-helical membrane proteins, achieving a correlation of 0.89 and mean absolute error (MAE) of 1.21 kcal/mol on a jack-knife test. Furthermore, a webserver for stability prediction was created and can be accessed freely at (https://web.iitm.ac.in/bioinfo2/TMHS/).
Article
Plant Sciences
Qiong Wang, Yuying Li, Ken-ichi Kosami, Chaochao Liu, Jing Li, Dan Zhang, Daisuke Miki, Yoji Kawano
Summary: This study reveals the contribution of the CC domain of the rice NLR gene Pit to self-association and shows that its function differs from that of barley MLA10 and Arabidopsis RPM1.
PLANT CELL AND ENVIRONMENT
(2022)
Article
Acoustics
Fangjie Zhang, Jian Li, Weixin Meng, Xiaodong Li, Chengshi Zheng
Summary: This paper presents a new database for evaluating ASLT algorithms, which utilizes a planar array with 32 MEMS microphones to record a large number of vehicle whistles in outdoor environments. The paper also provides an example demonstrating the localization of the vehicle whistle database using a specific sound source localization method.
Article
Biochemistry & Molecular Biology
Andras Zeke, Laszlo Dobson, Levente Istvan Szekeres, Tamas Lango, Gabor E. Tusnady
Summary: The article introduces a comprehensive database containing experimentally verified mammalian proteins displaying polarized sorting or secretion, with a focus on epithelial cells. This database provides various information relevant to cell secretion and sorting, which can be valuable for researchers in conducting related studies or comparative analyses.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Gergely Rona, Andras Zeke, Bearach Miwatani-Minter, Maren de Vries, Ramanjit Kaur, Austin Schinlever, Sheena Faye Garcia, Hailey Goldberg, Hui Wang, Thomas R. Hinds, Fabrice Bailly, Ning Zheng, Philippe Cotelle, Didier Desmaele, Nathaniel R. Landau, Meike Dittmann, Michele Pagano
Summary: A novel NSP14-NSP10 inhibitor, sofalcone, was found to enhance the efficacy of remdesivir and exhibit inhibitory activity against various coronaviruses in vitro. This provides proof-of-concept for the NSP14 complex as a therapeutic target.
CELL DEATH AND DIFFERENTIATION
(2022)
Article
Biochemistry & Molecular Biology
Manjeet Kumar, Sushama Michael, Jesus Alvarado-Valverde, Balint Meszaros, Hugo Samano-Sanchez, Andras Zeke, Laszlo Dobson, Tamas Lazar, Mihkel Ord, Anurag Nagpal, Nazanin Farahi, Melanie Kaser, Ramya Kraleti, Norman E. Davey, Rita Pancsa, Lucia B. Chemes, Toby J. Gibson
Summary: The Eukaryotic Linear Motif (ELM) resource remains a crucial source of information for motif-mediated protein-protein interactions, with the current update adding new motif classes focused on various cellular processes. The resource continues to face challenges in keeping up-to-date due to the increasing number of SLiM-mediated interactions being discovered.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Federica Quaglia, Balint Meszaros, Edoardo Salladini, Andras Hatos, Rita Pancsa, Lucia B. Chemes, Matyas Pajkos, Tamas Lazar, Samuel Pena-Diaz, Jaime Santos, Veronika Acs, Nazanin Farahi, Erzsebet Ficho, Maria Cristina Aspromonte, Claudio Bassot, Anastasia Chasapi, Norman E. Davey, Radoslav Davidovic, Laszlo Dobson, Arne Elofsson, Gabor Erdos, Pascale Gaudet, Michelle Giglio, Juliana Glavina, Javier Iserte, Valentin Iglesias, Zsofia Kalman, Matteo Lambrughi, Emanuela Leonardi, Sonia Longhi, Sandra Macedo-Ribeiro, Emiliano Maiani, Julia Marchetti, Cristina Marino-Buslje, Attila Meszaros, Alexander Miguel Monzon, Giovanni Minervini, Suvarna Nadendla, Juliet F. Nilsson, Marian Novotny, Christos A. Ouzounis, Nicolas Palopoli, Elena Papaleo, Pedro Jose Barbosa Pereira, Gabriele Pozzati, Vasilis J. Promponas, Jordi Pujols, Alma Carolina Sanchez Rocha, Martin Salas, Luciana Rodriguez Sawicki, Eva Schad, Aditi Shenoy, Tamas Szaniszlo, Konstantinos D. Tsirigos, Nevena Veljkovic, Gustavo Parisi, Salvador Ventura, Zsuzsanna Dosztanyi, Peter Tompa, Silvio C. E. Tosatto, Damiano Piovesan
Summary: The latest update of DisProt version 9 includes a restyled web interface, refactored IDPO, improvements in curation process, and around 30% content growth. The newly implemented reviewing process and curator training aim to provide higher quality and more consistent annotations. Integration with APICURON and adoption of MIADE standard, along with collaborations with GO and ECO consortia and support from ELIXIR infrastructure, enhance interoperability.
NUCLEIC ACIDS RESEARCH
(2022)
Review
Cell Biology
Andras Zeke, Eva Schad, Tamas Horvath, Rawan Abukhairan, Beata Szabo, Agnes Tantos
Summary: This article summarizes the current state of structural knowledge on the RNA binding modes of disordered protein regions and proposes a classification system based on their sequential and structural properties. Through detailed structural analysis of complexes containing disordered protein regions binding to RNA, two major binding modes representing different recognition strategies and functions were identified. Comparisons with DNA binding disordered proteins revealed key differences and similar binding strategies, suggesting a wider substrate acceptance by these proteins.
WILEY INTERDISCIPLINARY REVIEWS-RNA
(2022)
Article
Biochemistry & Molecular Biology
Neha Singh, Andras Zeke, Attila Remenyi
Summary: This study reveals the presence of FBXW7-binding phosphodegrons in various important functional proteins involved in chromatin regulation and cytoskeletal regulation. The FBXW7-mediated degradation of these key regulatory proteins is diminished in the presence of different MAPKs, highlighting the importance of the MAPK and FBXW7 partnership in directly affecting the protein levels of key regulators.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Oncology
David Dora, Christopher Rivard, Hui Yu, Shivaun Lueke Pickard, Viktoria Laszlo, Tunde Harko, Zsolt Megyesfalvi, Csongor Gerdan, Elek Dinya, Konrad Hoetzenecker, Fred R. Hirsch, Zoltan Lohinai, Balazs Dome
Summary: This study characterizes the microenvironment of SCLC and identifies potential therapeutic targets by analyzing the expression patterns of SCLC subtype markers and immune checkpoints. The results show that STING and MHCII are expressed in SCLC, and increased immune infiltration and STING expression are associated with better prognosis. These findings suggest that STING may be a promising therapeutic target for limited-stage SCLC.
CANCER IMMUNOLOGY IMMUNOTHERAPY
(2023)
Article
Multidisciplinary Sciences
Gergo Gogl, Boglarka Zambo, Camille Kostmann, Alexandra Cousido-Siah, Bastien Morlet, Fabien Durbesson, Luc Negroni, Pascal Eberling, Pau Jane, Yves Nomine, Andras Zeke, Soren Ostergaard, Elodie Monsellier, Renaud Vincentelli, Gilles Trave
Summary: Protein networks have been extensively studied, but most binding affinities are still unknown, which hinders the quantitative interpretation of interactomes. In this study, the authors measured the affinities of 65,000 interactions involving PDZ domains and target PDZ-binding motifs, providing new methods for quantitative interactome studies.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Andras Zeke, Tamas Takacs, Peter Sok, Krisztina Nemeth, Klara Kirsch, Peter Egri, Adam Levente Poti, Isabel Bento, Gabor E. Tusnady, Attila Remenyi
Summary: This study investigates the structural details of the control of SHP2 phosphatase activity through serine/threonine phosphorylation sites. The research reveals a direct link between these phosphorylation sites and the regulation of specific phosphotyrosine phosphatases, indicating a complex regulatory mechanism for SHP2.
NATURE COMMUNICATIONS
(2022)
Article
Mathematical & Computational Biology
David Dora, Timea Dora, Gabor Szegvari, Csongor Gerdan, Zoltan Lohinai
Summary: This article introduces a simple, transparent, user-friendly drug repurposing software that aims to facilitate collaborative work in the field of cancer research. The platform integrates data from various databases and provides rich background information and relevant literature to assist researchers in target selection and functional validation assays.
Article
Mathematical & Computational Biology
Zsofia E. Kalman, Daniel Dudola, Balint Meszaros, Zoltan Gaspari, Laszlo Dobson
Summary: The postsynaptic region is crucial for fundamental mechanisms such as learning and memory, and a comprehensive understanding of its protein-protein interactions (PPIs) is necessary. To address the scattered nature of PPI data, a freely available resource called the Postsynaptic Interaction Database (PSINDB) was developed. PSINDB contains detailed structural and biological information for thousands of PPIs, providing a valuable tool for molecular neurobiology research.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2022)
