Article
Biochemistry & Molecular Biology
Ben M. Smith, Pamela J. E. Rowling, Christopher M. Dobson, Laura S. Itzhaki
Summary: The study investigates the interaction between beta-catenin and TCF7L2, revealing the kinetic characteristics through a fluorescence reporter system and mutagenesis analysis. The results suggest a complex two-site avidity mechanism of binding, with the involvement of transient contacts and alternative dissociation pathways. The study provides insights into the molecular recognition of a long intrinsically disordered region with an elongated repeat-protein surface, involving parallel routes and sequential steps.
Article
Biochemical Research Methods
Mitchell R. Vollger, Peter Kerpedjiev, Adam M. Phillippy, Evan E. Eichler
Summary: StainedGlass is a new visualization tool that can depict the identity and orientation of multi-megabase tandem repeat structures at a genome-wide scale, aiding in the inference of evolutionary history for complex regions of genomes.
Article
Biochemistry & Molecular Biology
Broto Chakrabarty, Nita Parekh
Summary: Recent research has focused on repeat proteins due to stable folds, high conservation, and diverse functions they offer. A database called DbStRiPs was developed for annotation and classification of tandem structural repeat proteins, integrating sequence and structure information to refine annotations and identify novel repeat families. Analysis revealed novel protein repeat families and clusters, enhancing understanding of repeat protein diversity and function.
Article
Biochemistry & Molecular Biology
Paula Nazarena Arrias, Alexander Miguel Monzon, Damiano Clementel, Soroush Mozaffari, Damiano Piovesan, Andrey V. Kajava, Silvio C. E. Tosatto
Summary: Structured tandem repeat proteins (STRPs) are characterized by a modular and repetitive three-dimensional structure arrangement. Previously overlooked Box repeats, a type of STRP fold, have been identified in the DNA sliding clamp processivity factors.
JOURNAL OF STRUCTURAL BIOLOGY
(2023)
Article
Biochemical Research Methods
Soroosh Gholamizoj, Bin Ma
Summary: SPEQ is a spectrum quality assessment tool that classifies spectra into high-quality and low-quality using a deep neural network, which has demonstrated improved prediction accuracy compared to other models.
Article
Biochemical Research Methods
Shinichi Morishita, Kazuki Ichikawa, Eugene W. Myers
Summary: This study presents an efficient algorithm that utilizes the characteristics of repetitive sequences to address the issue of high error rates in long-read sequencing technologies. The algorithm first estimates regions that may contain tandem repeats, and then assembles the k-mers of these regions into a consensus repeat unit by greedily traversing a de Bruijn graph. Experimental results demonstrate that the proposed algorithm outperforms the widely used Tandem Repeats Finder in terms of sensitivity.
Review
Biophysics
Mark Petersen, Doug Barrick
Summary: This article discusses the cooperativity in protein folding and the thermodynamic origins of cooperativity, using tandem repeat proteins as an experimental system. The study analyzes the structure of repeat proteins and classifies them based on their degree of cooperativity, introducing statistical thermodynamic models for analysis. These models are used to analyze data for different classes of repeat proteins, fitting parameters to overall structural features.
ANNUAL REVIEW OF BIOPHYSICS, VOL 50, 2021
(2021)
Article
Biochemistry & Molecular Biology
Tomasz Zok, Natalia Kraszewska, Joanna Miskiewicz, Paulina Pielacinska, Michal Zurkowski, Marta Szachniuk
Summary: ONQUADRO is an advanced database system that supports the study of canonical and non-canonical quadruplex structures, providing comprehensive information and functions for calculating structure parameters and statistical analysis. Users can view and download descriptions of tetrads, quadruplexes, and G4-helices. The database is freely available and can be used on both desktop computers and mobile devices.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Liman Ma, Wenji Wang, Ying Qu, Dongguo Wang
Summary: This study analyzed the genetic features of KPC-2 core structures in Klebsiella pneumoniae strain F94 and found that the strain was resistant to most tested antibiotics, especially to low levels of ceftazidime/avibactam, but sensitive to high levels. The study also revealed that plasmids with multiple KPC-2 core structures have highly similar multidrug resistance regions.
SCIENTIFIC REPORTS
(2023)
Article
Multidisciplinary Sciences
Igor Stevanovski, Sanjog R. Chintalaphani, Hasindu Gamaarachchi, James M. Ferguson, Sandy S. Pineda, Carolin K. Scriba, Michel Tchan, Victor Fung, Karl Ng, Andrea Cortese, Henry Houlden, Carol Dobson-Stone, Lauren Fitzpatrick, Glenda Halliday, Gianina Ravenscroft, Mark R. Davis, Nigel G. Laing, Avi Fellner, Marina Kennerson, Kishore R. Kumar, Ira W. Deveson
Summary: This article describes a method for genotyping neurological STR expansions using targeted long-read sequencing with Oxford Nanopore's ReadUntil function. The method allows for accurate DNA analysis and haplotype-resolved assembly, and successfully diagnoses patients with neurogenetic diseases. Long-read sequencing solves large and complex STR expansions and reveals a diversity of STR alleles.
Article
Entomology
Qian Li, Yi-Feng Zhang, Tian-Min Zhang, Jia-Hui Wan, Yu-Dan Zhang, Hui Yang, Yuan Huang, Chang Xu, Gang Li, Hui-Meng Lu
Summary: In this study, a new platform called iORbase was constructed for the structural and functional analysis of insect olfactory receptors (iORs). iORbase supports the prediction of structure and function of user-submitted iORs or pheromones and contains well-analyzed results of iORs and their 3D protein structures identified from various insect species. This study has implications in improving experimental efficiency and success rate, identifying new targets for insecticides, and developing electronic nose technology.
Article
Biochemical Research Methods
Jozef Sitarcik, Tomas Vinar, Brona Brejova, Werner Krampl, Jaroslav Budis, Jan Radvanszky, Maria Lucka
Summary: WarpSTR is a new method that characterizes both simple and complex tandem repeats directly from raw nanopore signals using a finite-state automaton and a search algorithm analogous to dynamic time warping.
Article
Chemistry, Medicinal
Marius T. Wenz, Miriam Bertazzon, Jana Sticht, Stevan Aleksic, Daniela Gjorgjevikj, Christian Freund, Bettina G. Keller
Summary: This study identifies and characterizes two complex structures of tandem WW domains and their natural binding partner peptide sequence. The findings contribute to understanding the versatility and specificity of protein-protein interactions.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Chemistry, Medicinal
Yuqi Zhang, Marton Vass, Da Shi, Esam Abualrous, Jennifer M. Chambers, Nikita Chopra, Christopher Higgs, Koushik Kasavajhala, Hubert Li, Prajwal Nandekar, Hideyuki Sato, Edward B. Miller, Matthew P. Repasky, Steven Jerome
Summary: The AlphaFold2 (AF2) algorithm predicts proteins' 3D structures from amino acid sequences. The open AlphaFold protein structure database covers the complete human proteome. Through virtual screening, AF2 structures show comparable early enrichment of known active compounds to apo structures, and with refinement using an induced-fit protocol, the performance in structure-based virtual screening can be improved. Thus, AF2 structures hold promise for in silico hit identification.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Biochemical Research Methods
Atheer Matroud, Christopher Tuffley, Michael Hendy
Summary: Tandem repeats are repetitive structures in DNA sequences that can serve as important markers for phylogenetic and population genetic studies. Estimating the evolutionary distance between sequences with homologous motifs is the first step in using tandem repeats for phylogenetic studies. We present an algorithm that estimates this distance using an asymmetric alignment algorithm, which can also handle more complex repetitive structures.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Juliet F. F. Nilsson, Hakima Baroudi, Frank Gondelaud, Giulia Pesce, Christophe Bignon, Denis Ptchelkine, Joseph Chamieh, Herve Cottet, Andrey V. V. Kajava, Sonia Longhi
Summary: The Nipah and Hendra viruses, classified as Henipaviruses, are highly dangerous human pathogens that counteract the host immune response. A recent study found that a short region within the shared N-terminal domain (PNT3) of the Phosphoprotein (P protein) can form amyloid-like structures. This study evaluated the role of specific tyrosine residues within this region in fibrillation. Results showed that removal of a single tyrosine significantly decreases fibril formation, mainly affecting the elongation phase, and the C-terminal half of PNT3 inhibits fibril formation. The study sheds light on the molecular mechanisms of fibril formation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemical Research Methods
Eric W. Deutsch, Juan Antonio Vizcaino, Andrew R. Jones, Pierre-Alain Binz, Henry Lam, Joshua Klein, Wout Bittremieux, Yasset Perez-Riverol, David L. Tabb, Mathias Walzer, Sylvie Ricard-Blum, Henning Hermjakob, Steffen Neumann, Tytus D. Mak, Shin Kawano, Luis Mendoza, Tim Van Den Bossche, Ralf Gabriels, Nuno Bandeira, Jeremy Carver, Benjamin Pullman, Zhi Sun, Nils Hoffmann, Jim Shofstahl, Yunping Zhu, Luana Licata, Federica Quaglia, Silvio C. E. Tosatto, Sandra E. Orchard
Summary: The Human Proteome Organization (HUPO) Proteomics Standards Initiative (PSI) has been developing guidelines and standards for the proteomics community for 20 years. The organization describes its operation, the current state of existing standards, and the proposals currently being developed. They emphasize the importance of community participation and collaboration with other organizations to promote data sharing and accelerate progress in proteomics.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Damiano Piovesan, Alessio Del Conte, Damiano Clementel, Alexander Miguel Monzon, Martina Bevilacqua, Maria Cristina Aspromonte, Javier A. Iserte, Fernando E. Orti, Cristina Marino-Buslje, Silvio C. E. Tosatto
Summary: The MobiDB database is a knowledge base of intrinsically disordered proteins, which collects annotations and predictions to provide new knowledge about the functional significance of disordered regions. The latest release of MobiDB focuses on improving user experience and database content, integrating AlphaFoldDB predictions and implementing the homology transfer pipeline.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Typhaine Paysan-Lafosse, Matthias Blum, Sara Chuguransky, Tiago Grego, Beatriz Lazaro Pinto, Gustavo A. Salazar, Maxwell L. Bileschi, Peer Bork, Alan Bridge, Lucy Colwell, Julian Gough, Daniel H. Haft, Ivica Letunic, Aron Marchler-Bauer, Huaiyu Mi, Darren A. Natale, Christine A. Orengo, Arun P. Pandurangan, Catherine Rivoire, Christian J. A. Sigrist, Ian Sillitoe, Narmada Thanki, Paul D. Thomas, Silvio C. E. Tosatto, Cathy H. Wu, Alex Bateman
Summary: The InterPro database has been updated with new data content and website features, providing a more user-friendly access to protein sequence classification and functional domain identification. It has also integrated features from the retiring Pfam website and developed a card game to engage the non-scientific community. Furthermore, the database explores the benefits and challenges of using artificial intelligence for protein structure prediction.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Diana Piol, Laura Tosatto, Emanuela Zuccaro, Eric N. Anderson, Antonella Falconieri, Maria J. Polanco, Caterina Marchioretti, Federica Lia, Joseph White, Elisa Bregolin, Giovanni Minervini, Sara Parodi, Xavier Salvatella, Giorgio Arrigoni, Andrea Ballabio, Albert R. La Spada, Silvio C. E. Tosatto, Fabio Sambataro, Diego L. Medina, Udai B. Pandey, Manuela Basso, Maria Plennuto
Summary: Spinal and bulbar muscular atrophy is caused by polyglutamine expansions in androgen receptor, leading to gain-of-function toxicity. This study investigates the phosphorylation of polyglutamine-expanded receptor and its role in neurodegeneration. The researchers find that certain kinases and phosphatases can modify the function and toxicity of the receptor, and targeting these enzymes can potentially be used as a therapeutic approach.
Article
Biochemistry & Molecular Biology
Giorgia F. Camagni, Giovanni Minervini, Silvio C. E. Tosatto
Summary: The Prolyl Hydroxylases (PHDs) are a family of enzymes that regulate cell oxygen-sensing by hydroxylating hypoxia-inducible transcription factors alpha (HIFs-alpha) and promoting their degradation. Hypoxia inhibits PHDs activity, leading to HIFs-alpha stabilization and cell adaptation to low oxygen levels. The different isoforms of PHDs have varying effects on tumor progression. Molecular dynamics simulations, conservation analysis, and binding free energy calculations were used to study the binding properties and substrate affinity of PHD2 with HIF-1 alpha and HIF-2 alpha. The findings suggest that the PHD2 C-terminus may play a role in regulating PHD activity.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Alessio Del Conte, Adel Bouhraoua, Mahta Mehdiabadi, Damiano Clementel, Alexander Miguel Monzon, Damiano CAID Predictors, Silvio C. E. Tosatto, Damiano Piovesan
Summary: Intrinsic disorder (ID) in proteins is a well-established phenomenon in structural biology, but measuring its behavior on a large scale is challenging. To address this issue, CAID benchmarks ID predictors and creates a web server, the CAID Prediction Portal, which executes all CAID methods on user-defined sequences. The server generates standardized output, facilitates comparison between methods, and provides a valuable resource for researchers studying ID in proteins.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Elizabeth Martinez-Perez, Matyas Pajkos, Silvio C. E. Tosatto, Toby J. Gibson, Zsuzsanna Dosztanyi, Cristina Marino-Buslje
Summary: DisProt is a curated database of Intrinsically Disordered Proteins (IDPs) with strong experimental support. Transferring annotations regarding disorder state and functions to homologous proteins in other species is important for understanding their biological roles. With the use of a pipeline, it is possible to transfer annotations from DisProt proteins to their orthologs, resulting in a large number of transferred terms by homology.
Article
Biochemistry & Molecular Biology
Jingchao Guo, Liyun Zhang, Yongxia Zhao, Awais Ihsan, Xu Wang, Yanfei Tao
Summary: Drug abuse is common in livestock and poultry production, leading to low residues of drugs in eggs that pose potential threats to human safety. This study uses LC-MS/MS to detect residual Enrofloxacin (EF) and tilmicosin (TIM) in laying hens and investigates the effect of TIM on EF metabolism. The results show that the combination of EF and TIM increases EF residues in eggs, decreases EF elimination rate, and prolongs EF half-life. Therefore, caution should be exercised when using EF and TIM in combination, and stronger supervision is needed to avoid risks to human health.
Article
Biochemistry & Molecular Biology
Maria Cristina Aspromonte, Maria Victoria Nugnes, Federica Quaglia, Adel Bouharoua, DisProt Consortium, Silvio C. E. Tosatto, Damiano Piovesan
Summary: DisProt is a gold standard database for intrinsically disordered proteins and regions, providing valuable information about their functions. The latest version of DisProt brings significant advancements in function representation and curation process, increasing both the coverage and quality of annotations. Moreover, DisProt offers a comparison with AlphaFold2 predictions, demonstrating its utility in explaining the uncertainty of predicted structures.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Alessio Del Conte, Mahta Mehdiabadi, Adel Bouhraoua, Alexander M. Mozon, Silvio C. E. Tosatto, Damiano Piovesan
Summary: Protein intrinsic disorder is a complex and challenging phenomenon for prediction methods due to its diverse nature and context-dependent transitions. The CAID2 challenge evaluated different prediction methods using benchmarks and the annotation provided by the DisProt database. The challenge demonstrated the need for versatile and efficient prediction software, and highlighted the varying performance of different methods.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2023)
Review
Biochemistry & Molecular Biology
Yongxia Zhao, Xiaochun Ye, Zhifeng Xiong, Awais Ihsan, Irma Ares, Marta Martinez, Bernardo Lopez-Torres, Maria-Rosa Martinez-Larranaga, Arturo Anadon, Xu Wang, Maria-Aranzazu Martinez
Summary: This review summarizes the role of increased ROS in DNA damage and the apoptosis of cancer cells caused by changes in cancer cell metabolism, as well as various anticancer therapies targeting ROS generation, in order to provide references for cancer therapies based on ROS generation.
Article
Biochemical Research Methods
Alessio Del Conte, Alexander Miguel Monzon, Damiano Clementel, Giorgia F. Camagni, Giovanni Minervini, Silvio C. E. Tosatto, Damiano Piovesan
Summary: RING-PyMOL is a plugin for PyMOL that enhances the analysis and visualization of structural ensembles and molecular dynamic simulations. It combines residue interaction networks and structural clustering to provide a powerful tool for studying conformational complexity. It can identify correlating contacts, interaction patterns, and explain structural heterogeneity and molecular function. RING-PyMOL is easy to use, fast, and generates interactive plots and output files for further analysis.