Review
Biochemistry & Molecular Biology
Ranran Chen, Xinlu Li, Yaqing Yang, Xixi Song, Cheng Wang, Dongdong Qiao
Summary: This paper presents a comprehensive overview of recently published predictors for intrinsically disordered protein (IDP) binding site prediction. The authors collected 30 representative predictors and summarized their databases, features, and algorithms. The predictors were divided into scoring functions, machine learning-based prediction, and consensus approaches, with detailed descriptions of their algorithms and performances. This study not only provides a full picture of the current status of IDP binding prediction, but also serves as a guide for selecting different methods and inspires future development trends and principles.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Biochemical Research Methods
Jacob Verburgt, Zicong Zhang, Daisuke Kihara
Summary: This study evaluates the performance of three IDP-receptor modeling tools and shows that they are able to accurately identify the general binding site but face challenges in capturing biophysical interactions.
Article
Biochemistry & Molecular Biology
Estella A. Newcombe, Catarina B. Fernandes, Jeppe E. Lundsgaard, Inna Brakti, Kresten Lindorff-Larsen, Annette E. Langkilde, Karen Skriver, Birthe B. Kragelund
Summary: Motifs within proteins help categorize their functions;Intrinsically disordered proteins (IDPs) rich in short linear motifs with various roles;Study found calcium-binding motifs in IDPs may serve various underreported structural and functional roles.
Article
Biochemistry & Molecular Biology
Letizia Pontoriero, Marco Schiavina, Sophie M. Korn, Andreas Schlundt, Roberta Pierattelli, Isabella C. Felli
Summary: This study identifies the crucial role of the intrinsically disordered regions (IDRs) of the SARS-CoV-2 nucleocapsid (N) protein in RNA recognition. By using NMR spectroscopy, the researchers provide atomic-level details of the interplay between folded and disordered regions of N during RNA interaction, offering insights into the replication process of the SARS-CoV-2 virus.
Review
Biochemistry & Molecular Biology
Shasha Chong, Mustafa Mir
Summary: The proteome contains a significant portion of intrinsically disordered regions (IDRs) that perform various biological functions and are linked to different diseases despite lacking well-defined 3D structures. Recent discoveries of functionally relevant biomolecular assemblies, some forming through liquid-liquid phase separation, have brought attention to IDRs. Weak, multivalent, but selective interactions between IDRs primarily drive the formation of these biomolecular assemblies according to emerging experimental and computational studies.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Review
Biochemical Research Methods
Sun Canzhuang, Feng Yonge
Summary: A multi-feature fusion model was constructed to accurately predict the disordered regions in intrinsically disordered proteins, with the best performance achieved when combining codon frequencies with chemical shifts as features, reaching an accuracy of 83.173%. The results demonstrate a good prediction outcome of the model, surpassing existing methods in identifying disordered regions.
CURRENT BIOINFORMATICS
(2021)
Review
Biochemistry & Molecular Biology
David Moses, Garrett M. Ginell, Alex S. Holehouse, Shahar Sukenik
Summary: Intrinsically disordered proteins and protein regions (IDRs) play essential roles in eukaryotic organisms. Unlike folded proteins, IDRs exist in a conformational ensemble influenced by sequence-dependent interactions. The absence of a stable 3D structure and high solvent accessibility make IDRs inherently sensitive to environmental changes, allowing them to act as sensors and actuators of cellular physicochemistry.
TRENDS IN BIOCHEMICAL SCIENCES
(2023)
Article
Biology
Taraneh Zarin, Bob Strome, Gang Peng, Iva Pritisanac, Julie D. Forman-Kay, Alan M. Moses
Summary: This study aims to utilize molecular features within the intrinsically disordered regions (IDRs) of proteins to predict specific biological functions and identify associated features. The results show diverse predictable functions, with some features consistent with previous reports and others previously unknown. Feature analysis represents a new systematic approach to understanding how biological functions of IDRs are determined by their protein sequences.
Article
Multidisciplinary Sciences
Chen Qiu, Zihan Zhang, Robert N. Wine, Zachary T. Campbell, Jun Zhang, Traci M. Tanaka Hall
Summary: This study reveals that the intrinsically disordered region (IDR) at the C-terminus of FBF-2 protein autoinhibits its RNA-binding affinity. The interaction between LST-1 and the C-terminal region of FBF-2 releases the autoinhibition and increases the RNA-binding affinity. This regulatory mechanism explains the interdependence of FBF-2 and LST-1 in germline stem cell self-renewal.
NATURE COMMUNICATIONS
(2023)
Review
Cell Biology
Alex S. Holehouse, Birthe B. Kragelund
Summary: Intrinsically disordered protein regions, lacking a stable 3D structure, are structurally heterogeneous and widely present in all kingdoms of life. Despite their lack of a defined structure, these regions play essential roles in cellular processes and can be regulated by their structural and chemical context. Recent studies have advanced our understanding of the link between protein sequence and conformational behavior in disordered regions, but the connection between sequence and molecular function is still not well defined.
NATURE REVIEWS MOLECULAR CELL BIOLOGY
(2023)
Editorial Material
Cell Biology
Sarah E. Bondos, A. Keith Dunker, Vladimir N. Uversky
Summary: The sequence -> structure -> function paradigm is primarily applicable to enzymes, transmembrane proteins, and signaling domains, while the sequence -> IDP/IDR ensemble -> function paradigm is primarily applicable to signaling and regulatory proteins and regions. Disorder contributes to signaling in a broad spectrum of species, playing diverse roles in responding to signals and orchestrating organismal processes.
CELL COMMUNICATION AND SIGNALING
(2021)
Review
Chemistry, Multidisciplinary
Matti Mar, Kateryna Nitsenko, Petur O. Heidarsson
Summary: Eukaryotic transcription factors play a crucial role in integrating molecular feedback and regulating gene expression. They consist of structured DNA-binding domains and long intrinsically disordered regions (IDRs). The dynamic multifunctionality of IDRs is essential for their functions in genome regulation. This review analyzes the chemical features of TF IDRs and their involvement in protein interactions, DNA binding, chromatin opening, and phase separation. Suggestions are given for future research to integrate experiments and simulations in understanding TF functions.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Deepak Chaurasiya, Rajkrishna Mondal, Tapobrata Lahiri, Asmita Tripathi, Tejas Ghinmine
Summary: The discovery of intrinsically disordered proteins (IDPs) and protein hybrids has changed the understanding of the sequence-structure-function paradigm of proteins. IDPs, which lack persistent structure, are found in all organisms and play crucial roles in biological processes. However, accurately characterizing and predicting the behavior of these proteins remains a challenge.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biology
Shih-Hui Chiu, Wen-Lin Ho, Yung-Chen Sun, Jean-Cheng Kuo, Jie-rong Huang
Summary: The intrinsically disordered regions (IDRs) among paralogs have different physicochemical properties but converge on the same biophysical function. The diversity of IDRs can lead to different traits, but they ultimately evolve to achieve a converged function.
COMMUNICATIONS BIOLOGY
(2022)
Article
Biology
Raghavendar R. Sanganna Gari, Grigory Tagiltsev, Ruth A. Pumroy, Yining Jiang, Martin Blackledge, Vera Y. Moiseenkova-Bell, Simon Scheuring
Summary: This study used high-speed atomic force microscopy to image TRPV2 channels in membranes and found that the N-terminal intrinsically disordered regions (IDRs) were involved in intermolecular interactions. The results provide evidence about the 'structure' of TRPV2 IDRs and suggest their potential role in mediating protein-protein interactions.
COMMUNICATIONS BIOLOGY
(2023)
Review
Biochemical Research Methods
Zhourun Wu, Qing Liao, Bin Liu
BRIEFINGS IN BIOINFORMATICS
(2020)
Article
Biochemical Research Methods
Chen-Chen Li, Bin Liu
BRIEFINGS IN BIOINFORMATICS
(2020)
Article
Biochemical Research Methods
Jiangyi Shao, Ke Yan, Bin Liu
Summary: The FoldRec-C2C predictor globally incorporates protein interactions for protein fold recognition, treating it as an information retrieval task in natural language processing. Tested on the LINDAHL dataset, FoldRec-C2C outperforms 34 state-of-the-art methods in the field.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemical Research Methods
Jiangyi Shao, Bin Liu
Summary: This study introduces a network-based predictor ProtFold-DFG for protein fold recognition, utilizing Directed Fusion Graph (DFG), KL divergence, and PageRank algorithm to enhance recognition accuracy. Experimental results demonstrate that ProtFold-DFG outperforms 35 other methods on the LINDAHL dataset, making it a promising approach for protein fold recognition.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biology
Hang Wei, Yuxin Ding, Bin Liu
COMPUTATIONAL BIOLOGY AND CHEMISTRY
(2020)
Article
Biochemistry & Molecular Biology
Jun Zhang, Qingcai Chen, Bin Liu
JOURNAL OF MOLECULAR BIOLOGY
(2020)
Article
Biochemical Research Methods
Yichen Guo, Ke Yan, Hao Wu, Bin Liu
ANALYTICAL BIOCHEMISTRY
(2020)
Article
Biochemical Research Methods
Ke Yan, Jie Wen, Jin-Xing Liu, Yong Xu, Bin Liu
Summary: The study proposed two novel algorithms, TSVM-fold and ESVM-fold, utilizing sequence similarity scores generated by multiple template-based methods for protein fold recognition prediction. Experimental results showed that these algorithms outperform some state-of-the-art methods in rigorous benchmark datasets.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2021)
Article
Biochemical Research Methods
Hang Wei, Qing Liao, Bin Liu
Summary: Identifying lncRNA-disease associations is crucial for exploring disease mechanisms and molecular drug discovery. However, current fusion strategies fail to remove noisy and irrelevant information, leading to low predictive performance. iLncRNAdis-FB proposes a new computational predictor based on CNN to integrate feature blocks from different data sources, achieving better prediction accuracy.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2021)
Article
Biochemical Research Methods
Yumeng Liu, Xiaolong Wang, Bin Liu
Summary: Intrinsically disordered proteins/regions (IDPs/IDRs) are important for biological functions, and accurate prediction is crucial for protein structure and function predictions. However, most existing methods tend to predict fully ordered proteins as disordered, ignoring the fact that most newly sequenced proteins are fully ordered. The proposed RFPR-IDP method, trained on both ordered and disordered proteins, outperforms existing predictors in predicting both ordered and disordered proteins.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemical Research Methods
Zhourun Wu, Qing Liao, Bin Liu
Summary: Protein complexes are key units for studying a cell system, and high-throughput approaches have enabled the determination of PPI data. The proposed mutual important interacting partner relation and the new algorithm idenPC-MIIP show improved performance in identifying protein complexes compared to existing methods.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Computer Science, Artificial Intelligence
Ke Yan, Jie Wen, Yong Xu, Bin Liu
Summary: Protein fold recognition is crucial for understanding protein functions and drug design. New methods (MVLR and MLDH-Fold) were proposed to improve predictive performance by combining different views of protein sequences. Experimental results show that these computational methods outperform other predictors, indicating their usefulness for protein fold recognition.
Article
Biochemical Research Methods
Hang Wei, Bin Liu
BRIEFINGS IN BIOINFORMATICS
(2020)
Article
Biochemical Research Methods
Bin Liu, Shuangyan Jiang, Quan Zou
BRIEFINGS IN BIOINFORMATICS
(2020)