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Relevant bibliographies by topics / IDPs/IDRs

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Academic literature on the topic 'IDPs/IDRs'

Author: Grafiati

Published: 25 May 2024

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Journal articles on the topic "IDPs/IDRs"

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Han, Bingqing, Chongjiao Ren, Wenda Wang, Jiashan Li, and Xinqi Gong. "Computational Prediction of Protein Intrinsically Disordered Region Related Interactions and Functions." Genes 14, no. 2 (2023): 432. http://dx.doi.org/10.3390/genes14020432.

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Intrinsically Disordered Proteins (IDPs) and Regions (IDRs) exist widely. Although without well-defined structures, they participate in many important biological processes. In addition, they are also widely related to human diseases and have become potential targets in drug discovery. However, there is a big gap between the experimental annotations related to IDPs/IDRs and their actual number. In recent decades, the computational methods related to IDPs/IDRs have been developed vigorously, including predicting IDPs/IDRs, the binding modes of IDPs/IDRs, the binding sites of IDPs/IDRs, and the m

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Coskuner-Weber, Orkid, and Vladimir N. Uversky. "Current Stage and Future Perspectives for Homology Modeling, Molecular Dynamics Simulations, Machine Learning with Molecular Dynamics, and Quantum Computing for Intrinsically Disordered Proteins and Proteins with Intrinsically Disordered Regions." Current Protein & Peptide Science 25, no. 2 (2024): 163–71. http://dx.doi.org/10.2174/0113892037281184231123111223.

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Abstract:: The structural ensembles of intrinsically disordered proteins (IDPs) and proteins with intrinsically disordered regions (IDRs) cannot be easily characterized using conventional experimental techniques. Computational techniques complement experiments and provide useful insights into the structural ensembles of IDPs and proteins with IDRs. Herein, we discuss computational techniques such as homology modeling, molecular dynamics simulations, machine learning with molecular dynamics, and quantum computing that can be applied to the studies of IDPs and hybrid proteins with IDRs. We also

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Liu, Meili, Akshaya K. Das, James Lincoff, et al. "Configurational Entropy of Folded Proteins and Its Importance for Intrinsically Disordered Proteins." International Journal of Molecular Sciences 22, no. 7 (2021): 3420. http://dx.doi.org/10.3390/ijms22073420.

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Many pairwise additive force fields are in active use for intrinsically disordered proteins (IDPs) and regions (IDRs), some of which modify energetic terms to improve the description of IDPs/IDRs but are largely in disagreement with solution experiments for the disordered states. This work considers a new direction—the connection to configurational entropy—and how it might change the nature of our understanding of protein force field development to equally well encompass globular proteins, IDRs/IDPs, and disorder-to-order transitions. We have evaluated representative pairwise and many-body pro

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Felli, Isabella C., Wolfgang Bermel, and Roberta Pierattelli. "Exclusively heteronuclear NMR experiments for the investigation of intrinsically disordered proteins: focusing on proline residues." Magnetic Resonance 2, no. 1 (2021): 511–22. http://dx.doi.org/10.5194/mr-2-511-2021.

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Abstract. NMR represents a key spectroscopic technique that contributes to the emerging field of highly flexible, intrinsically disordered proteins (IDPs) or protein regions (IDRs) that lack a stable three-dimensional structure. A set of exclusively heteronuclear NMR experiments tailored for proline residues, highly abundant in IDPs/IDRs, are presented here. They provide a valuable complement to the widely used approach based on amide proton detection, filling the gap introduced by the lack of amide protons in proline residues within polypeptide chains. The novel experiments have very interest

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Ahmed, Shehab S., Zaara T. Rifat, Ruchi Lohia, et al. "Characterization of intrinsically disordered regions in proteins informed by human genetic diversity." PLOS Computational Biology 18, no. 3 (2022): e1009911. http://dx.doi.org/10.1371/journal.pcbi.1009911.

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All proteomes contain both proteins and polypeptide segments that don’t form a defined three-dimensional structure yet are biologically active—called intrinsically disordered proteins and regions (IDPs and IDRs). Most of these IDPs/IDRs lack useful functional annotation limiting our understanding of their importance for organism fitness. Here we characterized IDRs using protein sequence annotations of functional sites and regions available in the UniProt knowledgebase (“UniProt features”: active site, ligand-binding pocket, regions mediating protein-protein interactions, etc.). By measuring th

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Alshehri, Manal A., Manee M. Manee, Mohamed B. Al-Fageeh, and Badr M. Al-Shomrani. "Genomic Analysis of Intrinsically Disordered Proteins in the Genus Camelus." International Journal of Molecular Sciences 21, no. 11 (2020): 4010. http://dx.doi.org/10.3390/ijms21114010.

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Intrinsically disordered proteins/regions (IDPs/IDRs) fail to fold completely into 3D structures, but have major roles in determining protein function. While natively disordered proteins/regions have been found to fulfill a wide variety of primary cellular roles, the functions of many disordered proteins in numerous species remain to be uncovered. Here, we perform the first large-scale study of IDPs/IDRs in the genus Camelus, one of the most important mammalians in Asia and North Africa, in order to explore the biological roles of these proteins. The study includes the prediction of disordered

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Medvedev, Kirill E., Jimin Pei, and Nick V. Grishin. "DisEnrich: database of enriched regions in human dark proteome." Bioinformatics 38, no. 7 (2022): 1870–76. http://dx.doi.org/10.1093/bioinformatics/btac051.

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Abstract Motivation Intrinsically disordered proteins (IDPs) are involved in numerous processes crucial for living organisms. Bias in amino acid composition of these proteins determines their unique biophysical and functional features. Distinct intrinsically disordered regions (IDRs) with compositional bias play different important roles in various biological processes. IDRs enriched in particular amino acids in human proteome have not been described consistently. Results We developed DisEnrich—the database of human proteome IDRs that are significantly enriched in particular amino acids. Each

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Kastano, Kristina, Gábor Erdős, Pablo Mier, et al. "Evolutionary Study of Disorder in Protein Sequences." Biomolecules 10, no. 10 (2020): 1413. http://dx.doi.org/10.3390/biom10101413.

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Intrinsically disordered proteins (IDPs) contain regions lacking intrinsic globular structure (intrinsically disordered regions, IDRs). IDPs are present across the tree of life, with great variability of IDR type and frequency even between closely related taxa. To investigate the function of IDRs, we evaluated and compared the distribution of disorder content in 10,695 reference proteomes, confirming its high variability and finding certain correlation along the Euteleostomi (bony vertebrates) lineage to number of cell types. We used the comparison of orthologs to study the function of disorde

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McFadden, William M., and Judith L. Yanowitz. "idpr: A package for profiling and analyzing Intrinsically Disordered Proteins in R." PLOS ONE 17, no. 4 (2022): e0266929. http://dx.doi.org/10.1371/journal.pone.0266929.

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Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) are proteins or protein-domains that do not have a single native structure, rather, they are a class of flexible peptides that can rapidly adopt multiple conformations. IDPs are quite abundant, and their dynamic characteristics provide unique advantages for various biological processes. The field of “unstructured biology” has emerged, in part, because of numerous computational studies that had identified the unique characteristics of IDPs and IDRs. The package ‘idpr’, short for Intrinsically Disordered Protein

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Saito, Akatsuki, Maya Shofa, Hirotaka Ode, et al. "How Do Flaviviruses Hijack Host Cell Functions by Phase Separation?" Viruses 13, no. 8 (2021): 1479. http://dx.doi.org/10.3390/v13081479.

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Viral proteins interact with different sets of host cell components throughout the viral life cycle and are known to localize to the intracellular membraneless organelles (MLOs) of the host cell, where formation/dissolution is regulated by phase separation of intrinsically disordered proteins and regions (IDPs/IDRs). Viral proteins are rich in IDRs, implying that viruses utilize IDRs to regulate phase separation of the host cell organelles and augment replication by commandeering the functions of the organelles and/or sneaking into the organelles to evade the host immune response. This review

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Dissertations / Theses on the topic "IDPs/IDRs"

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Bruley, Apolline. "Exploitation de signatures des repliements protéiques pour décrire le continuum ordre/désordre au sein des protéomes." Electronic Thesis or Diss., Sorbonne université, 2022. http://www.theses.fr/2022SORUS474.

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Une fraction significative des protéomes reste non annotée, laissant inaccessible une partie du répertoire fonctionnel de la vie, incluant des innovations moléculaires ayant une valeur thérapeutique ou environnementale. Le manque d'annotation fonctionnelle est en partie dû aux limites des approches actuelles pour la détection de relations cachées, ou à des caractéristiques spécifiques telles que le désordre. L'objectif de ma thèse a été de développer des approches méthodologiques reposant sur les signatures structurales des domaines repliés, afin de caractériser plus avant les séquences protéi

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Book chapters on the topic "IDPs/IDRs"

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Holehouse, Alex S. "IDPs and IDRs in biomolecular condensates." In Intrinsically Disordered Proteins. Elsevier, 2019. http://dx.doi.org/10.1016/b978-0-12-816348-1.00007-7.

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Zheng, Wenwei, and Hoi Sung Chung. "Single-molecule fluorescence studies of IDPs and IDRs." In Intrinsically Disordered Proteins. Elsevier, 2019. http://dx.doi.org/10.1016/b978-0-12-816348-1.00004-1.

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Salvi, Nicola. "Ensemble descriptions of IDPs and IDRs: Integrating simulation and experiment." In Intrinsically Disordered Proteins. Elsevier, 2019. http://dx.doi.org/10.1016/b978-0-12-816348-1.00002-8.

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Bolik-Coulon, Nicolas, Guillaume Bouvignies, Ludovic Carlier, and Fabien Ferrage. "Experimental characterization of the dynamics of IDPs and IDRs by NMR." In Intrinsically Disordered Proteins. Elsevier, 2019. http://dx.doi.org/10.1016/b978-0-12-816348-1.00003-x.

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