دورية أكاديمية
Modeling Side Chains in the Three-Dimensional Structure of Proteins for Post-Translational Modifications.
| العنوان: | Modeling Side Chains in the Three-Dimensional Structure of Proteins for Post-Translational Modifications. |
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| المؤلفون: | Petrovskiy DV; Institute of Biomedical Chemistry, 119121 Moscow, Russia., Nikolsky KS; Institute of Biomedical Chemistry, 119121 Moscow, Russia., Rudnev VR; Institute of Biomedical Chemistry, 119121 Moscow, Russia., Kulikova LI; Institute of Biomedical Chemistry, 119121 Moscow, Russia., Butkova TV; Institute of Biomedical Chemistry, 119121 Moscow, Russia., Malsagova KA; Institute of Biomedical Chemistry, 119121 Moscow, Russia., Kopylov AT; Institute of Biomedical Chemistry, 119121 Moscow, Russia., Kaysheva AL; Institute of Biomedical Chemistry, 119121 Moscow, Russia. |
| المصدر: | International journal of molecular sciences [Int J Mol Sci] 2023 Aug 30; Vol. 24 (17). Date of Electronic Publication: 2023 Aug 30. |
| نوع المنشور: | Journal Article |
| اللغة: | English |
| بيانات الدورية: | Publisher: MDPI Country of Publication: Switzerland NLM ID: 101092791 Publication Model: Electronic Cited Medium: Internet ISSN: 1422-0067 (Electronic) Linking ISSN: 14220067 NLM ISO Abbreviation: Int J Mol Sci Subsets: MEDLINE |
| أسماء مطبوعة: | Original Publication: Basel, Switzerland : MDPI, [2000- |
| مواضيع طبية MeSH: | Amino Acids* , Algorithms*, Amino Acid Substitution ; Databases, Protein ; Protein Processing, Post-Translational |
| مستخلص: | Amino acid substitutions and post-translational modifications (PTMs) play a crucial role in many cellular processes by directly affecting the structural and dynamic features of protein interaction. Despite their importance, the understanding of protein PTMs at the structural level is still largely incomplete. The Protein Data Bank contains a relatively small number of 3D structures having post-translational modifications. Although recent years have witnessed significant progress in three-dimensional modeling (3D) of proteins using neural networks, the problem related to predicting accurate PTMs in proteins has been largely ignored. Predicting accurate 3D PTM models in proteins is closely related to another fundamental problem: predicting the correct side-chain conformations of amino acid residues in proteins. An analysis of publications as well as the paid and free software packages for modeling three-dimensional structures showed that most of them focus on working with unmodified proteins and canonical amino acid residues; the number of articles and software packages placing emphasis on modeling three-dimensional PTM structures is an order of magnitude smaller. This paper focuses on modeling the side-chain conformations of proteins containing PTMs (nonstandard amino acid residues). We collected our own libraries comprising the most frequently observed PTMs from the PDB and implemented a number of algorithms for predicting the side-chain conformation at modification points and in the immediate environment of the protein. A comprehensive analysis of both the algorithms per se and compared to the common Rosetta and FoldX structure modeling packages was also carried out. The proposed algorithmic solutions are comparable in their characteristics to the well-known Rosetta and FoldX packages for the modeling of three-dimensional structures and have great potential for further development and optimization. The source code of algorithmic solutions has been deposited to and is available at the GitHub source. |
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| معلومات مُعتمدة: | 122092200056-9 Russian Federation Fundamental Research Program |
| فهرسة مساهمة: | Keywords: modeling side chains; non-canonical amino acid; phosphorylation; post-translational modifications; rotamer library |
| المشرفين على المادة: | 0 (Amino Acids) |
| تواريخ الأحداث: | Date Created: 20230909 Date Completed: 20230911 Latest Revision: 20230911 |
| رمز التحديث: | 20240829 |
| مُعرف محوري في PubMed: | PMC10488155 |
| DOI: | 10.3390/ijms241713431 |
| PMID: | 37686234 |
| قاعدة البيانات: | MEDLINE |
Full Text Finder | تدمد: | 1422-0067 |
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| DOI: | 10.3390/ijms241713431 |