Proteins-Structure Function and Bioinformatics最新文献

{"title":"Simpler Protein Domain Identification Using Spectral Clustering.","authors":"Frédéric Cazals, Jules Herrmann, Edoardo Sarti","doi":"10.1002/prot.26808","DOIUrl":"10.1002/prot.26808","url":null,"abstract":"<p><p>The decomposition of a biomolecular complex into domains is an important step to investigate biological functions and ease structure determination. A successful approach to do so is the SPECTRUS algorithm, which provides a segmentation based on spectral clustering applied to a graph coding inter-atomic fluctuations derived from an elastic network model. We present SPECTRALDOM, which makes three straightforward and useful additions to SPECTRUS. For single structures, we show that high quality partitionings can be obtained from a graph Laplacian derived from pairwise interactions-without normal modes. For sets of homologous structures, we introduce a Multiple Sequence Alignment mode, exploiting both the sequence based information (MSA) and the geometric information embodied in experimental structures. Finally, we propose to analyze the clusters/domains delivered using the so-called <math> <semantics><mrow><mi>D</mi></mrow> </semantics> </math> -family-matching algorithm, which establishes a correspondence between domains yielded by two decompositions, and can be used to handle fragmentation issues. Our domains compare favorably to those of the original SPECTRUS, and those of the deep learning based method Chainsaw. Using two complex cases, we show in particular that SPECTRALDOM is the only method handling complex conformational changes involving several sub-domains. Finally, a comparison of SPECTRALDOM and Chainsaw on the manually curated domain classification ECOD as a reference shows that high quality domains are obtained without using any evolutionary related piece of information. SPECTRALDOM is provided in the Structural Bioinformatics Library, see http://sbl.inria.fr and https://sbl.inria.fr/doc/Spectral_domain_explorer-user-manual.html.</p>","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":"1212-1225"},"PeriodicalIF":3.2,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143411913","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cloning, Characterization, and Computer-Aided Evolution of a Thermostable Laccase of the DUF152 Family From Klebsiella michiganensis.","authors":"Ting Cui, Kathrin Brückner, Stephan Schilling, Hans-Jürgen Mägert","doi":"10.1002/prot.26784","DOIUrl":"10.1002/prot.26784","url":null,"abstract":"<p><p>Bacterial laccases exhibit relatively high optimal reaction temperatures and possess a broad substrate spectrum, thereby expanding the range of potential applications for laccase enzymes. This study aims to investigate the molecular evolution of bacterial laccases using computational 3D-structure prediction and molecular docking tools such as AlphaFold2, Metal3D, AutoDockVina, and Rosetta. We isolated a bacterium with laccase activities from fecal samples from a Hermann's tortoise (Testudo hermanni), identified it as Klebsiella michiganensis using 16S rRNA sequencing and nanopore genome sequencing, and then identified a sequence encoding a laccase with a predicted molecular weight of approximately 27.5 kDa. Expression of the corresponding, chemically synthesized DNA fragment resulted in the isolation of an active laccase. The enzyme showed considerable thermostability, retaining 21% of its activity after boiling for 30 min. Using state-of-the-art information technology and machine learning techniques, we conducted 3D-structure prediction on this sequence, predicted its copper-ion binding sites, and validated these predictions through site-directed mutagenesis and expression. Subsequently, we performed computer-aided evolution studies on this sequence and found that 90% of the results from the selected mutations exhibited improved performance. In summary, this study not only revealed a novel laccase but also demonstrated an efficient approach for advancing research on the molecular evolution of bacterial laccases using cutting-edge machine learning, next-generation sequencing, traditional bioinformatics approaches, and laboratory techniques, providing an effective strategy for discovering and design new bacterial laccases.</p>","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":"1226-1237"},"PeriodicalIF":3.2,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12127718/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143416025","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction to Rigidifying Flexible Sites: A Promising Strategy to Improve Thermostability of Lysophospholipase From Pyrococcus abyssi.","authors":"","doi":"10.1002/prot.26804","DOIUrl":"10.1002/prot.26804","url":null,"abstract":"","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":"1295"},"PeriodicalIF":3.2,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143071260","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Skittles: GNN-Assisted Pseudo-Ligands Generation and Its Application for Binding Sites Classification and Affinity Prediction.","authors":"Sergei Evteev, Alexey Ereshchenko, Denis Adjugim, Alexey Vyacheslavov, Anna Pastukhova, Alexander Malyshev, Victor Terentiev, Yan Ivanenkov","doi":"10.1002/prot.26816","DOIUrl":"10.1002/prot.26816","url":null,"abstract":"<p><p>Nowadays, multiple solutions are known for identifying ligand-protein binding sites. Another important task is labeling each point of a binding site with the appropriate atom type, a process known as pseudo-ligand generation. The number of solutions for pseudo-ligand generation is limited, and, to our knowledge, the influence of machine learning techniques has not been studied previously. Here, we describe Skittles, a new graph neural network-assisted pseudo-ligand generation approach, and compare it with known force-field-based methods. We also demonstrate the application of Skittles-based data for solving several important problems in structural biology, including ligand-protein binding site classification and ligand-protein affinity prediction.</p>","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":"1269-1280"},"PeriodicalIF":3.2,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143525333","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"SARS-CoV-2 Mpro Dihedral Angles Reveal Allosteric Signaling.","authors":"Daniel Evans, Samreen Sheraz, Albert Y Lau","doi":"10.1002/prot.26814","DOIUrl":"10.1002/prot.26814","url":null,"abstract":"<p><p>In allosteric proteins, identifying the pathways that signals take from allosteric ligand-binding sites to enzyme active sites or binding pockets and interfaces remains challenging. This avenue of research is motivated by the goals of understanding particular macromolecular systems of interest and creating general methods for their study. An especially important protein that is the subject of many investigations in allostery is the SARS-CoV-2 main protease (Mpro), which is necessary for coronaviral replication. It is both an attractive drug target and, due to intense interest in it for the development of pharmaceutical compounds, a gauge of the state of the art approaches in studying protein inhibition. Here we develop a computational method for characterizing protein allostery and use it to study Mpro. We propose a role of the protein's C-terminal tail in allosteric modulation and warn of unintuitive traps that can plague studies of the role of protein dihedral angles in transmitting allosteric signals.</p>","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":"1281-1289"},"PeriodicalIF":3.2,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12129682/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143544684","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structural Insight Into the SKP1-CUL1-FBXO3-RBX1 Complex.","authors":"Jiajia Wei, Chao Xu","doi":"10.1002/prot.26809","DOIUrl":"10.1002/prot.26809","url":null,"abstract":"<p><p>The cryo-EM structure of human SCF^FBXO3, which consists of CUL1, RBX1, SKP1 and FBXO3 was solved at a nominal resolution of 3.70 Å. Although a previous study reported the crystal structure of the FBXO3 ApaG domain, how FBXO3 is incorporated into the SCF complex remains elusive. In the cryo-EM structure of SCF^FBXO3, the F-box domain of FBXO3 primarily associates with SKP1 via extensive hydrophobic interactions and interacts with the N-terminal region of CUL1 via hydrophobic interactions. The weak cryo-EM map of the RBX1 globular region is close to the FBXO3 ApaG domain, suggesting that unmodified SCF^FBXO3 exhibits a closed conformation and that CUL1 neddylation is likely required to achieve high E3 activity. The structural study provides insight into the assembly of SCF^FBXO3 and its activation mediated by CUL1 neddylation.</p>","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":"1290-1294"},"PeriodicalIF":3.2,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143375054","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evaluation of the Ability of Wasp Venom Bioinspired Peptides (Fraternine-10 and Octovespin) in the Disaggregation and Anti-Aggregation of Amyloid-β Fibrils.","authors":"Yuri Alves de Oliveira Só, Caio Vinícius Sousa Costa, Luana Cristina Camargo, Letícia Germino Veras, Luiz Antônio Ribeiro Júnior, Márcia Renata Mortari, Ricardo Gargano","doi":"10.1002/prot.26806","DOIUrl":"10.1002/prot.26806","url":null,"abstract":"<p><p>Many neurodegenerative diseases are directly related to the formation of toxic protein aggregates, such as Alzheimer's disease, which is associated with the aggregation of amyloid-beta (Aβ). In this context, protein fibrils are the hallmark of these neurodegenerative diseases. In this sense, developing compounds capable of preventing or reducing the formation of protein aggregation in the brain can be of fundamental importance for the curative treatment of these diseases. Animals' venom compounds are known to be selected for nervous system targets, therefore, they are considered an interesting platform for developing pharmacological tools. This work presents a study of the ligands Octovespin (bioinspired by the wasp venom Polybia occidentalis) and Fraternine-10 (bioinspired by the wasp venom Parachartergus fraternus) concerning the disaggregation and anti-aggregation of fibrils of Aβ(17-42) sheets. First, we performed in silico calculations using molecular docking and molecular dynamics simulations with 200 ns. The results indicate that Octovespin and Fraternine-10 interact with the Aβ protein fibrils throughout all simulation time. The RMSD, RMSF, number of hydrogen and radius of gyration values and the interactions with amino acids responsible for fibril aggregation demonstrate that both Octovespin and Fraternine-10 have a significant disaggregation potential, which corroborates the in vitro and in vivo experimental observations. Furthermore, experimental data of Fraternine-10 demonstrated an anti-aggregation effect, indicating that it can promote fibril disaggregation and prevent them from aggregating again to form oligomers. However, in vivo data of Fraternine-10 did not show improvement. Even though in vivo results were not promising, the in vitro and in silico discoveries qualify these molecules as potential sources for developing new candidates to become medicines against Alzheimer's disease.</p>","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":"1257-1268"},"PeriodicalIF":3.2,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143484969","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Double the Double: Revisiting BCL11B's Multimerization.","authors":"Anne Susemihl, Norman Geist, Piotr Grabarczyk, Christian A Schmidt, Mihaela Delcea, Lukas Schulig","doi":"10.1002/prot.26811","DOIUrl":"10.1002/prot.26811","url":null,"abstract":"<p><p>The transcription factor B Cell Lymphoma/Leukemia 11B (BCL11B) exerts a bi-directional function in cancer, with its role as an emerging therapeutic target in cancer treatment being particularly intriguing. BCL11B knockouts in cultured T cells revealed the acquisition of properties characteristic of natural killer cells, hinting at its importance in innate versus adaptive immune regulation. Our previous studies using Förster Resonance Energy Transfer-assisted Fluorescence-Activated Cell Sorting and Hybrid Solvent Replica-Exchange Simulations indicated that BCL11B forms dimers, with this being a prerequisite for its activity. However, size exclusion chromatography and crosslinking experiments have challenged this view, suggesting that BCL11B forms tetramers instead. An atypical CCHC zinc finger motif within the N-terminal region of the protein mediates multimerization and a novel 3D structure is presented based on extensive replica-exchange simulations in strong agreement with experimental data. The physiological relevance of multimer formation of this zinc finger protein has been demonstrated previously. Therefore, understanding the nature of BCL11B's multimerization could potentially enhance our ability to target this protein effectively, hopefully paving the way for novel BCL11B-targeted therapies.</p>","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":"1205-1211"},"PeriodicalIF":3.2,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12127727/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143460943","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Enhancing Functional Protein Design Using Heuristic Optimization and Deep Learning for Anti-Inflammatory and Gene Therapy Applications.","authors":"Ayşenur Soytürk Patat, Özkan Ufuk Nalbantoğlu","doi":"10.1002/prot.26810","DOIUrl":"10.1002/prot.26810","url":null,"abstract":"<p><p>Protein sequence design is a highly challenging task, aimed at discovering new proteins that are more functional and producible under laboratory conditions than their natural counterparts. Deep learning-based approaches developed to address this problem have achieved significant success. However, these approaches often do not adequately emphasize the functional properties of proteins. In this study, we developed a heuristic optimization method to enhance key functionalities such as solubility, flexibility, and stability, while preserving the structural integrity of proteins. This method aims to reduce laboratory demands by enabling a design that is both functional and structurally sound. This approach is particularly valuable for the synthetic production of proteins with anti-inflammatory properties and those used in gene therapy. The designed proteins were initially evaluated for their ability to preserve natural structures using recovery and confidence metrics, followed by assessments with the AlphaFold tool. Additionally, natural protein sequences were mutated using a genetic algorithm and compared with those designed by our method. The results demonstrate that the protein sequences generated by our method exhibit much greater similarity to native protein sequences and structures. The code and sequences for the designed proteins are available at https://github.com/aysenursoyturk/HMHO.</p>","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":"1238-1256"},"PeriodicalIF":3.2,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12127714/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143476550","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Lysine Acetylation of Plant α-Tubulins: Scaling Up the Local Effect to Large System Transformations.","authors":"Alexey Rayevsky, Elijah Bulgakov, Rostyslav Blume, Dmytro Novozhylov, Mariia Stykhylias, Serhii Ozheredov, Pavlo Karpov, Yaroslav Blume","doi":"10.1002/prot.26846","DOIUrl":"https://doi.org/10.1002/prot.26846","url":null,"abstract":"<p><p>Cell migration and motility, cell division, biogenesis and renewal of cell and tissue integrity, and the assembly and retention of cell or tissue architecture, to name but a few, represent increasingly vital processes at the cellular and whole-body levels. These biological processes are closely connected with the major structural transformations that cytoskeletal proteins undergo due to numerous post-translational modifications, including acetylation, tyrosynation, polyglutamylation, etc. We collected all the information on tubulin acetylation and data on related cellular manifestations. This work expands upon our previous investigations into PTM-associated microtubule remodeling by incorporating K60, K163, and K326 into our analysis. Subsequently, we applied the refined protocol to examine the impact of acetylation on the most prevalent tubulin isoforms: TBA1, TBA2, and TBA3. Our analysis identified three distinct patterns on the α-tubulin surface where interactions with neighboring subunits were altered upon acetylation. These findings suggest that acetylation significantly influences the inter-subunit interactions within the microtubule polymer. To assess the likelihood of rearrangement at each of the three acetylation sites (K60, K163, K326), we conducted a series of simulations involving nine tubulin molecules (representing a microtubule lattice). These simulations aimed to quantify the degree of dissociation susceptibility upon acetylation at each of these specific lysine residues while focusing on residues that serve as substrates for HDAC6 deacetylation in plants, K60, K163, and K326. In this study, we have gathered all relevant evidence for the impact of different acetylation points on the assembly and lifespan of microtubule organelles, using A. thaliana tubulins as a model object.</p>","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144217647","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}