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An accelerated molecular dynamics study for investigating protein pathways using the bond-boost hyperdynamics method. 一种加速分子动力学研究,用于研究蛋白质途径,使用bond-boost超动力学方法。
IF 4.5 3区 生物学
Protein Science Pub Date : 2025-03-01 DOI: 10.1002/pro.70073
Soon Woo Park, Moon-Ki Choi, Byung Ho Lee, Sangjae Seo, Woo Kyun Kim, Moon Ki Kim
{"title":"An accelerated molecular dynamics study for investigating protein pathways using the bond-boost hyperdynamics method.","authors":"Soon Woo Park, Moon-Ki Choi, Byung Ho Lee, Sangjae Seo, Woo Kyun Kim, Moon Ki Kim","doi":"10.1002/pro.70073","DOIUrl":"10.1002/pro.70073","url":null,"abstract":"<p><p>Molecular dynamics (MD) simulation is an important tool for understanding protein dynamics and the thermodynamic properties of proteins. However, due to the high computational cost of MD simulations, it is still challenging to explore a wide conformational space. To solve this problem, a variety of accelerated MD (aMD) schemes have been proposed over the past few decades. The bond-boost method (BBM) is one of such aMD schemes, which expedites escape events from energy basins by adding a bias potential based on changes in bond length. In this paper, we present a new methodology based on the BBM for accelerating the conformational transition of proteins. In our modified BBM, the bias potential is constructed using the dihedral angle and hydrogen bond, which are more suitable variables to monitor the conformational change in proteins. Additionally, we have developed an efficient algorithm compatible with the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) package. The method is validated with the conformational change of ribose binding protein and adenylate kinase by comparing the conventional and accelerated MD simulation results. Based on the aMD results, the characteristics of the proteins are investigated by monitoring the conformational transition pathways. Moreover, the free energy landscape calculated using umbrella sampling confirms all the states identified by the aMD simulation are the free energy minima, and the system makes transitions following the path indicated by the free energy landscape. Our efficient approach is expected to play a key role in investigating transition pathways in a wide range of protein simulations.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 3","pages":"e70073"},"PeriodicalIF":4.5,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11854359/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143503768","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Unraveling the molecular grammar and the structural transitions underlying the fibrillation of a viral fibrillogenic domain. 揭示病毒纤维原结构域颤动的分子语法和结构转变。
IF 4.5 3区 生物学
Protein Science Pub Date : 2025-03-01 DOI: 10.1002/pro.70068
Frank Gondelaud, Julien Leval, Lisha Arora, Anuja Walimbe, Christophe Bignon, Denis Ptchelkine, Stefania Brocca, Samrat Mukhopadyay, Sonia Longhi
{"title":"Unraveling the molecular grammar and the structural transitions underlying the fibrillation of a viral fibrillogenic domain.","authors":"Frank Gondelaud, Julien Leval, Lisha Arora, Anuja Walimbe, Christophe Bignon, Denis Ptchelkine, Stefania Brocca, Samrat Mukhopadyay, Sonia Longhi","doi":"10.1002/pro.70068","DOIUrl":"10.1002/pro.70068","url":null,"abstract":"<p><p>Hendra virus (HeV) is a biosafety level 4 human pathogen belonging to the Henipavirus genus within the Paramyxoviridae family. In HeV, the phosphoprotein-encoding gene also drives the synthesis of the V and W proteins that are two major players in the host innate immune response evasion. These three proteins share a common intrinsically disordered N-terminal domain (NTD) and have distinct C-terminal domains. We recently reported the ability of a short region (i.e., PNT3), located within the shared NTD, to form fibrils. We subsequently identified a PNT3 motif (EYYY) critically involved in fibrillation and deciphered the contribution of each tyrosine to the process. Herein, we combined mutational studies with various biochemical and biophysical approaches to further investigate the molecular mechanisms underlying PNT3 fibrillation. The results show that (i) lysine residues play a critical role in driving fibrillation, (ii) hydrophobic residues affect the nucleation step, and (iii) charge distribution strongly affects the fibrillation propensities. Vibrational Raman spectroscopy data further validated the role of lysine residues in promoting fibrillation and enabled documenting the formation of cross-β amyloid structures. Altogether, these results illuminate the molecular mechanisms involved in fibril formation and pave the way towards the rational design of inhibitors.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 3","pages":"e70068"},"PeriodicalIF":4.5,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11845978/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143477089","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Interfacing bacterial microcompartment shell proteins with genetically encoded condensates. 细菌微室壳蛋白与基因编码凝聚物的接合。
IF 4.5 3区 生物学
Protein Science Pub Date : 2025-03-01 DOI: 10.1002/pro.70061
Michele Costantino, Eric J Young, Abesh Banerjee, Cheryl A Kerfeld, Giovanna Ghirlanda
{"title":"Interfacing bacterial microcompartment shell proteins with genetically encoded condensates.","authors":"Michele Costantino, Eric J Young, Abesh Banerjee, Cheryl A Kerfeld, Giovanna Ghirlanda","doi":"10.1002/pro.70061","DOIUrl":"10.1002/pro.70061","url":null,"abstract":"<p><p>Condensates formed by liquid-liquid phase separation are promising candidates for the development of synthetic cells and organelles. Here, we show that bacterial microcompartment shell proteins from Haliangium ochraceum (BMC-H) assemble into coatings on the surfaces of protein condensates formed by tandem RGG-RGG domains, an engineered construct derived from the intrinsically disordered region of the RNA helicase LAF-1. WT BMC-H proteins formed higher-order assemblies within RGG-RGG droplets; however, engineered BMC-H variants fused to RGG truncations formed coatings on droplet surfaces. These intrinsically disordered tags controlled the interaction with the condensed phase based on their length and sequence, and one of the designs, BMC-H-T2, assembled preferentially on the surface of the droplet and prevented droplet coalescence. The formation of the coatings is dependent on the pH and protein concentration; once formed, the coatings are stable and do not exchange with the dilute phase. Coated droplets could sequester and concentrate folded proteins, including TEV protease, with selectivity similar to uncoated droplets. Addition of TEV protease to coated droplets resulted in the digestion of RGG-RGG to RGG and a decrease in droplet diameter, but not in the dissolution of the coatings. BMC shell protein-coated protein condensates are entirely encodable and provide a way to control the properties of liquid-liquid phase-separated compartments in the context of synthetic biology.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 3","pages":"e70061"},"PeriodicalIF":4.5,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11837282/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143449969","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
PEG-mCherry interactions beyond classical macromolecular crowding. 超越经典大分子拥挤的PEG-mCherry相互作用。
IF 4.5 3区 生物学
Protein Science Pub Date : 2025-03-01 DOI: 10.1002/pro.5235
Liam Haas-Neill, Khalil Joron, Eitan Lerner, Sarah Rauscher
{"title":"PEG-mCherry interactions beyond classical macromolecular crowding.","authors":"Liam Haas-Neill, Khalil Joron, Eitan Lerner, Sarah Rauscher","doi":"10.1002/pro.5235","DOIUrl":"10.1002/pro.5235","url":null,"abstract":"<p><p>The dense cellular environment influences bio-macromolecular structure, dynamics, interactions, and function. Despite advancements in understanding protein-crowder interactions, predicting their precise effects on protein structure and function remains challenging. Here, we elucidate the effects of PEG-induced crowding on the fluorescent protein mCherry using molecular dynamics simulations and fluorescence-based experiments. We identify and characterize specific PEG-induced structural and dynamical changes in mCherry. Importantly, we find interactions in which PEG molecules wrap around specific surface-exposed residues in a binding mode previously observed in protein crystal structures. Fluorescence correlation spectroscopy experiments capture PEG-induced changes, including aggregation, suggesting a potential role for the specific PEG-mCherry interactions identified in simulations. Additionally, mCherry fluorescence lifetimes are influenced by PEG and not by the bulkier crowder dextran or by another linear polymer, polyvinyl alcohol, highlighting the importance of crowder-protein soft interactions. This work augments our understanding of macromolecular crowding effects on protein structure and dynamics.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 3","pages":"e5235"},"PeriodicalIF":4.5,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11836898/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143449999","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Functional characterization of two AA10 lytic polysaccharide monooxygenases from Cellulomonas gelida. 凝胶胞单胞菌两种AA10多糖单加氧酶的功能表征。
IF 4.5 3区 生物学
Protein Science Pub Date : 2025-03-01 DOI: 10.1002/pro.70060
Rosaliina Turunen, Tina R Tuveng, Zarah Forsberg, Valerie C Schiml, Vincent G H Eijsink, Magnus Ø Arntzen
{"title":"Functional characterization of two AA10 lytic polysaccharide monooxygenases from Cellulomonas gelida.","authors":"Rosaliina Turunen, Tina R Tuveng, Zarah Forsberg, Valerie C Schiml, Vincent G H Eijsink, Magnus Ø Arntzen","doi":"10.1002/pro.70060","DOIUrl":"10.1002/pro.70060","url":null,"abstract":"<p><p>Lytic polysaccharide monooxygenases (LPMOs) are redox enzymes targeting the crystalline region of recalcitrant polysaccharides such as cellulose and chitin. Functional characterization of two LPMOs from the cellulose-degrading soil bacterium Cellulomonas gelida, CgLPMO10A and CgLPMO10B, showed expected activities on cellulose but also revealed novel features of AA10 LPMOs. While clustering together with strictly C1-oxidizing and strictly cellulose-active AA10 LPMOs, CgLPMO10A exhibits activity on both cellulose and chitin, oxidizing the C1 carbon of both substrates. This combination of substrate and oxidative specificity has not been previously observed for family 10 LPMOs and may be due to a conspicuous divergence in two hydrophobic residues on the substrate-binding surface. CgLPMO10B oxidizes cellulose at both the C1 and C4 positions and is also active on chitin, in line with predictions based on phylogeny. Interestingly, while coming from the same organism and both acting on cellulose, the two enzymes have markedly different redox properties with CgLPMO10B displaying the lowest redox potential and the highest oxidase activity observed for an AA10 LPMO so far. These results provide insight into the LPMO machinery of C. gelida and expand the known catalytic repertoire of bacterial LPMOs.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 3","pages":"e70060"},"PeriodicalIF":4.5,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11837042/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143449944","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Understanding dry proteins and their protection with solid-state hydrogen-deuterium exchange. 了解干蛋白及其在固态氢-氘交换中的保护作用。
IF 4.5 3区 生物学
Protein Science Pub Date : 2025-03-01 DOI: 10.1002/pro.70075
Julia A Brom, Gary J Pielak
{"title":"Understanding dry proteins and their protection with solid-state hydrogen-deuterium exchange.","authors":"Julia A Brom, Gary J Pielak","doi":"10.1002/pro.70075","DOIUrl":"10.1002/pro.70075","url":null,"abstract":"<p><p>Protein-based drugs are among our most powerful therapeutics, but their manufacture, storage, and distribution are hindered by solution instability and the expense of the necessary refrigeration. Formulating proteins as dry products, which is an almost entirely empirical endeavor, can ameliorate the problem, but recovery of an acceptable product upon resuspension is not always possible. Additional knowledge about dry protein structure and protection is necessary to make dry formulation both more rational and effective. While most biophysical and biochemical techniques necessitate solvated protein, solid-state hydrogen-deuterium exchange enables the study of dry proteins. Fourier-transform infrared spectroscopy, mass spectrometry, and liquid-observed vapor exchange nuclear magnetic resonance have all been used to measure isotopic exchange. These methods report on secondary structure, peptide, and residue level exposure, respectively. Recent studies using solid-state hydrogen-deuterium exchange provide insight into the mechanisms of dry protein protection and uncover stabilizing and destabilizing interactions, bringing us closer to rational formulation of these lifesaving products.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 3","pages":"e70075"},"PeriodicalIF":4.5,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11854353/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143503777","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A robust fluorogenic substrate for chikungunya virus protease (nsP2) activity. 基孔肯雅病毒蛋白酶(nsP2)活性的强荧光底物。
IF 4.5 3区 生物学
Protein Science Pub Date : 2025-03-01 DOI: 10.1002/pro.70069
Sparsh Makhaik, Wioletta Rut, Shruti Choudhary, Tulsi Upadhyay, Chenzhou Hao, Michael Westberg, Cedric Bobst, Euna Yoo, Jasna Fejzo, Michael Z Lin, Matthew Bogyo, Paul Thompson, Marcin Drag, Jeanne A Hardy
{"title":"A robust fluorogenic substrate for chikungunya virus protease (nsP2) activity.","authors":"Sparsh Makhaik, Wioletta Rut, Shruti Choudhary, Tulsi Upadhyay, Chenzhou Hao, Michael Westberg, Cedric Bobst, Euna Yoo, Jasna Fejzo, Michael Z Lin, Matthew Bogyo, Paul Thompson, Marcin Drag, Jeanne A Hardy","doi":"10.1002/pro.70069","DOIUrl":"10.1002/pro.70069","url":null,"abstract":"<p><p>Chikungunya virus (CHIKV) is an emerging pathogen with pandemic potential. CHIKV infection in humans is transmitted by mosquitoes and induces common symptoms of high fever, arthralgia and myalgia. Because no specific antiviral drugs for treatment of CHIKV infection are available, drug development remains a central goal. The chikungunya virus protease from nsP2 (CHIKVP) has emerged as a key drug target due to its indispensable role in viral replication via cleavage of the viral polyprotein. To date, effective tools for screening for CHIKVP inhibitors that reflect the most critical polyprotein cleavage sites have been lacking, hampering drug-development efforts. We found that the recognition ability of CHIKVP is sensitive to the length of peptide substrates. In this study, we report a robust fluorogenic substrate comprising a 15-mer peptide derived from the nsP3/4 junction from the CHIKV polyprotein. This peptide is flanked by an ACC-Lys(dnp) donor-quencher pair. Our new substrate acc-CHIK<sub>15</sub>-dnp shows a 30-fold improved signal-to-noise ratio as compared to the previously reported edab<sub>8</sub> substrate, which is also based on the nsP3/4 junction. We found acc-CHIK<sub>15</sub>-dnp is recognized only by CHIKVP but not by other alphavirus proteases. This is surprising due to the high level of sequence conservation in the alpha virus polyprotein junctions and indicates that the P-side residues are more important than the P'-side sequence for effective CHIKVP cleavage. The robust signal-to-noise ratio obtained using acc-CHIK<sub>15</sub>-dnp derived from the nsP3/4 cleavage site enabled much improved small molecule HTS on CHIKV relative to other fluorogenic reporters.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 3","pages":"e70069"},"PeriodicalIF":4.5,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11843719/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143468889","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Stabilization of a protein by a single halogen-based aromatic amplifier. 用单卤素基芳香放大器稳定蛋白质。
IF 4.5 3区 生物学
Protein Science Pub Date : 2025-03-01 DOI: 10.1002/pro.70064
Krystel El Hage, Balamurugan Dhayalan, Yen-Shan Chen, Nelson B Phillips, Jonathan Whittaker, Kelley Carr, Linda Whittaker, Manijeh H Phillips, Faramarz Ismail-Beigi, Markus Meuwly, Michael A Weiss
{"title":"Stabilization of a protein by a single halogen-based aromatic amplifier.","authors":"Krystel El Hage, Balamurugan Dhayalan, Yen-Shan Chen, Nelson B Phillips, Jonathan Whittaker, Kelley Carr, Linda Whittaker, Manijeh H Phillips, Faramarz Ismail-Beigi, Markus Meuwly, Michael A Weiss","doi":"10.1002/pro.70064","DOIUrl":"10.1002/pro.70064","url":null,"abstract":"<p><p>The utility of halogenation in protein design is investigated by a combination of quantitative atomistic simulations and experiment. Application to insulin is of complementary basic and translational interest. In a singly halogenated aromatic ring, regiospecific inductive effects were predicted to modulate multiple surrounding electrostatic (weakly polar) interactions, thereby amplifying changes in thermodynamic stability. In accordance with the simulations, we demonstrated stabilization of insulin by single halogen atoms at the ortho position of an invariant phenylalanine (2-F-Phe<sup>B24</sup>, 2-Cl-Phe<sup>B24</sup>, and 2-Br-Phe<sup>B24</sup>; ΔΔG<sub>u</sub> = -0.5 to -1.0 kcal/mol) located at the edge of a protein crevice; corresponding meta and para substitutions had negligible effects. Although receptor-binding affinities were generally decreased (in accordance with packing of the native Phe at the hormone-receptor interface), the ortho-analogs retained biological activity in mammalian cells and in a rat model of diabetes mellitus. Further, the ortho-modified analogs exhibited enhanced resistance to fibrillation above room temperature in two distinct assays of physical stability. Regiospecific halo-aromatic stabilization may thus augment the shelf life of pharmaceutical insulin formulations under real-world conditions. This approach, extending principles of medicinal chemistry, promises to apply to a broad range of therapeutic proteins and vaccines whose biophysical stabilization would enhance accessibility in the developing world.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 3","pages":"e70064"},"PeriodicalIF":4.5,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11837044/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143450197","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Docking guidance with experimental ligand structural density improves docking pose prediction and virtual screening performance. 利用实验配体结构密度进行对接指导可提高对接姿势预测和虚拟筛选性能。
IF 4.5 3区 生物学
Protein Science Pub Date : 2025-03-01 DOI: 10.1002/pro.70082
Althea T Hansel-Harris, Andreas F Tillack, Diogo Santos-Martins, Matthew Holcomb, Stefano Forli
{"title":"Docking guidance with experimental ligand structural density improves docking pose prediction and virtual screening performance.","authors":"Althea T Hansel-Harris, Andreas F Tillack, Diogo Santos-Martins, Matthew Holcomb, Stefano Forli","doi":"10.1002/pro.70082","DOIUrl":"10.1002/pro.70082","url":null,"abstract":"<p><p>Recent advances in structural biology have led to the publication of a wealth of high-resolution x-ray crystallography (XRC) and cryo-EM macromolecule structures, including many complexes with small molecules of interest for drug design. While it is common to incorporate information from the atomic coordinates of these complexes into docking (e.g., pharmacophore models or scaffold hopping), there are limited methods to directly leverage the underlying density information. This is desirable because it does not rely on the determination of relevant coordinates, which may require expert intervention, but instead interprets all density as indicative of regions to which a ligand may be bound. To do so, we have developed CryoXKit, a tool to incorporate experimental densities from either cryo-EM or XRC as a biasing potential on heavy atoms during docking. Using this structural density guidance with AutoDock-GPU, we found significant improvements in re-docking and cross-docking, important pose prediction tasks, compared with the unmodified AutoDock4 force field. Failures in cross-docking tasks are additionally reflective of changes in the positioning of pharmacophores in the site, suggesting it is a fundamental limitation of transferring information between complexes. We additionally found, against a set of targets selected from the LIT-PCBA dataset, that rescoring of these improved poses leads to better discriminatory power in virtual screenings for selected targets. Overall, CryoXKit provides a user-friendly method for improving docking performance with experimental data while requiring no a priori pharmacophore definition and at virtually no computational expense. Map-modification code available at: https://github.com/forlilab/CryoXKit.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 3","pages":"e70082"},"PeriodicalIF":4.5,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11854350/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143503771","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
An improved variant of tobacco etch virus (TEV) protease that does not need reducing agents. 一种不需要还原剂的烟草蚀刻病毒(TEV)蛋白酶的改进变体。
IF 4.5 3区 生物学
Protein Science Pub Date : 2025-03-01 DOI: 10.1002/pro.70049
Stella M Davis, Bryn L Romig, Alyssa A Abe, Nikolaus M Loening
{"title":"An improved variant of tobacco etch virus (TEV) protease that does not need reducing agents.","authors":"Stella M Davis, Bryn L Romig, Alyssa A Abe, Nikolaus M Loening","doi":"10.1002/pro.70049","DOIUrl":"10.1002/pro.70049","url":null,"abstract":"<p><p>Here we show that a combination of previously suggested mutations for tobacco etch virus (TEV) protease results in a TEV protease mutant that maintains the same catalytic efficiency as previously described mutants but has enhanced stability and solubility. Another advantage of this new variant of TEV protease is that it does not need the inclusion of a reducing agent to maintain its effectiveness, making it easier to generate, store, and use in cleavage reactions compared to previous TEV protease mutants and, in particular, makes it a good choice for cleaving proteins that contain disulfide bonds that would otherwise be altered by the inclusion of a reducing agent. We also provide a straightforward purification protocol for generating this new version of TEV protease.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 3","pages":"e70049"},"PeriodicalIF":4.5,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11837032/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143449965","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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