Protein Science最新文献

{"title":"Doses for X-ray and electron diffraction: New features in RADDOSE-3D including intensity decay models.","authors":"Joshua L Dickerson, Patrick T N McCubbin, Jonathan C Brooks-Bartlett, Elspeth F Garman","doi":"10.1002/pro.5005","DOIUrl":"10.1002/pro.5005","url":null,"abstract":"<p><p>New features in the dose estimation program RADDOSE-3D are summarised. They include the facility to enter a diffraction intensity decay model which modifies the \"Diffraction Weighted Dose\" output from a \"Fluence Weighted Dose\" to a \"Diffraction-Decay Weighted Dose\", a description of RADDOSE-ED for use in electron diffraction experiments, where dose is historically quoted in electrons/Ų rather than in gray (Gy), and finally the development of a RADDOSE-3D GUI, enabling easy access to all the options available in the program.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"33 7","pages":"e5005"},"PeriodicalIF":4.5,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11196903/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141458958","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}

{"title":"Conformational diversity of human HP1α.","authors":"Tina Ukmar-Godec, Taekyung Yu, Alain Ibanez de Opakua, Christian F Pantoja, Francesca Munari, Markus Zweckstetter","doi":"10.1002/pro.5079","DOIUrl":"10.1002/pro.5079","url":null,"abstract":"<p><p>Heterochromatin protein 1 alpha (HP1α) is an evolutionarily conserved protein that binds chromatin and is important for gene silencing. The protein comprises 191 residues arranged into three disordered regions and two structured domains, the chromo and chromoshadow domain, which associates into a homodimer. While high-resolution structures of the isolated domains of HP1 proteins are known, the structural properties of full-length HP1α remain largely unknown. Using a combination of NMR spectroscopy and structure predictions by AlphaFold2 we provide evidence that the chromo and chromoshadow domain of HP1α engage in direct contacts resulting in a compact chromo/chromoshadow domain arrangement. We further show that HP1β and HP1γ have increased interdomain dynamics when compared to HP1α which may contribute to the distinct roles of different Hp1 isoforms in gene silencing and activation.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"33 7","pages":"e5079"},"PeriodicalIF":4.5,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11187854/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141420600","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}

{"title":"A new lysine biosynthetic enzyme from a bacterial endosymbiont shaped by genetic drift and genome reduction.","authors":"Jenna M Gilkes, Rebekah A Frampton, Amanda J Board, André O Hudson, Thomas G Price, Vanessa K Morris, Deborah L Crittenden, Andrew C Muscroft-Taylor, Campbell R Sheen, Grant R Smith, Renwick C J Dobson","doi":"10.1002/pro.5083","DOIUrl":"10.1002/pro.5083","url":null,"abstract":"<p><p>The effect of population bottlenecks and genome reduction on enzyme function is poorly understood. Candidatus Liberibacter solanacearum is a bacterium with a reduced genome that is transmitted vertically to the egg of an infected psyllid-a population bottleneck that imposes genetic drift and is predicted to affect protein structure and function. Here, we define the function of Ca. L. solanacearum dihydrodipicolinate synthase (CLsoDHDPS), which catalyzes the committed branchpoint reaction in diaminopimelate and lysine biosynthesis. We demonstrate that CLsoDHDPS is expressed in Ca. L. solanacearum and expression is increased ~2-fold in the insect host compared to in planta. CLsoDHDPS has decreased thermal stability and increased aggregation propensity, implying mutations have destabilized the enzyme but are compensated for through elevated chaperone expression and a stabilized oligomeric state. CLsoDHDPS uses a ternary-complex kinetic mechanism, which is to date unique among DHDPS enzymes, has unusually low catalytic ability, but an unusually high substrate affinity. Structural studies demonstrate that the active site is more open, and the structure of CLsoDHDPS with both pyruvate and the substrate analogue succinic-semialdehyde reveals that the product is both structurally and energetically different and therefore evolution has in this case fashioned a new enzyme. Our study suggests the effects of genome reduction and genetic drift on the function of essential enzymes and provides insights on bacteria-host co-evolutionary associations. We propose that bacteria with endosymbiotic lifestyles present a rich vein of interesting enzymes useful for understanding enzyme function and/or informing protein engineering efforts.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"33 7","pages":"e5083"},"PeriodicalIF":4.5,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11201819/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141458954","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}

{"title":"Characterization of βB2-crystallin tryptophan mutants reveals two different folding states in solution.","authors":"Jiayue Sun, Ken Morishima, Rintaro Inoue, Masaaki Sugiyama, Takumi Takata","doi":"10.1002/pro.5092","DOIUrl":"10.1002/pro.5092","url":null,"abstract":"<p><p>Conserved tryptophan residues are critical for the structure and the stability of β/γ-crystallin in the lenses of vertebrates. During aging, in which the lenses are continuously exposed to ultraviolet irradiation and other environmental stresses, oxidation of tryptophan residues in β/γ-crystallin is triggered and impacts the lens proteins to varying degrees. Kynurenine derivatives, formed by oxidation of tryptophan, accumulate, resulting in destabilization and insolubilization of β/γ-crystallin, which correlates with age-related cataract formation. To understand the contribution of tryptophan modification on the structure and stability of human βB2-crystallin, five tryptophan residues were mutated to phenylalanine considering its similarity in structure and hydrophilicity to kynurenine. Among all mutants, W59F and W151F altered the stability and homo-oligomerization of βB2-crystallin-W59F promoted tetramerization whereas W151F blocked oligomerization. Most W59F dimers transformed into tetramer in a month, and the separated dimer and tetramer of W59F demonstrated different structures and hydrophobicity, implying that the biochemical properties of βB2-crystallin vary over time. By using SAXS, we found that the dimer of βB2-crystallin in solution resembled the lattice βB1-crystallin dimer (face-en-face), whereas the tetramer of βB2-crystallin in solution resembled its lattice tetramer (domain-swapped). Our results suggest that homo-oligomerization of βB2-crystallin includes potential inter-subunit reactions, such as dissociation, unfolding, and re-formation of the dimers into a tetramer in solution. The W>F mutants are useful in studying different folding states of βB2-crystallin in lens.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"33 7","pages":"e5092"},"PeriodicalIF":4.5,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11201810/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141458957","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}

{"title":"Periplasmic electron transfer network in Geobacter sulfurreducens revealed by biomolecular interaction studies.","authors":"Marisa R Ferreira, Leonor Morgado, Carlos A Salgueiro","doi":"10.1002/pro.5082","DOIUrl":"https://doi.org/10.1002/pro.5082","url":null,"abstract":"<p><p>Multiheme cytochromes located in different compartments are crucial for extracellular electron transfer in the bacterium Geobacter sulfurreducens to drive important environmental processes and biotechnological applications. Recent studies have unveiled that for particular sets of electron terminal acceptors, discrete respiratory pathways selectively recruit specific cytochromes from both the inner and outer membranes. However, such specificity was not observed for the abundant periplasmic cytochromes, namely the triheme cytochrome family PpcA-E. In this work, the distinctive NMR spectroscopic signatures of these proteins in different redox states were explored to monitor pairwise interactions and electron transfer reactions between each pair of cytochromes. The results showed that the five proteins interact transiently and can exchange electrons between each other revealing intra-promiscuity within the members of this family. This discovery is discussed in the light of the establishment of an effective electron transfer network by this pool of cytochromes. This network is advantageous to the bacteria as it enables the maintenance of the functional working potential redox range within the cells.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"33 7","pages":"e5082"},"PeriodicalIF":4.5,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11210610/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141470348","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}

{"title":"Interplay between protease and reverse transcriptase dimerization in a model HIV-1 polyprotein.","authors":"Brisa Caroline Alves Chagas, Xiaohong Zhou, Michel Guerrero, Tatiana V Ilina, Rieko Ishima","doi":"10.1002/pro.5080","DOIUrl":"10.1002/pro.5080","url":null,"abstract":"<p><p>The Gag-Pol polyprotein in human immunodeficiency virus type I (HIV-1) encodes enzymes that are essential for virus replication: protease (PR), reverse transcriptase (RT), and integrase (IN). The mature forms of PR, RT and IN are homodimer, heterodimer and tetramer, respectively. The precise mechanism underlying the formation of dimer or tetramer is not yet understood. Here, to gain insight into the dimerization of PR and RT in the precursor, we prepared a model precursor, PR-RT, incorporating an inactivating mutation at the PR active site, D25A, and including two residues in the p6* region, fused to a SUMO-tag, at the N-terminus of the PR region. We also prepared two mutants of PR-RT containing a dimer dissociation mutation either in the PR region, PR(T26A)-RT, or in the RT region, PR-RT(W401A). Size exclusion chromatography showed both monomer and dimer fractions in PR-RT and PR(T26A)-RT, but only monomer in PR-RT(W401A). SEC experiments of PR-RT in the presence of protease inhibitor, darunavir, significantly enhanced the dimerization. Additionally, SEC results suggest an estimated PR-RT dimer dissociation constant that is higher than that of the mature RT heterodimer, p66/p51, but slightly lower than the premature RT homodimer, p66/p66. Reverse transcriptase assays and RT maturation assays were performed as tools to assess the effects of the PR dimer-interface on these functions. Our results consistently indicate that the RT dimer-interface plays a crucial role in the dimerization in PR-RT, whereas the PR dimer-interface has a lesser role.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"33 7","pages":"e5080"},"PeriodicalIF":4.5,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11187873/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141420603","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}

{"title":"How arginine inhibits substrate-binding domain 2 elucidated using molecular dynamics simulations.","authors":"Maximilian Kienlein, Martin Zacharias","doi":"10.1002/pro.5077","DOIUrl":"10.1002/pro.5077","url":null,"abstract":"<p><p>The substrate-binding domain 2 (SBD2) is an important part of the bacterial glutamine (GLN) transporter and mediates binding and delivery of GLN to the transporter translocation subunit. The SBD2 consists of two domains, D1 and D2, that bind GLN in the space between domains in a closed structure. In the absence of ligand, the SBD2 adopts an open conformation with larger space between domains. The GLN binding and closing are essential for the subsequent transport into the cell. Arginine (ARG) can also bind to SBD2 but does not induce closing and inhibits GLN transport. We use atomistic molecular dynamics (MD) simulations in explicit solvent to study ARG binding in the presence of the open SBD2 structure and observed reversible binding to the native GLN binding site with similar contacts but no transition to a closed SBD2 state. Absolute binding free energy simulations predict a considerable binding affinity of ARG and GLN to the binding site on the D1 domain. Free energy simulations to induce subsequent closing revealed a strong free energy penalty in case of ARG binding in contrast to GLN binding that favors the closed SBD2 state but still retains a free energy barrier for closing. The simulations allowed the identification of the molecular origin of the closing penalty in case of bound ARG and suggested a mutation of lysine at position 373 to alanine that strongly reduced the penalty and allowed closing even in the presence of bound ARG. The study offers an explanation of the molecular mechanism of how ARG competitively inhibits GLN from binding to SBD2 and from triggering the transition to a closed conformation. The proposed Lys373Ala mutation shows promise as a potential tool to validate whether a conformational mismatch between open SBD2 and the translocator is responsible for preventing ARG uptake to the cell.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"33 7","pages":"e5077"},"PeriodicalIF":4.5,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11184577/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141420602","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}

{"title":"Structure‐aware deep learning model for peptide toxicity prediction","authors":"Hossein Ebrahimikondori, Darcy Sutherland, Anat Yanai, Amelia Richter, Ali Salehi, Chenkai Li, Lauren Coombe, Monica Kotkoff, René L. Warren, Inanc Birol","doi":"10.1002/pro.5076","DOIUrl":"https://doi.org/10.1002/pro.5076","url":null,"abstract":"Antimicrobial resistance is a critical public health concern, necessitating the exploration of alternative treatments. While antimicrobial peptides (AMPs) show promise, assessing their toxicity using traditional wet lab methods is both time‐consuming and costly. We introduce tAMPer, a novel multi‐modal deep learning model designed to predict peptide toxicity by integrating the underlying amino acid sequence composition and the three‐dimensional structure of peptides. tAMPer adopts a graph‐based representation for peptides, encoding ColabFold‐predicted structures, where nodes represent amino acids and edges represent spatial interactions. Structural features are extracted using graph neural networks, and recurrent neural networks capture sequential dependencies. tAMPer's performance was assessed on a publicly available protein toxicity benchmark and an AMP hemolysis data we generated. On the latter, tAMPer achieves an F1‐score of 68.7%, outperforming the second‐best method by 23.4%. On the protein benchmark, tAMPer exhibited an improvement of over 3.0% in the F1‐score compared to current state‐of‐the‐art methods. We anticipate tAMPer to accelerate AMP discovery and development by reducing the reliance on laborious toxicity screening experiments.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"159 1","pages":""},"PeriodicalIF":8.0,"publicationDate":"2024-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141506685","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Screening a knowledge‐based library of low molecular weight compounds against the proline biosynthetic enzyme 1‐pyrroline‐5‐carboxylate 1 (PYCR1)","authors":"Kaylen R. Meeks, Alexandra N. Bogner, John J. Tanner","doi":"10.1002/pro.5072","DOIUrl":"https://doi.org/10.1002/pro.5072","url":null,"abstract":"Δ<jats:sup>1</jats:sup>‐pyrroline‐5‐carboxylate reductase isoform 1 (PYCR1) is the last enzyme of proline biosynthesis and catalyzes the NAD(P)H‐dependent reduction of Δ<jats:sup>1</jats:sup>‐pyrroline‐5‐carboxylate to <jats:sc>L</jats:sc>‐proline. High PYCR1 gene expression is observed in many cancers and linked to poor patient outcomes and tumor aggressiveness. The knockdown of the <jats:italic>PYCR1</jats:italic> gene or the inhibition of PYCR1 enzyme has been shown to inhibit tumorigenesis in cancer cells and animal models of cancer, motivating inhibitor discovery. We screened a library of 71 low molecular weight compounds (average MW of 131 Da) against PYCR1 using an enzyme activity assay. Hit compounds were validated with X‐ray crystallography and kinetic assays to determine affinity parameters. The library was counter‐screened against human Δ<jats:sup>1</jats:sup>‐pyrroline‐5‐carboxylate reductase isoform 3 and proline dehydrogenase (PRODH) to assess specificity/promiscuity. Twelve PYCR1 and one PRODH inhibitor crystal structures were determined. Three compounds inhibit PYCR1 with competitive inhibition parameter of 100 μM or lower. Among these, (<jats:italic>S</jats:italic>)‐tetrahydro‐2H‐pyran‐2‐carboxylic acid (70 μM) has higher affinity than the current best tool compound <jats:italic>N</jats:italic>‐formyl‐<jats:sc>l</jats:sc>‐proline, is 30 times more specific for PYCR1 over human Δ<jats:sup>1</jats:sup>‐pyrroline‐5‐carboxylate reductase isoform 3, and negligibly inhibits PRODH. Structure‐affinity relationships suggest that hydrogen bonding of the heteroatom of this compound is important for binding to PYCR1. The structures of PYCR1 and PRODH complexed with 1‐hydroxyethane‐1‐sulfonate demonstrate that the sulfonate group is a suitable replacement for the carboxylate anchor. This result suggests that the exploration of carboxylic acid isosteres may be a promising strategy for discovering new classes of PYCR1 and PRODH inhibitors. The structure of PYCR1 complexed with <jats:sc>l</jats:sc>‐pipecolate and NADH supports the hypothesis that PYCR1 has an alternative function in lysine metabolism.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"54 1","pages":""},"PeriodicalIF":8.0,"publicationDate":"2024-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141523453","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"In silico identification of a novel Cdc2-like kinase 2 (CLK2) inhibitor in triple negative breast cancer.","authors":"Cheng-Chiao Huang, Chia-Ming Hsu, Min-Wu Chao, Kai-Cheng Hsu, Tony Eight Lin, Shih-Chung Yen, Huang-Ju Tu, Shiow-Lin Pan","doi":"10.1002/pro.5004","DOIUrl":"10.1002/pro.5004","url":null,"abstract":"<p><p>Dysregulation of RNA splicing processes is intricately linked to tumorigenesis in various cancers, especially breast cancer. Cdc2-like kinase 2 (CLK2), an oncogenic RNA-splicing kinase pivotal in breast cancer, plays a significant role, particularly in the context of triple-negative breast cancer (TNBC), a subtype marked by substantial medical challenges due to its low survival rates. In this study, we employed a structure-based virtual screening (SBVS) method to identify potential CLK2 inhibitors with novel chemical structures for treating TNBC. Compound 670551 emerged as a novel CLK2 inhibitor with a 50% inhibitory concentration (IC₅₀) value of 619.7 nM. Importantly, Compound 670551 exhibited high selectivity for CLK2 over other protein kinases. Functionally, this compound significantly reduced the survival and proliferation of TNBC cells. Results from a cell-based assay demonstrated that this inhibitor led to a decrease in RNA splicing proteins, such as SRSF4 and SRSF6, resulting in cell apoptosis. In summary, we identified a novel CLK2 inhibitor as a promising potential treatment for TNBC therapy.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"33 6","pages":"e5004"},"PeriodicalIF":4.5,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11081522/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140899317","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}