Protein Science最新文献

{"title":"Insights into the flexibility of the domain-linking loop in actinobacterial coproheme decarboxylase through structures and molecular dynamics simulations.","authors":"Gaurav Patil, Diego Javier Alonso de Armiño, Yirui Guo, Paul G Furtmüller, Dominika Borek, Dario A Estrin, Stefan Hofbauer","doi":"10.1002/pro.70027","DOIUrl":"10.1002/pro.70027","url":null,"abstract":"<p><p>Prokaryotic heme biosynthesis in Gram-positive bacteria follows the coproporphyrin-dependent heme biosynthesis pathway. The last step in this pathway is catalyzed by the enzyme coproheme decarboxylase, which oxidatively transforms two propionate groups into vinyl groups yielding heme b. The catalytic reaction cycle of coproheme decarboxylases exhibits four different states: the apo-form, the substrate (coproheme)-bound form, a transient three-propionate intermediate form (monovinyl, monopropionate deuteroheme; MMD), and the product (heme b)-bound form. In this study, we used cryogenic electron microscopy single-particle reconstruction (cryo-EM SPR) to characterize structurally the apo and heme b-bound forms of actinobacterial coproheme decarboxylase from Corynebacterium diphtheriae. The flexible loop that connects the N-terminal and the C-terminal ferredoxin domains of coproheme decarboxylases plays an important role in interactions between the enzyme and porphyrin molecule. To understand the role of this flexible loop, we performed molecular dynamics simulations on the apo and heme b coproheme decarboxylase from Corynebacterium diphtheriae. Our results are discussed in the context of the published structural information on coproheme-bound and MMD-bound coproheme decarboxylase and with respect to the reaction mechanism. Having structural information of all four enzymatically relevant states helps in understanding structural restraints with a functional impact.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 2","pages":"e70027"},"PeriodicalIF":4.5,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11761711/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143047691","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":"AggNet: Advancing protein aggregation analysis through deep learning and protein language model.","authors":"Wenjia He, Xiaopeng Xu, Haoyang Li, Juexiao Zhou, Xin Gao","doi":"10.1002/pro.70031","DOIUrl":"10.1002/pro.70031","url":null,"abstract":"<p><p>Protein aggregation is critical to various biological and pathological processes. Besides, it is also an important property in biotherapeutic development. However, experimental methods to profile protein aggregation are costly and labor-intensive, driving the need for more efficient computational alternatives. In this study, we introduce \"AggNet,\" a novel deep learning framework based on the protein language model ESM2 and AlphaFold2, which utilizes physicochemical, evolutionary, and structural information to discriminate amyloid and non-amyloid peptides and identify aggregation-prone regions (APRs) in diverse proteins. Benchmark comparisons show that AggNet outperforms existing methods and achieves state-of-the-art performance on protein aggregation prediction. Also, the predictive ability of AggNet is stable across proteins with different secondary structures. Feature analysis and visualizations prove that the model effectively captures peptides' physicochemical properties effectively, thereby offering enhanced interpretability. Further validation through a case study on MEDI1912 confirms AggNet's practical utility in analyzing protein aggregation and guiding mutation for aggregation mitigation. This study enhances computational tools for predicting protein aggregation and highlights the potential of AggNet in protein engineering. Finally, to improve the accessibility of AggNet, the source code can be accessed at: https://github.com/Hill-Wenka/AggNet.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 2","pages":"e70031"},"PeriodicalIF":4.5,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11751882/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143010356","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":"Loop engineering of enzymes to control their immobilization and ultimately fabricate more efficient heterogeneous biocatalysts.","authors":"Nicoll Zeballos, Irene Ginés-Alcober, Javier Macías-León, Daniel Andrés-Sanz, Andrés Manuel González-Ramírez, Mercedes Sánchez-Costa, Pedro Merino, Ramón Hurtado-Guerrero, Fernando López-Gallego","doi":"10.1002/pro.70040","DOIUrl":"10.1002/pro.70040","url":null,"abstract":"<p><p>Enzyme immobilization is indispensable for enhancing enzyme performance in various industrial applications. Typically, enzymes require specific spatial arrangements for optimal functionality, underscoring the importance of correct orientation. Despite well-known N- or C-terminus tailoring techniques, alternatives for achieving orientation control are limited. Here, we propose a novel approach that tailors the enzyme surface with engineered His-rich loops. To that aim, we first solve the X-ray crystal structure of a hexameric alcohol dehydrogenase from Thermus thermophilus HB27 (TtHBDH) (PDB: 9FBD). Guided by this 3D structure, we engineer the enzyme surface with a new loop enriched with six His residues to control enzyme orientation. Molecular dynamics simulations reveal that the engineered loop's imidazole rings have greater solvent accessibility than those in native His residues, allowing for more efficient enzyme immobilization on certain metal chelate-functionalized carriers. Using carriers functionalized with iron (III)-catechol, the apparent V_max of the immobilized loop variant doubles the immobilized His-tagged one, and vice versa when both variants are immobilized on carriers functionalized with copper (II)-imidodiacetic acid. His-tagged and loop-engineered TtHBDH show high operational stability reaching 100% bioconversion after 10 reaction cycles, yet the loop variant is faster than the His-tagged one.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 2","pages":"e70040"},"PeriodicalIF":4.5,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11751856/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143010467","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":"Applicability of AlphaFold2 in the modeling of dimeric, trimeric, and tetrameric coiled-coil domains.","authors":"Rafal Madaj, Mikel Martinez-Goikoetxea, Kamil Kaminski, Jan Ludwiczak, Stanislaw Dunin-Horkawicz","doi":"10.1002/pro.5244","DOIUrl":"10.1002/pro.5244","url":null,"abstract":"<p><p>Coiled coils are a common protein structural motif involved in cellular functions ranging from mediating protein-protein interactions to facilitating processes such as signal transduction or regulation of gene expression. They are formed by two or more alpha helices that wind around a central axis to form a buried hydrophobic core. Various forms of coiled-coil bundles have been reported, each characterized by the number, orientation, and degree of winding of the constituent helices. This variability is underpinned by short sequence repeats that form coiled coils and whose properties determine both their overall topology and the local geometry of the hydrophobic core. The strikingly repetitive sequence has enabled the development of accurate sequence-based coiled-coil prediction methods; however, the modeling of coiled-coil domains remains a challenging task. In this work, we evaluated the accuracy of AlphaFold2 in modeling coiled-coil domains, both in modeling local geometry and in predicting global topological properties. Furthermore, we show that the prediction of the oligomeric state of coiled-coil bundles can be achieved by using the internal representations of AlphaFold2, with a performance better than any previous state-of-the-art method (code available at https://github.com/labstructbioinf/dc2_oligo).</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 1","pages":"e5244"},"PeriodicalIF":4.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11651203/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142839011","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":"Allosteric regulation of the tyrosine phosphatase PTP1B by a protein-protein interaction.","authors":"Cassandra A Chartier, Virgil A Woods, Yunyao Xu, Anne E van Vlimmeren, Andrew C Johns, Marko Jovanovic, Ann E McDermott, Daniel A Keedy, Neel H Shah","doi":"10.1002/pro.70016","DOIUrl":"10.1002/pro.70016","url":null,"abstract":"<p><p>The rapid identification of protein-protein interactions has been significantly enabled by mass spectrometry (MS) proteomics-based methods, including affinity purification-MS, crosslinking-MS, and proximity-labeling proteomics. While these methods can reveal networks of interacting proteins, they cannot reveal how specific protein-protein interactions alter protein function or cell signaling. For instance, when two proteins interact, there can be emergent signaling processes driven purely by the individual activities of those proteins being co-localized. Alternatively, protein-protein interactions can allosterically regulate function, enhancing or suppressing activity in response to binding. In this work, we investigate the interaction between the tyrosine phosphatase PTP1B and the adaptor protein Grb2, which have been annotated as binding partners in a number of proteomics studies. This interaction has been postulated to co-localize PTP1B with its substrate IRS-1 by forming a ternary complex, thereby enhancing the dephosphorylation of IRS-1 to suppress insulin signaling. Here, we report that Grb2 binding to PTP1B also allosterically enhances PTP1B catalytic activity. We show that this interaction is dependent on the proline-rich region of PTP1B, which interacts with the C-terminal SH3 domain of Grb2. Using NMR spectroscopy and hydrogen-deuterium exchange mass spectrometry (HDX-MS) we show that Grb2 binding alters PTP1B structure and/or dynamics. Finally, we use MS proteomics to identify other interactors of the PTP1B proline-rich region that may also regulate PTP1B function similarly to Grb2. This work presents one of the first examples of a protein allosterically regulating the enzymatic activity of PTP1B and lays the foundation for discovering new mechanisms of PTP1B regulation in cell signaling.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 1","pages":"e70016"},"PeriodicalIF":4.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11670308/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142897217","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":"The structural influence of the oncogenic driver mutation N642H in the STAT5B SH2 domain.","authors":"Liam Haas-Neill, Deniz Meneksedag-Erol, Ayesha Chaudhry, Masha Novoselova, Qirat F Ashraf, Elvin D de Araujo, Derek J Wilson, Sarah Rauscher","doi":"10.1002/pro.70022","DOIUrl":"10.1002/pro.70022","url":null,"abstract":"<p><p>The point mutation N642H of the signal transducer and activator of transcription 5B (STAT5B) protein is associated with aggressive and drug-resistant forms of leukemia. This mutation is thought to promote cancer due to hyperactivation of STAT5B caused by increased stability of the active, parallel dimer state. However, the molecular mechanism leading to this stabilization is not well understood as there is currently no structure of the parallel dimer. To investigate the mutation's mechanism of action, we conducted extensive all-atom molecular dynamics simulations of multiple oligomeric forms of both STAT5B and STAT5B^N642H, including a model for the parallel dimer. The N642H mutation directly affects the hydrogen bonding network within the phosphotyrosine (pY)-binding pocket of the parallel dimer, enhancing the pY-binding interaction. The simulations indicate that apo STAT5B is highly flexible, exploring a diverse conformational space. In contrast, apo STAT5B^N642H accesses two distinct conformational states, one of which resembles the conformation of the parallel dimer. The simulation predictions of the effects of the mutation on structure and dynamics are supported by the results of hydrogen-deuterium exchange (HDX) mass spectrometry measurements carried out on STAT5B and STAT5B^N642H in which a phosphopeptide was used to mimic the effects of parallel dimerization on the SH2 domain. The molecular-level information uncovered in this work contributes to our understanding of STAT5B hyperactivation by the N642H mutation and could help pave the way for novel therapeutic strategies targeting this mutation.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 1","pages":"e70022"},"PeriodicalIF":4.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11670306/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142896822","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":"The role of amphipathic and cationic helical peptides in Parkinson's disease.","authors":"Carlos Pintado-Grima, Salvador Ventura","doi":"10.1002/pro.70020","DOIUrl":"10.1002/pro.70020","url":null,"abstract":"<p><p>Peptides are attracting a growing interest for therapeutic applications in biomedicine. In Parkinson's disease (PD), different human endogenous peptides have been associated with beneficial effects, including protein aggregation inhibition, reduced inflammation, or the protection of dopaminergic neurons. Such effects seem to be connected to the spatial arrangement of peptide side chains, and many of these human molecules share common conformational traits, displaying a distinctive amphipathic and cationic helical structure, which is believed to be crucial for their activities. This review delves into the relationship between these structural properties and the current evidence connecting biogenic peptides to the amelioration of PD symptoms. We discuss their implications in the disease, the different mechanisms of action, their state of validation, and their therapeutic potential.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 1","pages":"e70020"},"PeriodicalIF":4.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11669119/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142886269","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":"Bioisosteric replacement of pyridoxal-5'-phosphate to pyridoxal-5'-tetrazole targeting Bacillus subtilis GabR.","authors":"Nicholas E Kaley, Zachary J Liveris, Maxwell Moore, Cory T Reidl, Zdzislaw Wawrzak, Daniel P Becker, Dali Liu","doi":"10.1002/pro.70014","DOIUrl":"10.1002/pro.70014","url":null,"abstract":"<p><p>Antimicrobial resistance is a significant cause of mortality globally due to infections, a trend that is expected to continue to rise. As existing treatments fail and new drug discovery slows, the urgency to develop novel antimicrobial therapeutics grows stronger. One promising strategy involves targeting bacterial systems exclusive to pathogens, such as the transcription regulator protein GabR. Expressed in diverse bacteria including Escherichia coli, Bordetella pertussis, and Klebsiella pneumoniae, GabR has no homolog in eukaryotes, making it an ideal therapeutic target. Bacillus subtilis GabR (bsGabR), the most studied variant, regulates its own transcription and activates genes for GABA aminotransferase (GabT) and succinic semialdehyde dehydrogenase (GabD). This intricate regulatory system presents a compelling antimicrobial target with the potential for agonistic intervention to disrupt bacterial gene expression and induce cellular dysfunction, especially in bacterial stress responses. To explore manipulation of this system and the potential of this protein as an antimicrobial target, an in-depth understanding of the unique PLP-dependent transcription regulation is critical. Herein, we report the successful structural modification of the cofactor PLP and demonstrate the biochemical reactivity of the PLP analog pyridoxal-5'-tetrazole (PLT). Through both spectrophotometric and X-ray crystallographic analyses, we explore the interaction between bsGabR and PLT, together with a synthesized GABA derivative (S)-4-amino-5-phenoxypentanoate (4-phenoxymethyl-GABA or 4PMG). Most notably, we present a crystal structure of the condensed, external aldimine complex within bsGabR. While PLT alone is not a drug candidate, it can act as a probe to study the detailed mechanism of GabR-mediated function. PLT employs a tetrazole moiety as a bioisosteric replacement for phosphate in PLP. In addition, the PLP-4PMG adduct observed in the structure may serve as a novel chemical scaffold for subsequent structure-based antimicrobial design.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 1","pages":"e70014"},"PeriodicalIF":4.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11669113/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142886127","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":"Design of a yeast SUMO tag to eliminate internal translation initiation.","authors":"Jamison D Law, Yuan Gao, Vicki H Wysocki, Venkat Gopalan","doi":"10.1002/pro.5256","DOIUrl":"10.1002/pro.5256","url":null,"abstract":"<p><p>After overexpression in a suitable host, recombinant protein purification often relies on affinity (e.g., poly-histidine) and solubility-enhancing (e.g., small ubiquitin-like-modifier [SUMO]) tags. Following purification, these tags are removed to avoid their interference with target protein structure and function. The wide use of N-terminal His₆-SUMO fusions is partly due to efficient cleavage of the SUMO tag's C-terminal Gly-Gly motif by the Ulp1 SUMO protease and generation of the native N-terminus of the target protein. While adopting this system to purify the Salmonella homodimeric FraB deglycase, we discovered that Shine-Dalgarno (SD) sequences in the eukaryotic SUMO tag resulted in truncated proteins. This finding has precedents for synthesis of partial proteins in Escherichia coli from cryptic ribosome-binding sites within eukaryotic coding sequences. The SUMO open reading frame has two \"GGNGGN\" motifs that resemble SD sequences, one of which encodes the Gly-Gly motif required for Ulp1 cleavage. By mutating these SD sequences, we generated SUMO^NIT (no internal translation), a variant that eliminated production of the truncated proteins without affecting the levels of full-length His₆-SUMO-FraB or Ulp1 cleavage. SUMO^NIT should be part of the toolkit for enhancing SUMO fusion protein yield, purity, and homogeneity (especially for homo-oligomers). Moreover, we showcase the value of native mass spectrometry in revealing the complications that arise from generation of truncated proteins, as well as oxidation events and protease inhibitor adducts, which are indiscernible by commonly employed lower resolution methods.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 1","pages":"e5256"},"PeriodicalIF":4.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11653089/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142847548","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":"Heat-sterilizable antibody mimics designed on the cold shock protein scaffold from hyperthermophile Thermotoga maritima.","authors":"Hiroshi Amesaka, Marin Tachibana, Mizuho Hara, Shuntaro Toya, Haruki Nakagawa, Hiroyoshi Matsumura, Azumi Hirata, Masahiro Fujihashi, Kazufumi Takano, Shun-Ichi Tanaka","doi":"10.1002/pro.70018","DOIUrl":"10.1002/pro.70018","url":null,"abstract":"<p><p>Antibodies and antibody mimics are extensively used in the pharmaceutical industry, where stringent safety standards are required. Implementing heat sterilization during or after the manufacturing process could help prevent contamination by viruses and bacteria. However, conventional antibodies and antibody mimics are not suitable for heat sterilization because they irreversibly denature at high temperatures. In this study, we focused on the refolding property of the cold shock protein from the hyperthermophile Thermotoga maritima (TmCSP), which denatures at elevated temperatures but regains its native structure upon re-cooling. We designed and constructed a mutant library of TmCSP in which amino acid residues in its three surface loops were diversified. From the library, mutant TmCSPs that bind to each of eight target proteins were selected by phage and yeast surface display methods. We confirmed that the secondary structure and binding affinity of all the selected mutants were restored after heat treatment followed by cooling. Additionally, freeze-drying did not impair their binding affinity. The crystal structure of a mutant TmCSP in complex with its target, the esterase from Alicyclobacillus acidocaldarius, revealed specific interactions between them. These results clearly demonstrate the feasibility of creating heat-sterilizable antibody mimics using TmCSP as a scaffold.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 1","pages":"e70018"},"PeriodicalIF":4.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11670304/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142896572","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}