Protein Science最新文献

Human recombinant tyrosinase destabilization caused by the double mutation R217Q/R402Q. 由R217Q/R402Q双突变引起的重组酪氨酸酶失稳。

IF 4.5 3区生物学

Protein Science Pub Date : 2025-02-01 DOI: 10.1002/pro.70029

Sarah Toay, Narin Sheri, Ian MacDonald, Yuri V Sergeev

引用次数: 0

α-N-Methyltransferase regiospecificity is mediated by proximal, redundant enzyme-substrate interactions. α- n -甲基转移酶区域特异性是由近端冗余酶-底物相互作用介导的。

IF 4.5 3区生物学

Protein Science Pub Date : 2025-02-01 DOI: 10.1002/pro.70021

Kathryn K Crone, Jason W Labonte, Mikael H Elias, Michael F Freeman

{"title":"α-N-Methyltransferase regiospecificity is mediated by proximal, redundant enzyme-substrate interactions.","authors":"Kathryn K Crone, Jason W Labonte, Mikael H Elias, Michael F Freeman","doi":"10.1002/pro.70021","DOIUrl":"10.1002/pro.70021","url":null,"abstract":"N-Methylation of the peptide backbone confers pharmacologically beneficial characteristics to peptides that include greater membrane permeability and resistance to proteolytic degradation. The borosin family of ribosomally synthesized and post-translationally modified peptides offer a post-translational route to install amide backbone α-N-methylations. Previous work has elucidated the substrate scope and engineering potential of two examples of type I borosins, which feature autocatalytic precursors that encode N-methyltransferases that methylate their own C-termini in trans. We recently reported the first discrete N-methyltransferase and precursor peptide from Shewanella oneidensis MR-1, a minimally iterative, type IV borosin that allowed the first detailed kinetic analyses of borosin N-methyltransferases. Herein, we characterize the substrate scope and resilient regiospecificity of this discrete N-methyltransferase by comparison of relative rates and methylation patterns of over 40 precursor peptide variants along with structure analyses of nine enzyme-substrate complexes. Sequences critical to methylation are identified and demonstrated in assaying minimal peptide substrates and non-native peptide sequences for assessment of secondary structure requirements and engineering potential. This work grants understanding towards the mechanism of substrate recognition and iterative activity by discrete borosin N-methyltransferases.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 2","pages":"e70021"},"PeriodicalIF":4.5,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11751858/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143010486","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

Super-resolution imaging of proteins inside live mammalian cells with mLIVE-PAINT.

IF 4.5 3区生物学

Protein Science Pub Date : 2025-02-01 DOI: 10.1002/pro.70008

Haresh Bhaskar, Zoe Gidden, Gurvir Virdi, Dirk-Jan Kleinjan, Susan J Rosser, Sonia Gandhi, Lynne Regan, Mathew H Horrocks

引用次数: 0

LEA_4 motifs function alone and in conjunction with synergistic cosolutes to protect a labile enzyme during desiccation. LEA_4基序单独发挥作用，并与协同辅质结合，在干燥过程中保护不稳定的酶。

IF 4.5 3区生物学

Protein Science Pub Date : 2025-02-01 DOI: 10.1002/pro.70028

Vincent Nicholson, Kenny Nguyen, Edith Gollub, Mary McCoy, Feng Yu, Alex S Holehouse, Shahar Sukenik, Thomas C Boothby

{"title":"LEA_4 motifs function alone and in conjunction with synergistic cosolutes to protect a labile enzyme during desiccation.","authors":"Vincent Nicholson, Kenny Nguyen, Edith Gollub, Mary McCoy, Feng Yu, Alex S Holehouse, Shahar Sukenik, Thomas C Boothby","doi":"10.1002/pro.70028","DOIUrl":"10.1002/pro.70028","url":null,"abstract":"Organisms from all kingdoms of life depend on Late Embryogenesis Abundant (LEA) proteins to survive desiccation. LEA proteins are divided into broad families distinguished by the presence of family-specific motif sequences. The LEA_4 family, characterized by 11-residue motifs, plays a crucial role in the desiccation tolerance of numerous species. However, the role of these motifs in the function of LEA_4 proteins is unclear, with some studies finding that they recapitulate the function of full-length LEA_4 proteins in vivo, and other studies finding the opposite result. In this study, we characterize the ability of LEA_4 motifs to protect a desiccation-sensitive enzyme, citrate synthase (CS), from loss of function during desiccation. We show here that LEA_4 motifs not only prevent the loss of function of CS during desiccation but also that they can do so more robustly via synergistically interactions with cosolutes. Our analysis further suggests that cosolutes induce synergy with LEA_4 motifs in a manner that correlates with transfer free energy. This research advances our understanding of LEA_4 proteins by demonstrating that during desiccation their motifs can protect specific clients to varying degrees and that their protective capacity is modulated by their chemical environment. Our findings extend beyond the realm of desiccation tolerance, offering insights into the interplay between IDPs and cosolutes. By investigating the function of LEA_4 motifs, we highlight broader strategies for understanding protein stability and function.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 2","pages":"e70028"},"PeriodicalIF":4.5,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11751883/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143010423","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

Translation of the downstream ORF from bicistronic mRNAs by human cells: Impact of codon usage and splicing in the upstream ORF. 人类细胞对双频mrna下游ORF的翻译：上游ORF中密码子使用和剪接的影响

IF 4.5 3区生物学

Protein Science Pub Date : 2025-02-01 DOI: 10.1002/pro.70036

Philippe Paget-Bailly, Alexandre Helpiquet, Mathilde Decourcelle, Roxane Bories, Ignacio G Bravo

{"title":"Translation of the downstream ORF from bicistronic mRNAs by human cells: Impact of codon usage and splicing in the upstream ORF.","authors":"Philippe Paget-Bailly, Alexandre Helpiquet, Mathilde Decourcelle, Roxane Bories, Ignacio G Bravo","doi":"10.1002/pro.70036","DOIUrl":"10.1002/pro.70036","url":null,"abstract":"Biochemistry textbooks describe eukaryotic mRNAs as monocistronic. However, increasing evidence reveals the widespread presence and translation of upstream open reading frames preceding the \"main\" ORF. DNA and RNA viruses infecting eukaryotes often produce polycistronic mRNAs and viruses have evolved multiple ways of manipulating the host's translation machinery. Here, we introduce an experimental model to study gene expression regulation from virus-like bicistronic mRNAs in human cells. The model consists of a short upstream ORF and a reporter downstream ORF encoding a fluorescent protein. We have engineered synonymous variants of the upstream ORF to explore large parameter space, including codon usage preferences, mRNA folding features, and splicing propensity. We show that human translation machinery can translate the downstream ORF from bicistronic mRNAs, albeit reporter protein levels are thousand times lower than those from the upstream ORF. Furthermore, synonymous recoding of the upstream ORF exclusively during elongation significantly influences its own translation efficiency, reveals cryptic splice signals, and modulates the probability of downstream ORF translation. Our results are consistent with a leaky scanning mechanism facilitating downstream ORF translation from bicistronic mRNAs in human cells, offering new insights into the role of upstream ORFs in translation regulation.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 2","pages":"e70036"},"PeriodicalIF":4.5,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11751868/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143010482","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

The multifaceted role of XCL1 in health and disease. XCL1在健康和疾病中的多方面作用。

IF 4.5 3区生物学

Protein Science Pub Date : 2025-02-01 DOI: 10.1002/pro.70032

Muhammed Syed, Acacia F Dishman, Brian F Volkman, Tara L Walker

{"title":"The multifaceted role of XCL1 in health and disease.","authors":"Muhammed Syed, Acacia F Dishman, Brian F Volkman, Tara L Walker","doi":"10.1002/pro.70032","DOIUrl":"10.1002/pro.70032","url":null,"abstract":"The chemokine XC motif chemokine ligand 1 (XCL1) is an unusually specialized member of a conserved family of around 50 small, secreted proteins that are best known for their ability to stimulate the directional migration of cells. All chemokines adopt a very similar folded structure that binds a specific G protein-coupled receptor (GPCR), and most chemokines bind extracellular matrix glycosaminoglycans, often in a dimeric or oligomeric form. Owing in part to the lack of a disulfide bond that is conserved in all other chemokines, XCL1 interconverts between two distinct structures with distinct functions. One XCL1 fold resembles the structure of all other chemokines (chemokine fold), while the other does not (alternate fold). The chemokine fold of XCL1 displays high affinity for the GPCR XCR1, while the alternative fold binds GAGs and exhibits antimicrobial activity. Although the canonical role of XCL1 as a CD8+ dendritic cell chemoattractant was defined more than a decade ago, the misconception that XCL1 is a lymphocyte-specific chemoattractant still prevails in the recent literature. This review aims to highlight the structure-guided functions of XCL1 and reclarify its immunological role. In addition, the implications of this metamorphic chemokine in vaccine development and emerging functions in the nervous system will be explored.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 2","pages":"e70032"},"PeriodicalIF":4.5,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11751857/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143010477","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

GDFold2: A fast and parallelizable protein folding environment with freely defined objective functions.

IF 4.5 3区生物学

Protein Science Pub Date : 2025-02-01 DOI: 10.1002/pro.70041

Tianyu Mi, Nan Xiao, Haipeng Gong

{"title":"GDFold2: A fast and parallelizable protein folding environment with freely defined objective functions.","authors":"Tianyu Mi, Nan Xiao, Haipeng Gong","doi":"10.1002/pro.70041","DOIUrl":"10.1002/pro.70041","url":null,"abstract":"An important step of mainstream protein structure prediction is to model the 3D protein structure based on the predicted 2D inter-residue geometric information. This folding step has been integrated into a unified neural network to allow end-to-end training in state-of-the-art methods like AlphaFold2, but is separately implemented using the Rosetta folding environment in some traditional methods like trRosetta. Despite the inferiority in prediction accuracy, the conventional approach allows for the sampling of various protein conformations compatible with the predicted geometric constraints, partially capturing the dynamic information. Here, we propose GDFold2, a novel protein folding environment, to address the limitations of Rosetta. On the one hand, GDFold2 is highly computationally efficient, capable of accomplishing multiple folding processes in parallel within the time scale of minutes for generic proteins. On the other hand, GDFold2 supports freely defined objective functions to fulfill diversified optimization requirements. Moreover, we propose a quality assessment (QA) model to provide reliable prediction on the quality of protein structures folded by GDFold2, thus substantially simplifying the selection of structural models. GDFold2 and the QA model could be combined to investigate the transition path between protein conformational states, and the online server is available at https://structpred.life.tsinghua.edu.cn/server_gdfold2.html.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 2","pages":"e70041"},"PeriodicalIF":4.5,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11773392/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143053470","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

Investigation into the effect of phenylalanine gating on anaerobic haem breakdown using the energy landscape approach.

IF 4.5 3区生物学

Protein Science Pub Date : 2025-02-01 DOI: 10.1002/pro.5243

Alasdair D Keith, Elizabeth B Sawyer, Desmond C Y Choy, James L Cole, Cheng Shang, George S Biggs, Oskar James Klein, Paul D Brear, David J Wales, Paul D Barker

{"title":"Investigation into the effect of phenylalanine gating on anaerobic haem breakdown using the energy landscape approach.","authors":"Alasdair D Keith, Elizabeth B Sawyer, Desmond C Y Choy, James L Cole, Cheng Shang, George S Biggs, Oskar James Klein, Paul D Brear, David J Wales, Paul D Barker","doi":"10.1002/pro.5243","DOIUrl":"10.1002/pro.5243","url":null,"abstract":"We have recently demonstrated a novel anaerobic NADH-dependent haem breakdown reaction, which is carried out by a range of haemoproteins. The Yersinia enterocolitica protein, HemS, is the focus of further research presented in the current paper. Using conventional experimental methods, bioinformatics, and energy landscape theory (ELT), we provide new insight into the mechanism of the novel breakdown process. Of particular interest is the behavior of a double phenylalanine gate, which opens and closes according to the relative situations of haem and NADH within the protein pocket. This behavior suggests that the double phe-gate fulfills a regulatory role within the pocket, controlling the access of NADH to haem. Additionally, stopped-flow spectroscopy results provide kinetic comparisons between the wild-type and the selected mutants. We also present a fully resolved crystal structure for the F104AF199A HemS monomer, including its extensive loop, the first such structure to be completely resolved for HemS or any of its close homologues. The energy landscapes approach provided key information regarding the gating strategy employed by HemS, compensating for current limitations with conventional biophysical and molecular dynamics approaches. We propose that ELT become more widely used in the field, particularly in the investigation of the dynamics and interactions of weak-binding ligands, and for gating features, within protein cavities.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 2","pages":"e5243"},"PeriodicalIF":4.5,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11773379/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143053473","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

AFFIPred: AlphaFold2 structure-based Functional Impact Prediction of missense variations. 基于AlphaFold2结构的错义变异功能影响预测。

IF 4.5 3区生物学

Protein Science Pub Date : 2025-02-01 DOI: 10.1002/pro.70030

Mustafa S Pir, Emel Timucin

{"title":"AFFIPred: AlphaFold2 structure-based Functional Impact Prediction of missense variations.","authors":"Mustafa S Pir, Emel Timucin","doi":"10.1002/pro.70030","DOIUrl":"10.1002/pro.70030","url":null,"abstract":"Protein structure holds immense potential for pathogenicity prediction, albeit structure-based predictors are limited compared to the sequence-based counterparts due to the \"structure knowledge gap\" between large number of available protein sequences and relatively limited number of structures. Leveraging the highly accurate protein structures predicted by AlphaFold2 (AF2), we introduce AFFIPred, an ensemble machine learning classifier that combines sequence and AF2-based structural characteristics to predict missense variant pathogenicity. Based on the assessments on unseen datasets, AFFIPred reached a comparable level of performance with the state-of-the-art predictors such as AlphaMissense. We also showed that the recruitment of AF2 structures that are full-length and represent the unbound states ensures more precise SASA calculations compared to the recruitment of experimental structures. In line with the completeness of the AF2 structures, their use provide a more comprehensive view of the structural characteristics of the missense variation datasets by capturing all variants. AFFIPred maintains high-level accuracy without the limitations of PDB-based classifiers. AFFIPred has predicted over 210 million variations of the human proteome, which are accessible at https://affipred.timucinlab.com/.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 2","pages":"e70030"},"PeriodicalIF":4.5,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11751861/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143010354","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

NumSimEX: A method using EXX hydrogen exchange mass spectrometry to map the energetics of protein folding landscapes.

IF 4.5 3区生物学

Protein Science Pub Date : 2025-02-01 DOI: 10.1002/pro.70045

Jasper A G Flint, Jacob Witten, Isabella Han, John Strahan, Jovan Damjanovic, Nevon Song, Tim Poterba, Alexis Jaramillo Cartagena, Angelika Hirsch, Tony Ni, Julie L Sohl, Amy S Wagaman, Sheila S Jaswal

{"title":"NumSimEX: A method using EXX hydrogen exchange mass spectrometry to map the energetics of protein folding landscapes.","authors":"Jasper A G Flint, Jacob Witten, Isabella Han, John Strahan, Jovan Damjanovic, Nevon Song, Tim Poterba, Alexis Jaramillo Cartagena, Angelika Hirsch, Tony Ni, Julie L Sohl, Amy S Wagaman, Sheila S Jaswal","doi":"10.1002/pro.70045","DOIUrl":"10.1002/pro.70045","url":null,"abstract":"Hydrogen exchange mass spectrometry (HXMS) is a powerful tool to understand protein folding pathways and energetics. However, HXMS experiments to date have used exchange conditions termed EX1 or EX2 which limit the information that can be gained compared to the more general EXX exchange regime. If EXX behavior could be understood and analyzed, a single HXMS timecourse on an intact protein could fully map its folding landscape without requiring denaturation. To address this challenge, we developed a numerical simulation method called NumSimEX that models EXX exchange for arbitrarily complex folding pathways. NumSimEx fits protein folding dynamics to experimental HXMS data by iteratively comparing the simulated and experimental timecourses, allowing for determination of both kinetic and thermodynamic protein folding parameters. After analytically verifying NumSimEX's accuracy, we demonstrated its power on HXMS data from beta-2 microglobulin (β2M), a protein involved in dialysis-related amyloidosis. In particular, using NumSimEX, we identified three-state kinetics that near-perfectly matched experimental observation. This proof-of-principle application of NumSimEX sets the stage for harnessing HXMS to expand our understanding of proteins currently excluded from traditional protein folding methods. NumSimEX is freely available at https://github.com/JaswalLab/NumSimEX_Public.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 2","pages":"e70045"},"PeriodicalIF":4.5,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11761709/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143047692","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