Protein Engineering Design & Selection最新文献

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Rapid selection of high-affinity DARPins using click display. 快速选择高亲和力的darpin使用点击显示。
IF 3.5 4区 生物学
Protein Engineering Design & Selection Pub Date : 2026-01-09 DOI: 10.1093/protein/gzag028
Joshua D Bryant, Yu Zeng, Monisha Yerram, Karuppiah Chockalingam, Michael Woolley, Raghav Sehgal, Vikas Chonira, Zhilei Chen
{"title":"Rapid selection of high-affinity DARPins using click display.","authors":"Joshua D Bryant, Yu Zeng, Monisha Yerram, Karuppiah Chockalingam, Michael Woolley, Raghav Sehgal, Vikas Chonira, Zhilei Chen","doi":"10.1093/protein/gzag028","DOIUrl":"10.1093/protein/gzag028","url":null,"abstract":"<p><p>Rapid and scalable protein binder discovery platforms are essential for accelerating therapeutic and diagnostic development. Click display is a cell-free protein display technology that covalently links nascent proteins to their encoding cDNA in a one-pot reaction within 2 h, enabling rapid in vitro selection. Although previously demonstrated to support directed evolution, enrichment efficiency during biopanning was slower than conventional phage display. Here, we report two modifications that significantly enhance click display selection efficiency: (i) selective elution of target-bound complexes using a cleavable biotin linker, and (ii) competitive displacement of non-specific bead binders using a biotinylated blocking protein. These improvements dramatically reduce amplification of non-specific binders and enable efficient enrichment of target-specific binders within three to four rounds of panning. Using a naïve DARPin library, we rapidly enriched binders to interleukin-10 (IL-10) and transforming growth factor-β1 (TGF-β1), identifying clones with low nanomolar binding affinities and receptor-blocking activity. We further applied the optimized protocol to affinity maturation of a PD-L1-binding DARPin, achieving >400-fold improved binding affinity. The best candidate, 1D10, exhibits sub-nanomolar PD-1 inhibition in competition ELISA. These results demonstrate that the optimized click display workflow enables rapid enrichment and affinity maturation of high-affinity DARPins across diverse targets. The platform provides a streamlined, transformation-free approach for accelerating protein engineering and directed evolution.</p>","PeriodicalId":54543,"journal":{"name":"Protein Engineering Design & Selection","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2026-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13654297/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149118483","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Towards directed evolution of rare earth element binding peptides using genetically encoded sensitizing amino acids. 利用基因编码致敏氨基酸定向进化稀土元素结合肽。
IF 3.5 4区 生物学
Protein Engineering Design & Selection Pub Date : 2026-01-09 DOI: 10.1093/protein/gzag026
Riley M Bednar, Jason G Marmorstein, Kathleen J Stebe, E James Petersson
{"title":"Towards directed evolution of rare earth element binding peptides using genetically encoded sensitizing amino acids.","authors":"Riley M Bednar, Jason G Marmorstein, Kathleen J Stebe, E James Petersson","doi":"10.1093/protein/gzag026","DOIUrl":"10.1093/protein/gzag026","url":null,"abstract":"<p><p>As demand for the rare earth elements (REEs) that power new and emerging technologies increases rapidly, there is a growing need for next-generation separations systems that can provide more selective isolation of these critical, but difficult-to-purify materials. Due to their evolvability and compatibility with existing separations platforms, polypeptides represent an ideal and environmentally-friendly chassis with which to meet this challenge; however, there exist no high-throughput approaches to selecting polypeptides with improved affinity and selectivity towards the various REEs, chiefly due to the difficulty of detecting a selectable phenotype. Here, we present work towards overcoming this obstacle by developing a bacterial display platform for the direct sensing of REE binding in living bacterial cells. Our approach exploits the antenna effect, which allows a sufficiently proximal fluorophore to sensitize a bound europium ion and stimulate emission through resonant energy transfer, and makes use of genetic code expansion to insert a fluorescent amino acid directly into the polypeptide backbone in cellulo. We find that targeting a model lanthanide-binding peptide to the periplasm enables the accumulation of sufficient concentrations of this binder in an easily accessible subcellular localization such that robust signal can be detected. Through optimization of encoding, sensitization, and handling, we further improve our signal up to >20-fold over control cells lacking binders and demonstrate facile differentiation and characterization of several variant peptides. Our work paves the way for high-throughput synthetic evolution of REE binding polypeptides with expanded functionality.</p>","PeriodicalId":54543,"journal":{"name":"Protein Engineering Design & Selection","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2026-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13625638/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148992506","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Bind, catalyze, and quantify: a modern protein and enzyme engineering toolbox of genetically encoded non-canonical amino acids. 结合,催化和量化:基因编码非规范氨基酸的现代蛋白质和酶工程工具箱。
IF 3.5 4区 生物学
Protein Engineering Design & Selection Pub Date : 2026-01-09 DOI: 10.1093/protein/gzag007
Søren C Spina, Joseph S Bailey, Blaise R Kimmel
{"title":"Bind, catalyze, and quantify: a modern protein and enzyme engineering toolbox of genetically encoded non-canonical amino acids.","authors":"Søren C Spina, Joseph S Bailey, Blaise R Kimmel","doi":"10.1093/protein/gzag007","DOIUrl":"10.1093/protein/gzag007","url":null,"abstract":"<p><p>Non-canonical amino acids (ncAAs) are versatile molecular building blocks that can enhance nearly every aspect of protein engineering, from improving binding affinity to enabling precise quantitative analyses. This review highlights advances from 2020-2025 that demonstrate how expanding the amino acid repertoire unlocks new functionalities. We examine how genetically encoded ncAAs diversify and tune metal-binding properties, enabling programmable coordination and redox behavior in engineered enzymes. Further, we explore biocatalytic applications, including multi-fold activity enhancements in natural enzymes and the introduction of entirely novel reactivity in artificial systems. Finally, we discuss the growing use of ncAAs as intrinsic biophysical reporters, which support a wide range of spectroscopic methods for tracking structure, dynamics, and interactions at residue-level resolution. These capabilities establish ncAAs as essential tools that can be deployed at any stage of the protein design process, from constructing new catalytic centers to quantifying molecular behaviors in real time.</p>","PeriodicalId":54543,"journal":{"name":"Protein Engineering Design & Selection","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2026-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147370270","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Prioritizing stability-enhancing mutations using the ESM protein language model in conjunction with physics-based MM/GBSA predictions. 结合基于物理的MM/GBSA预测,利用ESM蛋白质语言模型对稳定性增强突变进行优先排序。
IF 3.5 4区 生物学
Protein Engineering Design & Selection Pub Date : 2026-01-09 DOI: 10.1093/protein/gzag016
Emily R Rhodes, Guido Scarabelli, Jonathan Jou, Jacob Byerly, Kayla G Sprenger, Eliud O Oloo
{"title":"Prioritizing stability-enhancing mutations using the ESM protein language model in conjunction with physics-based MM/GBSA predictions.","authors":"Emily R Rhodes, Guido Scarabelli, Jonathan Jou, Jacob Byerly, Kayla G Sprenger, Eliud O Oloo","doi":"10.1093/protein/gzag016","DOIUrl":"10.1093/protein/gzag016","url":null,"abstract":"<p><p>Directed evolution for protein engineering, as currently practiced in the biotechnology and pharmaceutical industries, is both tedious and expensive. Computationally driven protein design has the potential to expedite the engineering process and generate high-quality variants at a lower cost than traditional approaches. We investigated the effectiveness of two different computational methods as triaging tools for prioritizing target positions and identifying specific mutations that are likely to improve protein thermodynamic stability. Our benchmarking study used a comprehensive dataset consisting of 174,945 mutations across 180 distinct proteins and evaluated the ESM (Evolutionary Scale Modeling) protein language model alongside a physics-based method, MM/GBSA (Molecular Mechanics Generalized Born Surface Area). We found prediction biases in each method but also determined that these biases can be mitigated by applying the two methods in a complementary manner. We propose a hybrid mutation prioritization and selection strategy that achieves better accuracy than either method alone. Through re-ranking, the combined prioritization strategy attained a higher overall average ROC (receiver operating characteristic) AUC (area under curve) of 0.743 across the dataset compared to either MM/GBSA alone (0.685) or ESM Log Odds alone (0.597). The integrated framework can be adapted and applied to newer AI and physics-based models as the field advances.</p>","PeriodicalId":54543,"journal":{"name":"Protein Engineering Design & Selection","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2026-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148392187","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Engineering of tandem bispecific IL-7 receptor agonist antibody promoting selective T cell expansion. 串联双特异性IL-7受体激动剂抗体促进选择性T细胞扩增的工程研究。
IF 3.5 4区 生物学
Protein Engineering Design & Selection Pub Date : 2026-01-09 DOI: 10.1093/protein/gzag017
Jun-Kook Park, Inseong Jung, Seunghyun Lee, Jisuk Kim, Sanghee Shin, Jiwon Shin, Soojeong Noh, Dahye Kwon, Chaerin Nam, Hyunwook Kim, Hongsoo Choi, Kyungmoo Yea
{"title":"Engineering of tandem bispecific IL-7 receptor agonist antibody promoting selective T cell expansion.","authors":"Jun-Kook Park, Inseong Jung, Seunghyun Lee, Jisuk Kim, Sanghee Shin, Jiwon Shin, Soojeong Noh, Dahye Kwon, Chaerin Nam, Hyunwook Kim, Hongsoo Choi, Kyungmoo Yea","doi":"10.1093/protein/gzag017","DOIUrl":"10.1093/protein/gzag017","url":null,"abstract":"<p><p>Interleukin-7 (IL-7) is indispensable for T cell development and homeostasis, and clinical studies have demonstrated its ability to restore T cell numbers in lymphopenic conditions. However, the therapeutic application of IL-7 has been limited by its short half-life and potential immunogenicity of recombinant variants. To overcome these challenges, we engineered a fully human tandem bispecific antibody, TB4, that functions as a potent IL-7 receptor agonist by cis-targeting IL-7 receptor alpha (IL-7Rα) and the common γ chain (γc). The tetravalent tandem scFv-Fc architecture, coupled with optimized linker length, conferred markedly enhanced binding affinity and avidity compared to the knobs-into-holes bispecific format, with domain orientation designed to limit unintended γc binding. At the cellular level, TB4 engaged both receptor subunits and exhibited reduced internalization dynamics, features that are likely to contribute to the sustained STAT5 phosphorylation observed in primary human T cells. Functionally, TB4 supported long-term T cell survival and expansion, but selectively promoted the expansion of CD4+ memory subsets, especially effector memory cells re-expressing CD45RA populations, in contrast to the broader effects of native IL-7. Transcriptomic profiling further revealed that while both TB4 and IL-7 activated proliferative gene programs, TB4 uniquely drove an antiviral and innate immune signature. Collectively, these findings establish TB4 as a next-generation IL-7R agonist antibody with a differentiated mechanism of action and potential as a precision immunomodulator that can selectively expand and reprogram T cells.</p>","PeriodicalId":54543,"journal":{"name":"Protein Engineering Design & Selection","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2026-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148406778","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Experimental analyses of RFdiffusion designed Miniproteins for binding to SARS-CoV-2 nucleocapsid protein. RFdiffusion设计的与SARS-CoV-2核衣壳蛋白结合的微小蛋白的实验分析
IF 3.5 4区 生物学
Protein Engineering Design & Selection Pub Date : 2025-12-23 DOI: 10.1093/protein/gzag004
Zeenat Khakerwala, Ashwani Kumar, Sujay S Gaikwad, Truptimayee Barik, Shweta Singh, Gagan Deep Gupta, Ravindra D Makde
{"title":"Experimental analyses of RFdiffusion designed Miniproteins for binding to SARS-CoV-2 nucleocapsid protein.","authors":"Zeenat Khakerwala, Ashwani Kumar, Sujay S Gaikwad, Truptimayee Barik, Shweta Singh, Gagan Deep Gupta, Ravindra D Makde","doi":"10.1093/protein/gzag004","DOIUrl":"10.1093/protein/gzag004","url":null,"abstract":"<p><p>Miniprotein designs are emerging as promising antibody alternatives for therapeutic and diagnostic use. Using RFdiffusion, we designed 538 binder candidates targeting both N and C-terminal domains of the SARS-CoV-2 nucleocapsid protein, selecting 19 for recombinant production in E. coli. All were soluble and purified (8-10 mg/L yield), though 13 unexpectedly formed oligomers. CD spectroscopy confirmed proper folding and thermal refolding, with 9 miniproteins exhibiting Tm > 75°C. Binding assay revealed three miniproteins with affinities of 115 nM, 4.8 μM, and 7.32 μM. The 1.8 Å resolution crystal structure of one binder (Gpx62) matched the predicted design. However, predictive metrics (like ipTM of AlphaFold3 and computational simulations) did not align with experimental data. Together, these results reveal unintended oligomerization as a major, previously underappreciated barrier in miniprotein binder discovery, demonstrating that while RFdiffusion reliably predicts structural integrity and stability of miniprotein, its current metrics do not account for the oligomeric behavior that might critically limit binding competence.</p>","PeriodicalId":54543,"journal":{"name":"Protein Engineering Design & Selection","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146151262","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Rhizavidin engineered for eukaryotic expression. 根际亲和素真核表达工程研究
IF 3.5 4区 生物学
Protein Engineering Design & Selection Pub Date : 2025-12-23 DOI: 10.1093/protein/gzag002
Brian Cieslewicz, Cullen Roeder, Dara Bree, Renuka Haridas, Anastassia Kozlova, Tatiana Vasquez, Primit Desai, Julianna Paone, Ian Tonkiss, Gilles Besin, Teresa Broering, Cary Liptak, Heidi Burke
{"title":"Rhizavidin engineered for eukaryotic expression.","authors":"Brian Cieslewicz, Cullen Roeder, Dara Bree, Renuka Haridas, Anastassia Kozlova, Tatiana Vasquez, Primit Desai, Julianna Paone, Ian Tonkiss, Gilles Besin, Teresa Broering, Cary Liptak, Heidi Burke","doi":"10.1093/protein/gzag002","DOIUrl":"10.1093/protein/gzag002","url":null,"abstract":"<p><p>Several technologies leverage avidin/biotin interactions for complexation, including the MAPS vaccine technology which utilizes rhizavidin, a biotin-binding protein derived from the proteobacterium Rhizobium etli, to complex antigens with biotinylated polysaccharides. Rhizavidin possesses five potential N-linked glycosylation sites which are not glycosylated in the native bacterium or when rhizavidin is recombinantly expressed in Escherichia coli. However, when expressed in eukaryotic cell systems, these sites undergo variable and non-physiologically relevant glycosylation that complicates purification. To overcome these challenges, we engineered rhizavidin with substitutions that abolish unnatural N-linked glycosylation while maintaining rhizavidin's biotin-binding functionality. As a proof of concept, this construct was genetically fused to the receptor binding domain of the spike protein from the SARS-CoV-2 virus, expressed in mammalian cells, and was successfully incorporated into MAPS technology-based vaccines. This newly engineered rhizavidin enhances the versatility of the MAPS technology, enabling the targeting of viruses and tumor-associated antigens that often require mammalian post-translational modifications.</p>","PeriodicalId":54543,"journal":{"name":"Protein Engineering Design & Selection","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146068693","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
VIF-Ig: a novel fc framework for ADCC by incorporation of VHH unit. VIF-Ig:一种结合VHH单元的ADCC Fc框架。
IF 3.5 4区 生物学
Protein Engineering Design & Selection Pub Date : 2025-12-23 DOI: 10.1093/protein/gzag003
Yaohui Li, Yichen Huang, Yingdan Duan, He Zhao, Shanshan Wang, Jiefu Li, Hua Jing, Kebing Yu, Chih-Chuan Chang, Feng Wang
{"title":"VIF-Ig: a novel fc framework for ADCC by incorporation of VHH unit.","authors":"Yaohui Li, Yichen Huang, Yingdan Duan, He Zhao, Shanshan Wang, Jiefu Li, Hua Jing, Kebing Yu, Chih-Chuan Chang, Feng Wang","doi":"10.1093/protein/gzag003","DOIUrl":"10.1093/protein/gzag003","url":null,"abstract":"<p><p>Antibody-dependent cellular cytotoxicity is a key mechanism for antibody-based therapeutics, and current engineering strategies to enhance ADCC primarily rely on two approaches: Fc mutations to improve the antibody's intrinsic CD16a affinity, or the fusion of binding-modules targeting NK cell receptors. The former often compromises antibody stability and induces CD16a downregulation; the latter occupies sites critical for target association and limits the assembly of multi-specific therapeutics. Here, we introduce a novel Fc engineering approach wherein the CH2 domain of the Fc region is replaced with an anti-NKp46 VHH named VIF-Ig. It has been reported that NKp46 expression remains unaltered after NK cell activation across various tumor microenvironments, addressing a key limitation of CD16a-dependent strategies. The novel molecules exhibit potent ADCC, high thermal stability, and retain FcRn binding for favorable pharmacokinetic profiles. Furthermore, we demonstrate that VIF-Ig can accommodate VHHs to target various epitopes. Thus, this versatile modular platform is suitable for developing next-generation NK cell or even other cell engagers with enhanced efficacy and tunable specificity, especially for emerging multi-specific immune cell engagers.</p>","PeriodicalId":54543,"journal":{"name":"Protein Engineering Design & Selection","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146068714","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Rapid isolation and characterization of high-affinity single-domain antibodies for broad-Spectrum detection of SARS-CoV-2 variants. 用于SARS-CoV-2变异体广谱检测的高亲和力单域抗体的快速分离和鉴定
IF 3.5 4区 生物学
Protein Engineering Design & Selection Pub Date : 2025-12-23 DOI: 10.1093/protein/gzag001
Ah Hyun Cho, Hee Eon Lee, Ji Hyun Lee, Won-Kyu Lee, Songyeol Yun, Sukmook Lee
{"title":"Rapid isolation and characterization of high-affinity single-domain antibodies for broad-Spectrum detection of SARS-CoV-2 variants.","authors":"Ah Hyun Cho, Hee Eon Lee, Ji Hyun Lee, Won-Kyu Lee, Songyeol Yun, Sukmook Lee","doi":"10.1093/protein/gzag001","DOIUrl":"10.1093/protein/gzag001","url":null,"abstract":"<p><p>The rapid evolution of SARS-CoV-2 presents substantial challenges to maintaining diagnostic accuracy. Single-domain antibodies (variable domains of camelid heavy-chain antibodies, VHHs), commonly referred to as nanobodies, are attractive tools for diagnostic applications due to their high specificity, stability, affinity and expression yield. In this study, three high-affinity VHHs that recognize the receptor-binding domain (RBD) of the SARS-CoV-2 BA.2 variant were isolated from a large naïve alpaca VHH phage display library. These nanobodies exhibited nanomolar affinities and high thermal stability. Notably, reformatting one VHH into a bivalent VHH-Fc fusion construct, K115.2-Fc, enhanced binding affinity 24-fold, achieving an equilibrium dissociation constant of 68.3 picomolar. Functional characterization demonstrated that K115.2-Fc cross-reacted with the Wuhan SARS-CoV-2 RBD and multiple variants, including Alpha, Beta, Gamma, Delta, Kappa, BA.1, BA.2, and BA.4/5. In indirect enzyme-linked immunosorbent assay, K115.2-Fc detected full-length spike protein with a limit of detection of 8.1 pM. Moreover, it enabled sensitive detection in western blotting and flow cytometry, highlighting its applicability across diverse diagnostic applications. Collectively, these findings identify K115.2-Fc as a promising candidate with potential for SARS-CoV-2 diagnostic utility.</p>","PeriodicalId":54543,"journal":{"name":"Protein Engineering Design & Selection","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146013409","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Toward an official model protein system, with GFP as an exemplar. 以绿色荧光蛋白为例,建立正式的蛋白质系统模型。
IF 3.5 4区 生物学
Protein Engineering Design & Selection Pub Date : 2025-12-23 DOI: 10.1093/protein/gzaf014
Marc Zimmer
{"title":"Toward an official model protein system, with GFP as an exemplar.","authors":"Marc Zimmer","doi":"10.1093/protein/gzaf014","DOIUrl":"10.1093/protein/gzaf014","url":null,"abstract":"<p><p>Model organisms significantly advance research because scientific communities recognize their value, develop infrastructure around them, and utilize them to address questions relevant to multiple species. I propose adopting a similar approach at the molecular level by establishing an official model protein system. This system would acknowledge five proteins that are already informally recognized as models in protein science: GFP, lysozyme, hemoglobin/myoglobin, RNase A, and bacteriorhodopsin. Formal recognition of these proteins would create standardized reporting requirements, shared benchmarks, and reference datasets, enhancing reproducibility, comparability, and educational resources. GFP serves as a prime example of this concept: it is a single-gene, genetically portable protein with a conserved structure and a measurable phenotype that effectively connects computation and experimental research. This paper identifies the criteria for model protein designation, presents a minimal reporting checklist, and outlines initial steps for implementation at the system level.</p>","PeriodicalId":54543,"journal":{"name":"Protein Engineering Design & Selection","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145483944","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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