Protein Science最新文献

{"title":"Non-canonical ORFs-derived protein products in mitochondria: A multifaceted exploration of their functions in health and disease.","authors":"Ikram Ajala, Benoît Vanderperre","doi":"10.1002/pro.70053","DOIUrl":"10.1002/pro.70053","url":null,"abstract":"<p><p>Traditionally, eukaryotic mRNAs were perceived as inherently monocistronic. However, recent insights from ribosome profiling (Ribo-seq) and proteomics studies challenge this paradigm. These investigations reveal that, beyond the currently annotated reference proteins (RefProts), there exist additional proteins known as alternative proteins (AltProts) and small open reading frames derived microproteins encoded in regions of mRNAs previously considered untranslated or in non-coding transcripts. This experimental evidence broadens the spectrum of functional proteins within cells, tissues, and organs, potentially offering crucial insights into biological processes. Notably, a significant proportion of these newly identified AltProts and microproteins demonstrates localization in mitochondria, contributing to the functions of mitochondrial complexes. This review delves into the overlooked realm of the alternative proteome within mitochondria, exploring the role of nuclear or mitochondrial-genome-encoded AltProts and microproteins in physiological and pathological cellular processes.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 3","pages":"e70053"},"PeriodicalIF":4.5,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11837024/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143450033","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":"Exploring P450 superfamily diversity with P450Atlas - Online tool for automated subfamily assignment.","authors":"Dominik Gront, Khajamohiddin Syed, David R Nelson","doi":"10.1002/pro.70057","DOIUrl":"10.1002/pro.70057","url":null,"abstract":"<p><p>Cytochrome P450 monooxygenases (CYPs/P450s) are heme-containing enzymes known to biology for more than six decades. Their stereo- and regio-specific enzymatic activities on various compounds led to exploring their potential in almost all areas of life. The P450 superfamily, encompassing nearly 10,000 known families, boasts a staggering diversity represented by numerous families, highlighting its immense scale within the realm of enzymes. In this contribution, we describe the P450Atlas website: the ultimate source of information about all named P450 families and subfamilies. The website's main functionality is the automated assignment of a query sequence to one of the known subfamilies. The new subfamily assignment algorithm relies on Hidden Markov Models (HMM) and has been extensively tested and compared to an approach based on the BLAST program. Extensive validation shows that the HMM approach is more sensitive than the latter one, offering almost perfect automated P450 sequence assignment to subfamilies. A user can also browse and search through the online list of families across the Tree of Life. We believe that the P450Atlas website (https://p450atlas.org) will become a comprehensive and unified source of information on cytochrome 450 nomenclature.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 3","pages":"e70057"},"PeriodicalIF":4.5,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11837033/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143449924","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":"ShiftScan: A tool for rapid analysis of high-throughput differential scanning fluorimetry data and compound prioritization.","authors":"Samantha C Waterworth, Shilpa R Shenoy, Nirmala D Sharma, Chris Wolcott, Duncan E Donohue, Barry R O'Keefe, John A Beutler","doi":"10.1002/pro.70055","DOIUrl":"10.1002/pro.70055","url":null,"abstract":"<p><p>Differential scanning fluorimetry (DSF) can be an effective high-throughput screening assay in drug discovery for detecting protein-compound interactions that stabilize or destabilize macromolecules. Due to the magnitude and quality of the data produced by this biophysical assay, analyzing and prioritizing compounds from large-scale DSF data sets has proven challenging to the research community. Here, we present ShiftScan-a powerful, stand-alone tool designed for the rapid analysis of DSF data and compound prioritization based on thermal transition patterns. ShiftScan accurately and quickly predicts melting temperatures (Tm values) from both canonical and non-canonical transition patterns, efficiently filtering out spurious data to minimize false positives. We report on the use of this tool for data analysis of screens involving both pure compound and natural product fraction libraries and provide the software to the screening community to aid in the discovery of molecularly-targeted compounds. Instructions for installation and usage of ShiftScan can be found at our GitHub repository: https://github.com/samche42/ShiftScan.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 3","pages":"e70055"},"PeriodicalIF":4.5,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11848206/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143483816","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":"Exploring the proton transport mechanism of the mitochondrial ADP/ATP carrier: FA-cycling hypothesis and beyond.","authors":"Elena E Pohl, Mario Vazdar, Jürgen Kreiter","doi":"10.1002/pro.70047","DOIUrl":"10.1002/pro.70047","url":null,"abstract":"<p><p>The mitochondrial ADP/ATP carrier (AAC, ANT), a member of the SLC25 family of solute carriers, plays a critical role in transporting purine nucleotides (ATP and ADP) as well as protons across the inner mitochondrial membrane. However, the precise mechanism and physiological significance of proton transport by ADP/ATP carrier remain unclear. Notably, the presence of uncouplers-such as long-chain fatty acids (FA) or artificial compounds like dinitrophenol (DNP)-is essential for this process. We explore two potential mechanisms that describe ADP/ATP carrier as either (i) a proton carrier that functions in the presence of FA or DNP, or (ii) an anion transporter (FA^- or DNP). In the latter case, the proton is translocated by the neutral form of FA, which carries it from the matrix to the intermembrane space (FA-cycling hypothesis). Our recent results support this hypothesis. We describe a four-step mechanism for the \"sliding\" of the FA anion from the matrix to the mitochondrial intermembrane space and discuss a possible generalization of this mechanism to other SLC25 carriers.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 3","pages":"e70047"},"PeriodicalIF":4.5,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11837047/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143449926","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":"Engineering IGF2 for Lysosome-targeting chimeras development to target drug-resistant membrane proteins in tumor therapy.","authors":"Yanchao Pan, Qing Xiang, Kai Deng, Muhammad I Anwar, Leiming Wang, Yuan Wang, Qiulian Liang, Lirou Shen, Jing Yang, Zhongyu Hou, Weijun Shen","doi":"10.1002/pro.70051","DOIUrl":"10.1002/pro.70051","url":null,"abstract":"<p><p>Lysosome-targeting chimeras (LYTACs) represent a promising approach for the targeted degradation of membrane proteins. Currently, two primary methods for LYTAC development involve chemically modified antibodies and wild-type insulin-like growth factor 2 (IGF2) fusion proteins (iLYTACs). However, LYTACs necessitate intricate chemical modification processes, while wild-type IGF2 in iLYTAC technology binds to IGF1R, potentially triggering carcinogenesis. To tackle this challenge, we introduce specific IGF2R-binding lysosomal targeting chimeras (sLYTACs), a novel technology utilizing engineered IGF2 mutant fusion antibodies for the degradation of endogenous membrane proteins. Diverging from iLYTACs, sLYTACs exhibit selective binding to IGF2R with increased affinity, significantly bolstering the anti-proliferative impact on drug-resistant tumor cells both in vitro and in vivo. By effectively degrading third-generation tyrosine kinase inhibitor-resistant EGFR mutants, masking binding epitope HER2, and concurrently targeting compensatory receptors interacting with these proteins, sLYTACs show great promise in drug development to overcome bypass signaling and combat drug resistance in tumors.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 3","pages":"e70051"},"PeriodicalIF":4.5,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11837023/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143449919","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":"Refinement and curation of homologous groups facilitated by structure prediction.","authors":"Richard Dustin Schaeffer, Jimin Pei, Jing Zhang, Qian Cong, Nick V Grishin","doi":"10.1002/pro.70074","DOIUrl":"10.1002/pro.70074","url":null,"abstract":"<p><p>Domain classification of protein predictions released in the AlphaFold Database (AFDB) has been a recent focus of the Evolutionary Classification of protein Domains (ECOD). Although a primary focus of our recent work has been the partition and assignment of domains from these predictions, we here show how these diverse predictions can be used to examine the reference domain set more closely. Using results from DPAM, our AlphaFold-specific domain parsing algorithm, we examine hierarchical groupings that share significant levels of homologous links, both between groups that were not previously assessed to be definitively homologous and between groups that were not previously observed to share significant homologous links. Combined with manual analysis, these large datasets of structural and sequence similarities allow us to merge homologous groups in multiple cases which we detail within. These domains tend to be families of domains from families that are either small, previously had few experimental representatives, or had unknown function. The exception to this is the chromodomains, a large homologous group which were increased from \"possibly homologous\" to \"definitely homologous\" to increase the consistency of ECOD based their strong homologous links to the SH3 domains.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 3","pages":"e70074"},"PeriodicalIF":4.5,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11836899/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143450195","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":"From duplication to fusion: Expanding Dayhoff's model of protein evolution.","authors":"Yusran Abdillah Muthahari, Lilian Magnus, Paola Laurino","doi":"10.1002/pro.70054","DOIUrl":"10.1002/pro.70054","url":null,"abstract":"<p><p>Dayhoff's hypothesis suggests that complex proteins emerged from simpler peptides or domains, which duplicated and fused to create more complex proteins and novel functions. These processes expanded and diversified the protein repertoire within organisms. Extensive studies and reviews over the past two decades have highlighted the impact of gene duplication on protein evolution. However, the role of fusion in this evolutionary narrative remains less understood. This perspective seeks to address this gap by emphasizing the role of fusion in evolution. Fusion is critical in determining the evolutionary fate of duplicated protomers, either preserving their ancestral function or evolving entirely new functions. It complements mutations, insertions, and deletions as evolutionary steps to enhance protein evolvability by expanding the capacity of the protein to explore new structural and functional space.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 3","pages":"e70054"},"PeriodicalIF":4.5,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11837038/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143449942","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":"Insights into the low-temperature adaptation of an enzyme as studied through ancestral sequence reconstruction.","authors":"Shuang Cui, Subrata Dasgupta, Sota Yagi, Madoka Kimura, Ryutaro Furukawa, Shunsuke Tagami, Satoshi Akanuma","doi":"10.1002/pro.70071","DOIUrl":"10.1002/pro.70071","url":null,"abstract":"<p><p>For billions of years, enzymes have evolved in response to the changing environments in which their host organisms lived. Various lines of evidence suggest the earliest primitive organisms inhabited high-temperature environments and possessed enzymes adapted to such conditions. Consequently, extant mesophilic and psychrophilic enzymes are believed to have adapted to lower temperatures during the evolutionary process. Herein, we analyzed this low-temperature adaptation using ancestral sequence reconstruction. Previously, we generated the phylogenetic tree of 3-isopropylmalate dehydrogenases (IPMDHs) and reconstructed the sequence of the last bacterial common ancestor. The corresponding ancestral enzyme displayed high thermostability and catalytic activity at elevated temperatures but moderate activity at low temperatures (Furukawa et al., Sci. Rep., 2020;10:15493). Here, to identify amino acid residues that are responsible for the low-temperature adaptation, we reconstructed and characterized all 11 evolutionary intermediates that sequentially connect the last bacterial common ancestor with extant mesophilic IPMDH from Escherichia coli. A remarkable change in catalytic properties, from those suited for high reaction temperatures to those adapted for low temperatures, occurred between two consecutive evolutionary intermediates. Using a combination of sequence comparisons between ancestral proteins and site-directed mutagenesis analyses, three key amino acid substitutions were identified that enhance low-temperature catalytic activity. Intriguingly, amino acid substitutions that had the most significant impact on activity at low temperatures displayed no discernable effect on thermostability. However, these substitutions markedly reduced the activation energy for catalysis, thereby improving low-temperature activity. The results were further investigated by molecular dynamics simulations of the predicted structures of the ancestral enzymes. Our findings exemplify how ancestral sequence reconstruction can identify residues crucial for adaptation to low temperatures.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 3","pages":"e70071"},"PeriodicalIF":4.5,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11836894/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143449882","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":"Folding of a tandemly knotted protein: Evidence that a polypeptide chain can get out of deep kinetic traps.","authors":"Hongyu Zhang, Sophie E Jackson","doi":"10.1002/pro.70048","DOIUrl":"10.1002/pro.70048","url":null,"abstract":"<p><p>It is hard to imagine how proteins can thread and form knots in their polypeptide chains, but they do. These topologically complex structures have challenged the traditional protein folding views of simple funnel-shaped energy landscapes. Previous experimental studies on the folding mechanisms of deeply knotted proteins with a single trefoil knot have yielded evidence that this topology has a more complicated folding landscape than other simpler proteins. However, to date, there have been no attempts to study the folding of any protein in which multiple threading events are needed to create more than one knot within a single polypeptide chain. Here, we report the construction and characterization of an artificial tandemly knotted protein. We find compelling evidence that both domains of the protein form trefoil knots with similar structures and stabilities to the parent single trefoil-knotted protein. In addition, we show that this tandemly knotted protein has a complex folding pathway in which there are additional very slow folding phases that we propose correspond to the formation of the second knot within the system. We also find evidence that during folding this protein gets transiently trapped in deep kinetic traps, however, the majority of protein chains (>90%) manage to partially unfold and acquire the native tandem-knot topology. This work highlights the fact that Nature can tolerate more complex protein topologies than we thought, and despite considerable misfolding during folding, protein chains can find their way to the native state even in the absence of molecular chaperones.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 3","pages":"e70048"},"PeriodicalIF":4.5,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11837048/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143449940","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":"Torsional twist of the SARS-CoV and SARS-CoV-2 SUD-N and SUD-M domains.","authors":"Monica Rosas-Lemus, George Minasov, Joseph S Brunzelle, Taha Y Taha, Sofia Lemak, Shaohui Yin, Ludmilla Shuvalova, Julia Rosecrans, Kanika Khanna, H Steven Seifert, Alexei Savchenko, Peter J Stogios, Melanie Ott, Karla J F Satchell","doi":"10.1002/pro.70050","DOIUrl":"10.1002/pro.70050","url":null,"abstract":"<p><p>Coronavirus non-structural protein 3 (nsp3) forms hexameric crowns of pores in the double membrane vesicle that houses the replication-transcription complex. Nsp3 in SARS-like viruses has three unique domains absent in other coronavirus nsp3 proteins. Two of these, SUD-N (Macrodomain 2) and SUD-M (Macrodomain 3), form two lobes connected by a peptide linker and an interdomain disulfide bridge. We resolve the first complete x-ray structure of SARS-CoV SUD-N/M as well as a mutant variant of SARS-CoV-2 SUD-N/M modified to restore cysteines for interdomain disulfide bond naturally lost by evolution. Comparative analysis of all structures revealed SUD-N and SUD-M are not rigidly associated but rather have significant rotational flexibility. Phylogenetic analysis supports that the potential to form the disulfide bond is common across betacoronavirus isolates from many bat species and civets, but also one or both of the cysteines that form the disulfide bond are absent across isolates from bats and pangolins. The absence of these cysteines does not impact viral replication or protein translation.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 3","pages":"e70050"},"PeriodicalIF":4.5,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11837046/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143450198","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}