Protein Science最新文献_第5页

Ion mobility mass spectrometry unveils conformational effects of drug lead EPI-001 on the intrinsically disordered N-terminal domain of the androgen receptor. 离子迁移质谱揭示了药物铅EPI-001对雄激素受体内在无序n端结构域的构象影响。

IF 4.5 3区生物学

Protein Science Pub Date : 2025-01-01 DOI: 10.1002/pro.5254

Ikhlas M M Ahmed, Adam Rofe, Martyn C Henry, Eric West, Craig Jamieson, Iain J McEwan, Rebecca Beveridge

{"title":"Ion mobility mass spectrometry unveils conformational effects of drug lead EPI-001 on the intrinsically disordered N-terminal domain of the androgen receptor.","authors":"Ikhlas M M Ahmed, Adam Rofe, Martyn C Henry, Eric West, Craig Jamieson, Iain J McEwan, Rebecca Beveridge","doi":"10.1002/pro.5254","DOIUrl":"10.1002/pro.5254","url":null,"abstract":"Intrinsically disordered proteins (IDPs) are important drug targets as they are key actors within cell signaling networks. However, the conformational plasticity of IDPs renders them challenging to characterize, which is a bottleneck in developing small molecule drugs that bind to IDPs and modulate their behavior. In relation to this, ion mobility mass spectrometry (IM-MS) is a useful tool to investigate IDPs, as it can reveal their conformational preferences. It can also offer important insights in drug discovery, as it can measure binding stoichiometry and unveil conformational shifts of IDPs exerted by the binding of small drug-like molecules. Herein, we have used IM-MS to investigate the effect of drug lead EPI-001 on the disordered N-terminal domain of the androgen receptor (AR-NTD). Despite structural heterogeneity rendering the NTD a challenging region of the protein to drug, this domain harbors most, if not all, of the transcriptional activity. We quantify the stoichiometry of EPI-001 binding to various constructs corresponding to functional domains of AR-NTD and show that it binds to separate constructs containing transactivation unit (TAU)-1 and TAU-5, respectively, and that 1-2 molecules bind to a larger construct containing both sequences. We also identify a conformational shift upon EPI-001 binding to the TAU-5, and to a much lesser extent with TAU-1 containing constructs. This work provides novel insight on the interactions of EPI-001 with the AR-NTD, and the structural alterations that it exerts, and positions IM-MS as an informative tool that will enhance the tractability of IDPs, potentially leading to better therapies.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 1","pages":"e5254"},"PeriodicalIF":4.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11635395/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142813921","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

Structural dynamics and binding of Caenorhabditis elegans lifespan-extending lipid binding protein-3 to polyunsaturated fatty acids. 延长秀丽隐杆线虫寿命的脂质结合蛋白-3与多不饱和脂肪酸的结构动力学及结合。

IF 4.5 3区生物学

Protein Science Pub Date : 2025-01-01 DOI: 10.1002/pro.5249

André R Cuevas, Matthew C Tillman, Meng C Wang, Eric A Ortlund

{"title":"Structural dynamics and binding of Caenorhabditis elegans lifespan-extending lipid binding protein-3 to polyunsaturated fatty acids.","authors":"André R Cuevas, Matthew C Tillman, Meng C Wang, Eric A Ortlund","doi":"10.1002/pro.5249","DOIUrl":"10.1002/pro.5249","url":null,"abstract":"Intracellular lipid binding proteins (iLBPs) play crucial roles in lipid transport and cellular metabolism across the animal kingdom. Recently, a fat-to-neuron axis was described in Caenorhabditis elegans, in which lysosomal activity in the fat liberates polyunsaturated fatty acids (PUFAs) that signal to neurons and extend lifespan with durable fecundity. In this study, we investigate the structure and binding mechanisms of a lifespan-extending lipid chaperone, lipid binding protein-3 (LBP-3), which shuttles dihomo-γ-linolenic (DGLA) acid from intestinal fat to neurons. We present the first high-resolution crystal structure of LBP-3, which reveals a classic iLBP fold with an unexpected and unique homodimeric arrangement via interstrand interactions that is incompatible with ligand binding. We identify key ionic interactions that mediate DGLA binding within the lipid binding pocket. Molecular dynamics simulations further elucidate LBP-3's preferential binding to DGLA due to its rotational freedom and access to favorable binding conformations compared to other 20-carbon PUFAs. We also propose that LBP-3 dimerization may be a unique regulatory mechanism for lipid chaperones.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 1","pages":"e5249"},"PeriodicalIF":4.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11633055/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142807872","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

A crucial active site network of titratable residues guides catalysis and NAD⁺ binding in human succinic semialdehyde dehydrogenase. 可滴定残基的关键活性位点网络指导人类琥珀半醛脱氢酶的催化和NAD+结合。

IF 4.5 3区生物学

Protein Science Pub Date : 2025-01-01 DOI: 10.1002/pro.70024

Samuele Cesaro, Marco Orlando, Ilaria Bettin, Carmen Longo, Giulia Spagnoli, Patrizia Polverino de Laureto, Gianluca Molla, Mariarita Bertoldi

{"title":"A crucial active site network of titratable residues guides catalysis and NAD+ binding in human succinic semialdehyde dehydrogenase.","authors":"Samuele Cesaro, Marco Orlando, Ilaria Bettin, Carmen Longo, Giulia Spagnoli, Patrizia Polverino de Laureto, Gianluca Molla, Mariarita Bertoldi","doi":"10.1002/pro.70024","DOIUrl":"10.1002/pro.70024","url":null,"abstract":"Human succinic semialdehyde dehydrogenase is a mitochondrial enzyme fundamental in the neurotransmitter γ-aminobutyric acid catabolism. It catalyzes the NAD+-dependent oxidative degradation of its derivative, succinic semialdehyde, to succinic acid. Mutations in its gene lead to an inherited neurometabolic rare disease, succinic semialdehyde dehydrogenase deficiency, characterized by mental and developmental delay. Due to the poor characterization of this enzyme, we carried out evolutionary and kinetic investigations to contribute to its functional behavior, a prerequisite to interpreting pathogenic variants. An in silico analysis shows that succinic semialdehyde dehydrogenases belong to two families, one human-like and the other of bacterial origin, differing in the oligomeric state and in a network of active site residues. This information is coupled to the biophysical-biochemical characterization of the human recombinant enzyme uncovering that (i) catalysis proceeds by an ordered bi-bi mechanism with NAD+ binding before the aldehyde that exerts a partial non-competitive inhibition; (ii) a stabilizing complex between the catalytic Cys340 and NAD+ is observed and interpreted as a protective mechanism; and (iii) a concerted non-covalent network assists the action of the catalytic residues Cys340 and Glu306. Through mutational analyses of Lys214, Glu306, Cys340, and Glu515 associated with pH studies, we showed that NAD+ binding is controlled by the dyad Lys214-Glu515. Moreover, catalysis is assured by proton transfer exerted by the same dyad networked with the catalytic Glu306, involved in catalytic Cys340 deprotonation/reprotonation. The identification of this weak bond network essential for cofactor binding and catalysis represents a first step to tackling the molecular basis for its deficiency.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 1","pages":"e70024"},"PeriodicalIF":4.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11681614/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142897212","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

Restoring adapter protein complex 4 function with small molecules: an in silico approach to spastic paraplegia 50. 用小分子恢复适配蛋白复合体的功能：痉挛截瘫的计算机方法[j]。

IF 4.5 3区生物学

Protein Science Pub Date : 2025-01-01 DOI: 10.1002/pro.70006

Serena Francisco, Lorenzo Lamacchia, Attilio Turco, Giuseppe Ermondi, Giulia Caron, Matteo Rossi Sebastiano

{"title":"Restoring adapter protein complex 4 function with small molecules: an in silico approach to spastic paraplegia 50.","authors":"Serena Francisco, Lorenzo Lamacchia, Attilio Turco, Giuseppe Ermondi, Giulia Caron, Matteo Rossi Sebastiano","doi":"10.1002/pro.70006","DOIUrl":"10.1002/pro.70006","url":null,"abstract":"This study focuses on spastic paraplegia type 50 (SPG50), an adapter protein complex 4 deficiency syndrome caused by mutations in the adapter protein complex 4 subunit mu-1 (AP4M1) gene, and on the downstream alterations of the AP4M1 protein. We applied a battery of heterogeneous computational resources, encompassing two in-house tools described here for the first time, to (a) assess the druggability potential of AP4M1, (b) characterize SPG50-associated mutations and their 3D scenario, (c) identify mutation-tailored drug candidates for SPG50, and (d) elucidate their mechanisms of action by means of structural considerations on homology models of the adapter protein complex 4 core. Altogether, the collected results indicate R367Q as the mutation with the most promising potential of being corrected by small-molecule drugs, and the flavonoid rutin as best candidate for this purpose. Rutin shows promise in rescuing the interaction between the AP4M1 and adapter protein complex subunit beta-1 (AP4B1) subunits by means of a glue-like mode of action. Overall, this approach offers a framework that could be systematically applied to the investigation of mutation-wise molecular mechanisms in different hereditary spastic paraplegias, too.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 1","pages":"e70006"},"PeriodicalIF":4.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11670165/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142896636","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

Streptococcus pneumoniae GAPN is a key metabolic player necessary for host infection. 肺炎链球菌GAPN是宿主感染所必需的关键代谢因子。

IF 4.5 3区生物学

Protein Science Pub Date : 2025-01-01 DOI: 10.1002/pro.5253

Eunjeong Lee, Anthony Saviola, Shaun Bevers, Jasmina S Redzic, Sean P Maroney, Steven Shaw, Emily Tamkin, Sam Fulte, Travis Nemkov, Nancy Meyer, Angelo D'Alessandro, Kirk C Hansen, Sarah E Clark, Elan Eisenmesser

{"title":"Streptococcus pneumoniae GAPN is a key metabolic player necessary for host infection.","authors":"Eunjeong Lee, Anthony Saviola, Shaun Bevers, Jasmina S Redzic, Sean P Maroney, Steven Shaw, Emily Tamkin, Sam Fulte, Travis Nemkov, Nancy Meyer, Angelo D'Alessandro, Kirk C Hansen, Sarah E Clark, Elan Eisenmesser","doi":"10.1002/pro.5253","DOIUrl":"10.1002/pro.5253","url":null,"abstract":"Streptococcus pneumoniae (S. pneumoniae) employs various metabolic pathways to generate nicotinamide adenine dinucleotide phosphate (NADPH), which is essential for redox balance, fatty acid synthesis, and energy production. GAPN, a non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase, plays a role in this process by directly reducing NADP+ to NADPH, effectively contributing to glucose metabolism. However, its relative importance for S. pneumoniae metabolism and infection has remained unknown. Here, we performed a comprehensive characterization of S. pneumoniae GAPN through kinetic assays, isothermal titration calorimetry (ITC), cryo-EM, mass spectrometry, and infection assays. Despite its structural similarities to its homologues in other species, S. pneumoniae GAPN exhibits negative cooperativity with respect to its substrate, glyceraldehyde-3-phosphate (G3P), suggesting a unique regulatory mechanism. Our results demonstrate that GAPN knockout leads to significant metabolic reprogramming, including increased glycogen storage that leads to enhanced fatty acid metabolism. This collectively reduces the ability of S. pneumoniae to manage oxidative stress and sustain infection. Our findings highlight GAPN as a critical enzyme for S. pneumoniae metabolic balance and suggest that its inhibition could serve as a potential strategy for therapeutic intervention in pneumococcal diseases.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 1","pages":"e5253"},"PeriodicalIF":4.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11633051/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142807870","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

In situ characterization of amine-forming enzymes shows altered oligomeric state. 在原位表征的胺形成酶显示改变寡聚状态。

IF 4.5 3区生物学

Protein Science Pub Date : 2025-01-01 DOI: 10.1002/pro.5248

Adam A Caparco, Bettina R Bommarius, Laurine Ducrot, Julie A Champion, Carine Vergne-Vaxelaire, Andreas S Bommarius

{"title":"In situ characterization of amine-forming enzymes shows altered oligomeric state.","authors":"Adam A Caparco, Bettina R Bommarius, Laurine Ducrot, Julie A Champion, Carine Vergne-Vaxelaire, Andreas S Bommarius","doi":"10.1002/pro.5248","DOIUrl":"10.1002/pro.5248","url":null,"abstract":"Enzyme stability can be measured in a number of ways, including melting temperature, activity retention, and size analysis. However, these measurements are often conducted in an idealized storage buffer and not in the relevant enzymatic reaction media. Particularly for reactions that occur in alkaline, volatile, and high ionic strength media, typical analyses using differential scanning calorimetry, light scattering, and sodium dodecyl-sulfate polyacrylamide gel electrophoresis are not satisfactory to track the stability of these enzymes. In this work, we monitor the stability of engineered and native dehydrogenases that require a high amount of ammonia for their reaction to occur. We demonstrate the benefits of analyzing these enzymes in their reaction buffer, uncovering trends that were not observable in the typical phosphate storage buffer. This work provides a framework for analyzing the stability of many other enzymes whose reaction media is not suitable for traditional techniques. We introduce several strategies for measuring the melting temperature, oligomeric state, and activity of these enzymes in their reaction media. Further, we have identified opportunities for integration of computational tools into this workflow to engineer enzymes more effectively for solvent tolerance and improved stability.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 1","pages":"e5248"},"PeriodicalIF":4.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11669115/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142886253","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

Role of amino acid substitutions on proteolytic stability of histatin 5 in the presence of secreted aspartyl proteases and salivary proteases. 在分泌的天冬氨酸蛋白酶和唾液蛋白酶存在下，氨基酸取代对组蛋白5蛋白水解稳定性的影响。

IF 4.5 3区生物学

Protein Science Pub Date : 2025-01-01 DOI: 10.1002/pro.70011

Wright K Makambi, Victoria L Chiu, Lydia Kasper, Bernhard Hube, Amy J Karlsson

{"title":"Role of amino acid substitutions on proteolytic stability of histatin 5 in the presence of secreted aspartyl proteases and salivary proteases.","authors":"Wright K Makambi, Victoria L Chiu, Lydia Kasper, Bernhard Hube, Amy J Karlsson","doi":"10.1002/pro.70011","DOIUrl":"10.1002/pro.70011","url":null,"abstract":"Histatin 5 (Hst5) is a 24-amino-acid peptide naturally present in human saliva that has been proposed as a potential antifungal therapeutic. However, Hst5 is susceptible to degradation by secreted aspartyl proteases (Saps) produced by Candida albicans, which could limit its efficacy as a therapeutic. To better understand the role of the lysine residues of Hst5 in proteolysis by C. albicans Saps (Sap1, Sap2, Sap3, Sap5, Sap6, Sap9, and Sap10), we studied variants of Hst5 with substitutions to leucine or arginine at the lysine residues (K5, K11, K13, and K17). Sap5, Sap6, and Sap10 did not degrade Hst5 or the variants. However, we observed degradation of the peptides by Sap1, Sap2, Sap3, and Sap9, and the degradation depended on the site of substitution and the substituent residue. Some modifications, such as K11L and K13L, were particularly susceptible to proteolysis by Sap1, Sap2, Sap3, and Sap9. In contrast, the K17L modification substantially increased the stability and antifungal activity of Hst5 in the presence of Saps. We used mass spectrometry to characterize the proteolysis products, which allowed us to identify fragments likely to have maintained or lost antifungal activity. We also evaluated the proteolytic stability of the Hst5 variants in saliva. Both K17L and K5R showed improved stability; however, the enhancements were modest, suggesting that further engineering is required to achieve significant improvements. Our approach demonstrates the potential of simple, rational substitutions to enhance peptide efficacy and proteolytic stability, providing a promising strategy for improving the properties of antifungal peptides.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 1","pages":"e70011"},"PeriodicalIF":4.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11669118/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142886264","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

An in silico framework to visualize how cancer-associated mutations influence structural plasticity of the chemokine receptor CCR3. 一个可视化癌症相关突变如何影响趋化因子受体CCR3结构可塑性的计算机框架。

IF 4.5 3区生物学

Protein Science Pub Date : 2025-01-01 DOI: 10.1002/pro.70013

Evan J van Aalst, Benjamin J Wylie

{"title":"An in silico framework to visualize how cancer-associated mutations influence structural plasticity of the chemokine receptor CCR3.","authors":"Evan J van Aalst, Benjamin J Wylie","doi":"10.1002/pro.70013","DOIUrl":"10.1002/pro.70013","url":null,"abstract":"G protein Coupled Receptors (GPCRs) are the largest family of cell surface receptors in humans. Somatic mutations in GPCRs are implicated in cancer progression and metastasis, but mechanisms are poorly understood. Emerging evidence implicates perturbation of intra-receptor activation pathway motifs whereby extracellular signals are transmitted intracellularly. Recently, sufficiently sensitive methodology was described to calculate structural strain as a function of missense mutations in AlphaFold-predicted model structures, which was extensively validated on experimental and predicted structural datasets. When paired with Molecular Dynamics (MD) simulations, these tools provide a facile approach to screen mutations in silico. We applied this framework to calculate the structural and dynamic effects of cancer-associated mutations in the chemokine receptor CCR3, a Class A GPCR involved in cancer and autoimmune disorders. Residue-residue contact scoring refined effective strain results, highlighting significant remodeling of inter- and intra-motif contacts along the highly conserved GPCR activation pathway network. We then integrated AlphaFold-derived predicted Local Distance Difference Test scores with per-residue Root Mean Square Fluctuations and activation pathway Contact Analysis (CONAN) from coarse grain MD simulations to identify statistically significant changes in receptor dynamics upon mutation. Finally, analysis of negative control mutants suggests false positive results in AlphaFold pipelines should be considered but can be mitigated with stricter control of statistical analysis. Our results indicate selected mutants influence structural plasticity of CCR3 related to ligand interaction, activation, and G protein coupling, using a framework that could be applicable to a wide range of biochemically relevant protein targets following further validation.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 1","pages":"e70013"},"PeriodicalIF":4.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11670309/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142897239","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

Protein stability models fail to capture epistatic interactions of double point mutations. 蛋白质稳定性模型无法捕捉双点突变的表观相互作用。

IF 4.5 3区生物学

Protein Science Pub Date : 2025-01-01 DOI: 10.1002/pro.70003

Henry Dieckhaus, Brian Kuhlman

{"title":"Protein stability models fail to capture epistatic interactions of double point mutations.","authors":"Henry Dieckhaus, Brian Kuhlman","doi":"10.1002/pro.70003","DOIUrl":"10.1002/pro.70003","url":null,"abstract":"There is strong interest in accurate methods for predicting changes in protein stability resulting from amino acid mutations to the protein sequence. Recombinant proteins must often be stabilized to be used as therapeutics or reagents, and destabilizing mutations are implicated in a variety of diseases. Due to increased data availability and improved modeling techniques, recent studies have shown advancements in predicting changes in protein stability when a single-point mutation is made. Less focus has been directed toward predicting changes in protein stability when there are two or more mutations. Here, we analyze the largest available dataset of double point mutation stability and benchmark several widely used protein stability models on this and other datasets. We find that additive models of protein stability perform surprisingly well on this task, achieving similar performance to comparable non-additive predictors according to most metrics. Accordingly, we find that neither artificial intelligence-based nor physics-based protein stability models consistently capture epistatic interactions between single mutations. We observe one notable deviation from this trend, which is that epistasis-aware models provide marginally better predictions than additive models on stabilizing double point mutations. We develop an extension of the ThermoMPNN framework for double mutant modeling, as well as a novel data augmentation scheme, which mitigates some of the limitations in currently available datasets. Collectively, our findings indicate that current protein stability models fail to capture the nuanced epistatic interactions between concurrent mutations due to several factors, including training dataset limitations and insufficient model sensitivity.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 1","pages":"e70003"},"PeriodicalIF":4.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11659742/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142865268","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

Proline variants in the BRCA1 coiled-coil domain disrupt folding and binding to PALB2. BRCA1 螺旋线圈结构域中的脯氨酸变体会破坏折叠和与 PALB2 的结合。

IF 4.5 3区生物学

Protein Science Pub Date : 2025-01-01 DOI: 10.1002/pro.5240

Chrissy N S Baker, Precious Grace C Pajela, Davis E Martin, Sergei V Dzyuba, Mikaela D Stewart

{"title":"Proline variants in the BRCA1 coiled-coil domain disrupt folding and binding to PALB2.","authors":"Chrissy N S Baker, Precious Grace C Pajela, Davis E Martin, Sergei V Dzyuba, Mikaela D Stewart","doi":"10.1002/pro.5240","DOIUrl":"10.1002/pro.5240","url":null,"abstract":"Inherited mutations in the genes coding for the tumor suppressor proteins BRCA1 and PALB2 can lead to increased risk of breast and ovarian cancer. Upon DNA damage, these two proteins form a complex to promote double-stranded break repair via homologous recombination. Missense mutations in either BRCA1 or PALB2 that disrupt this important interaction result in loss of effective DNA damage repair and are associated with breast tumorigenesis. However, the overwhelming majority of missense mutations found in the binding domains of these two genes remain classified as variants of unknown significance. Here we report an in vitro assay for assessing the effect of variants of unknown significance on the heterodimerization of PALB2 and BRCA1 that recapitulates the effect of the known deleterious mutations. We apply the assay to several variants of unknown significance in BRCA1 which reveals other mutations in this region that also disrupt binding, including a mutation of a residue not predicted to directly interact with PALB2. Structural analysis indicates that all BRCA1 mutations to proline tested disrupt α-helix formation and therefore are not well tolerated even when located at positions outside of the PALB2-binding interface. This assay and the structural hypothesis described will be helpful for assessing risk for variants identified in the future in the BRCA1/PALB2 interaction domains.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 1","pages":"e5240"},"PeriodicalIF":4.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11645666/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142823938","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