Proteins-Structure Function and Bioinformatics最新文献_第6页

De Novo Design of Highly Stable Binders Targeting Dihydrofolate Reductase in Klebsiella pneumoniae. 靶向肺炎克雷伯菌二氢叶酸还原酶的高稳定性结合剂的重新设计。

IF 3.2 4区生物学

Proteins-Structure Function and Bioinformatics Pub Date : 2025-05-15 DOI: 10.1002/prot.26835

Ihteshamul Haq, Faheem Anwar, Yigang Tong

{"title":"De Novo Design of Highly Stable Binders Targeting Dihydrofolate Reductase in Klebsiella pneumoniae.","authors":"Ihteshamul Haq, Faheem Anwar, Yigang Tong","doi":"10.1002/prot.26835","DOIUrl":"https://doi.org/10.1002/prot.26835","url":null,"abstract":"The study aims to design novel therapeutic inhibitors targeting the DHFR protein of Klebsiella pneumoniae. However, challenges like bacterial resistance to peptides and the limitations of computational models in predicting in vivo behavior must be addressed to refine the design process and improve therapeutic efficacy. This study employed deep learning-based bioinformatics techniques to tackle these issues. The study involved retrieving DHFR protein sequences from Klebsiella strains, aligning them to identify conserved regions, and using deep learning models (OmegaFold, ProteinMPNN) to design de novo inhibitors. Cell-penetrating peptide (CPP) motifs were added to enhance delivery, followed by allergenicity and thermal stability assessments. Molecular docking and dynamics simulations evaluated the binding affinity and stability of the inhibitors with DHFR. A conserved 60-residue region was identified, and 60 de novo binders were generated, resulting in 7200 sequences. After allergenicity prediction and stability testing, 10 sequences with melting points near 70°C were shortlisted. Strong binding affinities were observed, especially for complexes 4OR7-1787 and 4OR7-1811, which remained stable in molecular dynamics simulations, indicating their potential as therapeutic agents. This study designed stable de novo peptides with cell-penetrating properties and strong binding affinity to DHFR. Future steps include in vitro validation to assess their effectiveness in inhibiting DHFR, followed by in vivo studies to evaluate their therapeutic potential and stability. These peptides offer a promising strategy against Klebsiella pneumoniae infections, providing potential alternatives to current antibiotics. Experimental validation will be key to assessing their clinical relevance.","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144082403","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

Molecular Basis for Vacuolar Iron Transport by OsVIT2, a Target for Iron Biofortification in Rice. 水稻铁生物强化靶点OsVIT2空泡铁运输的分子基础

IF 3.2 4区生物学

Proteins-Structure Function and Bioinformatics Pub Date : 2025-05-15 DOI: 10.1002/prot.26843

L B Arend, D S Lima, M G S Costa, F K Ricachenevsky, H Verli

{"title":"Molecular Basis for Vacuolar Iron Transport by OsVIT2, a Target for Iron Biofortification in Rice.","authors":"L B Arend, D S Lima, M G S Costa, F K Ricachenevsky, H Verli","doi":"10.1002/prot.26843","DOIUrl":"https://doi.org/10.1002/prot.26843","url":null,"abstract":"Iron deficiency is the prevalent and most widespread nutritional shortfall for humans, affecting over 30% of the global population and leading to anemia, particularly among preschool-aged children and pregnant women in developing countries. Simultaneously, while half of the world's population depends on rice (Oryza sativa L.) as a staple food, this cereal does not provide a sufficient amount of that micronutrient to meet these people's nutritional needs: even when iron is readily available in the soil, it does not accumulate in the consumed portion of the grain, namely, the starchy endosperm, being instead retained in the aleurone layer, in the pericarp and in the embryo. In this context, the present work applies computational biology tools-such as normal mode analysis and molecular dynamics simulations-to elucidate the behavior and transport mechanism of the Vacuolar Iron Transporter 2 (OsVIT2), a central protein for iron homeostasis in rice, with the objective of laying the foundations for future OsVIT2 engineering projects that could be articulated with ongoing efforts to promote iron biofortification in rice. We shed light on the interplay between protonation state, configuration and hydration of OsVIT2's pore; on the mechanics of its opening and on the ever-shifting hydrogen bond network contained within it. We also explore the potential contribution of the \"flexible arms\" to the iron-capturing function performed by the cytoplasmic domain.","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144082404","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

Phosphorylation Changes SARS-CoV-2 Nucleocapsid Protein's Structural Dynamics and Its Interaction With RNA. 磷酸化改变SARS-CoV-2核衣壳蛋白结构动力学及其与RNA的相互作用

IF 3.2 4区生物学

Proteins-Structure Function and Bioinformatics Pub Date : 2025-05-15 DOI: 10.1002/prot.26842

Stefan Loonen, Lina van Steenis, Marianne Bauer, Nikolina Šoštarić

{"title":"Phosphorylation Changes SARS-CoV-2 Nucleocapsid Protein's Structural Dynamics and Its Interaction With RNA.","authors":"Stefan Loonen, Lina van Steenis, Marianne Bauer, Nikolina Šoštarić","doi":"10.1002/prot.26842","DOIUrl":"https://doi.org/10.1002/prot.26842","url":null,"abstract":"The SARS-CoV-2 nucleocapsid protein, or N-protein, is a structural protein that plays an important role in the SARS-CoV-2 life cycle. The N-protein takes part in the regulation of viral RNA replication and drives highly specific packaging of full-length genomic RNA prior to virion formation. One regulatory mechanism that is proposed to drive the switch between these two operating modes is the phosphorylation state of the N-protein. Here, we assess the dynamic behavior of non-phosphorylated and phosphorylated versions of the N-protein homodimer through atomistic molecular dynamics simulations. We show that the introduction of phosphorylation yields a more dynamic protein structure and decreases the binding affinity between the N-protein and RNA. Furthermore, we find that secondary structure is essential for the preferential binding of particular RNA elements from the 5' UTR of the viral genome to the N-terminal domain of the N-protein. Altogether, we provide detailed molecular insights into N-protein dynamics, N-protein:RNA interactions, and phosphorylation. Our results corroborate the hypothesis that phosphorylation of the N-protein serves as a regulatory mechanism that determines N-protein function.","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144082407","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

3D-ΔΔG: A Dual-Channel Prediction Model for Protein-Protein Binding Affinity Changes Following Mutation Based on Protein 3D Structures. 3D-ΔΔG：基于蛋白质三维结构的蛋白质结合亲和力突变后变化的双通道预测模型。

IF 3.2 4区生物学

Proteins-Structure Function and Bioinformatics Pub Date : 2025-05-15 DOI: 10.1002/prot.26837

Yuxiang Wang, Yibo Zhu, Xiumin Shi, Lu Wang

{"title":"3D-ΔΔG: A Dual-Channel Prediction Model for Protein-Protein Binding Affinity Changes Following Mutation Based on Protein 3D Structures.","authors":"Yuxiang Wang, Yibo Zhu, Xiumin Shi, Lu Wang","doi":"10.1002/prot.26837","DOIUrl":"https://doi.org/10.1002/prot.26837","url":null,"abstract":"Protein-protein interactions are crucial for cellular regulation, antigen-antibody interactions, and other vital processes within living organisms. However, mutations in amino acid residues have the potential to induce changes in protein-protein binding affinity (ΔΔG), which may contribute to the onset and progression of disease. Existing methods for predicting ΔΔG use either protein sequence information or structural data. Furthermore, some methods are only applicable to single-point mutation cases. To address these limitations, we introduce a ΔΔG predictor that can handle complex scenarios involving multipoint mutations. In this investigation, a dual-channel deep learning model three-dimensional (3D)-ΔΔG is introduced, which is designed to predict ΔΔG by combining mutation information from side chain sequences and 3D structures. The proposed model employs a pre-trained protein language model to encode the side-chain amino acid sequence. A graph attention network is deployed to handle the graph representation of proteins simultaneously. Finally, a dual-channel processing module is implemented to facilitate depth fusion and extraction of both sequence and structural features. The model effectively captures the intricate alterations occurring pre- and post-protein mutation by integrating both sequence and 3D structural information. Results on the single-point mutation data set demonstrate a substantial improvement compared to state-of-the-art models. More significantly, 3D-ΔΔG exhibits superior performance when evaluated on the mixed mutation data sets, SKEMPIv1 and SKEMPIv2. The high level of agreement between the computationally predicted ΔΔG values and the experimentally determined values illustrates the potential of the 3D-ΔΔG model as an effective pre-screening tool in protein design and engineering.","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144082393","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

Structural and Functional Characterization of the 28 kDa Structured Core of BmSA1, the Major Surface Antigen of Babesia Microti. 微小巴贝斯虫主要表面抗原BmSA1 28 kDa结构核的结构与功能表征

IF 3.2 4区生物学

Proteins-Structure Function and Bioinformatics Pub Date : 2025-05-09 DOI: 10.1002/prot.26836

Assia Mouhand, Joana Pissarra, Philippe Barthe, Christian Roumestand, Stéphane Delbecq

{"title":"Structural and Functional Characterization of the 28 kDa Structured Core of BmSA1, the Major Surface Antigen of Babesia Microti.","authors":"Assia Mouhand, Joana Pissarra, Philippe Barthe, Christian Roumestand, Stéphane Delbecq","doi":"10.1002/prot.26836","DOIUrl":"https://doi.org/10.1002/prot.26836","url":null,"abstract":"Babesiosis is a tick-borne disease that poses a significant threat to animal health worldwide. In addition, climate change and the risk of human-to-human transmission through blood transfusion have made babesiosis an emerging disease in humans. Babesiosis is caused by the intraerythrocytic development of protozoan parasites from the genus Babesia, which belongs to the apicomplexan phylum that notably includes the more-widely studied causative agent of malaria, Plasmodium falciparum. Of the several hundred Babesia species identified so far, only a few are known to infect humans, with B. microti being the most prevalent and responsible for most of the clinical cases reported to date. There is no licensed vaccine for B. microti, and the development of a reliable serological diagnostic test would contribute to ensuring the safety of blood transfusions. The identification and characterization of parasite surface proteins are important steps in achieving this aim. One such protein is the GPI-anchored Major Surface Antigen BmSA1 (also known as BmGPI12), which is expressed at high levels at the surface of the merozoite. We present here the high-resolution solution structure of the 28 kDa structured core of BmSA1 (∆∆BmSA1) obtained through NMR spectroscopy. The structure of BmSA1 appears unrelated to the previously published structures of the major surface antigens of B. divergens (Bd37) or of B. canis (Bc28.1), which are thought to play a similar role in parasite invasion. We also define the erythrocyte binding function of ∆∆BmSA1, using NMR spectroscopy to map the binding interface. Finally, we used bioinformatic tools to map the potential epitopes of antibodies at the surface of the structured core of BmSA1.","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144008018","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

Structural Investigation of the Anti-CRISPR Protein AcrIE7. 抗crispr蛋白AcrIE7的结构研究

IF 3.2 4区生物学

Proteins-Structure Function and Bioinformatics Pub Date : 2025-05-03 DOI: 10.1002/prot.26832

Jeehee Kang, Changkon Park, Gyujin Lee, Jasung Koo, Hyejin Oh, Eun-Hee Kim, Euiyoung Bae, Jeong-Yong Suh

引用次数: 0

Structural and Functional Differences of Rhodostomin and Echistatin in Integrin Recognition and Biological Implications. 整合素识别中红吻合酶和紫组蛋白的结构和功能差异及其生物学意义。

IF 3.2 4区生物学

Proteins-Structure Function and Bioinformatics Pub Date : 2025-05-02 DOI: 10.1002/prot.26834

Yi-Chun Chen, Chun-Hao Huang, Yao-Tsung Chang, Chiu-Yueh Chen, Jia-Hau Shiu, Chun-Ho Cheng, Yu-Fang Su, Woei-Jer Chuang

{"title":"Structural and Functional Differences of Rhodostomin and Echistatin in Integrin Recognition and Biological Implications.","authors":"Yi-Chun Chen, Chun-Hao Huang, Yao-Tsung Chang, Chiu-Yueh Chen, Jia-Hau Shiu, Chun-Ho Cheng, Yu-Fang Su, Woei-Jer Chuang","doi":"10.1002/prot.26834","DOIUrl":"https://doi.org/10.1002/prot.26834","url":null,"abstract":"Rhodostomin (Rho) and Echistatin (Ech) are RGD-containing disintegrins with different sizes, disulfide bond patterns, and amino acid sequences in their RGD loops and C-termini. Cell adhesion analyzes showed that Rho exhibited a 5.2-, 18.9-, 2.2-, and 1.7-fold lower inhibitory activity against integrins αvβ3, α5β1, αIIbβ3, and αvβ5 in comparison with those of Ech. In contrast, Rho exhibited an 8.8-fold higher activity than Ech in inhibiting integrin αvβ6. The swapping of Ech's RGD loop and C-terminal sequences into those of Rho cannot increase its integrins' inhibitory activities. Interestingly, the mutation of Ech into Rho's RGD loop PRGDMP sequence and C-terminal YH sequence caused an 8.2-fold higher activity in inhibiting integrin αvβ6. Structural analyzes of Rho and Ech showed that they have similar conformations in their RGD loop and different conformations in their C-terminal regions. Molecular docking found that not only the RGD loop but also the C-terminal region of Rho and Ech interacted with integrins, showing that the C-terminal region is also important for integrin recognition. The docking of Rho into integrin αvβ6 showed that the C-terminal H68 residue of Rho interacted with D129 of β6. In contrast, the docking of Ech into integrin α5β1 showed that the C-terminal H44 residue of Ech interacted with Q191 of β1. Ech exhibited 78.5- and 10.9-fold higher activities in inhibiting HUVEC proliferation and A375 melanoma cell migration than those of Rho. These findings demonstrate that the disulfide bond pattern, RGD loop, and C-terminal region of disintegrins may cause their functional differences. The functional and structural differences between Rho and Ech support their potential as scaffolds to design drugs targeting their respective integrins.","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144047414","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

Characterization of the E26H Mutant Schistosoma japonicum Glutathione S-Transferase. 日本血吸虫谷胱甘肽s -转移酶E26H突变体的鉴定

IF 3.2 4区生物学

Proteins-Structure Function and Bioinformatics Pub Date : 2025-05-01 Epub Date: 2025-01-02 DOI: 10.1002/prot.26794

János András Mótyán, Ágota Nagyné Veres, József Tőzsér

{"title":"Characterization of the E26H Mutant Schistosoma japonicum Glutathione S-Transferase.","authors":"János András Mótyán, Ágota Nagyné Veres, József Tőzsér","doi":"10.1002/prot.26794","DOIUrl":"10.1002/prot.26794","url":null,"abstract":"Glutathione-S-transferase, such as that of Schistosoma japonicum (sjGST) belongs to the most widely utilized fusion tags in the recombinant protein technology. The E26H mutation of sjGST has already been found to remarkably improve its ability for binding divalent ions, enabling its purification with immobilized metal affinity chromatography (IMAC). Nevertheless, most characteristics of this mutant remained unexplored to date. In this study, we performed a comparative analysis of the wild-type and the E26H mutant sjGST by using in vitro as well as in silico approaches. We confirmed that the sjGST(E26H) protein exhibits significantly increased affinity for binding nickel ions as compared to the wild-type. In addition, we proved that the sjGST(E26H) can be purified efficiently either with glutathione- or immobilized metal ion-affinity chromatography, even in consecutive purification steps. The human retroviral-like aspartic protease 1 (ASPRV1) conjugated with the sjGST(E26H) fusion tag was also successfully purified by using both of these affinity chromatographic approaches. Our studies revealed that the E26H mutant sjGST can be used as a versatile affinity tag because the modified protein retains the kinetic features of the wild-type and its affinity towards glutathione, while can be purified efficiently by IMAC, as well.","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":"1054-1066"},"PeriodicalIF":3.2,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11968563/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142923493","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

Distribution of Polyphosphate Kinase 2 Genes in Bacteria Underscores a Dynamic Evolutionary History. 多磷酸激酶 2 基因在细菌中的分布证明了动态进化的历史

IF 3.2 4区生物学

Proteins-Structure Function and Bioinformatics Pub Date : 2025-05-01 Epub Date: 2024-12-18 DOI: 10.1002/prot.26780

Ryusei Matsumoto, Tomoaki Matsuura, Liam M Longo

{"title":"Distribution of Polyphosphate Kinase 2 Genes in Bacteria Underscores a Dynamic Evolutionary History.","authors":"Ryusei Matsumoto, Tomoaki Matsuura, Liam M Longo","doi":"10.1002/prot.26780","DOIUrl":"10.1002/prot.26780","url":null,"abstract":"Polyphosphate kinase 2 (PPK2) enzymes catalyze phosphoryl transfer from polyphosphate to nucleotides and are divided into three classes, each presumed to have different catalytic preferences. With relevance to biotechnology, medicine, and primitive biology, there is significant interest in understanding the evolutionary history of PPK2 enzymes and predicting their functional properties. We reasoned that the distribution and pairing preferences of PPK2 gene classes across the prokaryote tree of life may shed light on these questions. PPK2 was found to be a dynamic gene family, often present in only a subset of species within a clade, even when considering a single genus. Although all possible PPK2 pairs were observed, a ~2-fold enrichment for Class I enzymes in species with multiple PPK2 genes strongly shapes pairing preferences. PPK2 class preference in the absence of PPK1, which synthesizes rather than utilizes polyphosphate, indicates the potential for functional adaptation and/or promiscuity with respect to reaction directionality for all classes, a feature that has previously been associated only with Class I. Patterns of adjacent PPK2 genes revealed signatures of gene duplication, as adjacent genes overwhelmingly belonged to the same class, as well as the potential for an added layer of PPK2 dynamics: hetero-oligomerization of single-domain Class II enzymes to recapitulate the structure of two-domain Class II enzymes. Finally, an updated PPK2 tree constructed from domains instead of genes calls into question established narratives of PPK2 evolution, putting new limits on the extent to which nucleobase promiscuity can be invoked in the early evolution of this family.","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":"972-980"},"PeriodicalIF":3.2,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11968564/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142848566","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

Structural Insights Into the Impact of the Glycine-Rich Loop Mutation in Noonan Syndrome on the ATP Binding Pocket of CRAF Kinase. Noonan综合征中富含甘氨酸环突变对CRAF激酶ATP结合袋影响的结构见解。

IF 3.2 4区生物学

Proteins-Structure Function and Bioinformatics Pub Date : 2025-05-01 Epub Date: 2024-12-30 DOI: 10.1002/prot.26769

Fatemeh Janati-Fard, Mohammad R Housaindokht, Fatemeh Moosavi, Saeideh Nakhaei-Rad

{"title":"Structural Insights Into the Impact of the Glycine-Rich Loop Mutation in Noonan Syndrome on the ATP Binding Pocket of CRAF Kinase.","authors":"Fatemeh Janati-Fard, Mohammad R Housaindokht, Fatemeh Moosavi, Saeideh Nakhaei-Rad","doi":"10.1002/prot.26769","DOIUrl":"10.1002/prot.26769","url":null,"abstract":"The pathogenic G361A variant of CRAF, associated with increased intrinsic kinase activity in Noonan syndrome (NS), remains poorly understood in terms of its molecular and structural impact on kinase activity. To elucidate the mechanistic implications of the glycine to alanine substitution at residue 361 in CRAF, we employed molecular dynamics simulations. Our findings reveal that this mutation predominantly affects the ATP binding pocket and critical intermolecular interactions within the active cleft that favors the phosphate transfer reaction. Notably, our data highlight significant alterations in key interactions involving Lys470/Asp486 and ATP.Mg2+ in CRAFG361A that are absent in wild-type CRAF. Additionally, we identified a novel interaction mode between Lys431 and γ-phosphate in wild-type CRAF, a residue evolutionarily conserved in CRAFs but not in related kinases such as BRAF, ARAF, and KSR1/2. Furthermore, observed shifts in the αC-helix and G-loop relative to the wild-type correlate with an enlarged ATP-binding cavity in the mutant, reflecting structural adaptations due to these mutations. Overall, these structural insights underscore the elevated intrinsic kinase activity of the CRAFG361A variant and provide crucial mechanistic details that could inform the development of specific inhibitors targeting this variant.","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":"1022-1034"},"PeriodicalIF":3.2,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142911210","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