Pub Date : 2025-12-18DOI: 10.1016/j.crstbi.2025.100177
Elena Álvarez Sánchez , Simon Huet , Stéphane Téletchéa
Tumor Necrosis Factor alpha (TNFα) is a pro-inflammatory cytokine critical for regulating cell survival and death. Under pathological conditions, excessive TNFα activity can lead to chronic inflammation, contributing to diseases such as inflammatory bowel disease and other autoimmune disorders. While structural studies have elucidated the atomistic details of TNFα binding to its receptor, TNF Receptor 1 (TNFR1), the influence of the membrane environment on this interaction remains poorly characterized experimentally. In this study, we employed advanced all-atom Gaussian accelerated molecular dynamics simulations to investigate how lipid-mediated interactions modulate the TNFα–TNFR1 complex. We identified key residues on both the cytokine and its receptor that govern trimer assembly, receptor binding, and potential pathological alterations. Our analysis confirmed previously identified functional sites and revealed new residues likely to contribute to the structural stability and dynamics of the complex. These findings provide a more comprehensive understanding of the molecular determinants of TNF signaling and offer a foundation for future experimental investigations into the receptor-ligand interface and membrane-mediated regulation.
{"title":"Molecular determinants of TNFR1:TNFα binding and dynamics in a physiological membrane environment","authors":"Elena Álvarez Sánchez , Simon Huet , Stéphane Téletchéa","doi":"10.1016/j.crstbi.2025.100177","DOIUrl":"10.1016/j.crstbi.2025.100177","url":null,"abstract":"<div><div>Tumor Necrosis Factor alpha (TNFα) is a pro-inflammatory cytokine critical for regulating cell survival and death. Under pathological conditions, excessive TNFα activity can lead to chronic inflammation, contributing to diseases such as inflammatory bowel disease and other autoimmune disorders. While structural studies have elucidated the atomistic details of TNFα binding to its receptor, TNF Receptor 1 (TNFR1), the influence of the membrane environment on this interaction remains poorly characterized experimentally. In this study, we employed advanced all-atom Gaussian accelerated molecular dynamics simulations to investigate how lipid-mediated interactions modulate the TNFα–TNFR1 complex. We identified key residues on both the cytokine and its receptor that govern trimer assembly, receptor binding, and potential pathological alterations. Our analysis confirmed previously identified functional sites and revealed new residues likely to contribute to the structural stability and dynamics of the complex. These findings provide a more comprehensive understanding of the molecular determinants of TNF signaling and offer a foundation for future experimental investigations into the receptor-ligand interface and membrane-mediated regulation.</div></div>","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":"11 ","pages":"Article 100177"},"PeriodicalIF":2.7,"publicationDate":"2025-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145898003","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-01DOI: 10.1016/j.crstbi.2025.100175
Raneem Aldadah , Delila Lekic , Kanita Sabanovic , Boris Kovalenko , Muhamed Adilovic , Altijana Hromic-Jahjefendic , Vladimir N. Uversky
Bacterial cell poles play a fundamental role in several cellular processes, such as cell cycle, chemotaxis, cell differentiation, development, growth, and structure of the bacterial cell, as well as protein localization. Using a set of bioinformatics tools, we evaluated the probability of 19 bacterial cell pole-related proteins to be disordered and undergo spontaneous liquid-liquid phase separation (LLPS). Our analysis revealed that11 cell pole-related proteins are predicted to be highly disordered, 7 proteins are moderately disordered, and only one protein is expected to be highly ordered. Furthermore, this intrinsic disorder propensity is mostly evolutionary conserved. Most of the analyzed 19 cell pole-related proteins were found to be associated with the LLPS process, with TipN, PopZ, and PBP2A being capable of spontaneous phase separation, RacA, Noc, PBP1A/1B, ParB, PBP3, PBP2B, FtsZ, MipZ, MinD, and MreB being expected to potentially serve as droplet clients, and with the remaining proteins (DivIVA, ComN, Maf, PBP4, MinC, and MinJ) being predicted to be unrelated to LLPS. The results suggested that FtsZ, DivIVA, and MiPZ serve as the main regulatory proteins, being well-known for their role in forming the septum and chromosomal segregation. Furthermore, PopZ and TipN proteins contribute to high stress resistance. Clarifying the function and effects of each mechanism gives insight into the organization of bacterial cells and some strategies for antimicrobial targets.
{"title":"Looking at bacterial cell poles from a liquid-liquid phase separation of intrinsically disordered proteins perspective","authors":"Raneem Aldadah , Delila Lekic , Kanita Sabanovic , Boris Kovalenko , Muhamed Adilovic , Altijana Hromic-Jahjefendic , Vladimir N. Uversky","doi":"10.1016/j.crstbi.2025.100175","DOIUrl":"10.1016/j.crstbi.2025.100175","url":null,"abstract":"<div><div>Bacterial cell poles play a fundamental role in several cellular processes, such as cell cycle, chemotaxis, cell differentiation, development, growth, and structure of the bacterial cell, as well as protein localization. Using a set of bioinformatics tools, we evaluated the probability of 19 bacterial cell pole-related proteins to be disordered and undergo spontaneous liquid-liquid phase separation (LLPS). Our analysis revealed that11 cell pole-related proteins are predicted to be highly disordered, 7 proteins are moderately disordered, and only one protein is expected to be highly ordered. Furthermore, this intrinsic disorder propensity is mostly evolutionary conserved. Most of the analyzed 19 cell pole-related proteins were found to be associated with the LLPS process, with TipN, PopZ, and PBP2A being capable of spontaneous phase separation, RacA, Noc, PBP1A/1B, ParB, PBP3, PBP2B, FtsZ, MipZ, MinD, and MreB being expected to potentially serve as droplet clients, and with the remaining proteins (DivIVA, ComN, Maf, PBP4, MinC, and MinJ) being predicted to be unrelated to LLPS. The results suggested that FtsZ, DivIVA, and MiPZ serve as the main regulatory proteins, being well-known for their role in forming the septum and chromosomal segregation. Furthermore, PopZ and TipN proteins contribute to high stress resistance. Clarifying the function and effects of each mechanism gives insight into the organization of bacterial cells and some strategies for antimicrobial targets.</div></div>","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":"10 ","pages":"Article 100175"},"PeriodicalIF":2.7,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145614387","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-01DOI: 10.1016/j.crstbi.2025.100176
Sinethemba H. Yakobi, Uchechukwu U. Nwodo
Escalating antimicrobial resistance necessitates the development of alternative therapeutics that circumvent conventional enzymatic and efflux-based defence systems. Antimicrobial peptides (AMPs) represent a compelling class of innate immune effectors, however, their clinical translation is hindered by incomplete mechanistic understanding of how structural organization and conformational dynamics shape antimicrobial function. In this study, we performed an integrated comparative analysis of three mechanistically representative AMPs—LL-37, HNP-1, and magainin-2—to resolve how maturation pathways, fold topology, amphipathic architecture, and dynamic target engagement govern antimicrobial action. Consensus secondary-structure prediction, AlphaFold2/PEP-FOLD modelling, and physicochemical profiling revealed three distinct structural signatures. LL-37 exhibited a flexible disorder-to-helix transition enabling adaptive, curvature-driven membrane dissolution, HNP-1 adopted a rigid cysteine-stabilized β-sheet that promotes lipid clustering and entropic inhibition of membrane-associated enzymes, and magainin-2 formed a stable amphipathic α-helix optimized for toroidal pore initiation. Machine-learning classification corroborated strong antimicrobial likelihood for HNP-1 and magainin-2, with LL-37 displaying context-dependent activation. Protein–peptide docking and normal-mode elastic network modelling further demonstrated the possibility of LL-37 allosterically dampening conformational cycling of the MexB efflux pump, HNP-1 restricting catalytic-loop mobility in LpxC, and magainin-2 enhancing correlated β-barrel breathing in OprF to promote pore formation. These findings delineate three mechanistically distinct antimicrobial strategies—adaptive membrane dissolution, rigid pore-stacking inhibition, and dynamic pore initiation—linked directly to peptide structural organization. This framework provides a rational basis for mechanism-guided AMP optimization and the engineering of next-generation membrane-active therapeutics with reduced resistance susceptibility.
{"title":"Structural and mechanistic divergence in LL-37, HNP-1, and Magainin-2: An integrated computational and biophysical analysis","authors":"Sinethemba H. Yakobi, Uchechukwu U. Nwodo","doi":"10.1016/j.crstbi.2025.100176","DOIUrl":"10.1016/j.crstbi.2025.100176","url":null,"abstract":"<div><div>Escalating antimicrobial resistance necessitates the development of alternative therapeutics that circumvent conventional enzymatic and efflux-based defence systems. Antimicrobial peptides (AMPs) represent a compelling class of innate immune effectors, however, their clinical translation is hindered by incomplete mechanistic understanding of how structural organization and conformational dynamics shape antimicrobial function. In this study, we performed an integrated comparative analysis of three mechanistically representative AMPs—LL-37, HNP-1, and magainin-2—to resolve how maturation pathways, fold topology, amphipathic architecture, and dynamic target engagement govern antimicrobial action. Consensus secondary-structure prediction, AlphaFold2/PEP-FOLD modelling, and physicochemical profiling revealed three distinct structural signatures. LL-37 exhibited a flexible disorder-to-helix transition enabling adaptive, curvature-driven membrane dissolution, HNP-1 adopted a rigid cysteine-stabilized β-sheet that promotes lipid clustering and entropic inhibition of membrane-associated enzymes, and magainin-2 formed a stable amphipathic α-helix optimized for toroidal pore initiation. Machine-learning classification corroborated strong antimicrobial likelihood for HNP-1 and magainin-2, with LL-37 displaying context-dependent activation. Protein–peptide docking and normal-mode elastic network modelling further demonstrated the possibility of LL-37 allosterically dampening conformational cycling of the MexB efflux pump, HNP-1 restricting catalytic-loop mobility in LpxC, and magainin-2 enhancing correlated β-barrel breathing in OprF to promote pore formation. These findings delineate three mechanistically distinct antimicrobial strategies—adaptive membrane dissolution, rigid pore-stacking inhibition, and dynamic pore initiation—linked directly to peptide structural organization. This framework provides a rational basis for mechanism-guided AMP optimization and the engineering of next-generation membrane-active therapeutics with reduced resistance susceptibility.</div></div>","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":"10 ","pages":"Article 100176"},"PeriodicalIF":2.7,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145614386","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The tyrosinase enzyme plays a pivotal role in melanin pigment production; however, heightened tyrosinase activity can lead to undesired pigmentation. Consequently, inhibiting this enzyme's function stands as a critical research avenue for devising effective strategies to mitigate pigmentation issues. This study aimed to forecast the biological activity of chemical compounds capable of inhibiting tyrosinase and elucidate pivotal elements influencing this enzyme's activity. To achieve this goal, we employed computational techniques to construct a model predicting the biological activity of these compounds. Initially, we identified 27 tyrosinase inhibitors from previous studies. Subsequently, after performing ADMET studies, we extracted and pre-processed the significant features of each compound to develop a Stepwise-MLR model. Moreover, with the help of this model, we were able to identify the most influential and novel structural features that directly affect enzyme activity and determine the importance factor of each feature. Furthermore, all derived inhibitors with evaluated inhibition constants were docked to the active site of target tyrosinase to investigate the binding mode of the compounds. Docking analysis indicated T1 as the most stable compound with a binding energy of −8.00 kcal/mol. T1 as the most active compound identified through these computational studies can be applied as a prospective tyrosinase inhibitor. The implications of our findings extend to the development of new therapies for pigmentation disorders, notably within the cosmetic and dermatological sectors.
{"title":"ADMET, QSAR and Docking studies to predict the activity of tyrosinase-derived medications inhibitors based on computational techniques","authors":"Adele Sadat Haghighat Hoseini , Abed Mohebshahedin , Shamim Ghiabi , Mahdi KhalatbariLimaki , Mahshid Arastonejad , Sorour Hassani , Mahsa Alem , Esmaeil Roohparvar Basmenj","doi":"10.1016/j.crstbi.2025.100174","DOIUrl":"10.1016/j.crstbi.2025.100174","url":null,"abstract":"<div><div>The <em>tyrosinase</em> enzyme plays a pivotal role in melanin pigment production; however, heightened <em>tyrosinase</em> activity can lead to undesired pigmentation. Consequently, inhibiting this enzyme's function stands as a critical research avenue for devising effective strategies to mitigate pigmentation issues. This study aimed to forecast the biological activity of chemical compounds capable of inhibiting <em>tyrosinase</em> and elucidate pivotal elements influencing this enzyme's activity. To achieve this goal, we employed computational techniques to construct a model predicting the biological activity of these compounds. Initially, we identified 27 <em>tyrosinase</em> inhibitors from previous studies. Subsequently, after performing ADMET studies, we extracted and pre-processed the significant features of each compound to develop a Stepwise-MLR model. Moreover, with the help of this model, we were able to identify the most influential and novel structural features that directly affect enzyme activity and determine the importance factor of each feature. Furthermore, all derived inhibitors with evaluated inhibition constants were docked to the active site of target <em>tyrosinase</em> to investigate the binding mode of the compounds. Docking analysis indicated T1 as the most stable compound with a binding energy of −8.00 kcal/mol. T1 as the most active compound identified through these computational studies can be applied as a prospective <em>tyrosinase</em> inhibitor. The implications of our findings extend to the development of new therapies for pigmentation disorders, notably within the cosmetic and dermatological sectors.</div></div>","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":"10 ","pages":"Article 100174"},"PeriodicalIF":2.7,"publicationDate":"2025-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145516630","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-08-08DOI: 10.1016/j.crstbi.2025.100173
Pragya Kesarwani , Durai Sundar
The CRISPR/Cas system is a potential tool for genome editing, yet it faces challenges due to off-target activity caused by mismatches at specific positions. However, Off-target activity can be minimized by optimal design of guide RNA (gRNA) but there remains a possibility of unintended cleavage, highlighting the role of the Cas nuclease in off-target recognition and binding the target site. This study focuses on comparing the conformational dynamics and stability of Wildtype, RR, RVR, RRm and RVRm variants of AsCas12a with gRNA-DNA bound complexes. It was found that the cross-correlation coefficient between His1167 of the NUC domain and Thr384 of the REC II domain significantly increased after the K949A mutation compared to other variants. The extensive spread of principal components also revealed flexibility in both Cas nuclease and gRNA-DNA hybrid of RVR variant and wildtype AsCas12a whereas the confined clusters in PCA plot suggests increased stability in both the variants after mutation. This study shows the role of K949A mutation in improving stability of PAM variants and predicted critical residues such as His1167, Thr384 and Ser959, in inducing stability in mutants of PAM variants.
{"title":"Conformational changes induced by K949A mutation in the CRISPR-Cas12a complex drives an effective target-binding mechanism","authors":"Pragya Kesarwani , Durai Sundar","doi":"10.1016/j.crstbi.2025.100173","DOIUrl":"10.1016/j.crstbi.2025.100173","url":null,"abstract":"<div><div>The CRISPR/Cas system is a potential tool for genome editing, yet it faces challenges due to off-target activity caused by mismatches at specific positions. However, Off-target activity can be minimized by optimal design of guide RNA (gRNA) but there remains a possibility of unintended cleavage, highlighting the role of the Cas nuclease in off-target recognition and binding the target site. This study focuses on comparing the conformational dynamics and stability of Wildtype, RR, RVR, RRm and RVRm variants of AsCas12a with gRNA-DNA bound complexes. It was found that the cross-correlation coefficient between His1167 of the NUC domain and Thr384 of the REC II domain significantly increased after the K949A mutation compared to other variants. The extensive spread of principal components also revealed flexibility in both Cas nuclease and gRNA-DNA hybrid of RVR variant and wildtype AsCas12a whereas the confined clusters in PCA plot suggests increased stability in both the variants after mutation. This study shows the role of K949A mutation in improving stability of PAM variants and predicted critical residues such as His1167, Thr384 and Ser959, in inducing stability in mutants of PAM variants.</div></div>","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":"10 ","pages":"Article 100173"},"PeriodicalIF":2.7,"publicationDate":"2025-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144841709","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Functional annotation of proteins is crucial in understanding the basic biology of organisms. In the context of pathogens, it can provide valuable insights towards its functional landscape contributing to understanding the molecular mechanisms of pathogenesis and survival. In this study, we explored the applications of sequence and AI-driven structure-based methods to functionally (re)annotate Mycobacteroides abscessus (MAB). MAB is an opportunistic pathogen responsible for causing infections in immunocompromised patients and exhibits resistance to several antibiotics. The global rise in drug-resistant strains and the recently identified potential for indirect human-to-human transmission emphasizes the importance of understanding MAB as a critical pathogen. However, there is a huge gap in our understanding of the MAB proteome, which is vital not only for understanding the functional aspects of various proteins but also for prioritizing drug targets for therapeutic development. Presently, 28 % of the MAB proteome, as available in UniProtKB, is poorly annotated, and more than a fourth of MAB proteome lack gene ontology (GO) terms, indicating a lack of standard functional descriptions. To this end, the present study aims to functionally (re)annotate MAB proteome using a combination of sequence and structure-based approaches in a systematic way. We performed sequence-based similarity search against NR database and performed HMM based search for functional domains with Pfam and CATH. Then, we utilized MAB AlphaFold-predicted structures to annotate MAB proteins with structure-based similarity search using Foldseek to identify proteins and transfer their gene ontology (GO) annotations. We assigned new GO annotations (374 proteins) and refined the existing annotations (885 proteins) for previously unannotated essential genes of MAB. In addition, we also performed annotations using an integrated sequence and structure-based approach for the 29 proteins for which AlphaFold structures were not available. In the end, structural comparisons of a few proteins that were similar to Mycobacterium tuberculosis were explored, revealing residue-level differences in MAB linked to drug resistance. Our study highlights a combined sequence- and AI-driven structure-based approach for large-scale proteome functional annotation, which can be applied to any organism of interest.
{"title":"Functional (re)annotation of Mycobacteroides abscessus proteome using integrative sequence and AI-based structural approaches","authors":"Pranavathiyani Gnanasekar , Simran Gambhir , Priyadarshan Kinatukara , Anshu Bhardwaj","doi":"10.1016/j.crstbi.2025.100172","DOIUrl":"10.1016/j.crstbi.2025.100172","url":null,"abstract":"<div><div>Functional annotation of proteins is crucial in understanding the basic biology of organisms. In the context of pathogens, it can provide valuable insights towards its functional landscape contributing to understanding the molecular mechanisms of pathogenesis and survival. In this study, we explored the applications of sequence and AI-driven structure-based methods to functionally (re)annotate <em>Mycobacteroides abscessus</em> (MAB). MAB is an opportunistic pathogen responsible for causing infections in immunocompromised patients and exhibits resistance to several antibiotics. The global rise in drug-resistant strains and the recently identified potential for indirect human-to-human transmission emphasizes the importance of understanding MAB as a critical pathogen. However, there is a huge gap in our understanding of the MAB proteome, which is vital not only for understanding the functional aspects of various proteins but also for prioritizing drug targets for therapeutic development. Presently, 28 % of the MAB proteome, as available in UniProtKB, is poorly annotated, and more than a fourth of MAB proteome lack gene ontology (GO) terms, indicating a lack of standard functional descriptions. To this end, the present study aims to functionally (re)annotate MAB proteome using a combination of sequence and structure-based approaches in a systematic way. We performed sequence-based similarity search against NR database and performed HMM based search for functional domains with Pfam and CATH. Then, we utilized MAB AlphaFold-predicted structures to annotate MAB proteins with structure-based similarity search using Foldseek to identify proteins and transfer their gene ontology (GO) annotations. We assigned new GO annotations (374 proteins) and refined the existing annotations (885 proteins) for previously unannotated essential genes of MAB. In addition, we also performed annotations using an integrated sequence and structure-based approach for the 29 proteins for which AlphaFold structures were not available. In the end, structural comparisons of a few proteins that were similar to <em>Mycobacterium tuberculosis</em> were explored, revealing residue-level differences in MAB linked to drug resistance. Our study highlights a combined sequence- and AI-driven structure-based approach for large-scale proteome functional annotation, which can be applied to any organism of interest.</div></div>","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":"10 ","pages":"Article 100172"},"PeriodicalIF":2.7,"publicationDate":"2025-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144863978","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-06-27DOI: 10.1016/j.crstbi.2025.100170
Jiaan Yang , Wenxin Ji , Wen Xiang Cheng , Gang Wu , Si Tong Sheng , Peng Zhang , Jun Lin , Xiaojia Chen , Qiong Shi
The folding conformation of native protein has flexibility in different degrees, which may bring difficulty in presenting the structures, and also it causes complexity in understanding the relationship between structure and functions. Although many methods and databases provide information for intrinsically disordered protein (IDP), they are mainly limited to determining the intrinsically disordered regions (IDR) lacking knowledge of possible folding patterns. To overcome the barrier, the protein structure fingerprint technology has been developed, which includes PFSC (Protein Folding Shape Code) (Yang, 2008) and PFVM (Protein Folding Variation Matrix) (Yang et al., 2022) algorithms as well as FiveFold (Yang et al., 2025) approach for protein structure prediction, which are able explicitly to expose the possible conformational structures for intrinsically disordered protein. Three proteins, human cellular tumor antigen P53, human alpha-synuclein, and human protamine-2, are taken as samples for demonstration of how to obtain their folding conformation structures for intrinsically disordered proteins. The folding features for intrinsically disordered proteins with given structures may be revealed by the alignment of PFSC strings, and the folding possibility for intrinsically disordered proteins without a given structure can be exhibited by the local folding variations in PFVM. Furthermore, the multiple conformational 3D structures for intrinsically disordered protein can be predicted by FiveFold approach, which provides a significant tool further to understand the intrinsic disorder of proteins.
{"title":"Expose flexible conformations for intrinsically disordered protein","authors":"Jiaan Yang , Wenxin Ji , Wen Xiang Cheng , Gang Wu , Si Tong Sheng , Peng Zhang , Jun Lin , Xiaojia Chen , Qiong Shi","doi":"10.1016/j.crstbi.2025.100170","DOIUrl":"10.1016/j.crstbi.2025.100170","url":null,"abstract":"<div><div>The folding conformation of native protein has flexibility in different degrees, which may bring difficulty in presenting the structures, and also it causes complexity in understanding the relationship between structure and functions. Although many methods and databases provide information for intrinsically disordered protein (IDP), they are mainly limited to determining the intrinsically disordered regions (IDR) lacking knowledge of possible folding patterns. To overcome the barrier, the protein structure fingerprint technology has been developed, which includes PFSC (Protein Folding Shape Code) (Yang, 2008) and PFVM (Protein Folding Variation Matrix) (Yang et al., 2022) algorithms as well as FiveFold (Yang et al., 2025) approach for protein structure prediction, which are able explicitly to expose the possible conformational structures for intrinsically disordered protein. Three proteins, human cellular tumor antigen P53, human alpha-synuclein, and human protamine-2, are taken as samples for demonstration of how to obtain their folding conformation structures for intrinsically disordered proteins. The folding features for intrinsically disordered proteins with given structures may be revealed by the alignment of PFSC strings, and the folding possibility for intrinsically disordered proteins without a given structure can be exhibited by the local folding variations in PFVM. Furthermore, the multiple conformational 3D structures for intrinsically disordered protein can be predicted by FiveFold approach, which provides a significant tool further to understand the intrinsic disorder of proteins.</div></div>","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":"10 ","pages":"Article 100170"},"PeriodicalIF":2.7,"publicationDate":"2025-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144534378","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-06-20DOI: 10.1016/j.crstbi.2025.100171
Nabila Hadiah Akbar , Farendina Suarantika , Taufik Muhammad Fakih , Ariranur Haniffadli , Khoirunnisa Muslimawati , Aditya Maulana Perdana Putra
Breast cancer remains the most commonly diagnosed cancer among women worldwide, with approximately 2.3 million new cases reported in 2022. In the United States alone, an estimated 310,720 new cases of female breast cancer are expected in 2024. HER2-positive breast cancer, characterized by the overexpression of the human epidermal growth factor receptor 2 (HER2), accounts for about 20 % of all breast cancer cases. The development of anti-HER2 therapies has significantly improved survival rates for patients with HER2-positive breast cancer. In this study, we employed in silico methods to evaluate the potential of natural alkaloids, Mitragynine and 7-Hydroxymitragynine, as HER2 inhibitors. Molecular docking revealed binding energies of −7.56 kcal/mol and −8.77 kcal/mol, respectively, with key interactions involving residues such as Leu726, Val734, Ala751, Lys753, Thr798, and Asp863. Molecular dynamics simulations demonstrated the stability of all three complexes, including Mitragynine, 7-Hydroxymitragynine, and Native (SYR127063), over the simulation period. Mitragynine exhibited stronger interaction stability, supported by a higher hydrogen bond occupancy of 39.19 %, compared to 4.32 % for 7-Hydroxymitragynine, while Native (SYR127063) displayed the highest occupancy at 49.66 %. MM-PBSA analysis further validated these findings, with Native (SYR127063) exhibiting the most favorable total binding energy of −163.448 ± 17.288 kJ/mol, followed by Mitragynine at −112.33 ± 22.41 kJ/mol, and 7-Hydroxymitragynine at −103.56 ± 15.61 kJ/mol. ADMET, physicochemical properties, and drug-likeness evaluations indicated that all compounds satisfy Lipinski, Ghose, Veber, Egan, and Muegge rules, confirming their suitability as lead-like molecules. Based on these findings, Mitragynine and 7-Hydroxymitragynine are promising candidates for HER2-targeted breast cancer therapy, with further experimental validation recommended to confirm their clinical potential.
{"title":"Screening, docking, and molecular dynamics analysis of Mitragyna speciosa (Korth.) compounds for targeting HER2 in breast cancer","authors":"Nabila Hadiah Akbar , Farendina Suarantika , Taufik Muhammad Fakih , Ariranur Haniffadli , Khoirunnisa Muslimawati , Aditya Maulana Perdana Putra","doi":"10.1016/j.crstbi.2025.100171","DOIUrl":"10.1016/j.crstbi.2025.100171","url":null,"abstract":"<div><div>Breast cancer remains the most commonly diagnosed cancer among women worldwide, with approximately 2.3 million new cases reported in 2022. In the United States alone, an estimated 310,720 new cases of female breast cancer are expected in 2024. HER2-positive breast cancer, characterized by the overexpression of the human epidermal growth factor receptor 2 (HER2), accounts for about 20 % of all breast cancer cases. The development of anti-HER2 therapies has significantly improved survival rates for patients with HER2-positive breast cancer. In this study, we employed in silico methods to evaluate the potential of natural alkaloids, Mitragynine and 7-Hydroxymitragynine, as HER2 inhibitors. Molecular docking revealed binding energies of −7.56 kcal/mol and −8.77 kcal/mol, respectively, with key interactions involving residues such as Leu726, Val734, Ala751, Lys753, Thr798, and Asp863. Molecular dynamics simulations demonstrated the stability of all three complexes, including Mitragynine, 7-Hydroxymitragynine, and Native (SYR127063), over the simulation period. Mitragynine exhibited stronger interaction stability, supported by a higher hydrogen bond occupancy of 39.19 %, compared to 4.32 % for 7-Hydroxymitragynine, while Native (SYR127063) displayed the highest occupancy at 49.66 %. MM-PBSA analysis further validated these findings, with Native (SYR127063) exhibiting the most favorable total binding energy of −163.448 ± 17.288 kJ/mol, followed by Mitragynine at −112.33 ± 22.41 kJ/mol, and 7-Hydroxymitragynine at −103.56 ± 15.61 kJ/mol. ADMET, physicochemical properties, and drug-likeness evaluations indicated that all compounds satisfy Lipinski, Ghose, Veber, Egan, and Muegge rules, confirming their suitability as lead-like molecules. Based on these findings, Mitragynine and 7-Hydroxymitragynine are promising candidates for HER2-targeted breast cancer therapy, with further experimental validation recommended to confirm their clinical potential.</div></div>","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":"10 ","pages":"Article 100171"},"PeriodicalIF":2.7,"publicationDate":"2025-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144366520","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The human reference proteome is routinely modelled with predictive tools such as AlphaFold2. We recently released a database in which, for each human protein, the AlphaFold2 model is paired with its ESMFold counterpart. The two predictive methods take advantage of different procedures and it is interesting to compare them in relation to their quality, particularly when an experimental protein structure is not available. Here, we select three state-of-the-art quality assessment methods and we adopt them to compare 42,942 pairs of models. This procedure helps to find the most reliable models for human proteins, particularly for the set of proteins for which structure prediction methods give dissimilar results. We obtain that when predicted structures are similar, AlphaFold2 models consistently receive higher scores than the ESMFold counterparts. When predicted structures differ, the ESMFold model is the best choice for 49 % of the proteins according to a consensus of the three QA tools.
{"title":"Evaluation of the structural models of the human reference proteome: AlphaFold2 versus ESMFold","authors":"Matteo Manfredi , Castrense Savojardo , Pier Luigi Martelli , Rita Casadio","doi":"10.1016/j.crstbi.2025.100167","DOIUrl":"10.1016/j.crstbi.2025.100167","url":null,"abstract":"<div><div>The human reference proteome is routinely modelled with predictive tools such as AlphaFold2. We recently released a database in which, for each human protein, the AlphaFold2 model is paired with its ESMFold counterpart. The two predictive methods take advantage of different procedures and it is interesting to compare them in relation to their quality, particularly when an experimental protein structure is not available. Here, we select three state-of-the-art quality assessment methods and we adopt them to compare 42,942 pairs of models. This procedure helps to find the most reliable models for human proteins, particularly for the set of proteins for which structure prediction methods give dissimilar results. We obtain that when predicted structures are similar, AlphaFold2 models consistently receive higher scores than the ESMFold counterparts. When predicted structures differ, the ESMFold model is the best choice for 49 % of the proteins according to a consensus of the three QA tools.</div></div>","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":"9 ","pages":"Article 100167"},"PeriodicalIF":2.7,"publicationDate":"2025-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144167366","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-04-09DOI: 10.1016/j.crstbi.2025.100166
Tuhin Manna , Subhamoy Dey , Monalisha Karmakar , Amiya Kumar Panda , Chandradipa Ghosh
During various stages of its life cycle, Vibrio cholerae initiate biofilm signalling cascade. Intercellular high level of the signalling nucleotide 3′-5′ cyclic dimeric guanosine monophosphate (c-di-GMP), synthesized by diguanylate cyclases (DGCs) from its precursor molecule GTP, is crucial for biofilm formation. Present study endeavours to in silico approaches in evaluating genomic, physicochemical, topological and functional properties of six c-di-GMP regulatory DGCs (CdgA, CdgH, CdgK, CdgL, CdgM, VpvC) of V. cholerae. Genomic investigations unveiled that codon preferences were inclined towards AU ending over GC ending codons and overall GC content ranged from 44.6 to 49.5 with codon adaptation index ranging from 0.707 to 0.783. Topological analyses deciphered the presence of transmembrane domains in all proteins. All the DGCs were acidic, hydrophilic and thermostable. Only CdgA, CdgH and VpvC were predicted to be stable during in vitro conditions. Non-polar amino acids with leucine being the most abundant amino acid among these DGCs with α-helix as the predominant secondary structure, responsible for forming the transmembrane regions by secondary structure analysis. Tertiary structures of the proteins were obtained by computation using AlphaFold and trRosetta. Predicted structures by both the servers were compared in various aspects using PROCHECK, ERRAT and Modfold8 servers. Selected 3D structures were refined using GalaxyRefine. InterPro Scan revealed presence of a conserved GGDEF domain in all DGCs and predicted the active site residues in the GGDEF domain. Molecular docking studies using CB-DOCK 2 tool revealed that among the DGCs, VpvC exhibited highest affinity for GTP (−5.6 kcal/mol), which was closely followed by CdgL (−5.5 kcal/mol). MD simulations depicted all DGC-GTP complexes to be stable due to its considerably low eigenvalues. Such studies are considered to provide maiden insights into the genomic and structural properties of V. cholerae DGCs, actively involved in biofilm signalling systems, and it is projected to be beneficial in the discovery of novel DGC inhibitors that can target and downregulate the c-di-GMP regulatory system to develop anti-biofilm strategies against the cholera pathogen.
{"title":"Investigations on genomic, topological and structural properties of diguanylate cyclases involved in Vibrio cholerae biofilm signalling using in silico techniques: Promising drug targets in combating cholera","authors":"Tuhin Manna , Subhamoy Dey , Monalisha Karmakar , Amiya Kumar Panda , Chandradipa Ghosh","doi":"10.1016/j.crstbi.2025.100166","DOIUrl":"10.1016/j.crstbi.2025.100166","url":null,"abstract":"<div><div>During various stages of its life cycle, <em>Vibrio cholerae</em> initiate biofilm signalling cascade. Intercellular high level of the signalling nucleotide 3′-5′ cyclic dimeric guanosine monophosphate (c-di-GMP), synthesized by diguanylate cyclases (DGCs) from its precursor molecule GTP, is crucial for biofilm formation. Present study endeavours to <em>in silico</em> approaches in evaluating genomic, physicochemical, topological and functional properties of six c-di-GMP regulatory DGCs (CdgA, CdgH, CdgK, CdgL, CdgM, VpvC) of <em>V. cholerae</em>. Genomic investigations unveiled that codon preferences were inclined towards AU ending over GC ending codons and overall GC content ranged from 44.6 to 49.5 with codon adaptation index ranging from 0.707 to 0.783. Topological analyses deciphered the presence of transmembrane domains in all proteins. All the DGCs were acidic, hydrophilic and thermostable. Only CdgA, CdgH and VpvC were predicted to be stable during <em>in vitro</em> conditions. Non-polar amino acids with leucine being the most abundant amino acid among these DGCs with α-helix as the predominant secondary structure, responsible for forming the transmembrane regions by secondary structure analysis. Tertiary structures of the proteins were obtained by computation using AlphaFold and trRosetta. Predicted structures by both the servers were compared in various aspects using PROCHECK, ERRAT and Modfold8 servers. Selected 3D structures were refined using GalaxyRefine. InterPro Scan revealed presence of a conserved GGDEF domain in all DGCs and predicted the active site residues in the GGDEF domain. Molecular docking studies using CB-DOCK 2 tool revealed that among the DGCs, VpvC exhibited highest affinity for GTP (−5.6 kcal/mol), which was closely followed by CdgL (−5.5 kcal/mol). MD simulations depicted all DGC-GTP complexes to be stable due to its considerably low eigenvalues. Such studies are considered to provide maiden insights into the genomic and structural properties of <em>V. cholerae</em> DGCs, actively involved in biofilm signalling systems, and it is projected to be beneficial in the discovery of novel DGC inhibitors that can target and downregulate the c-di-GMP regulatory system to develop anti-biofilm strategies against the cholera pathogen.</div></div>","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":"9 ","pages":"Article 100166"},"PeriodicalIF":2.7,"publicationDate":"2025-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143852140","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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