Proteins-Structure Function and Bioinformatics最新文献

{"title":"Sequence-Similar Protein Domain Pairs With Structural or Topological Dissimilarity.","authors":"Peter Røgen","doi":"10.1002/prot.26753","DOIUrl":"10.1002/prot.26753","url":null,"abstract":"<p><p>For a variety of applications, protein structures are clustered by sequence similarity, and sequence-redundant structures are disregarded. Sequence-similar chains are likely to have similar structures, but significant structural variation, as measured with RMSD, has been documented for sequence-similar chains and found usually to have a functional explanation. Moving two neighboring stretches of backbone through each other may change the chain topology and alter possible folding paths. The size of this motion is compatible to a variation in a flexible loop. We search and find domains with alternate chain topology in CATH4.2 sequence families relatively independent of sequence identity and of structural similarity as measured by RMSD. Structural, topological, and functional representative sets should therefore keep sequence-similar domains not just with structural variation but also with topological variation. We present BCAlign that finds Alignment and superposition of protein Backbone Curves by optimizing a user chosen convex combination of structural derivation and derivation between the structure-based sequence alignment and an input sequence alignment. Steric and topological obstructions from deforming a curve into an aligned curve are then found by a previously developed algorithm. For highly sequence-similar domains, sequence-based structural alignment better represents the chains motion and generally reveals larger structural and topological variation than structure-based does. Fold-switching protein pairs have been reported to be most frequent between X-ray and NMR structures and estimated to be underrepresented in the PDB as the alternate configuration is harder to resolve. Here we similarly find chain topology most frequently altered between X-ray and NMR structures.</p>","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":"588-597"},"PeriodicalIF":3.2,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11809131/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142402131","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}

{"title":"Exploring the Dynamic Interplay of Deleterious Variants on the RAF1-RAP1A Binding in Cancer: Conformational Analysis, Binding Free Energy, and Essential Dynamics.","authors":"Abbas Khan, Syed Shujait Ali, Muhammad Ammar Zahid, Shahenda Salah Abdelsalam, Noorah Albekairi, Raed M Al-Zoubi, Mohanad Shkoor, Dong-Qing Wei, Abdelali Agouni","doi":"10.1002/prot.26759","DOIUrl":"10.1002/prot.26759","url":null,"abstract":"<p><p>The RAF1-RAP1A interaction activates the MAPK/ERK pathway which is very crucial in the carcinogenesis process. This protein complex influences tumor formation, proliferation, and metastasis. Understanding aberrant interactions driven by clinical mutations is vital for targeted therapies. Hence, the current study focuses on the screening of clinically reported substitutions in the RAF1 and RAP1A genes using predictive algorithms integrated with all-atoms simulation, essential dynamics, and binding free energy methods. Survival analysis results revealed a strong association between RAF1 and RAP1A expression levels and diminished survival rates in cancer patients across different cancer types. Integrated machine learning algorithms showed that among the 134 mutations reported for these 2 proteins, only 13 and 35 were classified as deleterious mutations in RAF1 and RAP1P, respectively. Moreover, one mutation in RAF1 reported elevated levels of binding between RAF1 and RAP1P while in RAP1A, 7 mutations were reported to increase the binding affinity. The high-binding mutations, P34Q and V60F, were subjected to protein-protein coupling which confirmed the increase in the binding affinity. Wild-type and mutant RAF1-RAP1P bound complexes were subjected to molecular simulation investigation, revealing enhanced structural stability, increased compactness, and stabilized residue fluctuations of the mutant systems in contrast to the wild-type. In addition, hydrogen bonding analysis revealed a variation in the binding paradigm which further underscores the impact of these substitutions on the coupling of RAF1 and RAP1A. Principal component analysis (PCA) and free energy landscape (FEL) evaluation further determined dynamical variations in the wild-type and mutant complexes. Finally, the Gibbs free energy for each complex was estimated and found to be -71.94 ± 0.38 kcal/mol for the wild-type, -95.57 ± 0.37 kcal/mol for the V60F, and -85.76 ± 0.72 kcal/mol for P34Q complex. These findings confirm the effect of these variants on increasing the binding affinity of RAF1 to RAP1P. These mutations can therefore be targeted for cancer therapy to modulate the activity of the MAPK/ERK signaling pathway.</p>","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":"684-701"},"PeriodicalIF":3.2,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11809134/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142577358","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}

{"title":"Selective Inhibition of hsp90 Paralogs: Uncovering the Role of Helix 1 in Grp94-Selective Ligand Binding.","authors":"Nanette L S Que, Paul M Seidler, Wen J Aw, Gabriela Chiosis, Daniel T Gewirth","doi":"10.1002/prot.26756","DOIUrl":"10.1002/prot.26756","url":null,"abstract":"<p><p>Grp94 is the endoplasmic reticulum paralog of the hsp90 family of chaperones, which have been targeted for therapeutic intervention via their highly conserved ATP binding sites. The design of paralog-selective inhibitors relies on understanding the protein structural elements that drive higher affinity in selective inhibitors. Here, we determined the structures of Grp94 and Hsp90 in complex with the Grp94-selective inhibitor PU-H36, and of Grp94 with the non-selective inhibitor PU-H71. In Grp94, PU-H36 derives its higher affinity by utilizing Site 2, a Grp94-specific side pocket adjoining the ATP binding cavity, but in Hsp90 PU-H36 occupies Site 1, a side pocket that is accessible in all paralogs with which it makes lower affinity interactions. The structure of Grp94 in complex with PU-H71 shows only Site 1 binding. While changes in the conformation of helices 4 and 5 in the N-terminal domain occur when ligands bind to Site 1 of both Hsp90 and Grp94, large conformational shifts that also involve helix 1 are associated with the engagement of the Site 2 pocket in Grp94 only. Site 2 in Hsp90 is blocked and its helix 1 conformation is insensitive to ligand binding. To understand the role of helix 1 in ligand selectivity, we tested the binding of PU-H36 and other Grp94-selective ligands to chimeric Grp94/Hsp90 constructs. These studies show that helix 1 is the major determinant of selectivity for Site 2 targeted ligands and also influences the rate of ATPase activity in Hsp90 paralogs.</p>","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":"654-672"},"PeriodicalIF":3.2,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11810606/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142549199","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}

{"title":"Unraveling the Structural Basis of Biased Agonism in the β₂-Adrenergic Receptor Through Molecular Dynamics Simulations.","authors":"Wojciech Plazinski, Aneta Archala, Krzysztof Jozwiak, Anita Plazinska","doi":"10.1002/prot.26766","DOIUrl":"10.1002/prot.26766","url":null,"abstract":"<p><p>Biased agonism in G protein-coupled receptors is a phenomenon resulting in the selective activation of distinct intracellular signaling pathways by different agonists, which may exhibit bias toward either Gs, Gi, or arrestin-mediated pathways. This study investigates the structural basis of ligand-induced biased agonism within the context of the β₂-adrenergic receptor (β₂-AR). Atomistic molecular dynamics simulations were conducted for β₂-AR complexes with two stereoisomers of methoxynaphtyl fenoterol (MNFen), that is, compounds eliciting qualitatively different cellular responses. The simulations reveal distinct interaction patterns within the binding cavity, dependent on the stereoisomer. These changes propagate to the intracellular parts of the receptor, triggering various structural responses: the dynamic structure of the intracellular regions of the (R,R)-MNFen complex more closely resembles the \"G_s-compatible\" and \"β-arrestin-compatible\" conformation of β₂-AR, while both stereoisomers maintain structural responses equidistant from the inactive conformation. These findings are confirmed by independent coarse-grained simulations. In the context of deciphered molecular mechanisms, Trp313 plays a pivotal role, altering its orientation upon interactions with (R,R)-MNFen, along with the Lys305-Asp192 ionic bridge. This effect, accompanied by ligand interactions with residues on TM2, increases the strength of interactions within the extracellular region and the binding cavity, resulting in a slightly more open conformation and a minor (by ca. 0.2 nm) increase in the distance between the TM5-TM7, TM1-TM6, TM6-TM7, and TM1-TM5 pairs. On the other hand, an even slighter decrease in the distance between the TM1-TM4 and TM2-TM4 pairs is observed.</p>","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":"728-744"},"PeriodicalIF":3.2,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142645237","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}

{"title":"Unveiling the Complexity of cis-Regulation Mechanisms in Kinases: A Comprehensive Analysis.","authors":"Alvaro M Navarro, Macarena Alonso, Elizabeth Martínez-Pérez, Tamas Lazar, Toby J Gibson, Javier A Iserte, Peter Tompa, Cristina Marino-Buslje","doi":"10.1002/prot.26751","DOIUrl":"10.1002/prot.26751","url":null,"abstract":"<p><p>Protein cis-regulatory elements (CREs) are regions that modulate the activity of a protein through intramolecular interactions. Kinases, pivotal enzymes in numerous biological processes, often undergo regulatory control via inhibitory interactions in cis. This study delves into the mechanisms of cis regulation in kinases mediated by CREs, employing a combined structural and sequence analysis. To accomplish this, we curated an extensive dataset of kinases featuring annotated CREs, organized into homolog families through multiple sequence alignments. Key molecular attributes, including disorder and secondary structure content, active and ATP-binding sites, post-translational modifications, and disease-associated mutations, were systematically mapped onto all sequences. Additionally, we explored the potential for conformational changes between active and inactive states. Finally, we explored the presence of these kinases within membraneless organelles and elucidated their functional roles therein. CREs display a continuum of structures, ranging from short disordered stretches to fully folded domains. The adaptability demonstrated by CREs in achieving the common goal of kinase inhibition spans from direct autoinhibitory interaction with the active site within the kinase domain, to CREs binding to an alternative site, inducing allosteric regulation revealing distinct types of inhibitory mechanisms, which we exemplify by archetypical representative systems. While this study provides a systematic approach to comprehend kinase CREs, further experimental investigations are imperative to unravel the complexity within distinct kinase families. The insights gleaned from this research lay the foundation for future studies aiming to decipher the molecular basis of kinase dysregulation, and explore potential therapeutic interventions.</p>","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":"575-587"},"PeriodicalIF":3.2,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142376308","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}

{"title":"Based on Molecular Docking, Molecular Dynamics Simulation and MM/PB(GB)SA to Study Potential Inhibitors of PRRSV-Nsp4.","authors":"Tianyu Shi, Wenzhou Chang, Xinyu Wei, Yiling Kong, Ying Wei","doi":"10.1002/prot.26754","DOIUrl":"10.1002/prot.26754","url":null,"abstract":"<p><p>Porcine reproductive and respiratory syndrome (PRRS) is one of the most serious infectious immunosuppressive diseases in the world. The nonstructural protein Nsp4 can be used as an ideal target for anti-PRRSV replication inhibitors. However, little is known about potential inhibitors that target Nsp4 to affect PRRSV replication. The purpose of this study was to screen potential natural inhibitors that affect PRRSV replication by inhibiting Nsp4. Five compounds with strong binding affinity to Nsp4 were selected by structure-based molecular docking method. The complexes of naringin dihydrochalcone (NDC), agathisflavone (AGT), and amentoflavone (AMF) with Nsp4 were stable throughout the molecular dynamics simulation. According to MM/PBSA analysis, the free energies of binding of NDC, AGT, and AMF to Nsp4 were less than-30 Kcal/mol. In conclusion, these three compounds are worthy of further investigation as novel inhibitors of PRRSV. This study provides a theoretical basis for the development of anti-PRRSV natural drugs.</p>","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":"598-607"},"PeriodicalIF":3.2,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142402130","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}

{"title":"Insights Into the Molecular Interactions of MIC2 and M2AP: Role of TSR6 and Conservation Across Species.","authors":"Xu Xia, Chenqiang Du, Yang Wang, Gaojie Song","doi":"10.1002/prot.26758","DOIUrl":"10.1002/prot.26758","url":null,"abstract":"<p><p>Microneme protein 2 (MIC2) and its associated protein M2AP are pivotal for the gliding motility and host cell invasion by Toxoplasma gondii. In our prior work, we showed that M2AP binds specifically to the sixth TSR domain of MIC2, with this interaction mediated dominantly by the hotspot residue H620 situated at the center of TSR6. To delve deeper into the functional significance of H620 and explore the dynamic behavior of Y602, we conducted molecular dynamic (MD) simulations of the Toxoplasma TSR6-M2AP complex, encompassing both wild-type and mutant forms. Our findings underscore the critical role of H620 within TSR6, particularly its hydrogen bond interaction with K72 of M2AP. The H620A mutation disrupts the nearby hydrophobic network while minimally affecting other hydrophilic interactions. Furthermore, our data reveal a highly conserved binding pose between M2AP and TSR6 across different species, consistent with previous trans-genera studies, thereby offering insights for future strategies in infection control development.</p>","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":"620-628"},"PeriodicalIF":3.2,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142482017","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}

{"title":"Localized Amino Acid Enrichment Analysis as a Tool for Understanding Protein Extremophilicity.","authors":"Elliot Hill, Avery Hill, Elena Voisin, Amber Byrd, Allyn Schoeffler","doi":"10.1002/prot.26760","DOIUrl":"10.1002/prot.26760","url":null,"abstract":"<p><p>Sequence conservation analyses offer us a powerful glimpse of natural selection at work. Standard tools for measuring sequence conservation report conservation as a function of a specific location in a multiple sequence alignment and have proven indispensable in identifying highly constrained features such as active site residues. The advent of large-scale genomic sequencing efforts allows researchers to expand this paradigm and investigate more nuanced relationships between sequence and function. Here, we present a simple tool (SWiLoDD: Sliding Window Localized Differentiation Detection) that allows researchers to analyze local, rather than site-specific, conservation using a sliding window approach. Our tool accepts multiple sequence alignments partitioned based on a biological differentiator and returns alignment position-based, localized differential enrichment metrics for amino acids of choice. We present two case studies of this analysis in action: local-but-diffuse glycine enrichments in the ATPase subunits of thermophilic and psychrophilic bacterial gyrase homologs, and ligand- and interface-specific amino acid enrichments in halophilic bacterial crotonyl-CoA carboxylases/reductases. Though we have described examples of extremophilic bacterial proteins in this study, our tool may be used to investigate any set of homologous sequences from which sub-groups can be meaningfully partitioned. Our results suggest that investigating differential localized conservation in partitioned MSAs will expand our understanding of how sequence conservation and protein function are connected.</p>","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":"702-715"},"PeriodicalIF":3.2,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142606480","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}

{"title":"Skittles: GNN-Assisted Pseudo-Ligands Generation and Its Application for Binding Sites Classification and Affinity Prediction.","authors":"Sergei Evteev, Alexey Ereshchenko, Denis Adjugim, Alexey Vyacheslavov, Anna Pastukhova, Alexander Malyshev, Victor Terentiev, Yan Ivanenkov","doi":"10.1002/prot.26816","DOIUrl":"https://doi.org/10.1002/prot.26816","url":null,"abstract":"<p><p>Nowadays, multiple solutions are known for identifying ligand-protein binding sites. Another important task is labeling each point of a binding site with the appropriate atom type, a process known as pseudo-ligand generation. The number of solutions for pseudo-ligand generation is limited, and, to our knowledge, the influence of machine learning techniques has not been studied previously. Here, we describe Skittles, a new graph neural network-assisted pseudo-ligand generation approach, and compare it with known force-field-based methods. We also demonstrate the application of Skittles-based data for solving several important problems in structural biology, including ligand-protein binding site classification and ligand-protein affinity prediction.</p>","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143525333","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}

{"title":"Evaluation of the Ability of Wasp Venom Bioinspired Peptides (Fraternine-10 and Octovespin) in the Disaggregation and Anti-Aggregation of Amyloid-β Fibrils.","authors":"Yuri Alves de Oliveira Só, Caio Vinícius Sousa Costa, Luana Cristina Camargo, Letícia Germino Veras, Luiz Antônio Ribeiro Júnior, Márcia Renata Mortari, Ricardo Gargano","doi":"10.1002/prot.26806","DOIUrl":"https://doi.org/10.1002/prot.26806","url":null,"abstract":"<p><p>Many neurodegenerative diseases are directly related to the formation of toxic protein aggregates, such as Alzheimer's disease, which is associated with the aggregation of amyloid-beta (Aβ). In this context, protein fibrils are the hallmark of these neurodegenerative diseases. In this sense, developing compounds capable of preventing or reducing the formation of protein aggregation in the brain can be of fundamental importance for the curative treatment of these diseases. Animals' venom compounds are known to be selected for nervous system targets, therefore, they are considered an interesting platform for developing pharmacological tools. This work presents a study of the ligands Octovespin (bioinspired by the wasp venom Polybia occidentalis) and Fraternine-10 (bioinspired by the wasp venom Parachartergus fraternus) concerning the disaggregation and anti-aggregation of fibrils of Aβ(17-42) sheets. First, we performed in silico calculations using molecular docking and molecular dynamics simulations with 200 ns. The results indicate that Octovespin and Fraternine-10 interact with the Aβ protein fibrils throughout all simulation time. The RMSD, RMSF, number of hydrogen and radius of gyration values and the interactions with amino acids responsible for fibril aggregation demonstrate that both Octovespin and Fraternine-10 have a significant disaggregation potential, which corroborates the in vitro and in vivo experimental observations. Furthermore, experimental data of Fraternine-10 demonstrated an anti-aggregation effect, indicating that it can promote fibril disaggregation and prevent them from aggregating again to form oligomers. However, in vivo data of Fraternine-10 did not show improvement. Even though in vivo results were not promising, the in vitro and in silico discoveries qualify these molecules as potential sources for developing new candidates to become medicines against Alzheimer's disease.</p>","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143484969","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}