Proteins-Structure Function and Bioinformatics最新文献

{"title":"Structural Basis for the Essential Role of Ca²⁺ in the Lytic Activity of Staphylococcus aureus PlyGRCS Endolysin Targeting Methicillin-Resistant Staphylococcus aureus.","authors":"Gopinatha Krishnappa, Harshitha Nagaraj, Harshavardini Bakthavatsalam SureshKumar, Mitali Mandal, Sivaraman Padavattan, Veenakumari Haradara Bahubali, Saravanamuthu Thiyagarajan, Balasundaram Padmanabhan","doi":"10.1002/prot.26777","DOIUrl":"10.1002/prot.26777","url":null,"abstract":"<p><p>Staphylococcus aureus causes a wide range of infections, from mild skin conditions to severe, life-threatening diseases. Bacteriophage endolysins exhibit a selective capacity to degrade the peptidoglycan layer of Gram-positive bacteria, making promising biotherapeutic agents against antibiotic-resistant infections. PlyGRCS, a specific endolysin derived from S. aureus, comprises a catalytic CHAP domain and a cell-wall binding SH3_5 domain connected by a linker. Ca²⁺ ions are essential for the CHAP domain's catalytic function. The crystal structure of PlyGRCS, determined in the absence of Ca²⁺ and refined to a resolution of 1.67 Å, revealed significant conformational changes in the Ca²⁺ binding site. Antimicrobial assays with Ca²⁺-deficient PlyGRCS and mutants targeting key residues in the catalytic and Ca²⁺ binding regions highlighted the importance of specific functional residues for lytic activity against methicillin-resistant Staphylococcus aureus (MRSA). These structural and microbial studies provide valuable insights into the critical residues contributing to PlyGRCS's bacteriolytic efficacy against MRSA.</p>","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":"920-933"},"PeriodicalIF":3.2,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142807171","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":"Protein Complex Structure Prediction With AlphaFold-Enhanced HDOCK in CAPRI Rounds 47-55.","authors":"Hao Li, Peicong Lin, Yurui Li, Sheng-You Huang","doi":"10.1002/prot.26823","DOIUrl":"https://doi.org/10.1002/prot.26823","url":null,"abstract":"<p><p>Protein-protein interactions play a critical role in numerous biological processes, and understanding these interactions is essential for deciphering cellular mechanisms and designing therapeutic interventions. Predicting protein-protein complex structures by computational methods is an important approach to studying protein-protein interactions. The CAPRI (Critical Assessment of PRediction of Interactions) experiment has served as a benchmark for evaluating computational methods for predicting protein complex structures. We participated in CAPRI Rounds 47-55 and continuously refined our complex structure prediction strategies throughout this period. Initially, our approach was based on a hybrid docking strategy that combined template-based and ab initio docking methods. However, starting from Round 53, we integrated AlphaFold into our prediction pipeline. Inspired by the experiences of other participants in Round 54, we further refined our use of AlphaFold by enhancing the sampling strategy, which significantly improved our prediction accuracy in Round 55.</p>","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143756225","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":"Correction to \"AbDPP: Target-Oriented Antibody Design With Pretraining and Prior Biological Structure Knowledge\".","authors":"","doi":"10.1002/prot.26775","DOIUrl":"10.1002/prot.26775","url":null,"abstract":"","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":"945"},"PeriodicalIF":3.2,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142775189","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":"Conserved and Unique Mitochondrial Target Sequence of TRPV4 Can Independently Regulate Mitochondrial Functions.","authors":"Tusar Kanta Acharya, Parnasree Mahapatra, Shamit Kumar, Nishant Kumar Dubey, Srujanika Rajalaxmi, Arijit Ghosh, Ashutosh Kumar, Chandan Goswami","doi":"10.1002/prot.26772","DOIUrl":"10.1002/prot.26772","url":null,"abstract":"<p><p>Though mitochondria have their own genome and protein synthesis machineries, the majority of the mitochondrial proteins are actually encoded by the nuclear genome. Most of these mitochondrial proteins are imported into specific compartments of the mitochondria due to their mitochondrial target sequence (MTS). Unlike the nuclear target sequence, the MTS of most of the mitochondrial localized proteins remain poorly understood, mainly due to their variability, heterogeneity, unconventional modes of action, mitochondrial potential-dependent transport, and other complexities. Recently, we reported that transient receptor potential vanilloid subtype 4 (TRPV4), a thermosensitive cation channel, is physically located at the mitochondria. Here we characterize a small segment (AA 592-630) located at the TM4-loop4-TM5 segment of TRPV4 that acts as a novel MTS. The same region remains highly conserved in all vertebrates and contains a large number of point mutations each of which causes an diverse spectrum of diseases in human. Using confocal and super-resolution microscopy, we show that this MTS of TRPV4 or its mutants localizes to the mitochondria independently and also induces functional and quantitative changes in the mitochondria. By using conformal microscopy, we could detect the presence of the MTS region within the isolated mitochondria. These findings may be important to understand the complexity of MTS and TRPV4-induced channelopathies better.</p>","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":"908-919"},"PeriodicalIF":3.2,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11878201/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142796626","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":"MuGger Toxins: Exploring the Selective Binding Mechanism of Clostridial Glucosyltransferase Toxin B and Host GTPases.","authors":"Damla Nur Camli, Haci Aslan Onur Iscil, Saliha Ece Acuner","doi":"10.1002/prot.26770","DOIUrl":"10.1002/prot.26770","url":null,"abstract":"<p><p>(a) Clostridioides difficile ( C. difficile ) bacterium can cause severe diarrhea and its over-colonization in the host's intestinal tract lead to the development of pseudomembranous colitis, generally due to antibiotic usage. The primary exotoxins involved are toxin A (TcdA) and toxin B (TcdB), the latter being more pathogenic. TcdB has glucosyltransferase activity and mediates monoglycosylation by targeting host cell enzymes (mainly Rho and Ras family of GTPases) with differential selectivity. Here, we aim to provide structural and dynamic insights into how TcdB impacts the host's intestinal epithelial cells focusing on the glycosylation mechanism of Rho GTPases, Cdc42, and Rac1, at the molecular level. To this aim, we modeled the unknown TcdB-host protein complex structures, based on the available experimental structures of TcdB, through protein-protein docking. Then, we elaborated on TcdB-Rho GTPase models as TcdB is known to selectively interact with GDP-bound inactive states of Rho GTPases, over the GTP-bound active ones, but the mechanism is unclear. Through a total of 6 μs-long molecular dynamics simulation of TcdB and GTP/GDP-bound Rac1 and Cdc42 complexes, TcdB's selective binding mechanism was revealed for Rac1. TcdB-Rac1 complexes were further analyzed with enhanced sampling techniques such as well-tempered metadynamics simulations and umbrella sampling to reveal selective binding mechanism between TcdB and GDP-bound Rac1. Our results show that TcdB selectively binds to GDP-bound Rac1, over the GTP-bound one, driven by its affinity for the Mg²⁺ ion. A destabilized Mg²⁺ ion incapable of coordinating GDP disrupts Rac1's GTPase function, shedding light on the molecular basis of TcdB's pathogenic effects.</p>","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":"934-944"},"PeriodicalIF":3.2,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142820248","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":"Insight Into Factors Influencing the Aggregation Process in Wild-Type and P66R Mutant SOD1: Computational and Spectroscopic Approaches.","authors":"Roghayeh Farrokhzad, Bagher Seyedalipour, Payam Baziyar, Saman Hosseinkhani","doi":"10.1002/prot.26765","DOIUrl":"10.1002/prot.26765","url":null,"abstract":"<p><p>Disturbances in metal ion homeostasis associated with amyotrophic lateral sclerosis (ALS) have been described for several years, but the exact mechanism of involvement is not well understood. To elucidate the role of metalation in superoxide dismutase (SOD1) misfolding and aggregation, we comprehensively characterized the structural features (apo/holo forms) of WT-SOD1 and P66R mutant in loop IV. Using computational and experimental methodologies, we assessed the physicochemical properties of these variants and their correlation with protein aggregation at the molecular level. Modifications in apo-SOD1 compared to holo-SOD1 were more pronounced in flexibility, stability, hydrophobicity, and intramolecular interactions, as indicated by molecular dynamics simulations. The enzymatic activities of holo/apo-WT SOD1 were 1.30 and 1.88-fold of the holo/apo P66R mutant, respectively. Under amyloid-inducing conditions, decreased ANS fluorescence intensity in the apo-form relative to the holo-form suggested pre-fibrillar species and amyloid aggregate growth due to occluded hydrophobic pockets. FTIR spectroscopy revealed that apo-WT-SOD1 and apo-P66R exhibited a mixture of parallel and intermolecular β-sheet structures, indicative of aggregation propensity. Aggregate species were identified using TEM, Congo red staining, and ThT/ANS fluorescence spectroscopy. Thermodynamic analyses with GdnHCl demonstrated that metal deficit, mutation, and intramolecular disulfide bond reduction are essential for initiating SOD1 misfolding and aggregation. These disruptions destabilize the dimer-monomer equilibrium, promoting dimer dissociation into monomers and decreasing the thermodynamic stability of SOD1 variants, thus facilitating amyloid/amorphous aggregate formation. Our findings offer novel insights into protein aggregation mechanisms in disease pathology and highlight potential therapeutic strategies against toxic protein aggregation, including SOD1.</p>","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":"885-907"},"PeriodicalIF":3.2,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142792732","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":"Unraveling GPCRs Allosteric Modulation. Cannabinoid 1 Receptor as a Case Study.","authors":"Alejandro Cruz, Arieh Warshel","doi":"10.1002/prot.26762","DOIUrl":"10.1002/prot.26762","url":null,"abstract":"<p><p>G-protein-coupled receptors (GPCRs) constitute one of the most prominent families of integral membrane receptor proteins that mediate most transmembrane signaling processes. Malfunction of these signal transduction processes is one of the underlying causes of many human pathologies (Parkinson's, Huntington's, heart diseases, etc), provoking that GPCRs are the largest family of druggable proteins. However, these receptors have been targeted traditionally by orthosteric ligands, which usually causes side effects due to the simultaneous targeting of homologous receptor subtypes. Allosteric modulation offers a promising alternative approach to circumvent this problematic and, thus, comprehending its details is a most important task. Here we use the Cannabinoid type-1 receptor (CB1R) in trying to shed light on this issue, focusing on positive allosteric modulation. This is done by using the protein-dipole Langevin-dipole (PDLD) within the linear response approximation (LRA) framework (PDLD/S-2000) along with our coarse-grained (CG) model of membrane proteins to evaluate the dissociation constants (K _Bs) and cooperativity factors (αs) for a diverse series of CB1R positive allosteric modulators belonging to the 2-phenylindole structural class, considering CP55940 as an agonist. The agreement with the experimental data evinces that significantly populated allosteric modulator:CB1R and allosteric modulator:CP55940:CB1R complexes have been identified and characterized successfully. Analyzing them, it has been determined that CB1R positive allosteric modulation lies in an outwards displacement of transmembrane α helix (TM) 4 extracellular end and in the regulation of the range of motion of a compound TM7 movement for binary and ternary complexes, respectively. In this respect, we achieved a better comprehension of the molecular architecture of CB1R positive allosteric site, identifying Lys192^3.28 and Gly194^3.30 as key residues regarding electrostatic interactions inside this cavity, and to rationalize (at both structural and molecular level) the exhibited stereoselectivity in relation to positive allosteric modulation activity by considered CB1R allosteric modulators. Additionally, putative/postulated allosteric binding sites have been screened successfully, identifying the real CB1R positive allosteric site, and most structure-activity relationship (SAR) studies of CB1R 2-phenylindole allosteric modulators have been rationalized. All these findings point out towards the predictive value of the methodology used in the current work, which can be applied to other biophysical systems of interest. The results presented in this study contribute significantly to understand GPCRs allosteric modulation and, hopefully, will encourage a more thorough exploration of the topic.</p>","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":"763-785"},"PeriodicalIF":3.2,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11879764/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142711818","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":"The Crystal Structure of Human IgD-Fc Reveals Unexpected Differences With Other Antibody Isotypes.","authors":"Anna M Davies, Tam T T Bui, Raúl Pacheco-Gómez, Susan K Vester, Andrew J Beavil, Hannah J Gould, Brian J Sutton, James M McDonnell","doi":"10.1002/prot.26771","DOIUrl":"10.1002/prot.26771","url":null,"abstract":"<p><p>Of the five human antibody isotypes, the function of IgD is the least well-understood, although various studies point to a role for IgD in mucosal immunity. IgD is also the least well structurally characterized isotype. Until recently, when crystal structures were reported for the IgD Fab, the only structural information available was a model for intact IgD based on solution scattering data. We now report the crystal structure of human IgD-Fc solved at 3.0 Å resolution. Although similar in overall architecture to other human isotypes, IgD-Fc displays markedly different orientations of the Cδ3 domains in the Cδ3 domain dimer and the lowest interface area of all the human isotypes. The nature of the residues that form the dimer interface also differs from those conserved in the other isotypes. By contrast, the interface between the Cδ2 and Cδ3 domains in each chain is the largest among the human isotypes. This interface is characterized by two binding pockets, not seen in other isotypes, and points to a potential role for the Cδ2/Cδ3 interface in stabilizing the IgD-Fc homodimer. We investigated the thermal stability of IgD-Fc, alone and in the context of an intact IgD antibody, and found that IgD-Fc unfolds in a single transition. Human IgD-Fc clearly has unique structural features not seen in the other human isotypes, and comparison with other mammalian IgD sequences suggests that these unique features might be widely conserved.</p>","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":"786-800"},"PeriodicalIF":3.2,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11878202/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142711704","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":"PCANN Program for Structure-Based Prediction of Protein-Protein Binding Affinity: Comparison With Other Neural-Network Predictors.","authors":"Olga O Lebedenko, Mikhail S Polovinkin, Anastasiia A Kazovskaia, Nikolai R Skrynnikov","doi":"10.1002/prot.26821","DOIUrl":"https://doi.org/10.1002/prot.26821","url":null,"abstract":"<p><p>In this communication, we introduce a new structure-based affinity predictor for protein-protein complexes. This predictor, dubbed PCANN (Protein Complex Affinity by Neural Network), uses the ESM-2 language model to encode the information about protein binding interfaces and graph attention network (GAT) to parlay this information into <math> <semantics> <mrow><msub><mi>K</mi> <mi>d</mi></msub> </mrow> <annotation>$$ {K}_{mathrm{d}} $$</annotation></semantics> </math> predictions. In the tests employing two previously unused literature-extracted datasets, PCANN performed better than the best of the publicly available predictors, BindPPI, with mean absolute error (MAE) of 1.3 versus 1.4 kcal/mol. Further progress in the development of <math> <semantics> <mrow><msub><mi>K</mi> <mi>d</mi></msub> </mrow> <annotation>$$ {K}_{mathrm{d}} $$</annotation></semantics> </math> predictors using deep learning models is faced with two problems: (i) the amount of experimental data available to train and test new predictors is limited and (ii) the available <math> <semantics> <mrow><msub><mi>K</mi> <mi>d</mi></msub> </mrow> <annotation>$$ {K}_{mathrm{d}} $$</annotation></semantics> </math> data are often not very accurate and lack internal consistency with respect to measurement conditions. These issues can be potentially addressed through an AI-leveraged literature search followed by careful human curation and by introducing additional parameters to account for variations in experimental conditions.</p>","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143671758","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":"An Overview of Property, Design, and Functionality of Linkers for Fusion Protein Construction.","authors":"Hadis Chatrdooz, Javad Sargolzaei","doi":"10.1002/prot.26812","DOIUrl":"https://doi.org/10.1002/prot.26812","url":null,"abstract":"<p><p>Linkers are naturally occurring short amino acid sequences that are used to separate domains within a protein. The advent of recombinant DNA technology has made it possible to combine two interacting partners by introducing artificial linkers that often, allow for the production of stable and functional proteins. Glycine-rich linkers are useful for transient interactions, especially where the interaction is weak, by covalently linking proteins and forming a stable protein-protein complex. These linkers have also been used to generate covalently stable dimers and to connect two independent domains that create a ligand binding site or recognition sequence. Various structures of covalently linked protein complexes have been described using nuclear magnetic resonance methods, cryo-electron microscopy techniques, and X-ray crystallography; in addition, several structures where linkers have been used to generate stable protein-protein complexes, improve protein solubility, and obtain protein dimers are investigated, and also the design and engineering of the linker in fusion proteins is discussed. Therefore, one of the main factors for linker design and optimization is their flexibility, which can directly contribute to the physical distance between the domains of a fusion protein and describe the tendency of a linker to maintain a stable conformation during expression. We summarize the research on design and bioinformatics can be used to predict the spatial structure of the fusion protein. To perform simulations of spatial structures and drug molecule design, future research will concentrate on various correlation models.</p>","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143659812","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}