Advances in protein chemistry and structural biology最新文献_第3页

Antimicrobial peptides: Bridging mechanistic understanding and novel applications. 抗菌肽：桥接机制的理解和新的应用。

3区生物学

Advances in protein chemistry and structural biology Pub Date : 2026-01-01 Epub Date: 2025-08-30 DOI: 10.1016/bs.apcsb.2025.08.004

Wanzhen Dai, Bee K Tan, Jiamiao Hu

引用次数: 0

Unraveling the role of antimicrobial proteins in leptospirosis: A comprehensive transcriptomic analysis. 揭示抗菌蛋白在钩端螺旋体病中的作用：一项全面的转录组分析。

3区生物学

Advances in protein chemistry and structural biology Pub Date : 2026-01-01 Epub Date: 2025-05-30 DOI: 10.1016/bs.apcsb.2024.11.015

Nivedya Kottarath, Megha Hari, Prasanna Kumar Selvam, Karthick Vasudevan

{"title":"Unraveling the role of antimicrobial proteins in leptospirosis: A comprehensive transcriptomic analysis.","authors":"Nivedya Kottarath, Megha Hari, Prasanna Kumar Selvam, Karthick Vasudevan","doi":"10.1016/bs.apcsb.2024.11.015","DOIUrl":"10.1016/bs.apcsb.2024.11.015","url":null,"abstract":"Leptospirosis, caused by Leptospira bacteria, poses a significant global health threat with notable mortality rates. This study employs advanced transcriptomics to explore the complex interactions between host and pathogen, focusing on antimicrobial peptides (AMPs). Genomic data from mice infected with various Leptospira serotypes underwent rigorous quality control, alignment to the Mus musculus genome, and quantification using FeatureCounts. DESeq2 analysis revealed 491 differentially expressed genes (DEGs), shedding light on key molecular pathways crucial to leptospirosis pathogenesis, particularly involving AMP resistance mechanisms. Important molecular functions, KEGG pathways, cellular components, and biological processes linked to AMP resistance were revealed by functional enrichment analysis. These findings underscore roles in stress responses, immune modulation, and stimulus regulation. Utilizing Cytoscape, a protein-protein interaction network identified pivotal hub proteins such as Ptprc, Stat3, Syk, Stat5a, Stat1, Il18, Fcgr3, Jak2, Sell, and Jak1, integral to immune responses, signaling cascades, and cellular processes essential for AMP resistance. This comprehensive analysis provides valuable insights into the mechanisms underlying AMP resistance in leptospirosis. The identified biomarkers hold promise for developing targeted diagnostic tools and therapeutic strategies to combat AMP-resistant leptospirosis strains, potentially alleviating its global health impact. Further validation and comprehensive exploration are crucial to advancing our understanding and enhancing patient care strategies against antimicrobial resistance in leptospirosis.","PeriodicalId":7376,"journal":{"name":"Advances in protein chemistry and structural biology","volume":"149 ","pages":"333-352"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146045909","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Antimicrobial peptides act as a component of brain immunity against microbes in Alzheimer's disease. 在阿尔茨海默病中，抗菌肽是大脑对微生物免疫的一个组成部分。

3区生物学

Advances in protein chemistry and structural biology Pub Date : 2026-01-01 Epub Date: 2025-11-08 DOI: 10.1016/bs.apcsb.2025.10.016

Madhura Chandrashekar, Gowshika Velmurugan, Amit Mishra, Subashchandrabose Chinnathambi

{"title":"Antimicrobial peptides act as a component of brain immunity against microbes in Alzheimer's disease.","authors":"Madhura Chandrashekar, Gowshika Velmurugan, Amit Mishra, Subashchandrabose Chinnathambi","doi":"10.1016/bs.apcsb.2025.10.016","DOIUrl":"10.1016/bs.apcsb.2025.10.016","url":null,"abstract":"Alzheimer's disease is a most prevalent type of dementia in elderly people. Extracellular accumulation of Amyloid-β (Aβ) and intracellular aggregation of Tau NFTs in the brain is proposed to be a key factor in the development of Alzheimer's disease. A fast-growing body of evidence strengthened the infectious hypothesis of sporadic type of AD. Recent clinical studies focused on the characterizing of antimicrobial peptides (AMPs), because it has been documented that some pathogenic microorganism, such as herpesviruses and particular bacterial strains, are generally present in AD individuals. And also, the environmental factors, such as persistent bacterial or viral infections, change the blood-brain barrier's (BBB) permeability, making it easier for opportunistic pathogens to colonise the brain. This review highlights the potential role of Aβ, which perform antimicrobial activity against diverse pathogens, significantly encouraging its role in the innate immune response. While mammalian amyloid is linked with disease, numerous microbes form amyloid fibrils to embattle the biofilm that prevent the cells from the surrounding environment. According to the microbial AD hypothesis, Aβ clumps up to combat the microbial infection.","PeriodicalId":7376,"journal":{"name":"Advances in protein chemistry and structural biology","volume":"149 ","pages":"395-418"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146045996","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

G-protein coupled receptor regulates cytoskeletal remodelling of extracellular Tau in Alzheimer's disease. g蛋白偶联受体调控阿尔茨海默病中细胞外Tau的细胞骨架重塑。

3区生物学

Advances in protein chemistry and structural biology Pub Date : 2026-01-01 Epub Date: 2025-11-20 DOI: 10.1016/bs.apcsb.2025.10.018

Subashchandrabose Chinnathambi, Nagaraj Rangappa, Gowshika Velmurugan, Madhura Chandrashekar

引用次数: 0

Screening of prospective biofilm-inhibitory drug candidates aimed at the biofilm-associated protein (BAP) in Staphylococcus aureus: An in-silico investigation. 针对金黄色葡萄球菌生物膜相关蛋白（BAP）的前瞻性生物膜抑制候选药物筛选：一项计算机研究。

3区生物学

Advances in protein chemistry and structural biology Pub Date : 2026-01-01 Epub Date: 2026-05-12 DOI: 10.1016/bs.apcsb.2025.10.010

Sree Haryini, Mohanraj Gopikrishnan, Magesh Ramasamy, George Priya Doss C

{"title":"Screening of prospective biofilm-inhibitory drug candidates aimed at the biofilm-associated protein (BAP) in Staphylococcus aureus: An in-silico investigation.","authors":"Sree Haryini, Mohanraj Gopikrishnan, Magesh Ramasamy, George Priya Doss C","doi":"10.1016/bs.apcsb.2025.10.010","DOIUrl":"https://doi.org/10.1016/bs.apcsb.2025.10.010","url":null,"abstract":"Staphylococcus aureus is the leading pathogen responsible for hospital- and community-acquired infections. The increasing prevalence of nosocomial infections in healthcare settings presents a significant challenge, particularly due to the strong biofilm-forming capability of clinical strains, which contributes to biofilm-mediated multidrug resistance. The biofilm-associated protein (BAP) plays a pivotal role in the initial adhesion and maturation of biofilms, significantly increasing the likelihood of failure of conventional antimicrobial therapies. Given its crucial function in biofilm formation, BAP represents a promising target for anti-biofilm drug development. A high-throughput virtual screening technique was implemented to identify potent BAP inhibitors, utilizing triple-mode docking with the Glide module of the Schrödinger Maestro suite. About 28,831 compounds from the ENAMINE-targeted antibacterial library were screened against BAP in S. aureus. Among the selected ligands, Z1430813924 and Z1738791774 exhibited the lowest binding energy, demonstrating superior docking scores alongside favorable ADME and physicochemical properties, which suggests an enhanced inhibitory potential. To validate the docking findings, a 100-ns molecular dynamics simulation was employed to assess the stability of the protein-ligand complex within a dynamic environment. The essential dynamics analysis, including free energy landscape (FEL) and principal component analysis (PCA) evaluations, affirmed the stability and efficacy of the top compounds, Z1430813924 and Z1738791774, as promising BAP inhibitors. These insights provide a strong foundation for subsequent experimental validation and the potential development of novel anti-biofilm therapeutics targeting S. aureus infections.","PeriodicalId":7376,"journal":{"name":"Advances in protein chemistry and structural biology","volume":"153 ","pages":"485-504"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148443778","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Signaling cascades of microtubule-associated protein Tau in Alzheimer's disease. 阿尔茨海默病中微管相关蛋白Tau的信号级联反应。

3区生物学

Advances in protein chemistry and structural biology Pub Date : 2026-01-01 Epub Date: 2025-11-10 DOI: 10.1016/bs.apcsb.2025.10.013

Gowshika Velmurugan, Deena Krishnan, Riddhi Upadhyay, R Sivasamy, Murugan Sevanan, Subashchandrabose Chinnathambi

{"title":"Signaling cascades of microtubule-associated protein Tau in Alzheimer's disease.","authors":"Gowshika Velmurugan, Deena Krishnan, Riddhi Upadhyay, R Sivasamy, Murugan Sevanan, Subashchandrabose Chinnathambi","doi":"10.1016/bs.apcsb.2025.10.013","DOIUrl":"https://doi.org/10.1016/bs.apcsb.2025.10.013","url":null,"abstract":"Accumulation of neurofibrillary tangles (NFTs) in the neuronal cells is the predominant features of Alzheimer's diseases (AD) and other Tauopathies. Studies on molecular mechanism of human neurodegenerative disease shows that the substantial posttranslational modifications (PTMs) of Tau is essential for the conversion of monomeric soluble form into the aberrant insoluble aggregates in pathological condition. During pathogenesis of AD, Tau phosphorylation state is altered by the activation of various kinases and phosphates and eventually Tau become hyperphosphorylated. Hyperphosphorylated Tau detach from microtubules and aggregate intracellularly in affected neurons. This pathological Tau invades the subcellular organelles including mitochondria and leads to degeneration and cell death. Ageing is the crucial factor causing alteration in brain including, structural and functional role of Tau. Pathological Tau disrupts signaling cascades of mitochondria, energy-associated mechanism and this causes the elevation of oxidative stress in the neurons. Furthermore, hyperphosphorylated Tau also inhibits the mitophagy and autophagy-lysosomal pathway, resulting in the buildup of dysfunctional mitochondria in the affected neurons. This review highlights the major signaling cascades involved in Tau PTMs and its interlinked role in mitochondrial damage in aging population in AD.","PeriodicalId":7376,"journal":{"name":"Advances in protein chemistry and structural biology","volume":"153 ","pages":"169-190"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148443846","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Microbiome and microbial products as immunomodulators: Implications for gastrointestinal cancers. 微生物组和微生物产品作为免疫调节剂：对胃肠道癌症的影响。

3区生物学

Advances in protein chemistry and structural biology Pub Date : 2026-01-01 Epub Date: 2025-11-11 DOI: 10.1016/bs.apcsb.2025.10.008

Shriyans Reddy Yendreddy, Divya Patchigolla, Satyendra Singh, Kirti Baghel, Rupal Ojha, Vijay Kumar Prajapati

{"title":"Microbiome and microbial products as immunomodulators: Implications for gastrointestinal cancers.","authors":"Shriyans Reddy Yendreddy, Divya Patchigolla, Satyendra Singh, Kirti Baghel, Rupal Ojha, Vijay Kumar Prajapati","doi":"10.1016/bs.apcsb.2025.10.008","DOIUrl":"10.1016/bs.apcsb.2025.10.008","url":null,"abstract":"The Hippocratic adage \"all disease starts in the gut\" remains pertinent as research uncovers how the gut microbiome and its products influence immunity and gastrointestinal cancers. The immune system's remarkable paradox lies in its ability to distinguish and tolerate trillions of beneficial microbes while defending against harmful pathogens to maintain health. Disruptions to this delicate balance, known as dysbiosis, contribute to chronic inflammation and create a favourable tumour development and progression environment. Microbial metabolites, such as- short-chain fatty acids and secondary bile acids further modulate inflammation, gut barrier integrity, and immune checkpoint pathways. Emerging microbial biomarkers show promise in diagnosis and prognosis and compete with traditional clinical factors. Innovative therapeutic strategies are being explored to harness the microbiome's immunomodulatory potential. Integrating microbiome profiling into personalised medicine offers new opportunities to prevent, detect, and treat gastrointestinal cancers, shifting the microbiome from a passive disease marker to an active agent that modulates and influences the disease. This chapter discusses the emerging understanding of microbiomes and microbial products in gastrointestinal cancers, highlighting diagnostic advances and novel therapeutic approaches that leverage microbial interactions to improve patient outcomes.","PeriodicalId":7376,"journal":{"name":"Advances in protein chemistry and structural biology","volume":"152 ","pages":"1-35"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148003815","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Peptides and peptidomimetics as immunomodulator agents targeting neglected tropical diseases. 针对被忽视的热带病的多肽和拟肽制剂免疫调节剂。

3区生物学

Advances in protein chemistry and structural biology Pub Date : 2026-01-01 Epub Date: 2026-03-07 DOI: 10.1016/bs.apcsb.2026.02.001

Sheila Oliveira de Souza, Leandro Rocha Silva, Manuele Figueiredo da Silva, Maria Gabriele Cordeiro Domingos, Eziane Dantas da Silva, João Xavier de Araújo-Júnior, Paulo Fernando da Silva Santos-Júnior, Ana Catarina Rezende Leite, Edeildo Ferreira da Silva Júnior

{"title":"Peptides and peptidomimetics as immunomodulator agents targeting neglected tropical diseases.","authors":"Sheila Oliveira de Souza, Leandro Rocha Silva, Manuele Figueiredo da Silva, Maria Gabriele Cordeiro Domingos, Eziane Dantas da Silva, João Xavier de Araújo-Júnior, Paulo Fernando da Silva Santos-Júnior, Ana Catarina Rezende Leite, Edeildo Ferreira da Silva Júnior","doi":"10.1016/bs.apcsb.2026.02.001","DOIUrl":"10.1016/bs.apcsb.2026.02.001","url":null,"abstract":"The human immune system is a highly integrated and dynamic network designed to detect, respond to, and eliminate a wide range of infectious agents while preserving tissue homeostasis. This chapter provides an overview of the fundamental organization and function of innate and adaptive immunity, followed by a focused description of the human infection cycles of major pathogens of global health relevance, including Trypanosoma brucei (human African trypanosomiasis), T. cruzi (Chagas disease), Leishmania spp., Schistosoma mansoni, Plasmodium spp., and arboviruses such as Zika and dengue viruses. Emphasis is placed exclusively on the stages of each life cycle that occur within the human host, highlighting key cellular niches, tissue tropisms, and host-pathogen interactions that shape disease progression. In addition, the chapter discusses the diverse immunomodulatory strategies employed by these pathogens to evade immune detection, subvert effector mechanisms, and establish persistent or chronic infections. These mechanisms include antigenic variation, immune cell dysfunction, cytokine skewing, regulatory pathway activation, and molecular mimicry. By integrating immunological principles with pathogen-specific infection dynamics, this chapter aims to provide a coherent framework for understanding how immune responses are initiated, regulated, and manipulated during infection. Such knowledge is essential for the rational design of vaccines, immunotherapies, and host-directed interventions against parasitic and viral diseases.","PeriodicalId":7376,"journal":{"name":"Advances in protein chemistry and structural biology","volume":"152 ","pages":"141-189"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148003906","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Enzyme kinetics and engineering strategies for sustainable alternative protein production: From plant and microbial systems to cultivated meat. 可持续替代蛋白质生产的酶动力学和工程策略：从植物和微生物系统到养殖肉类。

3区生物学

Advances in protein chemistry and structural biology Pub Date : 2026-01-01 Epub Date: 2026-09-11 DOI: 10.1016/bs.apcsb.2026.08.008

Ramar Vanajothi, Chandrabose Yogeswari, Mani Jayaprakashvel, Deepali Desai, Munusamy Tharani, Elayaperumal Sumitha

{"title":"Enzyme kinetics and engineering strategies for sustainable alternative protein production: From plant and microbial systems to cultivated meat.","authors":"Ramar Vanajothi, Chandrabose Yogeswari, Mani Jayaprakashvel, Deepali Desai, Munusamy Tharani, Elayaperumal Sumitha","doi":"10.1016/bs.apcsb.2026.08.008","DOIUrl":"https://doi.org/10.1016/bs.apcsb.2026.08.008","url":null,"abstract":"The application of alternative proteins and their advanced techniques in various proteins including microbial, algal, plant-based and precision-fermented are highly used as alternative proteins. The cultivated meat approaches have intensified the need for optimized approaches in the process of enzymes. Enzyme kinetics and bioengineering play a significant role in the enhancement of protein functionality, flavor, texture, digestibility and overall process efficiency. The present book-chapters emphasize the basic principles enzyme kinetics, inhibition mechanisms, catalytic mechanisms and efficiency, also discussed the advanced kinetic models related to the heterogeneous protein substrates. Application of enzymes like transglutaminases, carbohydrase's and lipases are commonly used in alternative proteins production, with emphasis on microbial, algal, plant and cultivated systems. Engineering applications like rational design, immobilization approaches, directed evolution, computational biology are discussed as essential tools for the enhancement of enzymes, stability, specificity and industrial robustness. In addition, the integration of enzymatic kinetic modeling with bioreactor design process intensification to address the current challenges in the large scale-up and commercial applications. The present chapter highlights the advances in enzyme technology and bioprocessing, that are essential for developing sustainable, cost-effective and alternative protein products for the food industry.","PeriodicalId":7376,"journal":{"name":"Advances in protein chemistry and structural biology","volume":"154 ","pages":"357-382"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149007863","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Computational structure-based evaluation of antimicrobial peptides against OXA-51 β-lactamase in carbapenem-resistant Acinetobacter baumannii. 基于计算结构的抗碳青霉烯耐药鲍曼不动杆菌OXA-51 β-内酰胺酶抗菌肽评价。

3区生物学

Advances in protein chemistry and structural biology Pub Date : 2026-01-01 Epub Date: 2025-12-03 DOI: 10.1016/bs.apcsb.2025.09.003

Mohanraj Gopikrishnan, George Priya Doss C

{"title":"Computational structure-based evaluation of antimicrobial peptides against OXA-51 β-lactamase in carbapenem-resistant Acinetobacter baumannii.","authors":"Mohanraj Gopikrishnan, George Priya Doss C","doi":"10.1016/bs.apcsb.2025.09.003","DOIUrl":"10.1016/bs.apcsb.2025.09.003","url":null,"abstract":"Antimicrobial peptides (AMPs) constitute a promising class of next-generation therapeutics, exhibiting broad-spectrum efficacy and a diminished propensity for inducing resistance. Recent strides in computational biology have facilitated the rational design and high-throughput screening of AMPs tailored to target specific resistance mechanisms. In this study, we employed a structure-guided computational pipeline to identify and prioritize AMPs with inhibitory potential against OXA-51 β-lactamase, a pivotal enzyme contributing to carbapenem resistance in Acinetobacter baumannii. A comprehensive dataset comprising 300 AMPs, 250 of natural origin, and 50 synthetically engineered was curated through meta-analytical approaches. These peptides were systematically filtered based on key parameters, including physicochemical attributes, predicted toxicity, proteolytic stability, and aqueous solubility. Subsequent molecular docking analyses enabled the identification of eight high-affinity candidates, with AMP219 (NRC12), emerging as the top performer, exhibiting a binding energy of -214.98 kcal/mol. To further validate the binding stability and dynamic behavior of the AMP219 with the OXA-51 complex, a 300-nanosecond molecular dynamics simulation (MDS) was conducted. The results revealed sustained intermolecular interactions, persistent hydrogen bonding, and notable conformational rearrangements within the enzyme's active site, underscoring the peptide's inhibitory potential. Collectively, these findings emphasize the utility of integrative computational strategies in accelerating peptide-based drug discovery and provide a robust foundation for subsequent experimental validation against multidrug-resistant pathogens.","PeriodicalId":7376,"journal":{"name":"Advances in protein chemistry and structural biology","volume":"149 ","pages":"61-92"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146045881","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0