Advances in protein chemistry and structural biology最新文献

Engineering of antimicrobial peptides by surface display technologies. 表面显示技术在抗菌肽工程中的应用。

3区生物学

Advances in protein chemistry and structural biology Pub Date : 2026-01-01 Epub Date: 2025-05-12 DOI: 10.1016/bs.apcsb.2025.04.004

Sugra Yuceer, Husniye Tansel Yalcin, Sibel Kalyoncu

{"title":"Engineering of antimicrobial peptides by surface display technologies.","authors":"Sugra Yuceer, Husniye Tansel Yalcin, Sibel Kalyoncu","doi":"10.1016/bs.apcsb.2025.04.004","DOIUrl":"10.1016/bs.apcsb.2025.04.004","url":null,"abstract":"The emergence of antibiotic-resistant pathogens mostly due to intensive antibiotic use greatly endangers human health. For this reason, it has become necessary to search for new drugs or alternative treatments that are effective on resistant microorganisms. This review examines antimicrobial peptides (AMPs) which are part of the first primitive defense mechanism used by both eukaryotic and prokaryotic cells against many pathogens. AMPs are usually small (up to 50 amino acids), cationic peptides which make them bind to negatively charged cell membranes of pathogens for permeabilization and destruction. AMPs can act on antibiotic-resistant pathogens such as Enterococcus faecium, methicillin-resistant Staphylococcus aureus (MRSA), and Pseudomonas aeruginosa, and they offer unique advantages due to their membrane-active antimicrobial mechanisms that reduce the likelihood of developing resistance. AMPs have high therapeutic potential due to their broad-spectrum activities, and different mechanisms of action compared to traditional antibiotics. However, their practical application is often hampered by their limited activity, host toxicity and poor stability. To overcome these limitations, natural AMP sequences can be improved by protein engineering approaches. Surface display technology is one of the leading high-throughput protein engineering strategies where primary/secondary structures of AMPs can be modified and screened for various improvements. This review focuses on the key properties of antimicrobial peptides, as well as insights on the use of in vitro surface display techniques to develop next-generation AMPs for therapeutic uses.","PeriodicalId":7376,"journal":{"name":"Advances in protein chemistry and structural biology","volume":"149 ","pages":"115-141"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146045984","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

Molecular characterization and experimental models of chordoma: Foundations for rational therapy development. 脊索瘤的分子表征和实验模型：合理治疗发展的基础。

3区生物学

Advances in protein chemistry and structural biology Pub Date : 2026-01-01 Epub Date: 2026-06-26 DOI: 10.1016/bs.apcsb.2026.04.003

Christian Godinez, Matthew Holman, Emilija Sagaityte, Temitope Aina, Leah Shin, Kaylee Gallagher, Benjamín Córdova Herrera, Ziya L Gokaslan, Patricia L Zadnik Sullivan, Margot Martinez-Moreno

引用次数: 0

Computational exploration of high-throughput virtual screening and molecular dynamics analysis targeting BfmR in Acinetobacter baumannii: Towards anti-virulent therapeutics. 鲍曼不动杆菌靶向BfmR的高通量虚拟筛选和分子动力学分析的计算探索：面向抗病毒治疗。

3区生物学

Advances in protein chemistry and structural biology Pub Date : 2026-01-01 Epub Date: 2026-07-10 DOI: 10.1016/bs.apcsb.2026.06.013

Mohanraj Gopikrishnan, D Thirumal Kumar, George Priya Doss C

{"title":"Computational exploration of high-throughput virtual screening and molecular dynamics analysis targeting BfmR in Acinetobacter baumannii: Towards anti-virulent therapeutics.","authors":"Mohanraj Gopikrishnan, D Thirumal Kumar, George Priya Doss C","doi":"10.1016/bs.apcsb.2026.06.013","DOIUrl":"https://doi.org/10.1016/bs.apcsb.2026.06.013","url":null,"abstract":"The opportunistic pathogen Acinetobacter baumannii, a major cause of nosocomial infections, has exhibited a rapid increase in resistance to conventional antimicrobial therapies, emphasizing the urgent need for alternative strategies such as anti-virulence approaches. The response regulator BfmR is a critical mediator of biofilm formation and virulence, making it an attractive yet underexplored therapeutic target. In this study, we established a comprehensive in silico pipeline to identify potential BfmR inhibitors through large-scale virtual screening and advanced computational analyses. The crystal structure of BfmR (PDB ID: 5HM6) was prepared using Schrödinger's Protein Preparation Wizard with the OPLS3 force field. A compound library comprising 66,734 molecules from CMNPD, Enamine, ChemDiv, and Asinex databases was processed using LigPrep and Epik to generate appropriate protonation states and stereoisomers at physiological pH. Virtual screening was performed using GLIDE in a hierarchical workflow including HTVS, SP, and XP docking. Pharmacokinetic and toxicity profiles were assessed using QikProp to ensure drug-likeness. Top-scoring compounds were further evaluated using triplicate 500 ns molecular dynamics simulations in GROMACS 2023 with the CHARMM36 force field, employing TIP3P water models and system neutralization. Post-simulation analyses included RMSD, PCA, free energy landscape mapping, dynamic cross-correlation matrices, covariance analysis, and MM-PBSA binding energy calculations. Six lead compounds demonstrated stable binding, favorable energetics, and consistent interactions with key regulatory residues THR23, ARG29, and VAL109, highlighting their potential as promising anti-virulence agents against A. baumannii.","PeriodicalId":7376,"journal":{"name":"Advances in protein chemistry and structural biology","volume":"153 ","pages":"455-484"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148443847","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

Induced-pluripotent stem cell-derived immunotherapy for Tau and Alzheimer's disease. 诱导多能干细胞衍生免疫疗法治疗Tau蛋白和阿尔茨海默病。

3区生物学

Advances in protein chemistry and structural biology Pub Date : 2026-01-01 Epub Date: 2025-11-04 DOI: 10.1016/bs.apcsb.2025.10.005

Subashchandrabose Chinnathambi

引用次数: 0

Aptamers as immunomodulatory therapeutic alternatives targeting neglected tropical diseases (NTDs). 适体作为被忽视的热带病（NTDs）的免疫调节治疗选择。

3区生物学

Advances in protein chemistry and structural biology Pub Date : 2026-01-01 Epub Date: 2026-03-18 DOI: 10.1016/bs.apcsb.2026.02.010

Leandro Rocha Silva, Wadja Feitosa Dos Santos Silva, Ana Clara Ferreira de Melo, Érica Erlanny da Silva Rodrigues, Edeildo Ferreira da Silva-Júnior

{"title":"Aptamers as immunomodulatory therapeutic alternatives targeting neglected tropical diseases (NTDs).","authors":"Leandro Rocha Silva, Wadja Feitosa Dos Santos Silva, Ana Clara Ferreira de Melo, Érica Erlanny da Silva Rodrigues, Edeildo Ferreira da Silva-Júnior","doi":"10.1016/bs.apcsb.2026.02.010","DOIUrl":"10.1016/bs.apcsb.2026.02.010","url":null,"abstract":"Neglected tropical diseases (NTDs) comprise a heterogeneous group of infections that disproportionately affect populations in low- and middle-income countries, where limited access to diagnostics, therapeutics, and surveillance perpetuates disease burden. Conventional strategies based on antibodies and small-molecule drugs face major challenges, including high production costs, limited stability, cross-reactivity, toxicity, and the emergence of drug resistance. In this context, aptamers, short single-stranded nucleic acids selected by SELEX, have emerged as versatile immunomodulatory tools with significant potential for the diagnosis and treatment of NTDs. This chapter provides a comprehensive overview of aptamer-based strategies targeting major NTDs, with particular emphasis on human African trypanosomiasis and arboviral infections such as dengue, Zika, and chikungunya. Aptamers directed against conserved parasite and viral epitopes demonstrate the capacity to circumvent immune evasion mechanisms, including antigenic variation and serotype diversity, while enabling highly specific recognition and internalization. In African trypanosomes, RNA aptamers targeting variant surface glycoproteins exploit the flagellar pocket for targeted drug delivery, offering a novel approach to overcome therapeutic resistance. In arboviral diseases, aptamers have been successfully integrated into advanced diagnostic platforms, including competitive ELISA, electrochemical, and capacitive biosensors, achieving high sensitivity, rapid response times, and minimal cross-reactivity among closely related flaviviruses. Beyond diagnostics, selected aptamers exhibit neutralizing activity and immunomodulatory effects by interfering with host-pathogen interactions and innate immune signaling pathways.","PeriodicalId":7376,"journal":{"name":"Advances in protein chemistry and structural biology","volume":"152 ","pages":"191-244"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148004384","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

Mechanism of tau proteins differentially regulating the motility of different families of kinesin motors. tau蛋白差异调节不同家族运动的机制。

3区生物学

Advances in protein chemistry and structural biology Pub Date : 2026-01-01 Epub Date: 2025-11-25 DOI: 10.1016/bs.apcsb.2025.10.024

Ping Xie

{"title":"Mechanism of tau proteins differentially regulating the motility of different families of kinesin motors.","authors":"Ping Xie","doi":"10.1016/bs.apcsb.2025.10.024","DOIUrl":"10.1016/bs.apcsb.2025.10.024","url":null,"abstract":"It was shown experimentally that the motility of different families of kinesin motors can be differentially regulated by microtubule-associated tau proteins. However, the underlying mechanism is unclear. To address the mechanism, here we take three kinesin motors-kinesin-1, kinesin-3 and kinesin-8-as examples to study theoretically the motility of the kinesin motor within the tau island and at the island boundary. The theoretical results show that after landing within the tau island, a kinesin-8 motor can move processively for a long time of about 80 s and for a long run length of about 1.6 µm, a kinesin-1 motor can dissociate in a short time of about 0.35 s, while a kinesin-3 motor can dissociate in a much shorter time of about 0.01 s. The kinesin-8 motors can induce the receding of the tau island with a velocity similar to a kinesin-8 stepping within the island, kinesin-1 motors can hardly induce the island receding, while kinesin-3 motors have a much lower probability to induce the island receding than kinesin-1 motors. The theoretical results explain well the available experimental data. The studies indicate that the tau island differentially regulating the motility of different kinesin motors is due mainly to different residence times of the motors with a stationary small obstacle on the front tubulin.","PeriodicalId":7376,"journal":{"name":"Advances in protein chemistry and structural biology","volume":"150 ","pages":"377-396"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147571831","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 methods for alternative proteins. 替代蛋白的计算方法。

3区生物学

Advances in protein chemistry and structural biology Pub Date : 2026-01-01 Epub Date: 2026-08-25 DOI: 10.1016/bs.apcsb.2026.08.013

S Vyshnav, Vino Sundararajan, Sajitha Lulu Sudhakaran

{"title":"Computational methods for alternative proteins.","authors":"S Vyshnav, Vino Sundararajan, Sajitha Lulu Sudhakaran","doi":"10.1016/bs.apcsb.2026.08.013","DOIUrl":"https://doi.org/10.1016/bs.apcsb.2026.08.013","url":null,"abstract":"The growing demand for sustainable food systems has accelerated research into alternative proteins derived from plant sources, microorganisms, insects, and cultured animal cells. These protein systems offer promising solutions to environmental, ethical, and nutritional challenges associated with conventional livestock production. However, designing and optimizing alternative proteins requires deep understanding of molecular structures, biochemical properties, and production processes. Computational biology has emerged as a powerful approach to address these challenges by enabling predictive modeling, data-driven protein engineering, and large-scale bioinformatic analyses. This chapter provides a comprehensive overview of computational methods applied in alternative protein research and development. Key approaches discussed include sequence-based bioinformatics, structural modeling, molecular simulations, protein design algorithms, machine learning techniques, metabolic modeling, and process simulation. The chapter further explores how these computational frameworks support discovery of novel protein sources, optimization of functional properties, and scaling of industrial production processes. Challenges and future research directions are also discussed, particularly the integration of artificial intelligence, multi-omics data, and digital twin technologies for food manufacturing. Computational technologies are expected to play a pivotal role in shaping next-generation protein foods by accelerating innovation, reducing development costs, and enabling sustainable protein production systems.","PeriodicalId":7376,"journal":{"name":"Advances in protein chemistry and structural biology","volume":"154 ","pages":"383-439"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149007779","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

Algae and microbial proteins for alternative proteins: Untapped molecular resources. 藻类和微生物蛋白的替代蛋白：未开发的分子资源。

3区生物学

Advances in protein chemistry and structural biology Pub Date : 2026-01-01 Epub Date: 2026-08-26 DOI: 10.1016/bs.apcsb.2026.08.003

Maria P Spínola, Cátia F Martins, José A M Prates

{"title":"Algae and microbial proteins for alternative proteins: Untapped molecular resources.","authors":"Maria P Spínola, Cátia F Martins, José A M Prates","doi":"10.1016/bs.apcsb.2026.08.003","DOIUrl":"https://doi.org/10.1016/bs.apcsb.2026.08.003","url":null,"abstract":"Algal and microbial proteins constitute a vast, still underexploited pool of sustainable biomolecules with growing relevance to the future of alternative proteins. This chapter critically reviews the taxonomic, biochemical, and structural diversity of microalgae, cyanobacteria, yeasts, filamentous fungi, and bacterial platforms currently used for single-cell protein (SCP) production. Particular emphasis is placed on recent advances in extraction and downstream processing, including mechanical, enzymatic, chemical, and membrane-based strategies, to improve protein recovery while preserving structural integrity and minimising environmental impact. Molecular characterisation strategies are discussed to clarify how amino acid composition, structural organisation, and post-translational modifications shape key techno-functional properties, including solubility, emulsification, foaming, gelation, and film-forming capacity. The nutritional quality and bioactive potential of algal and microbial proteins are illustrated by selected examples, including Spirulina, Chlorella, fungal mycoprotein, and bacterial biomass, highlighting essential amino acid balance, digestibility, and the generation of bioactive peptides with antioxidant and immunomodulatory activities. In addition, regulatory frameworks, safety and allergenicity issues, sensory optimisation, and life-cycle assessment are examined to situate these protein sources within a broader context of sustainability and consumer acceptance. Finally, emerging advances in synthetic biology, adaptive laboratory evolution, metabolic engineering, and multi-omics-guided strain optimisation are discussed as enabling tools to improve functionality, scalability, and economic viability. By integrating molecular insights with process engineering and circular bioeconomy principles, this chapter positions algal and microbial proteins as credible and versatile building blocks for next-generation sustainable food systems.","PeriodicalId":7376,"journal":{"name":"Advances in protein chemistry and structural biology","volume":"154 ","pages":"257-306"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149007792","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

Blue proteins: Marine-derived alternatives for sustainable nutrition and climate-resilient food systems. 蓝色蛋白质：可持续营养和气候适应型粮食系统的海洋来源替代品。

3区生物学

Advances in protein chemistry and structural biology Pub Date : 2026-01-01 Epub Date: 2026-08-24 DOI: 10.1016/bs.apcsb.2026.08.002

Antony Likson, Kothaimanimaran Brindha, Deepali Desai, Solaiyappan Ramanathan, Sampath Bhuvaneshwari, Chandrabose Selvaraj

{"title":"Blue proteins: Marine-derived alternatives for sustainable nutrition and climate-resilient food systems.","authors":"Antony Likson, Kothaimanimaran Brindha, Deepali Desai, Solaiyappan Ramanathan, Sampath Bhuvaneshwari, Chandrabose Selvaraj","doi":"10.1016/bs.apcsb.2026.08.002","DOIUrl":"https://doi.org/10.1016/bs.apcsb.2026.08.002","url":null,"abstract":"The accelerating global demand for high-quality protein, coupled with escalating ecological pressures from terrestrial livestock systems, has intensified the search for sustainable alternative protein sources. Marine resources denote a promising frontier in addressing global protein security while reducing ecological footprints. This review explains the potential of alternative proteins derived from marine ecosystems, macroalgae (seaweed), fish protein hydrolysates, including microalgae, marine invertebrates, and low-trophic organisms. These resources offer great nutritional value, including balanced essential amino acid profiles, omega-3 fatty acids, vitamins, bioactive peptides and minerals, while generally requiring fewer land and freshwater inputs compared to conventional livestock production. Advances in green extraction technologies, biorefinery approaches, fermentation, and controlled enzymatic hydrolysis have enriched the functional and techno-economic viability of marine-derived proteins for food and nutraceutical applications. Furthermore, innovations such as sustainable harvesting frameworks, integrated multi-trophic aquaculture, and circular bioeconomy strategies strengthen environmental resilience and biodiversity conservation. Despite their promise, challenges remain regarding scalability, regulatory frameworks, allergenicity risks, and consumer acceptance and contamination concerns. Strategic research, policy support, and responsible commercialization pathways are important to unlock the full potential of marine alternative proteins. Overall, marine-based protein systems offer emerging solutions for climate mitigation, sustainable nutrition and resilient food systems in the context of a growing global population.","PeriodicalId":7376,"journal":{"name":"Advances in protein chemistry and structural biology","volume":"154 ","pages":"93-117"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149007794","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

Antibodies targeting amyloid-β and Tau oligomers in Alzheimer's disease. 针对阿尔茨海默病中淀粉样蛋白-β和Tau寡聚物的抗体。

3区生物学

Advances in protein chemistry and structural biology Pub Date : 2026-01-01 Epub Date: 2025-11-05 DOI: 10.1016/bs.apcsb.2025.10.002

Subashchandrabose Chinnathambi, Nagaraj Rangappa, Madhura Chandrashekar

{"title":"Antibodies targeting amyloid-β and Tau oligomers in Alzheimer's disease.","authors":"Subashchandrabose Chinnathambi, Nagaraj Rangappa, Madhura Chandrashekar","doi":"10.1016/bs.apcsb.2025.10.002","DOIUrl":"10.1016/bs.apcsb.2025.10.002","url":null,"abstract":"Alzheimer's disease is a leading neurodegenerative disorder, is characterized by cognitive decline linked to amyloid-beta plaques and Tau tangles. These pathological aggregates disrupt the neuronal communication, induce neuroinflammation, and contribute to synaptic dysfunction. Genetic mutations, aging, environmental and lifestyle factors exacerbate these mechanisms, promoting neurotoxicity. Advances in immunotherapy have targeted Aβ and Tau oligomers using several monoclonal antibodies and Tau-specific antibodies. These therapies aim to neutralize toxic aggregates, facilitate clearance, and slow cognitive decline. Dual-targeting approaches, such as bispecific antibodies, address both Aβ and Tau, enhancing therapeutic efficacy. Despite challenges-like limited blood-brain barrier penetration, off-target effects, and high production costs, innovations in nanobody technology and personalized medicine are the key players. Artificial intelligence-driven antibody design further accelerates development, offering hope for transformative Alzheimer's disease treatments. Future research focuses on optimizing safety and efficacy, paving the way for comprehensive management of this devastating disease.","PeriodicalId":7376,"journal":{"name":"Advances in protein chemistry and structural biology","volume":"151 ","pages":"225-265"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147939932","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