Advances in protein chemistry and structural biology最新文献

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Apolipoprotein E and Tau interaction in Alzheimer's disease. 载脂蛋白E和Tau在阿尔茨海默病中的相互作用。
3区 生物学
Advances in protein chemistry and structural biology Pub Date : 2025-01-01 Epub Date: 2024-12-07 DOI: 10.1016/bs.apcsb.2024.10.003
Subashchandrabose Chinnathambi, Anusree Adityan, Hariharakrishnan Chidambaram, Madhura Chandrashekar
{"title":"Apolipoprotein E and Tau interaction in Alzheimer's disease.","authors":"Subashchandrabose Chinnathambi, Anusree Adityan, Hariharakrishnan Chidambaram, Madhura Chandrashekar","doi":"10.1016/bs.apcsb.2024.10.003","DOIUrl":"https://doi.org/10.1016/bs.apcsb.2024.10.003","url":null,"abstract":"<p><p>Tau, an intrinsically disordered protein associated with microtubule stabilization, is crucial for cellular trafficking, and signaling pathways. Under pathological conditions, Tau undergoes post-translational modifications and structural changes, leading to its aggregation into neurofibrillary tangles (NFTs). The interactions between Tau and membrane lipids, including phospholipids like DOPC, DPPC, and proteins such as Apo E4, play a significant role in Tau aggregation. These interactions modulate Tau's structure, stabilization, and aggregation kinetics. Phospholipase C (PLC) and DEPC also influence Tau aggregation through signaling pathways and preservation of RNA integrity, respectively. Membrane lipid composition affects Tau-membrane interactions, which can promote Tau fibrillization and propagation, contributing to neurotoxicity in Alzheimer's disease (AD) and other Tauopathies. The disruption of lipid homeostasis by Apo E4, alterations in membrane fluidity and integrity by DPPC, and the influence of phospholipids on BBB functionality are significant in understanding Tau pathology.</p>","PeriodicalId":7376,"journal":{"name":"Advances in protein chemistry and structural biology","volume":"147 ","pages":"375-400"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145090766","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
The structure-based approaches to computing viral fitness. 基于结构的病毒适应度计算方法。
3区 生物学
Advances in protein chemistry and structural biology Pub Date : 2025-01-01 Epub Date: 2025-05-30 DOI: 10.1016/bs.apcsb.2024.11.004
Rukmankesh Mehra, Shivani Thakur
{"title":"The structure-based approaches to computing viral fitness.","authors":"Rukmankesh Mehra, Shivani Thakur","doi":"10.1016/bs.apcsb.2024.11.004","DOIUrl":"https://doi.org/10.1016/bs.apcsb.2024.11.004","url":null,"abstract":"<p><p>Viral fitness presents a complex challenge that requires a deep understanding of evolution and selection pressures. The swift emergence of mutations in viruses makes them ideal models for studying evolutionary dynamics. Recent advancements in biophysical methods and structural biology have facilitated insights into how these mutations influence evolutionary trajectories at the structural level. Computationally guided structural techniques are particularly valuable for analyzing the mutational landscape across all possible mutations in viral proteins under selection pressure. The virus often interacts via the receptor binding domain (RBD) of its surface protein with the receptor protein of the host cell. This binding is a key step for the viral entry in host cell and infection. In response, the host immune response or vaccines generate antibodies to neutralize the virus particles. This creates a competitive scenario where the viral surface protein competes for binding between host cell receptor and antibodies. The viral mutations supposedly evolve to effectively bind to host receptors while evading the antibody recognition. The differential binding affinity of the viral surface protein, preferably via RBD, between host receptor and antibodies may aid in defining the molecular level viral fitness function. The present chapter explores these dynamics through the lens of severe acute respiratory syndrome coronavirus 2 spike protein, binding to human angiotensin-converting enzyme 2 and circulating antibodies. Interestingly, this strategy utilized the wealth of protein structural data from cryo-electron microscopy and biochemical data on mutations.</p>","PeriodicalId":7376,"journal":{"name":"Advances in protein chemistry and structural biology","volume":"147 ","pages":"461-498"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145090845","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
Machine learning and molecular modeling based design of nanobodies targeting human serotonin transporter and receptor. 基于机器学习和分子模型的人类血清素转运体和受体纳米体设计。
3区 生物学
Advances in protein chemistry and structural biology Pub Date : 2025-01-01 Epub Date: 2024-12-22 DOI: 10.1016/bs.apcsb.2024.12.004
Binbin Xu, Jin Liu, Weiwei Xue
{"title":"Machine learning and molecular modeling based design of nanobodies targeting human serotonin transporter and receptor.","authors":"Binbin Xu, Jin Liu, Weiwei Xue","doi":"10.1016/bs.apcsb.2024.12.004","DOIUrl":"10.1016/bs.apcsb.2024.12.004","url":null,"abstract":"<p><p>Design of nanobodies have emerged as a new trend in antibody engineering, leveraging their unique properties including high stability, solubility, and the ability to bind to challenging targets such as membrane proteins. The application of computational strategies is pivotal for refining the efficacy of protein binders like nanobodies by broadening the sequence diversity, forecasting and bolstering their binding potency, selectivity, and overall performance. Recent advancements in computational techniques, such as machine learning algorithms and physics-based molecular modeling have significantly improved the design and development of nanobodies. These techniques allow for the precise modeling of nanobody-target interactions, enabling the identification of key residues responsible for binding and the prediction of potential conformational changes. In this study, five parental nanobodies binding to GPCRs and transporters were first used as template to create in silico nanobody libraries with the SCHEMA algorithm. Then, their binding potential and function to GPCRs or transporters were predicted by pre-trained machine learning models. The sequences above a threshold were processed with Rosetta and AlphaFold2 for 3D structural predictions. To further identify optimal conformations of specific nanobodies theoretically binding to 5-HT1AR or SERT, protein-protein docking by RosettaDock were performed. Finally, based on these model complexes, new nanobodies were redesigned, resulting in 21 and 18 candidates with enhanced binding to 5-HT1AR and SERT, respectively.</p>","PeriodicalId":7376,"journal":{"name":"Advances in protein chemistry and structural biology","volume":"147 ","pages":"535-558"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145090755","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
Nuclear transport protein suppresses Tau neurodegeneration. 核转运蛋白抑制Tau神经变性。
3区 生物学
Advances in protein chemistry and structural biology Pub Date : 2025-01-01 Epub Date: 2024-07-26 DOI: 10.1016/bs.apcsb.2024.07.001
Subashchandrabose Chinnathambi, Anusree Adithyan, Swathi Suresh, Gowshika Velmurugan, Madhura Chandrashekar, Surajita Sahu, Monalisa Mishra
{"title":"Nuclear transport protein suppresses Tau neurodegeneration.","authors":"Subashchandrabose Chinnathambi, Anusree Adithyan, Swathi Suresh, Gowshika Velmurugan, Madhura Chandrashekar, Surajita Sahu, Monalisa Mishra","doi":"10.1016/bs.apcsb.2024.07.001","DOIUrl":"10.1016/bs.apcsb.2024.07.001","url":null,"abstract":"<p><p>The nuclear pore complex, a large multimeric structure consists of numerous protein components, serves as a crucial gatekeeper for the transport of macromolecules across the nuclear envelope in eukaryotic cells. Dysfunction of the NPC has been implicated in various neurodegenerative diseases, including Alzheimer's disease. In AD, Tau aggregates interact with NPC proteins, known as nucleoporins, leading to disruptions in nuclear transport. Hyperphosphorylated Tau, a hallmark of AD pathology, interacts with central channel NUPs such as Nup62 and Nup98, causing cytoplasmic mis-localization of these proteins and impairing nuclear transport. Furthermore, Tau-NUP interactions promote Tau aggregation and the formation of neurofibrillary tangles, exacerbating neurodegeneration. Oligomeric Tau adheres to the lamin B receptor as well as nuclear lamin, preventing nucleocytoplasmic transport and resulting in heterochromatin unwinding, DNA damage, and neuronal death. The decrease in lamin B and increasing levels of lamin A along with C in AD-affected brain areas highlight the disease's intricacy. Furthermore, Tau internalization in the nucleus and interaction with nuclear pore complexes worsen NPC dysfunction, which contributes to neurotoxicity. Tau-DNA interactions suggest a chaperone-like role for Tau in DNA organization and repair, highlighting its involvement in maintaining genomic integrity. This review explores the intricate relationships between Tau, NPC components, and nuclear lamin in the context of AD, providing insights into the mechanisms underlying Tau-induced neurodegeneration and potential therapeutic targets.</p>","PeriodicalId":7376,"journal":{"name":"Advances in protein chemistry and structural biology","volume":"143 ","pages":"363-385"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143021801","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
Histone deacetylase's regulates Tau function in Alzheimer's disease. 组蛋白去乙酰化酶在阿尔茨海默病中调节Tau功能。
3区 生物学
Advances in protein chemistry and structural biology Pub Date : 2025-01-01 Epub Date: 2024-10-07 DOI: 10.1016/bs.apcsb.2024.09.008
Subashchandrabose Chinnathambi
{"title":"Histone deacetylase's regulates Tau function in Alzheimer's disease.","authors":"Subashchandrabose Chinnathambi","doi":"10.1016/bs.apcsb.2024.09.008","DOIUrl":"10.1016/bs.apcsb.2024.09.008","url":null,"abstract":"<p><p>Alzheimer's disease (AD) is a prevalent neurodegenerative disease associated with dementia and neuronal impairments in brain. AD is characterized histopathologically by two hallmark lesions: abnormally phosphorylated Tau inside neurons as intracellular NFTs and extracellular accumulation of amyloid β peptide (Aβ). Furthermore, it is unable to clarify the distinction between the brief association between the development and build-up of Aβ and the commencement of illness. Additionally, a number of experimental findings suggest that symptoms related to Aβ may only manifest within the framework of anabatic Tauopathies. Tau, a natively unfolded protein, essentially involved in microtubule binding and assembly. Tau protein consists of truncated segment and the purpose of this truncated fragment is to initiate and promote the conversion of soluble Tau into aggregates. The most common aberrant posttranslational change found in Neuro Fibrillary Tangles is hyperphosphorylation, which is essentially composed of aggregated Tau. Tau phosphorylation and acetylation of Tau protein at the locations controlled by histone deacetylase 6 compete, which modulates Tau function. Considering the potential benefits of targeting HDAC6 in AD, we propose focusing on the role of HDAC6 in regulating Tau functions and the other targets are the therapeutic understanding of AD.</p>","PeriodicalId":7376,"journal":{"name":"Advances in protein chemistry and structural biology","volume":"143 ","pages":"339-361"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143021782","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
Nuclear podosomes regulates cellular migration in Tau and Alzheimer's disease. 核足小体调节Tau和阿尔茨海默病的细胞迁移。
3区 生物学
Advances in protein chemistry and structural biology Pub Date : 2025-01-01 Epub Date: 2024-10-02 DOI: 10.1016/bs.apcsb.2024.09.009
Tazeen Qureshi, Madhura Chandrashekar, Vaishnavi Ananthanarayana, Murugappan Kumarappan, Nagaraj Rangappa, Gowshika Velmurugan, Subashchandrabose Chinnathambi
{"title":"Nuclear podosomes regulates cellular migration in Tau and Alzheimer's disease.","authors":"Tazeen Qureshi, Madhura Chandrashekar, Vaishnavi Ananthanarayana, Murugappan Kumarappan, Nagaraj Rangappa, Gowshika Velmurugan, Subashchandrabose Chinnathambi","doi":"10.1016/bs.apcsb.2024.09.009","DOIUrl":"10.1016/bs.apcsb.2024.09.009","url":null,"abstract":"<p><p>The neuronal cytoskeleton has remained a less explored area of research in establishing neuroprotection. HDAC6 has been studied with respect to many neurodegenerative diseases, especially AD. It exhibits the ability to interact with various cytoskeletal proteins and to promote migration in cells. Podosomes are actin microstructures that help cells to migrate in the extracellular environment. The aim of this review is to bring into focus the significance of studies on the involvement of podosomes in Alzheimer's disease. We have suggested that Histone Deacetylase 6 plays a vital role in AD, through its interactions with the various signalling processes in the cell, most importantly the cytoskeletal remodelling machinery within the podosomes.</p>","PeriodicalId":7376,"journal":{"name":"Advances in protein chemistry and structural biology","volume":"143 ","pages":"411-426"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143021796","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
Modifiable chemical risk factors for amyloid-β and Tau protein in Alzheimer's disease. 阿尔茨海默病中淀粉样蛋白-β和Tau蛋白可改变的化学危险因素。
3区 生物学
Advances in protein chemistry and structural biology Pub Date : 2025-01-01 Epub Date: 2024-11-14 DOI: 10.1016/bs.apcsb.2024.10.005
Subashchandrabose Chinnathambi, Sneha Malik, Murugappan Kumarappan, Madhura Chandrashekar
{"title":"Modifiable chemical risk factors for amyloid-β and Tau protein in Alzheimer's disease.","authors":"Subashchandrabose Chinnathambi, Sneha Malik, Murugappan Kumarappan, Madhura Chandrashekar","doi":"10.1016/bs.apcsb.2024.10.005","DOIUrl":"https://doi.org/10.1016/bs.apcsb.2024.10.005","url":null,"abstract":"<p><p>Alzheimer's disease (AD) is associated with numerous risk factors, many of them attributed to exposure to harmful chemical substances at levels higher than recommended. The exposure can happen through sources like food, water and the environment. A significant number of the risk factors are modifiable, that is; their effects can be altered by minor modifications kept under consideration. This article describes four such modifiable risk factors- exposure to metals, high levels of the amino acid homocysteine in the plasma, exposure to pesticides and chronic consumption of alcohol. Heavy metals can enter our bodies through various sources like water, food (through the soil), and through sources like cigarette smoke. They can alter normal brain functioning and increase the risk for neurodegenerative diseases, including AD. High levels of plasma homocysteine can also be a risk factor, with various proposed potential mechanisms. Pesticide use may have some alarming consequences. The effects of many pesticides on increasing the chances for AD are proven by many studies, which also show that occupational exposure to them is a great risk. Another risk factor discussed is the heavy consumption of alcohol, which plays a role in altering the neurotransmitter release, which may lead to it being a risk factor for AD. The type of alcohol consumed also had varied effects. Some strategies to mitigate the risk of the modifiable risk factors have been discussed.</p>","PeriodicalId":7376,"journal":{"name":"Advances in protein chemistry and structural biology","volume":"146 ","pages":"221-243"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144558790","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 blueprints: Guiding drug discovery through protein structure analysis. 分子蓝图:通过蛋白质结构分析指导药物发现。
3区 生物学
Advances in protein chemistry and structural biology Pub Date : 2025-01-01 Epub Date: 2025-05-08 DOI: 10.1016/bs.apcsb.2025.04.001
N Aiswarya, Sree Hima, Chandran Remya, D M Vasudevan, K V Dileep, Dileep Francis
{"title":"Molecular blueprints: Guiding drug discovery through protein structure analysis.","authors":"N Aiswarya, Sree Hima, Chandran Remya, D M Vasudevan, K V Dileep, Dileep Francis","doi":"10.1016/bs.apcsb.2025.04.001","DOIUrl":"https://doi.org/10.1016/bs.apcsb.2025.04.001","url":null,"abstract":"<p><p>The structural landscape of proteins serves as a molecular blueprint for drug discovery, offering critical insights into target interactions, binding mechanisms, and rational drug design. Advances in structural biology, including X-ray crystallography, cryo-electron microscopy, and computational modeling, have revolutionized the understanding of protein conformations and dynamics. By integrating structural insights with computational drug design, researchers can predict ligand-binding affinities, optimize drug candidates, and enhance target specificity in an effective manner. This approach has proven instrumental in developing novel therapeutics for diseases ranging from cancer to neurodegenerative disorders. Furthermore, techniques like structure-based drug discovery (SBDD), Ligand based drug design (LBDD), Pharmacophore based drug discovery and molecular dynamics enables the identification of allosteric sites, fostering the development of selective modulators with improved efficacy and reduced off-target effects. This review highlights the pivotal role of protein structure analysis in modern drug discovery, emphasizing its applications in hit identification, lead optimization, and the design of precision therapeutics. Understanding protein structure at atomic resolution remains the cornerstone of rational drug design, paving the way for more effective and personalized therapeutics.</p>","PeriodicalId":7376,"journal":{"name":"Advances in protein chemistry and structural biology","volume":"147 ","pages":"37-99"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145090758","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 analysis of natural compound inhibitors targeting KPC-2 and KPC-3 carbapenemases in Klebsiella pneumoniae: Virtual screening and molecular dynamics studies. 针对肺炎克雷伯菌KPC-2和KPC-3碳青霉烯酶的天然化合物抑制剂的计算分析:虚拟筛选和分子动力学研究。
3区 生物学
Advances in protein chemistry and structural biology Pub Date : 2025-01-01 Epub Date: 2025-05-15 DOI: 10.1016/bs.apcsb.2025.04.003
Mohanraj Gopikrishnan, Vishal Mohan Raj, Ashwin Balakumaran, Nandha Radhakrishnan, Affan Rais, George Priya Doss C
{"title":"Computational analysis of natural compound inhibitors targeting KPC-2 and KPC-3 carbapenemases in Klebsiella pneumoniae: Virtual screening and molecular dynamics studies.","authors":"Mohanraj Gopikrishnan, Vishal Mohan Raj, Ashwin Balakumaran, Nandha Radhakrishnan, Affan Rais, George Priya Doss C","doi":"10.1016/bs.apcsb.2025.04.003","DOIUrl":"https://doi.org/10.1016/bs.apcsb.2025.04.003","url":null,"abstract":"<p><p>Klebsiella pneumoniae, a Gram-negative bacterium, poses a significant public health threat due to its resistance to various antibiotics, including β-lactams and carbapenems. This resistance is mainly due to the production of Klebsiella pneumoniae carbapenemases (KPCs). The issue of KPC-2 and its variant, KPC-3, by K. pneumoniae strains, results in resistance to the substrate imipenem and β-lactamase inhibitors. Using Schrodinger software, we performed a high-throughput virtual screening of 374 compounds from the ChemDiv natural compound library in this study, targeting KPC-2 and KPC-3. The top compounds were identified using Extra Precision (XP) mode. Molecular dynamics simulations (MDS) were performed for 500 ns using GROMACS. Among the compounds, N075-0013 and N098-0051 for KPC-2 and N025-0014 and N099-0011 for KPC-3 exhibited binding energies ranging from -5.40 to -7.01 kcal/mol against both KPC-2 and KPC-3. The complexes formed with these compounds remained stable in their dynamic environments, suggesting their potential as effective inhibitors of KPC-2 and KPC-3. These results underscore the potential therapeutic promise of these compounds, justifying further in vitro and in vivo validation for their development as inhibitors of Klebsiella pneumoniae carbapenemases.</p>","PeriodicalId":7376,"journal":{"name":"Advances in protein chemistry and structural biology","volume":"147 ","pages":"177-205"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145090800","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
Revolutionizing structural biology: AI-driven protein structure prediction from AlphaFold to next-generation innovations. 结构生物学革命:人工智能驱动的蛋白质结构预测,从AlphaFold到下一代创新。
3区 生物学
Advances in protein chemistry and structural biology Pub Date : 2025-01-01 Epub Date: 2025-05-07 DOI: 10.1016/bs.apcsb.2025.04.002
Mowna Sundari Thangamalai, Deepali Desai, Chandrabose Selvaraj
{"title":"Revolutionizing structural biology: AI-driven protein structure prediction from AlphaFold to next-generation innovations.","authors":"Mowna Sundari Thangamalai, Deepali Desai, Chandrabose Selvaraj","doi":"10.1016/bs.apcsb.2025.04.002","DOIUrl":"https://doi.org/10.1016/bs.apcsb.2025.04.002","url":null,"abstract":"<p><p>Protein structure modeling from the prediction algorithm has become a valuable tool in biology and medicine with computational advances. Accurate protein structure prediction is critical in druglike compound discovery, disease mechanism understanding, and protein engineering because it provides molecular level insights into protein folding and its effects on molecular and cellular function. This chapter covers the evolution of protein structure prediction, from traditional methods like homology modeling, threading, and ab initio procedures and the new emerging AlphaFold's influence. AlphaFold's highly recognized precision level and open-access data democratized structural biology research, and that lead to inspiring new prediction models like RoseTTAFold and OmegaFold tools. Alpha Folds design, methodology, and highly accurate performance are thoroughly examined, and comparisons are performed with similar tools. We also highlight limitations, such as protein complex and dynamics forecasting, post-AlphaFold developments in structural databases, computer resources, and multi-scale modeling. Protein structure modeling and predictions have a wide range of applications in biomedical research, including drug discovery, functional annotation, and synthetic biology. Future directions include the integration of protein structure prediction with systems biology and genomics, as well as the use of next-generation AI and quantum computing to boost prediction accuracy. This research emphasizes AI's importance in structural biology and envisions a future in which predictive tools will provide comprehensive insights into protein function, dynamics, and therapeutic potential.</p>","PeriodicalId":7376,"journal":{"name":"Advances in protein chemistry and structural biology","volume":"147 ","pages":"1-19"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145090878","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
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