Advances in protein chemistry and structural biology最新文献_第7页

Nanoinformatics based insights into the interaction of blood plasma proteins with carbon based nanomaterials: Implications for biomedical applications. 基于纳米信息学洞察血浆蛋白与碳基纳米材料的相互作用：对生物医学应用的影响。

3区生物学

Advances in protein chemistry and structural biology Pub Date : 2024-01-01 Epub Date: 2024-02-19 DOI: 10.1016/bs.apcsb.2023.11.015

Abhishek Ramachandra Panigrahi, Abhinandana Sahu, Pooja Yadav, Samir Kumar Beura, Jyoti Singh, Krishnakanta Mondal, Sunil Kumar Singh

{"title":"Nanoinformatics based insights into the interaction of blood plasma proteins with carbon based nanomaterials: Implications for biomedical applications.","authors":"Abhishek Ramachandra Panigrahi, Abhinandana Sahu, Pooja Yadav, Samir Kumar Beura, Jyoti Singh, Krishnakanta Mondal, Sunil Kumar Singh","doi":"10.1016/bs.apcsb.2023.11.015","DOIUrl":"10.1016/bs.apcsb.2023.11.015","url":null,"abstract":"In the past three decades, interest in using carbon-based nanomaterials (CBNs) in biomedical application has witnessed remarkable growth. Despite the rapid advancement, the translation of laboratory experimentation to clinical applications of nanomaterials is one of the major challenges. This might be attributed to poor understanding of bio-nano interface. Arguably, the most significant barrier is the complexity that arises by interplay of several factors like properties of nanomaterial (shape, size, surface chemistry), its interaction with suspending media (surface hydration and dehydration, surface reconstruction and release of free surface energy) and the interaction with biomolecules (conformational change in biomolecules, interaction with membrane and receptor). Tailoring a nanomaterial that minimally interacts with protein and lipids in the medium while effectively acts on target site in biological milieu has been very difficult. Computational methods and artificial intelligence techniques have displayed potential in effectively addressing this problem. Through predictive modelling and deep learning, computer-based methods have demonstrated the capability to create accurate models of interactions between nanoparticles and cell membranes, as well as the uptake of nanomaterials by cells. Computer-based simulations techniques enable these computational models to forecast how making particular alterations to a material's physical and chemical properties could enhance functional aspects, such as the retention of drugs, the process of cellular uptake and biocompatibility. We review the most recent progress regarding the bio-nano interface studies between the plasma proteins and CBNs with a special focus on computational simulations based on molecular dynamics and density functional theory.","PeriodicalId":7376,"journal":{"name":"Advances in protein chemistry and structural biology","volume":"139 ","pages":"263-288"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140048547","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

A computational pipeline elucidating functions of conserved hypothetical Trypanosoma cruzi proteins based on public proteomic data. 基于公共蛋白质组数据阐明克氏锥虫保守假定蛋白功能的计算管道。

3区生物学

Advances in protein chemistry and structural biology Pub Date : 2024-01-01 Epub Date: 2024-01-04 DOI: 10.1016/bs.apcsb.2023.07.002

Janaina Macedo-da-Silva, Simon Ngao Mule, Livia Rosa-Fernandes, Giuseppe Palmisano

{"title":"A computational pipeline elucidating functions of conserved hypothetical Trypanosoma cruzi proteins based on public proteomic data.","authors":"Janaina Macedo-da-Silva, Simon Ngao Mule, Livia Rosa-Fernandes, Giuseppe Palmisano","doi":"10.1016/bs.apcsb.2023.07.002","DOIUrl":"10.1016/bs.apcsb.2023.07.002","url":null,"abstract":"The proteome is complex, dynamic, and functionally diverse. Functional proteomics aims to characterize the functions of proteins in biological systems. However, there is a delay in annotating the function of proteins, even in model organisms. This gap is even greater in other organisms, including Trypanosoma cruzi, the causative agent of the parasitic, systemic, and sometimes fatal disease called Chagas disease. About 99.8% of Trypanosoma cruzi proteome is not manually annotated (unreviewed), among which>25% are conserved hypothetical proteins (CHPs), calling attention to the knowledge gap on the protein content of this organism. CHPs are conserved proteins among different species of various evolutionary lineages; however, they lack functional validation. This study describes a bioinformatics pipeline applied to public proteomic data to infer possible biological functions of conserved hypothetical Trypanosoma cruzi proteins. Here, the adopted strategy consisted of collecting differentially expressed proteins between the epimastigote and metacyclic trypomastigotes stages of Trypanosoma cruzi; followed by the functional characterization of these CHPs applying a manifold learning technique for dimension reduction and 3D structure homology analysis (Spalog). We found a panel of 25 and 26 upregulated proteins in the epimastigote and metacyclic trypomastigote stages, respectively; among these, 18 CHPs (8 in the epimastigote stage and 10 in the metacyclic stage) were characterized. The data generated corroborate the literature and complement the functional analyses of differentially regulated proteins at each stage, as they attribute potential functions to CHPs, which are frequently identified in Trypanosoma cruzi proteomics studies. However, it is important to point out that experimental validation is required to deepen our understanding of the CHPs.","PeriodicalId":7376,"journal":{"name":"Advances in protein chemistry and structural biology","volume":"138 ","pages":"401-428"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139465928","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

Coordination, cooperation, competition, crowding and congestion of molecular motors: Theoretical models and computer simulations. 分子马达的协调、合作、竞争、拥挤和堵塞：理论模型和计算机模拟。

3区生物学

Advances in protein chemistry and structural biology Pub Date : 2024-01-01 Epub Date: 2024-01-20 DOI: 10.1016/bs.apcsb.2023.12.005

Aritra Sen, Debashish Chowdhury, Ambarish Kunwar

引用次数: 0

A crosstalk between 'osteocyte lacunal-canalicular system' and metabolism. 骨细胞腔-颅骨系统 "与新陈代谢之间的相互联系

3区生物学

Advances in protein chemistry and structural biology Pub Date : 2024-01-01 Epub Date: 2023-12-26 DOI: 10.1016/bs.apcsb.2023.12.019

Ebtesam A Al-Suhaimi, Sultan Akhtar, Fatima A Al Hubail, Hussain Alhawaj, Meneerah A Aljafary, Hamad S Alrumaih, Amira Daghestani, Alanwood Al-Buainain, Amer Lardhi, A M Homeida

{"title":"A crosstalk between 'osteocyte lacunal-canalicular system' and metabolism.","authors":"Ebtesam A Al-Suhaimi, Sultan Akhtar, Fatima A Al Hubail, Hussain Alhawaj, Meneerah A Aljafary, Hamad S Alrumaih, Amira Daghestani, Alanwood Al-Buainain, Amer Lardhi, A M Homeida","doi":"10.1016/bs.apcsb.2023.12.019","DOIUrl":"10.1016/bs.apcsb.2023.12.019","url":null,"abstract":"Considering the importance, bone physiology has long been studied to understand what systematic and cellular impact its cells and functions have. Exploring more questions is a substantially solid way to improve the understanding of bone physiological functions in/out sides. In adult bone, osteocytes (Ots) form about 95% of bone cells and live the longest lifespan inside their mineralized surroundings. Ots are the endocrine cells and originate from blood vessel's endothelial cells. In this work, we discussed the vital role of the \"Ots\". To determine the association between osteocytes' network with metabolic parameters in healthy mice, the experiments were performed on ten (10) adult C57BL6 male mice. Fasting blood and bone samples were collected weekly from mice for measurement of metabolic parameters and bone morphology. Scanning electron microscopy (SEM) revealed a 2D fine morphology of the bone which indicates a strong functional interconnection with bone nano/micro, and macro components of the organs. The long-branched canaliculi look like neurocytes in structure. The morphology and quantitative measurements of the osteocyte lacunal-canalicular system showed its wide spectrum spatial resolution of the positive and negative relationship within this system or metabolite parameters, confirming a strong cross connection between osteocyte lacunal-canalicular system and metabolism. We believe that the findings of this study can deliver a strategy about the potential roles of metabolic relation among osteocytes, insulin, and lipid in management of bone and metabolic diseases.","PeriodicalId":7376,"journal":{"name":"Advances in protein chemistry and structural biology","volume":"142 ","pages":"397-420"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141764726","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

Engineering high affinity antigen-binders: Beyond conventional antibodies. 设计高亲和力抗原结合体：超越传统抗体

3区生物学

Advances in protein chemistry and structural biology Pub Date : 2024-01-01 Epub Date: 2024-03-07 DOI: 10.1016/bs.apcsb.2023.12.014

Rajeev Kumar Pandey, Sanjana Mehrotra

{"title":"Engineering high affinity antigen-binders: Beyond conventional antibodies.","authors":"Rajeev Kumar Pandey, Sanjana Mehrotra","doi":"10.1016/bs.apcsb.2023.12.014","DOIUrl":"https://doi.org/10.1016/bs.apcsb.2023.12.014","url":null,"abstract":"For decades, antibodies have remained the archetypal binding proteins that can be rapidly produced with high affinity and specificity against virtually any target. A conventional antibody is still considered the prototype of a binding molecule. It is therefore not surprising that antibodies are routinely used in basic scientific and biomedical research, analytical workflows, molecular diagnostics etc. and represent the fastest growing sector in the field of biotechnology. However, several limitations associated with conventional antibodies, including stringent requirement of animal immunizations, mammalian cells for expression, issues on stability and aggregation, bulkier size and the overall time and cost of production has propelled evolution of concepts along alternative antigen binders. Rapidly evolving protein engineering approaches and high throughput screening platforms have further complemented the development of myriads of classes of non-conventional protein binders including antibody derived as well as non-antibody based molecular scaffolds. These non-canonical binders are finding use across disciplines of which diagnostics and therapeutics are the most noteworthy.","PeriodicalId":7376,"journal":{"name":"Advances in protein chemistry and structural biology","volume":"140 ","pages":"37-57"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140955600","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

MHC tetramer technology: Exploring T cell biology in health and disease. MHC 四聚体技术：探索健康和疾病中的 T 细胞生物学。

3区生物学

Advances in protein chemistry and structural biology Pub Date : 2024-01-01 Epub Date: 2024-03-19 DOI: 10.1016/bs.apcsb.2024.02.002

Rahul Tiwari, Vishal Kumar Singh, Rajneesh, Awnish Kumar, Vibhav Gautam, Rajiv Kumar

引用次数: 0

Functional proteomics based on protein microarray technology for biomedical research. 基于蛋白质微阵列技术的功能蛋白质组学用于生物医学研究。

3区生物学

Advances in protein chemistry and structural biology Pub Date : 2024-01-01 Epub Date: 2023-05-15 DOI: 10.1016/bs.apcsb.2023.04.002

Pablo Juanes-Velasco, Carlota Arias-Hidalgo, Alicia Landeira-Viñuela, Ana Nuño-Soriano, Marina Fuentes-Vacas, Rafa Góngora, Ángela-Patricia Hernández, Manuel Fuentes

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In silico network pharmacology analysis and molecular docking validation of Swasa Kudori tablet for screening druggable phytoconstituents of asthma. 对 Swasa Kudori 片剂进行硅网络药理学分析和分子对接验证，以筛选可用于治疗哮喘的植物成分。

3区生物学

Advances in protein chemistry and structural biology Pub Date : 2024-01-01 Epub Date: 2023-08-10 DOI: 10.1016/bs.apcsb.2023.07.001

Karthik Sekaran, Rinku Polachirakkal Varghese, Ashwini Karthik, K Sasikumar, M S Shree Devi, P Sathiyarajeswaran, C George Priya Doss

{"title":"In silico network pharmacology analysis and molecular docking validation of Swasa Kudori tablet for screening druggable phytoconstituents of asthma.","authors":"Karthik Sekaran, Rinku Polachirakkal Varghese, Ashwini Karthik, K Sasikumar, M S Shree Devi, P Sathiyarajeswaran, C George Priya Doss","doi":"10.1016/bs.apcsb.2023.07.001","DOIUrl":"10.1016/bs.apcsb.2023.07.001","url":null,"abstract":"Traditional medicines are impactful in treating a cluster of respiratory-related illnesses. This paper demonstrates screening active, druggable phytoconstituents from a classical Siddha-based poly-herbal formulation called Swasa Kudori Tablet to treat asthma. The phytoconstituents of Swasa Kudori are identified as Calotropis gigantea, Piper nigrum, and (Co-drug) Abies webbiana. Active chemical compounds are extracted with the Chemical Entities of Biological Interest (ChEBI) database. The gene targets of each compound are identified based on the pharmacological activity using the DIGEP-Pred database. Thirty-two genes showing Pa> 0.7 is screened, and the target markers are selected after performing gene overlap evaluation with the asthma genes reported in GeneCards and DisGeNET database. Ten markers are identified, such as ADIPOQ, CASP8, CAT, CCL2, CD86, FKBP5, HMOX1, NFE2L2, TIMP1, VDR, in common, listed as molecular targets. Pharmacokinetic assessment (ADME) revealed five natural drug compounds 2-5-7-trihydroxy-2-(4-hydroxyphenyl)-2,3-dihydro-4H-chromen-4-one, (+)-catechin-3'-methyl ether, futoenone, 5-hydroxy-4',7-dimethoxyflavanone, and pinocembrin showing better druggability. Further screening delineates the target (HMOX1) and drug (pinocembrin) for molecular docking evaluation. When docked with HO-1, Pinocembrin showed a binding affinity of -8.0 kcal/mol. MD simulation studies substantiate the docking studies as HO-1 in complex with pinocembrin remains stable in the simulated trajectory. The current findings exhibit the significance of traditional medicines as potential drug candidates against asthma.","PeriodicalId":7376,"journal":{"name":"Advances in protein chemistry and structural biology","volume":"138 ","pages":"257-274"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139465962","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 approaches for identifying disease-causing mutations in proteins. 识别蛋白质致病突变的计算方法。

3区生物学

Advances in protein chemistry and structural biology Pub Date : 2024-01-01 Epub Date: 2023-12-20 DOI: 10.1016/bs.apcsb.2023.11.007

Medha Pandey, Suraj Kumar Shah, M Michael Gromiha

引用次数: 0

Uncovering the secrets of resistance: An introduction to computational methods in infectious disease research. 揭开抗药性的秘密：传染病研究中的计算方法简介。

3区生物学

Advances in protein chemistry and structural biology Pub Date : 2024-01-01 Epub Date: 2024-02-15 DOI: 10.1016/bs.apcsb.2023.11.004

Aditya K Padhi, Shweata Maurya

{"title":"Uncovering the secrets of resistance: An introduction to computational methods in infectious disease research.","authors":"Aditya K Padhi, Shweata Maurya","doi":"10.1016/bs.apcsb.2023.11.004","DOIUrl":"10.1016/bs.apcsb.2023.11.004","url":null,"abstract":"Antimicrobial resistance (AMR) is a growing global concern with significant implications for infectious disease control and therapeutics development. This chapter presents a comprehensive overview of computational methods in the study of AMR. We explore the prevalence and statistics of AMR, underscoring its alarming impact on public health. The role of AMR in infectious disease outbreaks and its impact on therapeutics development are discussed, emphasizing the need for novel strategies. Resistance mutations are pivotal in AMR, enabling pathogens to evade antimicrobial treatments. We delve into their importance and contribution to the spread of AMR. Experimental methods for quantitatively evaluating resistance mutations are described, along with their limitations. To address these challenges, computational methods provide promising solutions. We highlight the advantages of computational approaches, including rapid analysis of large datasets and prediction of resistance profiles. A comprehensive overview of computational methods for studying AMR is presented, encompassing genomics, proteomics, structural bioinformatics, network analysis, and machine learning algorithms. The strengths and limitations of each method are briefly outlined. Additionally, we introduce ResScan-design, our own computational method, which employs a protein (re)design protocol to identify potential resistance mutations and adaptation signatures in pathogens. Case studies are discussed to showcase the application of ResScan in elucidating hotspot residues, understanding underlying mechanisms, and guiding the design of effective therapies. In conclusion, we emphasize the value of computational methods in understanding and combating AMR. Integration of experimental and computational approaches can expedite the discovery of innovative antimicrobial treatments and mitigate the threat posed by AMR.","PeriodicalId":7376,"journal":{"name":"Advances in protein chemistry and structural biology","volume":"139 ","pages":"173-220"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140048552","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