Advances in protein chemistry and structural biology最新文献_第8页

Exploring the effect of disease causing mutations in metal binding sites of human ARSA in metachromatic leukodystrophy. 探索变色性白质营养不良症中人类 ARSA 金属结合位点的致病突变的影响。

3区生物学

Advances in protein chemistry and structural biology Pub Date : 2024-01-01 Epub Date: 2024-06-25 DOI: 10.1016/bs.apcsb.2023.12.016

N Madhana Priya, N Sidharth Kumar, S Udhaya Kumar, G Mohanraj, R Magesh, Hatem Zayed, Karthick Vasudevan, George Priya Doss C

{"title":"Exploring the effect of disease causing mutations in metal binding sites of human ARSA in metachromatic leukodystrophy.","authors":"N Madhana Priya, N Sidharth Kumar, S Udhaya Kumar, G Mohanraj, R Magesh, Hatem Zayed, Karthick Vasudevan, George Priya Doss C","doi":"10.1016/bs.apcsb.2023.12.016","DOIUrl":"10.1016/bs.apcsb.2023.12.016","url":null,"abstract":"The arylsulfatase A (ARSA) gene is observed to be deficient in patients with metachromatic leukodystrophy (MLD), a type of lysosomal storage disease. MLD is a severe neurodegenerative disorder characterized by an autosomal recessive inheritance pattern. This study aimed to map the most deleterious mutations at the metal binding sites of ARSA and the amino acids in proximity to the mutated positions. We utilized an array of computational tools, including PredictSNP, MAPP, PhD-SNP, PolyPhen-1, PolyPhen-2, SIFT, SNAP, and ConSurf, to identify the most detrimental mutations potentially implicated in MLD collected from UniProt, ClinVar, and HGMD. Two mutations, D29N and D30H, as being extremely deleterious based on assessments of pathogenicity, conservation, biophysical characteristics, and stability analysis. The D29 and D30 are located at the metal-interacting regions of ARSA and found to undergo post-translational modification, specifically phosphorylation. Henceforth, the in-depth effect of metal binding upon mutation was examined using molecular dynamics simulations (MDS) before and after phosphorylation. The MDS results exhibited high deviation for the D29N and D30H mutations in comparison to the native, and the same was confirmed by significant residue fluctuation and reduced compactness. These structural alterations suggest that such mutations may influence protein functionality, offering potential avenues for personalized therapeutic and providing a basis for potential mutation-specific treatments for severe MLD patients.","PeriodicalId":7376,"journal":{"name":"Advances in protein chemistry and structural biology","volume":"141 ","pages":"203-221"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141496756","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 journey from omics to clinicomics in solid cancers: Success stories and challenges. 实体瘤从omics到clinicomics的历程：成功案例与挑战。

3区生物学

Advances in protein chemistry and structural biology Pub Date : 2024-01-01 Epub Date: 2024-02-21 DOI: 10.1016/bs.apcsb.2023.11.008

Sanjana Mehrotra, Sankalp Sharma, Rajeev Kumar Pandey

{"title":"A journey from omics to clinicomics in solid cancers: Success stories and challenges.","authors":"Sanjana Mehrotra, Sankalp Sharma, Rajeev Kumar Pandey","doi":"10.1016/bs.apcsb.2023.11.008","DOIUrl":"10.1016/bs.apcsb.2023.11.008","url":null,"abstract":"The word 'cancer' encompasses a heterogenous group of distinct disease types characterized by a spectrum of pathological features, genetic alterations and response to therapies. According to the World Health Organization, cancer is the second leading cause of death worldwide, responsible for one in six deaths and hence imposes a significant burden on global healthcare systems. High-throughput omics technologies combined with advanced imaging tools, have revolutionized our ability to interrogate the molecular landscape of tumors and has provided unprecedented understanding of the disease. Yet, there is a gap between basic research discoveries and their translation into clinically meaningful therapies for improving patient care. To bridge this gap, there is a need to analyse the vast amounts of high dimensional datasets from multi-omics platforms. The integration of multi-omics data with clinical information like patient history, histological examination and imaging has led to the novel concept of clinicomics and may expedite the bench-to-bedside transition in cancer. The journey from omics to clinicomics has gained momentum with development of radiomics which involves extracting quantitative features from medical imaging data with the help of deep learning and artificial intelligence (AI) tools. These features capture detailed information about the tumor's shape, texture, intensity, and spatial distribution. Together, the related fields of multiomics, translational bioinformatics, radiomics and clinicomics may provide evidence-based recommendations tailored to the individual cancer patient's molecular profile and clinical characteristics. In this chapter, we summarize multiomics studies in solid cancers with a specific focus on breast cancer. We also review machine learning and AI based algorithms and their use in cancer diagnosis, subtyping, prognosis and predicting treatment resistance and relapse.","PeriodicalId":7376,"journal":{"name":"Advances in protein chemistry and structural biology","volume":"139 ","pages":"89-139"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140048540","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 resources and chemoinformatics for translational health research. 用于转化健康研究的计算资源和化学信息学。

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.2023.11.003

Tripti Tripathi, Dev Bukhsh Singh, Timir Tripathi

引用次数: 0

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

引用次数: 0