Essays in biochemistry最新文献_第10页

Enzyme synergy for plant cell wall polysaccharide degradation. 植物细胞壁多糖降解的酶协同作用。

IF 6.4 2区生物学

Essays in biochemistry Pub Date : 2023-04-18 DOI: 10.1042/EBC20220166

Ahmed Khamassi, Claire Dumon

引用次数: 3

On the impact of carbohydrate-binding modules (CBMs) in lytic polysaccharide monooxygenases (LPMOs). 糖结合模块(CBMs)对多糖单加氧酶(LPMOs)的影响。

IF 6.4 2区生物学

Essays in biochemistry Pub Date : 2023-04-18 DOI: 10.1042/EBC20220162

Zarah Forsberg, Gaston Courtade

引用次数: 5

Butyrate-producing colonic clostridia: picky glycan utilization specialists. 产生丁酸的结肠梭菌:挑剔的聚糖利用专家。

IF 6.4 2区生物学

Essays in biochemistry Pub Date : 2023-04-18 DOI: 10.1042/EBC20220125

Maria Louise Leth, Michael Jakob Pichler, Maher Abou Hachem

{"title":"Butyrate-producing colonic clostridia: picky glycan utilization specialists.","authors":"Maria Louise Leth, Michael Jakob Pichler, Maher Abou Hachem","doi":"10.1042/EBC20220125","DOIUrl":"https://doi.org/10.1042/EBC20220125","url":null,"abstract":"Butyrate-producing human gut microbiota members are recognized for their strong association with a healthy immune-homeostasis and protection from inflammatory disorders and colorectal cancer. These effects are attributed to butyrate, the terminal electron sink of glycan fermentation by prevalent and abundant colonic Firmicutes from the Lachnospiraceae and Oscillospiraceae families. Remarkably, our insight into the glycan utilization mechanisms and preferences of butyrogenic Firmicutes remains very limited as compared with other gut symbionts, especially from the Bacteroides, Bifidobacterium, and Lactobacillus genera. Here, we summarize recent findings on the strategies that colonic butyrate producers have evolved to harvest energy from major dietary fibres, especially plant structural and storage glycans, such as resistant starch, xylans, and mannans. Besides dietary fibre, we also present the unexpected discovery of a conserved protein apparatus that confers the growth of butyrate producers on human milk oligosaccharides (HMOs), which are unique to mother's milk. The dual dietary fibre/HMO utilization machinery attests the adaptation of this group to both the infant and adult guts. These finding are discussed in relation to the early colonization of butyrogenic bacteria and the maturation of the microbiota during the transition from mother's milk to solid food. To date, the described butyrogenic Firmicutes are glycan utilization specialists that target only a few glycans in a highly competitive manner relying on co-regulated glycan utilization loci. We describe the common pillars of this machinery, highlighting butyrate producers as a source for discovery of biochemically and structurally novel carbohydrate active enzymes.","PeriodicalId":11812,"journal":{"name":"Essays in biochemistry","volume":"67 3","pages":"415-428"},"PeriodicalIF":6.4,"publicationDate":"2023-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9688388","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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: 7

A special issue of Essays in Biochemistry on current advances about CAZymes and their impact and key role in human health and environment. 《生物化学论文》的特刊，关于酶的最新进展及其对人类健康和环境的影响和关键作用。

IF 6.4 2区生物学

Essays in biochemistry Pub Date : 2023-04-18 DOI: 10.1042/EBC20230004

Mirjam Czjzek, Elizabeth Ficko-Blean, Jean-Guy Berrin

{"title":"A special issue of Essays in Biochemistry on current advances about CAZymes and their impact and key role in human health and environment.","authors":"Mirjam Czjzek, Elizabeth Ficko-Blean, Jean-Guy Berrin","doi":"10.1042/EBC20230004","DOIUrl":"https://doi.org/10.1042/EBC20230004","url":null,"abstract":"Carbohydrate active enzymes (CAZymes) and their biochemical characterization have been the subject of extensive research over the past ten years due to their importance to carbohydrate metabolism in different biological contexts. For instance, the understanding that 'polysaccharide utilizing loci' (PUL) systems hosted by specific 'carbohydrate degraders' in the intestinal microbiota play key roles in health and disease, such as Crohn's disease, ulcerative colitis or colorectal cancer to name the most well-characterized, has led to an outstanding effort in trying to decipher the molecular mechanisms by which these processes are organized and regulated. The past 10 years has also seen the expansion of CAZymes with auxiliary activities, such as lytic polysaccharide monooxygenases (LPMOs) or even sulfatases, and interest has grown in general about the enzymes needed to remove the numerous decorations and modifications of complex biomass, such as carbohydrate esterases (CE). Today, the characterization of these 'modifying' enzymes allows us to tackle a much more complex biomass, which presents sulfations, methylations, acetylations or interconnections with lignin. This special issue about CAZyme biochemistry covers all these aspects, ranging from implications in disease to environmental and biotechnological impact, with a varied collection of twenty-four review articles providing current biochemical, structural and mechanistic insights into their respective topics.","PeriodicalId":11812,"journal":{"name":"Essays in biochemistry","volume":"67 3","pages":"325-329"},"PeriodicalIF":6.4,"publicationDate":"2023-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9333206","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

In silico modelling of the function of disease-related CAZymes. 疾病相关CAZymes功能的计算机模拟。

IF 6.4 2区生物学

Essays in biochemistry Pub Date : 2023-04-18 DOI: 10.1042/EBC20220218

Alba Nin-Hill, Beatriz Piniello, Carme Rovira

{"title":"In silico modelling of the function of disease-related CAZymes.","authors":"Alba Nin-Hill, Beatriz Piniello, Carme Rovira","doi":"10.1042/EBC20220218","DOIUrl":"https://doi.org/10.1042/EBC20220218","url":null,"abstract":"In silico modelling of proteins comprises a diversity of computational tools aimed to obtain structural, electronic, and/or dynamic information about these biomolecules, capturing mechanistic details that are challenging to experimental approaches, such as elusive enzyme-substrate complexes, short-lived intermediates, and reaction transition states (TS). The present article gives the reader insight on the use of in silico modelling techniques to understand complex catalytic reaction mechanisms of carbohydrate-active enzymes (CAZymes), along with the underlying theory and concepts that are important in this field. We start by introducing the significance of carbohydrates in nature and the enzymes that process them, CAZymes, highlighting the conformational flexibility of their carbohydrate substrates. Three commonly used in silico methods (classical molecular dynamics (MD), hybrid quantum mechanics/molecular mechanics (QM/MM), and enhanced sampling techniques) are described for nonexpert readers. Finally, we provide three examples of the application of these methods to unravel the catalytic mechanisms of three disease-related CAZymes: β-galactocerebrosidase (GALC), responsible for Krabbe disease; α-mannoside β-1,6-N-acetylglucosaminyltransferase V (MGAT5), involved in cancer; and O-fucosyltransferase 1 (POFUT1), involved in several human diseases such as leukemia and the Dowling-Degos disease.","PeriodicalId":11812,"journal":{"name":"Essays in biochemistry","volume":"67 3","pages":"355-372"},"PeriodicalIF":6.4,"publicationDate":"2023-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/18/eb/ebc-67-ebc20220218.PMC10154626.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9408318","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Glycosyltransferase family 47 (GT47) proteins in plants and animals. 植物和动物的糖基转移酶家族47 (GT47)蛋白。

IF 6.4 2区生物学

Essays in biochemistry Pub Date : 2023-04-14 DOI: 10.1042/EBC20220152

Liang Zhang, Pradeep Kumar Prabhakar, Vivek S Bharadwaj, Yannick J Bomble, Maria J Peña, Breeanna R Urbanowicz

{"title":"Glycosyltransferase family 47 (GT47) proteins in plants and animals.","authors":"Liang Zhang, Pradeep Kumar Prabhakar, Vivek S Bharadwaj, Yannick J Bomble, Maria J Peña, Breeanna R Urbanowicz","doi":"10.1042/EBC20220152","DOIUrl":"https://doi.org/10.1042/EBC20220152","url":null,"abstract":"Glycosyltransferases (GTs) are carbohydrate-active enzymes that are encoded by the genomes of organisms spanning all domains of life. GTs catalyze glycosidic bond formation, transferring a sugar monomer from an activated donor to an acceptor substrate, often another saccharide. GTs from family 47 (GT47, PF03016) are involved in the synthesis of complex glycoproteins in mammals and insects and play a major role in the synthesis of almost every class of polysaccharide in plants, with the exception of cellulose, callose, and mixed linkage β-1,3/1,4-glucan. GT47 enzymes adopt a GT-B fold and catalyze the formation of glycosidic bonds through an inverting mechanism. Unlike animal genomes, which encode few GT47 enzymes, plant genomes contain 30 or more diverse GT47 coding sequences. Our current knowledge of the GT47 family across plant species brings us an interesting view, showcasing how members exhibit a great diversity in both donor and acceptor substrate specificity, even for members that are classified in the same phylogenetic clade. Thus, we discuss how plant GT47 family members represent a great case to study the relationship between substrate specificity, protein structure, and protein evolution. Most of the plant GT47 enzymes that are identified to date are involved in biosynthesis of plant cell wall polysaccharides, including xyloglucan, xylan, mannan, and pectins. This indicates unique and crucial roles of plant GT47 enzymes in cell wall formation. The aim of this review is to summarize findings about GT47 enzymes and highlight new challenges and approaches on the horizon to study this family.","PeriodicalId":11812,"journal":{"name":"Essays in biochemistry","volume":"67 3","pages":"639-652"},"PeriodicalIF":6.4,"publicationDate":"2023-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9333351","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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: 1

Mass spectrometric insights into protein aggregation. 蛋白质聚集的质谱分析。

IF 6.4 2区生物学

Essays in biochemistry Pub Date : 2023-03-29 DOI: 10.1042/EBC20220103

Tara L Pukala

{"title":"Mass spectrometric insights into protein aggregation.","authors":"Tara L Pukala","doi":"10.1042/EBC20220103","DOIUrl":"https://doi.org/10.1042/EBC20220103","url":null,"abstract":"Protein aggregation is now recognized as a generic and significant component of the protein energy landscape. Occurring through a complex and dynamic pathway of structural interconversion, the assembly of misfolded proteins to form soluble oligomers and insoluble aggregates remains a challenging topic of study, both in vitro and in vivo. Since the etiology of numerous human diseases has been associated with protein aggregation, and it has become a field of increasing importance in the biopharmaceutical industry, the biophysical characterization of protein misfolded states and their aggregation mechanisms continues to receive increased attention. Mass spectrometry (MS) has firmly established itself as a powerful analytical tool capable of both detection and characterization of proteins at all levels of structure. Given inherent advantages of biological MS, including high sensitivity, rapid timescales of analysis, and the ability to distinguish individual components from complex mixtures with unrivalled specificity, it has found widespread use in the study of protein aggregation, importantly, where traditional structural biology approaches are often not amenable. The present review aims to provide a brief overview of selected MS-based approaches that can provide a range of biophysical descriptors associated with protein conformation and the aggregation pathway. Recent examples highlight where this technology has provided unique structural and mechanistic understanding of protein aggregation.","PeriodicalId":11812,"journal":{"name":"Essays in biochemistry","volume":"67 2","pages":"243-253"},"PeriodicalIF":6.4,"publicationDate":"2023-03-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10070474/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9260339","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Mass spectrometry of intact membrane proteins: shifting towards a more native-like context. 完整膜蛋白的质谱分析:转向更原生的环境。

IF 6.4 2区生物学

Essays in biochemistry Pub Date : 2023-03-29 DOI: 10.1042/EBC20220169

Abraham Oluwole, Denis Shutin, Jani R Bolla

{"title":"Mass spectrometry of intact membrane proteins: shifting towards a more native-like context.","authors":"Abraham Oluwole, Denis Shutin, Jani R Bolla","doi":"10.1042/EBC20220169","DOIUrl":"https://doi.org/10.1042/EBC20220169","url":null,"abstract":"Integral membrane proteins are involved in a plethora of biological processes including cellular signalling, molecular transport, and catalysis. Many of these functions are mediated by non-covalent interactions with other proteins, substrates, metabolites, and surrounding lipids. Uncovering such interactions and deciphering their effect on protein activity is essential for understanding the regulatory mechanisms underlying integral membrane protein function. However, the detection of such dynamic complexes has proven to be challenging using traditional approaches in structural biology. Native mass spectrometry has emerged as a powerful technique for the structural characterisation of membrane proteins and their complexes, enabling the detection and identification of protein-binding partners. In this review, we discuss recent native mass spectrometry-based studies that have characterised non-covalent interactions of membrane proteins in the presence of detergents or membrane mimetics. We additionally highlight recent progress towards the study of membrane proteins within native membranes and provide our perspective on how these could be combined with recent developments in instrumentation to investigate increasingly complex biomolecular systems.","PeriodicalId":11812,"journal":{"name":"Essays in biochemistry","volume":"67 2","pages":"201-213"},"PeriodicalIF":6.4,"publicationDate":"2023-03-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10070488/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9268327","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

Fundamentals of HDX-MS. HDX-MS基本原理。

IF 6.4 2区生物学

Essays in biochemistry Pub Date : 2023-03-29 DOI: 10.1042/EBC20220111

Vanesa Vinciauskaite, Glenn R Masson

引用次数: 6

A special issue of Essays in Biochemistry on structural mass spectrometry. 关于结构质谱的《生物化学论文》特刊。

IF 6.4 2区生物学

Essays in biochemistry Pub Date : 2023-03-29 DOI: 10.1042/EBC20230006

Hannah M Britt, Rebecca Beveridge, Antonio N Calabrese

引用次数: 0