scholarly journals Application Fields, Positions, and Bioinformatic Mining of Non-active Sites: A Mini-Review

2021 ◽  
Vol 9 ◽  
Author(s):  
Xiaoxiao Wang ◽  
Qinyuan Ma ◽  
Jian Shen ◽  
Bin Wang ◽  
Xiuzhen Gao ◽  
...  
Keyword(s):  
Active Sites ◽  
Recent Progress ◽  
Molecular Mechanisms ◽  
Vital Role ◽  
Enzyme Engineering ◽  
Major Research ◽  
Enzyme Families ◽  
Application Fields ◽  
Enzymatic Mechanisms ◽  
Biocatalytic Process

Active sites of enzymes play a vital role in catalysis, and researchhas been focused on the interactions between active sites and substrates to understand the biocatalytic process. However, the active sites distal to the catalytic cavity also participate in catalysis by maintaining the catalytic conformations. Therefore, some researchers have begun to investigate the roles of non-active sites in proteins, especially for enzyme families with different functions. In this mini-review, we focused on recent progress in research on non-active sites of enzymes. First, we outlined two major research methodswith non-active sites as direct targets, including understanding enzymatic mechanisms and enzyme engineering. Second, we classified the positions of reported non-active sites in enzyme structures and studied the molecular mechanisms underlying their functions, according to the literature on non-active sites. Finally, we summarized the results of bioinformatic analysisof mining non-active sites as targets for protein engineering.

scholarly journals Study of Functional and Allosteric Sites in Protein Superfamilies

Acta Naturae ◽  
2015 ◽  
Vol 7 (4) ◽  
pp. 34-45 ◽  
Author(s):  
D. А. Suplatov ◽  
V. К. Švedas
Keyword(s):  
Structure Function ◽  
Binding Sites ◽  
Active Sites ◽  
Molecular Mechanisms ◽  
Protein Structures ◽  
Evolutionary Relationship ◽  
Enzyme Engineering ◽  
Homologous Proteins ◽  
Functional Sites ◽  
Protein Superfamilies

The interaction of proteins (enzymes) with a variety of low-molecular-weight compounds, as well as protein-protein interactions, is the most important factor in the regulation of their functional properties. To date, research effort has routinely focused on studying ligand binding to the functional sites of proteins (active sites of enzymes), whereas the molecular mechanisms of allosteric regulation, as well as binding to other pockets and cavities in protein structures, remained poorly understood. Recent studies have shown that allostery may be an intrinsic property of virtually all proteins. Novel approaches are needed to systematically analyze the architecture and role of various binding sites and establish the relationship between structure, function, and regulation. Computational biology, bioinformatics, and molecular modeling can be used to search for new regulatory centers, characterize their structural peculiarities, as well as compare different pockets in homologous proteins, study the molecular mechanisms of allostery, and understand the communication between topologically independent binding sites in protein structures. The establishment of an evolutionary relationship between different binding centers within protein superfamilies and the discovery of new functional and allosteric (regulatory) sites using computational approaches can improve our understanding of the structure-function relationship in proteins and provide new opportunities for drug design and enzyme engineering.

Antennal transcriptome analysis and candidate olfactory genes in Crematogaster rogenhoferi

2021 ◽  
pp. 1-12
Author(s):  
Xiang Zhou ◽  
Jixing Guo ◽  
Mingxia Zhang ◽  
Chunxiu Bai ◽  
Zheng Wang ◽  
...  
Keyword(s):  
Biological Control ◽  
Transcriptome Analysis ◽  
Molecular Basis ◽  
Molecular Mechanisms ◽  
Biological Control Agent ◽  
Control Agent ◽  
Vital Role ◽  
Neuron Membrane ◽  
Ionotropic Receptors ◽  
Soft Scale

Abstract Crematogaster rogenhoferi (Hymenoptera: Formicidae), an omnivorous ant, is one of the dominant predatory natural enemies of a soft scale pest, Parasaissetia nigra Nietner (Homoptera: Coccidae), and can effectively control P. nigra populations in rubber forests. Olfaction plays a vital role in the process of predation. However, the information about the molecular mechanism of olfaction-evoked behaviour in C. rogenhoferi is limited. In this study, we conducted antennal transcriptome analysis to identify candidate olfactory genes. We obtained 53,892 unigenes, 16,185 of which were annotated. Based on annotations, we identified 49 unigenes related to chemoreception, including four odourant-binding proteins, three chemosensory proteins, 37 odourant receptors, two odourant ionotropic receptors and three sensory neuron membrane proteins. This is the first report on the molecular basis of the chemosensory system of C. rogenhoferi. The findings provide a basis for elucidating the molecular mechanisms of the olfactory-related behaviours of C. rogenhoferi, which would facilitate a better application of C. rogenhoferi as a biological control agent.

scholarly journals Mechanistic strategies of microbial communities regulating lignocellulose deconstruction in a UK salt marsh

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Daniel R. Leadbeater ◽  
Nicola C. Oates ◽  
Joseph P. Bennett ◽  
Yi Li ◽  
Adam A. Dowle ◽  
...  
Keyword(s):  
Salt Marsh ◽  
Salt Marshes ◽  
Molecular Mechanisms ◽  
Surface Sediments ◽  
Gene Profiling ◽  
Oxidative Enzymes ◽  
Lignocellulose Degradation ◽  
Rrna Gene ◽  
Enzymatic Mechanisms

Abstract Background Salt marshes are major natural repositories of sequestered organic carbon with high burial rates of organic matter, produced by highly productive native flora. Accumulated carbon predominantly exists as lignocellulose which is metabolised by communities of functionally diverse microbes. However, the organisms that orchestrate this process and the enzymatic mechanisms employed that regulate the accumulation, composition and permanence of this carbon stock are not yet known. We applied meta-exo-proteome proteomics and 16S rRNA gene profiling to study lignocellulose decomposition in situ within the surface level sediments of a natural established UK salt marsh. Results Our studies revealed a community dominated by Gammaproteobacteria, Bacteroidetes and Deltaproteobacteria that drive lignocellulose degradation in the salt marsh. We identify 42 families of lignocellulolytic bacteria of which the most active secretors of carbohydrate-active enzymes were observed to be Prolixibacteracea, Flavobacteriaceae, Cellvibrionaceae, Saccharospirillaceae, Alteromonadaceae, Vibrionaceae and Cytophagaceae. These families secreted lignocellulose-active glycoside hydrolase (GH) family enzymes GH3, GH5, GH6, GH9, GH10, GH11, GH13 and GH43 that were associated with degrading Spartina biomass. While fungi were present, we did not detect a lignocellulolytic contribution from fungi which are major contributors to terrestrial lignocellulose deconstruction. Oxidative enzymes such as laccases, peroxidases and lytic polysaccharide monooxygenases that are important for lignocellulose degradation in the terrestrial environment were present but not abundant, while a notable abundance of putative esterases (such as carbohydrate esterase family 1) associated with decoupling lignin from polysaccharides in lignocellulose was observed. Conclusions Here, we identify a diverse cohort of previously undefined bacteria that drive lignocellulose degradation in the surface sediments of the salt marsh environment and describe the enzymatic mechanisms they employ to facilitate this process. Our results increase the understanding of the microbial and molecular mechanisms that underpin carbon sequestration from lignocellulose within salt marsh surface sediments in situ and provide insights into the potential enzymatic mechanisms regulating the enrichment of polyphenolics in salt marsh sediments.

Study on the Military Environmental Information Management with GIS

2010 ◽  
Vol 113-116 ◽  
pp. 561-564
Author(s):  
Jian Ding ◽  
Ke Hong Wu ◽  
Zhi Bing Ding
Keyword(s):  
Decision Making ◽  
Information Management ◽  
Transportation Planning ◽  
Vital Role ◽  
Environmental Information ◽  
Gis Technology ◽  
Important Conclusion ◽  
Model Calculations ◽  
Hazardous Chemical ◽  
Application Fields

The application of GIS technology to Military Environmental Information(MEI) management will play a vital role in MEI management, and can lead to better decision-making. This paper discusses both the management method and the application fields. Case studies, like information management, pollution coverage evaluating, military transportation planning and monitoring, and decision-making supporting, are presented in this paper. Detailed digital basemap database, Digital Elevation Model(DEM) data, Digital OrthoImage Model(DOM) data, image database of Remote Sensing, Social economic element database, and other informations related to military features, can be integrated into MEI GIS, and will meet the needs for later query and statistics. Spatial analysis is the bridge that links fundamental data models to GIS technology. While buffer analysis can be used for identifying the locations of hazardous chemical storage sites in relation to residents living area, and can facilitate the evaluation of the threatened area in the event of a leak or spill of hazardous materials. Network analysis can be used in military transportation planning and monitoring. GIS is particularly useful in providing composite visual representation of fairly complex underlying model calculations, analysts can draw implicit and important conclusion from the already known geographical data. The study shows that the management of MEI using GIS technology is reasonable and feasible, and GIS is a highly efficient tool in MEI management.

scholarly journals Pseudogene ACTBP2 increases blood–brain barrier permeability by promoting KHDRBS2 transcription through recruitment of KMT2D/WDR5 in Aβ1–42 microenvironment

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Qianshuo Liu ◽  
Xiaobai Liu ◽  
Defeng Zhao ◽  
Xuelei Ruan ◽  
Rui Su ◽  
...  
Keyword(s):  
Blood Brain Barrier ◽  
Molecular Mechanisms ◽  
Rna Binding ◽  
Vital Role ◽  
Brain Barrier ◽  
Blood Brain ◽  
Bbb Permeability ◽  
Novel Target ◽  
And Function

AbstractThe blood–brain barrier (BBB) has a vital role in maintaining the homeostasis of the central nervous system (CNS). Changes in the structure and function of BBB can accelerate Alzheimer’s disease (AD) development. β-Amyloid (Aβ) deposition is the major pathological event of AD. We elucidated the function and possible molecular mechanisms of the effect of pseudogene ACTBP2 on the permeability of BBB in Aβ1–42 microenvironment. BBB model treated with Aβ1–42 for 48 h were used to simulate Aβ-mediated BBB dysfunction in AD. We proved that pseudogene ACTBP2, RNA-binding protein KHDRBS2, and transcription factor HEY2 are highly expressed in ECs that were obtained in a BBB model in vitro in Aβ1–42 microenvironment. In Aβ1–42-incubated ECs, ACTBP2 recruits methyltransferases KMT2D and WDR5, binds to KHDRBS2 promoter, and promotes KHDRBS2 transcription. The interaction of KHDRBS2 with the 3′UTR of HEY2 mRNA increases the stability of HEY2 and promotes its expression. HEY2 increases BBB permeability in Aβ1–42 microenvironment by transcriptionally inhibiting the expression of ZO-1, occludin, and claudin-5. We confirmed that knocking down of Khdrbs2 or Hey2 increased the expression levels of ZO-1, occludin, and claudin-5 in APP/PS1 mice brain microvessels. ACTBP2/KHDRBS2/HEY2 axis has a crucial role in the regulation of BBB permeability in Aβ1–42 microenvironment, which may provide a novel target for the therapy of AD.

Nutrigenomics and Life Style Facet- A Modulatory Molecular Evidence in Progression of Breast and Colon Cancer with Emerging Importance

2021 ◽  
Vol 21 ◽  
Author(s):  
Suman Kumar Ray ◽  
Sukhes Mukherjee
Keyword(s):  
Colon Cancer ◽  
Molecular Mechanisms ◽  
Health Management ◽  
Vital Role ◽  
Molecular Evidence ◽  
Nutritional Interventions ◽  
Phenotypic Alteration ◽  
The Individual ◽  
Supplement Intake

: Legitimate nutrition assumes a significant role in preventing diseases and, in this way, nutritional interventions establish vital strategies in the area of public health. Nutrigenomics centres on the different genes and diet in an individual and how an individual’s genes influence the reaction to bioactive foodstuff. It targets considering the genetic and epigenetic interactions with nutrients to lead to a phenotypic alteration and consequently to metabolism, differentiation, or even apoptosis. Nutrigenomics and lifestyle factors play a vital role in health management and represent an exceptional prospect for the improvement of personalized diets to the individual at risk of developing diseases like cancer. Concerning cancer as a multifactorial genetic ailment, several aspects need to be investigated and analysed. Various perspectives should be researched and examined regarding the development and prognosis of breast and colon cancer. Malignant growth occurrence is anticipated to upsurge in the impending days, and an effective anticipatory strategy is required. The effect of dietary components, basically studied by nutrigenomics, looks at gene expression and molecular mechanisms. It also interrelates bioactive compounds and nutrients because of different 'omics' innovations. Several preclinical investigations demonstrate the pertinent role of nutrigenomics in breast and colon cancer, and change of dietary propensities is conceivably a successful methodology for reducing cancer risk. The connection between the genomic profile of patients with breast or colon cancer and their supplement intake, it is conceivable to imagine an idea of personalized medicine, including nutrition and medicinal services.

Parallel molecular mechanisms for enzyme temperature adaptation

Science ◽  
2021 ◽  
Vol 371 (6533) ◽  
pp. eaay2784
Author(s):  
Margaux M. Pinney ◽  
Daniel A. Mokhtari ◽  
Eyal Akiva ◽  
Filip Yabukarski ◽  
David M. Sanchez ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Interaction Networks ◽  
Temperature Adaptation ◽  
Mechanistic Studies ◽  
Sequence Analyses ◽  
Evolutionary Mechanisms ◽  
Ketosteroid Isomerase ◽  
Physical Mechanisms ◽  
Bacterial Enzyme ◽  
Enzyme Families

The mechanisms that underly the adaptation of enzyme activities and stabilities to temperature are fundamental to our understanding of molecular evolution and how enzymes work. Here, we investigate the molecular and evolutionary mechanisms of enzyme temperature adaption, combining deep mechanistic studies with comprehensive sequence analyses of thousands of enzymes. We show that temperature adaptation in ketosteroid isomerase (KSI) arises primarily from one residue change with limited, local epistasis, and we establish the underlying physical mechanisms. This residue change occurs in diverse KSI backgrounds, suggesting parallel adaptation to temperature. We identify residues associated with organismal growth temperature across 1005 diverse bacterial enzyme families, suggesting widespread parallel adaptation to temperature. We assess the residue properties, molecular interactions, and interaction networks that appear to underly temperature adaptation.

scholarly journals Exogenous Promoter Triggers APETALA3 Silencing through RNA-Directed DNA Methylation Pathway in Arabidopsis

2019 ◽  
Vol 20 (18) ◽  
pp. 4478 ◽  
Author(s):  
Benqi Wang ◽  
Jie Liu ◽  
Lei Chu ◽  
Xue Jing ◽  
Huadong Wang ◽  
...  
Keyword(s):  
Transgenic Plants ◽  
Molecular Mechanisms ◽  
Plant Reproduction ◽  
Vital Role ◽  
Abnormal Development ◽  
Class A ◽  
Methylation Pathway ◽  
Class B ◽  
Transgenic Lines ◽  
Morphological Defects

The development of floral organs plays a vital role in plant reproduction. In our research, the APETALA3 (AP3) promoter-transgenic lines showed abnormal developmental phenotypes in stamens and petals. The aim of this study is to understand the molecular mechanisms of the morphological defects in transgenic plants. By performing transgenic analysis, it was found that the AP3-promoted genes and the vector had no relation to the morphological defects. Then, we performed the expression analysis of the class A, B, and C genes. A dramatic reduction of transcript levels of class B genes (AP3 and PISTILLATA) was observed. Additionally, we also analyzed the methylation of the promoters of class B genes and found that the promoter of AP3 was hypermethylated. Furthermore, combining mutations in rdr2-2, drm1/2, and nrpd1b-11 with the AP3-silencing lines rescued the abnormal development of stamens and petals. The expression of AP3 was reactivated and the methylation level of AP3 promoter was also reduced in RdDM-defective AP3-silencing lines. Our results showed that the RdDM pathway contributed to the transcriptional silencing in the transgenic AP3-silencing lines. Moreover, the results revealed that fact that the exogenous fragment of a promoter could trigger the methylation of homologous endogenous sequences, which may be ubiquitous in transgenic plants.

Conductive Metal and Covalent Organic Frameworks for Electrocatalysis: Design Principles, Recent Progress and Perspective

Nanoscale ◽  
2021 ◽  
Author(s):  
Jinyan Wang ◽  
Hongyin Hu ◽  
Shuanglong Lu ◽  
Jundie Hu ◽  
Han Zhu ◽  
...  
Keyword(s):  
Active Sites ◽  
Recent Progress ◽  
Structural Diversity ◽  
Design Principles ◽  
Covalent Organic Frameworks

Metal and covalent organic frameworks (MOFs/COFs) are emerging promising candidates in the field of catalysts due to their porous nature, chemically well-defined active sites and structural diversity. However, they are...

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