Bioinformatic mapping of a more precise Aspergillus niger degradome

Zixing Dong; Shuangshuang Yang; Byong H. Lee

doi:10.1038/s41598-020-80028-3

Bioinformatic mapping of a more precise Aspergillus niger degradome

Scientific Reports ◽

10.1038/s41598-020-80028-3 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Zixing Dong ◽

Shuangshuang Yang ◽

Byong H. Lee

Keyword(s):

Aspergillus Niger ◽

Metal Binding ◽

Active Sites ◽

Biochemical Characterization ◽

Experimental Studies ◽

Matrix Remodeling ◽

Starting Point ◽

Merops Database ◽

Binding Residues ◽

Microbial Defense

AbstractAspergillus niger has the ability to produce a large variety of proteases, which are of particular importance for protein digestion, intracellular protein turnover, cell signaling, flavour development, extracellular matrix remodeling and microbial defense. However, the A. niger degradome (the full repertoire of peptidases encoded by the A. niger genome) available is not accurate and comprehensive. Herein, we have utilized annotations of A. niger proteases in AspGD, JGI, and version 12.2 MEROPS database to compile an index of at least 232 putative proteases that are distributed into the 71 families/subfamilies and 26 clans of the 6 known catalytic classes, which represents ~ 1.64% of the 14,165 putative A. niger protein content. The composition of the A. niger degradome comprises ~ 7.3% aspartic, ~ 2.2% glutamic, ~ 6.0% threonine, ~ 17.7% cysteine, ~ 31.0% serine, and ~ 35.8% metallopeptidases. One hundred and two proteases have been reassigned into the above six classes, while the active sites and/or metal-binding residues of 110 proteases were recharacterized. The probable physiological functions and active site architectures of these peptidases were also investigated. This work provides a more precise overview of the complete degradome of A. niger, which will no doubt constitute a valuable resource and starting point for further experimental studies on the biochemical characterization and physiological roles of these proteases.

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Machine learning differentiates enzymatic and non-enzymatic metals in proteins

Nature Communications ◽

10.1038/s41467-021-24070-3 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Ryan Feehan ◽

Meghan W. Franklin ◽

Joanna S. G. Slusky

Keyword(s):

Machine Learning ◽

Metal Binding ◽

Binding Sites ◽

Active Sites ◽

De Novo ◽

Enzyme Design ◽

Metal Binding Sites ◽

Ensemble Machine Learning ◽

Machine Learning Model ◽

Physicochemical Features

AbstractMetalloenzymes are 40% of all enzymes and can perform all seven classes of enzyme reactions. Because of the physicochemical similarities between the active sites of metalloenzymes and inactive metal binding sites, it is challenging to differentiate between them. Yet distinguishing these two classes is critical for the identification of both native and designed enzymes. Because of similarities between catalytic and non-catalytic metal binding sites, finding physicochemical features that distinguish these two types of metal sites can indicate aspects that are critical to enzyme function. In this work, we develop the largest structural dataset of enzymatic and non-enzymatic metalloprotein sites to date. We then use a decision-tree ensemble machine learning model to classify metals bound to proteins as enzymatic or non-enzymatic with 92.2% precision and 90.1% recall. Our model scores electrostatic and pocket lining features as more important than pocket volume, despite the fact that volume is the most quantitatively different feature between enzyme and non-enzymatic sites. Finally, we find our model has overall better performance in a side-to-side comparison against other methods that differentiate enzymatic from non-enzymatic sequences. We anticipate that our model’s ability to correctly identify which metal sites are responsible for enzymatic activity could enable identification of new enzymatic mechanisms and de novo enzyme design.

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In VivoImpact of Met221 Substitution in GOB Metallo-β-Lactamase

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.05418-11 ◽

2012 ◽

Vol 56 (4) ◽

pp. 1769-1773 ◽

Cited By ~ 5

Author(s):

Jorgelina Morán-Barrio ◽

María-Natalia Lisa ◽

Alejandro J. Vila

Keyword(s):

Antibiotic Resistance ◽

Protein Stability ◽

Metal Binding ◽

Active Sites ◽

Bacterial Resistance ◽

Structural Diversity ◽

Hydrophobic Core

ABSTRACTMetallo-β-lactamases (MβLs) represent one of the main mechanisms of bacterial resistance against β-lactam antibiotics. The elucidation of their mechanism has been limited mostly by the structural diversity among their active sites. All MβLs structurally characterized so far present a Cys or a Ser residue at position 221, which is critical for catalysis. GOB lactamases stand as an exception within this picture, possessing a Met residue in this location. We studied different mutants in this position, and we show that Met221 is essential for protein stability, most likely due to its involvement in a hydrophobic core. In contrast to other known MβLs, residue 221 is not involved in metal binding or in catalysis in GOB enzymes, further highlighting the structural diversity of MβLs. We also demonstrate the usefulness of protein periplasmic profiles to assess the contribution of protein stability to antibiotic resistance.

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Study on adsorption of CO and CO2 by graphene gas sensor

Modern Physics Letters B ◽

10.1142/s0217984921501542 ◽

2021 ◽

pp. 2150154

Author(s):

Wenchao Tian ◽

Jiahao Niu ◽

Wenhua Li ◽

Xiaohan Liu

Keyword(s):

Gas Sensors ◽

Active Sites ◽

Density Functional ◽

Gas Adsorption ◽

Experimental Studies ◽

Detection Accuracy ◽

Functional Theory ◽

Vacancy Defects ◽

Adsorption Of Co ◽

Detection Characteristics

The two-dimensional (2D) plane of graphene has many active sites for gas adsorption. It has broad application prospects in the field of MEMS gas sensors. At present, there are many experimental studies on graphene gas sensors, but it is difficult to accurately control various influencing factors in the experiments. Therefore, this paper applies the first principle based on density functional theory to study the adsorption and detection characteristics of graphene on CO and CO2. The first-principles analysis method was used to study the adsorption characteristics and sensitivity of graphene. The results show that the inductive graphene has a sensitivity of 1.55% and 0.77% for CO and CO2, respectively. The Stone–Wales defects and multi-vacancy defects have greatly improved the sensitivity of graphene to CO, which is 35.25% and 4.14%, respectively. Introduction of defects increases the sensitivity of detection of CO and CO2, but also improves the selective gas detection material of these two gases. Thus, the control and selectively introducing defects may improve the detection accuracy of the graphene CO and CO2.

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Biochemical characterization of xylanase GH11 isolated from Aspergillus niger BCC14405 (XylB) and its application in xylooligosaccharide production

Biotechnology Letters ◽

10.1007/s10529-021-03202-1 ◽

2021 ◽

Author(s):

Katesuda Aiewviriyasakul ◽

Benjarat Bunterngsook ◽

Hataikarn Lekakarn ◽

Wipawee Sritusnee ◽

Pattanop Kanokratana ◽

...

Keyword(s):

Aspergillus Niger ◽

Biochemical Characterization

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Experimental studies on equilibrium adsorption isosteres and determination of the thermodynamic quantities of polar media on alumina Al2O3

Acta Scientifica Naturalis ◽

10.1515/asn-2017-0006 ◽

2017 ◽

Vol 4 (1) ◽

pp. 34-45 ◽

Cited By ~ 2

Author(s):

Albena Yonova

Keyword(s):

Active Sites ◽

Adsorption Process ◽

Surface Acidity ◽

Experimental Studies ◽

Isosteric Heat ◽

Heat Of Adsorption ◽

Equilibrium Adsorption ◽

Thermodynamic Quantities ◽

Isosteric Heat Of Adsorption ◽

Adsorption Isosteres

Abstract The present work is a revieif of theoretical and experimental study on the adsorption performance of the adsorbent Alumina (Al2O3) used in the adsorption system. An experimental investigation on the equilibrium adsorption isosteres at low pressure (< 1 atm) of working pairs Al2O3/H2O and Al2O3/C2H6O2 is carried out. The isovolume measurement method is adopted in the test setup to directly measure the saturated vapor pressures of working pairs at vapor-liquid equilibrium (dG=0 and dμi=0). Quantity adsorbed is determined from pressure, volume and temperature using gas law. The isosteric heat of adsorption is calculated from the slope of the plot of lnP versus 1/T different amounts of adsorbate onto adsorbent as follows: 0,01 vol% Al2O3/H2O; 0,03 vol% Al2O3/H2O; 0,1 vol% Al2O3/H2O; 0,01 vol% Al2O3/C2H6O2; 0,03 vol% Al2O3/C2H6O2; 0,1 vol% Al2O3/C2H6O2. This study shows that adsorption working pair Al2O3 C2H6O2 has better adsorption performances than those of the A2O3/H2O. Surface acidity! is a most important property! far both adsorption and catalysis and therefore is examined structure of active sites of alumina surface. Thermodynamic parameters such as isosteric heat of adsorption, isosteric enthalpy and entropy of adsorption are critical design variables in estimating the performance and predicting the mechanism of an adsorption process and are also one of the basic requirements for the characterization and optimization of an adsorption process

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Bio-Templating: An Emerging Synthetic Technique for Catalysts. A Review

Catalysts ◽

10.3390/catal11111364 ◽

2021 ◽

Vol 11 (11) ◽

pp. 1364

Author(s):

M. Carmen Herrera-Beurnio ◽

Jesús Hidalgo-Carrillo ◽

Francisco J. López-Tenllado ◽

Juan Martin-Gómez ◽

Rafael C. Estévez ◽

...

Keyword(s):

Active Sites ◽

Experimental Studies ◽

Functional Materials ◽

Inorganic Materials ◽

Hierarchical Organization ◽

Materials Synthesis ◽

Energy Capture ◽

Wide Range ◽

Mineralization Processes ◽

And Storage

In the last few years, researchers have focused their attention on the synthesis of new catalyst structures based on or inspired by nature. Biotemplating involves the transfer of biological structures to inorganic materials through artificial mineralization processes. This approach offers the main advantage of allowing morphological control of the product, as a template with the desired morphology can be pre-determined, as long as it is found in nature. This way, natural evolution through millions of years can provide us with new synthetic pathways to develop some novel functional materials with advantageous properties, such as sophistication, miniaturization, hybridization, hierarchical organization, resistance, and adaptability to the required need. The field of application of these materials is very wide, covering nanomedicine, energy capture and storage, sensors, biocompatible materials, adsorbents, and catalysis. In the latter case, bio-inspired materials can be applied as catalysts requiring different types of active sites (i.e., redox, acidic, basic sites, or a combination of them) to a wide range of processes, including conventional thermal catalysis, photocatalysis, or electrocatalysis, among others. This review aims to cover current experimental studies in the field of biotemplating materials synthesis and their characterization, focusing on their application in heterogeneous catalysis.

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ANTIMICROBIAL ACTIVITY STUDY OF NEW QUINAZOLIN-4(3H)-ONES AGAINST STAPHYLOCOCCUS AUREUS AND STREPTOCOCCUS PNEUMONIAE

Pharmacy & Pharmacology ◽

10.19163/2307-9266-2021-9-4-318-329 ◽

2021 ◽

Vol 9 (4) ◽

pp. 318-329

Author(s):

M. A. Samotrueva ◽

A. A. Ozerov ◽

A. A. Starikova ◽

N. M. Gabitova ◽

D. V. Merezhkina ◽

...

Keyword(s):

Staphylococcus Aureus ◽

Antimicrobial Activity ◽

Streptococcus Pneumoniae ◽

Active Sites ◽

Wide Spectrum ◽

Experimental Studies ◽

Amide Group ◽

Pharmacological Effect ◽

Dilution Method

Quinazolin-4(3H)-one derivatives exhibiting a wide spectrum of a pharmacological activity, represent a promising class of substances used to obtain antibacterial agents, which is especially important in the context of the emergence of pathogenic microorganisms’ resistance to drugs used in medicine. It has been proved that compounds having a naphthyl radical in the molecule, as well as an amide group bound to the benzene ring as quinazolinone substituents, are characterized by a pronounced antimicrobial activity against Staphylococcus aureus and Streptococcus pneumoniae.The aim of the research is a primary microbiological screening of the in vitro antimicrobial activity of new quinazolin-4(3H)-one derivatives against Staphylococcus aureus and Streptococcus pneumoniae, as well as the assessment of the relationship between the pharmacological effect and the structural transformation of the substance molecule, lipophilicity and the possibility of forming resistance to them.Materials and methods. The experimental studies have been carried out using well-known nosocomial pathogens of infectious and inflammatory diseases Staphylococcus aureus and Streptococcus pneumoniae by a serial dilution method.Results. A compound containing a naphthyl radical in its structure, which contributes to an increase in the hydrophobicity of the substance and its solubility in the membrane of a bacterial cell, has a bacteriostatic effect against both Staphylococcus aureus and Streptococcus pneumoniae. A similar pharmacological effect is exhibited by a derivative with an amide group as a substituent of the quinazolinone nucleus linked to a phenyl radical, which probably contributes to an increase in the degree of binding to active sites of enzymes involved in the DNA replication, and protein synthesis. Obviously, the increased lipophilicity, which promotes better binding to the efflux protein, cannot serve as objective characteristics of the emergence possibility of the pathogen’s resistance to this substance.Conclusion. Among the synthesized compounds, the leading substances that exhibit an antimicrobial activity against Staphylococcus aureus and Streptococcus pneumonia, have been identified. The assessment of the chemical structure made it possible to substantiate their pharmacological action and draw conclusions about the possibility of developing resistance to it in microbial cells.

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Biochemical characterization of a glycoside hydrolase family 43 β-D-galactofuranosidase from the fungus Aspergillus niger

10.1101/2021.10.27.466152 ◽

2021 ◽

Author(s):

Gregory S Bulmer ◽

Fang Wei Yuen ◽

Naimah Begum ◽

Bethan S Jones ◽

Sabine S Flitsch ◽

...

Keyword(s):

Aspergillus Niger ◽

Glycoside Hydrolase ◽

Biochemical Characterization ◽

Maximum Activity ◽

Glycoside Hydrolase Family ◽

Enzyme Specificity ◽

Fungal Enzymes ◽

Glycoside Hydrolase Family 43 ◽

Hydrolase Family

β-D-Galactofuranose (Galf) and its polysaccharides are found in bacteria, fungi and protozoa but do not occur in mammalian tissues, and thus represent a specific target for anti-pathogenic drugs. Understanding the enzymatic degradation of these polysaccharides is therefore of great interest, but the identity of fungal enzymes with exclusively galactofuranosidase activity has so far remained elusive. Here we describe the identification and characterization of a galactofuranosidase from the industrially important fungus Aspergillus niger. Phylogenetic analysis of glycoside hydrolase family 43 subfamily 34 (GH43_34) members revealed the occurrence of three distinct clusters and, by comparison with specificities of characterized bacterial members, suggested a basis for prediction of enzyme specificity. Using this rationale, in tandem with molecular docking, we identified a putative β-D-galactofuranosidase from A. niger which was recombinantly expressed in Escherichia coli. The Galf-specific hydrolase, encoded by xynD demonstrates maximum activity at pH 5, 25 °C towards 4-Nitrophenyl-β-galactofuranoside (pNP-βGalf), with a Km of 17.9 ± 1.9 mM and Vmax of 70.6 ± 5.3 μmol min-1. The characterization of this first fungal GH43 galactofuranosidase offers further molecular insight into the degradation of Galf-containing structures and may inform clinical treatments against fungal pathogens.

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Platinum–copper single atom alloy catalysts with high performance towards glycerol hydrogenolysis

Nature Communications ◽

10.1038/s41467-019-13685-2 ◽

2019 ◽

Vol 10 (1) ◽

Cited By ~ 33

Author(s):

Xi Zhang ◽

Guoqing Cui ◽

Haisong Feng ◽

Lifang Chen ◽

Hui Wang ◽

...

Keyword(s):

Active Sites ◽

High Performance ◽

Reaction Pathway ◽

Theoretical Calculations ◽

Experimental Studies ◽

Value Added ◽

Catalytic Performance ◽

Single Atom ◽

Glycerol Hydrogenolysis ◽

Single Atom Alloy

AbstractSelective hydrogenolysis of biomass-derived glycerol to propanediol is an important reaction to produce high value-added chemicals but remains a big challenge. Herein we report a PtCu single atom alloy (SAA) catalyst with single Pt atom dispersed on Cu nanoclusters, which exhibits dramatically boosted catalytic performance (yield: 98.8%) towards glycerol hydrogenolysis to 1,2-propanediol. Remarkably, the turnover frequency reaches up to 2.6 × 103 molglycerol·molPtCu–SAA−1·h−1, which is to our knowledge the largest value among reported heterogeneous metal catalysts. Both in situ experimental studies and theoretical calculations verify interface sites of PtCu–SAA serve as intrinsic active sites, in which the single Pt atom facilitates the breakage of central C–H bond whilst the terminal C–O bond undergoes dissociation adsorption on adjacent Cu atom. This interfacial synergistic catalysis based on PtCu–SAA changes the reaction pathway with a decreased activation energy, which can be extended to other noble metal alloy systems.

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