scholarly journals Exploring the Role of L10 Loop in New Delhi Metallo-β-lactamase (NDM-1): Kinetic and Dynamic Studies

Molecules ◽  
2021 ◽  
Vol 26 (18) ◽  
pp. 5489
Author(s):  
Alessandra Piccirilli ◽  
Emanuele Criscuolo ◽  
Fabrizia Brisdelli ◽  
Paola Sandra Mercuri ◽  
Sabrina Cherubini ◽  
...  
Keyword(s):  
Enzyme Activity ◽  
Amino Acid ◽  
Double Mutant ◽  
Amino Acid Substitutions ◽  
New Delhi ◽  
Kinetic Behavior ◽  
Dynamic Studies ◽  
The Stability

Four NDM-1 mutants (L218T, L221T, L269H and L221T/Y229W) were generated in order to investigate the role of leucines positioned in L10 loop. A detailed kinetic analysis stated that these amino acid substitutions modified the hydrolytic profile of NDM-1 against some β-lactams. Significant reduction of kcat values of L218T and L221T for carbapenems, cefazolin, cefoxitin and cefepime was observed. The stability of the NDM-1 and its mutants was explored by thermofluor assay in real-time PCR. The determination of TmB and TmD demonstrated that NDM-1 and L218T were the most stable enzymes. Molecular dynamic studies were performed to justify the differences observed in the kinetic behavior of the mutants. In particular, L218T fluctuated more than NDM-1 in L10, whereas L221T would seem to cause a drift between residues 75 and 125. L221T/Y229W double mutant exhibited a decrease in the flexibility with respect to L221T, explaining enzyme activity improvement towards some β-lactams. Distances between Zn1-Zn2 and Zn1-OH- or Zn2-OH- remained unaffected in all systems analysed. Significant changes were found between Zn1/Zn2 and first sphere coordination residues.

scholarly journals Effects of Amino Acid Substitutions at Conserved and Acidic Residues within Region 1.1 of Escherichia coli ς70

2000 ◽  
Vol 182 (1) ◽  
pp. 221-224 ◽  
Author(s):  
Christina Wilson Bowers ◽  
Andrea McCracken ◽  
Alicia J. Dombroski
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Aspartic Acid ◽  
Transcription Initiation ◽  
Amino Acid Substitutions ◽  
Conserved Residues ◽  
Acidic Residues

ABSTRACT Amino acid substitutions in Escherichia coliς70 were generated and characterized in an analysis of the role of region 1.1 in transcription initiation. Several acidic and conserved residues are tolerant of substitution. However, replacement of aspartic acid 61 with alanine results in inactivity caused by structural and functional thermolability.

scholarly journals Avaliação da estabilidade de agregados e a vulnerabilidade à erosão ao longo de uma vertente no município de Araruna, região noroeste do Paraná-Brasil / Evaluation of aggregates stability and vulnerability to erosion along a shed in the municipality of Araruna, northwest region of Paraná-Brazil

2018 ◽  
Vol 28 (55) ◽  
pp. 845-862
Author(s):  
Fabiana Barros Medeiros ◽  
Francieli Sant'ana Marcatto ◽  
Hélio Silveira ◽  
MariaTeresa De Nóbrega
Keyword(s):  
Structural Analysis ◽  
Soil Cover ◽  
Morphological Characteristics ◽  
Soil Horizons ◽  
Water Flows ◽  
Sandstone Formation ◽  
The Stability ◽  
Northwest Region

Esta pesquisa tem como objetivo estudar a vulnerabilidade à erosão dos solos da zona de contato do arenito da Formação Caiuá com o basalto da Formação Serra Geral, no município de Araruna, Mesorregião Noroeste Paranaense, dando enfoque ao papel da estabilidade da estrutura atual dos solos, considerando-se as alterações produzidas pelas formas de uso e ocupação da área. A análise realizada também considerou as variações das características morfológicas dos solos em perfil e ao longo da litossequência (sistema pedológico), assim como os seus reflexos na geração de setores mais ou menos suscetíveis à erosão na vertente. Para o levantamento dos solos ao longo da vertente foram utilizados os procediments propostos pela Análise Estrutural da Cobertura Pedológica e a coleta de amostras para a determinação da granulometria e estabilidade de agregados. Os resultados indicaram a ação dos fluxos de água laterais e verticais, atuando na transformação dos horizontes dos solos ao longo da vertente e uma variação da estabilidade estrutural associada as características morfológicas dos solos e ao tipo de uso e manejo empregado. Os Argissolos apresentaram agregados pequenos e um gradiente textural entre o horizonte superficial e subsuperficial, lhe conferindo uma forte suscetibilidade a erosão. O Nitossolo não apresentou grande diferenciação no tamanho dos agregados, exceto no horizonte Bw, onde a redução no tamanho dos agregados se associaram a mudança morfológica da estrutura do solo.AbstractThis research aims to study the vulnerability to soil erosion of the contact zone of the sandstone Formation Caiuá with basalt of the Serra Geral Formation, in the municipality of Araruna, Paraná Northwest Region, giving focus to the role of the stability of the current structure of soils, considering the changes produced by the forms of use and occupation of the area. The analysis also considered variations of morphological characteristics of soils in profile and along the lithosactivity (pedological system), as well as your reflexes in the generation of sectors more or less susceptible to erosion in the shed. For the survey of the soils along the strand, the procedures proposed by the Structural Analysis of the Pedological Coverage and the collection of samples for the determination of the granulometry and stability of aggregates were used. The results indicated the action of the lateral and vertical water flows, acting on the transformation of the soil horizons along the slope and a variation of the structural stability associated with the morphological characteristics of the soils and the type of use and management used. The Argisols presented small aggregates and a textural gradient between the surface and subsurface horizon, giving it a strong susceptibility to erosion. The Nitossolo did not show great differentiation in the size of the aggregates, except in the Bw horizon, where the reduction in the size of the aggregates was associated to the morphological change of the soil structure.Keywords: structural analysis of the soil cover, stability of aggregates, susceptibility to erosion, pedological systems.

D-Serine metabolism: new insights into the modulation of D-amino acid oxidase activity

2013 ◽  
Vol 41 (6) ◽  
pp. 1551-1556 ◽  
Author(s):  
Silvia Sacchi
Keyword(s):  
Enzyme Activity ◽  
Amino Acid ◽  
Oxidase Activity ◽  
Acid Oxidase ◽  
Endogenous Ligand ◽  
Amino Acid Oxidase ◽  
The Brain ◽  
Serine Metabolism ◽  
Synthesis And Degradation

Over the years, accumulating evidence has indicated that D-serine represents the main endogenous ligand of NMDA (N-methyl-D-aspartate) receptors. In the brain, the concentration of D-serine stored in cells is defined by the activity of two enzymes: serine racemase (responsible for both the synthesis and degradation) and D-amino acid oxidase (which catalyses D-serine degradation). The present review is focused on human D-amino acid oxidase, discussing the mechanisms involved in modulating enzyme activity and stability, with the aim to substantiate the pivotal role of D-amino acid oxidase in brain D-serine metabolism.

Role of charged amino acid side chains in the stability and lipid binding ofManduca sexta apolipophorin III

1995 ◽  
Vol 30 (2-3) ◽  
pp. 211-223 ◽  
Author(s):  
Minal Upadhyaya ◽  
Kim Oikawa ◽  
Cyril M. Kay ◽  
Douglas G. Scraba ◽  
Roger Bradley ◽  
...  
Keyword(s):  
Amino Acid ◽  
Lipid Binding ◽  
Side Chains ◽  
Apolipophorin Iii ◽  
Amino Acid Side Chains ◽  
The Stability

scholarly journals Additivity of the Stabilization Effect of Single Amino Acid Substitutions in Triple Mutants of Recombinant Formate Dehydrogenase from the Soybean Glycine max

Acta Naturae ◽  
2015 ◽  
Vol 7 (3) ◽  
pp. 55-64 ◽  
Author(s):  
A. A. Alekseeva ◽  
I. S. Kargov ◽  
S. Yu. Kleimenov ◽  
S. S. Savin ◽  
V I. Tishkov
Keyword(s):  
Thermal Stability ◽  
Glycine Max ◽  
Amino Acid ◽  
Formate Dehydrogenase ◽  
Single Amino Acid ◽  
Inactivation Kinetics ◽  
Amino Acid Substitutions ◽  
Stabilization Effect ◽  
The Stability ◽  
Thermal Stability Of

Recently, we demonstrated that the amino acid substitutions Ala267Met and Ala267Met/Ile272Val (Alekseeva et al., Biochemistry, 2012), Phe290Asp, Phe290Asn and Phe290Ser (Alekseeva et al., Prot. Eng. Des. Select, 2012) in recombinant formate dehydrogenase from soya Glycine max (SoyFDH) lead to a significant (up to 30-100 times) increase in the thermal stability of the enzyme. The substitutions Phe290Asp, Phe290Asn and Phe290Ser were introduced into double mutant SoyFDH Ala267Met/Ile272Val by site-directed mutagenesis. Combinations of three substitutions did not lead to a noticeable change in the catalytic properties of the mutant enzymes. The stability of the resultant triple mutants was studied through thermal inactivation kinetics and differential scanning calorimetry. The thermal stability of the new mutant SoyFDHs was shown to be much higher than that of their precursors. The stability of the best mutant SoyFDH Ala267Met/Ile272Val/Phe290Asp turned out to be comparable to that of the most stable wild-type formate dehydrogenases from other sources. The results obtained with both methods indicate a great synergistic contribution of individual amino acid substitutions to the common stabilization effect.

scholarly journals Gamma Irradiation of Aqueos Solution of L-Aspartic Acid, L-Aspartic Acid in Solid State, and L-Aspartic Acid Adsorbed into Na-Montmorillonite: Its Relevance in Chemistry Prebiotic

2021 ◽  
Vol 8 (2) ◽  
pp. 105-108
Author(s):  
A. Meléndez-López ◽  
M. F. García-Hurtado ◽  
J. Cruz-Castañeda ◽  
A. Negrón-Mendoza ◽  
S. Ramos-Bernal ◽  
...  
Keyword(s):  
Organic Matter ◽  
Amino Acid ◽  
Solid State ◽  
Aspartic Acid ◽  
Prebiotic Chemistry ◽  
High Energy ◽  
Energy Conditions ◽  
Gamma Radiolysis ◽  
The Stability

Aspartic acid is an amino acid present in the modern proteins, however, is considered a primitive amino acid hence its importance in prebiotic chemistry experiments studies. In some works of prebiotic chemistry have been studied the synthesis and the stability of organic matter under high energy sources, and the role of clays has been highlighted due to clays that can affect the reaction mechanisms in the radiolytic processes. The present work is focused on the study of the role of Namontmorillonite in the gamma radiolysis processes of L-aspartic acid. Gamma radiolysis processes were carried out in three different systems a) L-aspartic acid in aqueous solution; b) L-aspartic acid in solid-state; and c) L-aspartic acid adsorbed into Na-montmorillonite. L-aspartic acid was analyzed by high-performance liquid chromatography−electrospray ionization−mass spectrometry (HPLCESI-MS). The results showed that the decomposition of L-aspartic acid considerably decreased in the presence of clay thus highlighting the protector role of clays and favors the stability of organic matter even under the possible high energy conditions of primitive environments. The principal product ofgamma radiolysis of L-aspartic acid was succinic acid produced by deamination reaction. On the other hand, when aspartic acid was irradiated in solid-state the main product was the L-aspartic acid dimer. Both radiolysis products are important for chemical evolution processes for L-aspartic acid in primitive environments.

scholarly journals Functional role of catalytic triad and oxyanion hole-forming residues on enzyme activity of Escherichia coli thioesterase I/protease I/phospholipase L1

2006 ◽  
Vol 397 (1) ◽  
pp. 69-76 ◽  
Author(s):  
Li-Chiun Lee ◽  
Ya-Lin Lee ◽  
Ruey-Jyh Leu ◽  
Jei-Fu Shaw
Keyword(s):  
Escherichia Coli ◽  
Enzyme Activity ◽  
Amino Acid ◽  
Water Molecule ◽  
Acyl Chain ◽  
Residual Activity ◽  
Catalytic Triad ◽  
The Other ◽  
Oxyanion Hole

Escherichia coli TAP (thioesterase I, EC 3.1.2.2) is a multifunctional enzyme with thioesterase, esterase, arylesterase, protease and lysophospholipase activities. Previous crystal structural analyses identified its essential amino acid residues as those that form a catalytic triad (Ser10-Asp154-His157) and those involved in forming an oxyanion hole (Ser10-Gly44-Asn73). To gain an insight into the biochemical roles of each residue, site-directed mutagenesis was employed to mutate these residues to alanine, and enzyme kinetic studies were conducted using esterase, thioesterase and amino-acid-derived substrates. Of the residues, His157 is the most important, as it plays a vital role in the catalytic triad, and may also play a role in stabilizing oxyanion conformation. Ser10 also plays a very important role, although the small residual activity of the S10A variant suggests that a water molecule may act as a poor substitute. The water molecule could possibly be endowed with the nucleophilic-attacking character by His157 hydrogen-bonding. Asp154 is not as essential compared with the other two residues in the triad. It is close to the entrance of the substrate tunnel, therefore it predominantly affects substrate accessibility. Gly44 plays a role in stabilizing the oxyanion intermediate and additionally in acyl-enzyme-intermediate transformation. N73A had the highest residual enzyme activity among all the mutants, which indicates that Asn73 is not as essential as the other mutated residues. The role of Asn73 is proposed to be involved in a loop75–80 switch-move motion, which is essential for the accommodation of substrates with longer acyl-chain lengths.

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