scholarly journals Investigation the role of mutations M182T and Q39K in structure of beta-lactamase TEM-72 by molecular dynamics method

2016 ◽  
Vol 62 (5) ◽  
pp. 527-534
Author(s):  
D.S. Shcherbinin ◽  
M.Yu. Rubtsova ◽  
V.G. Grigorenko ◽  
I.V. Uporov ◽  
A.V. Veselovsky ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Enzyme Activity ◽  
High Temperature ◽  
Active Site ◽  
Bacterial Resistance ◽  
Beta Lactamase ◽  
Amino Acid Residues ◽  
The Common ◽  
Dynamics Method

Synthesis of b-lactamases is one of the common mechanisms of bacterial resistance to b-lactam antibiotics including penicillins and cephalosporins. The widespread use of antibiotics results in appearance of numerous extended-spectrum b-lactamase variants or resistance to inhibitors. Mutations of 92 residues of TEM type were found. Several mutations are the key mutations that determine the extension of spectrum of substrates. However, roles of the most associated mutations, located far from active site, remain unknown. We have investigated the role of associated mutations in structure of b-lactamase TEM-72, which contain two key mutation (G238S, E240K) and two associated mutations (Q39K, M182T) by means of simulation of molecular dynamics. The key mutation lead to destabilization of the protein globule, characterized by increased mobility of amino acid residues at high temperature of modelling. Mutation M182T lead to stabilization protein, whereas mutation Q39K is destabilizing mutation. It seems that the last mutation serves for optimization of conformational mobility of b-lactamase and may influence on enzyme activity.

scholarly journals Significant role of Asn-247 and Arg-64 residues in close proximity of the active site in maintaining the catalytic function of CTX-M-15 type β-lactamase

RSC Advances ◽  
2019 ◽  
Vol 9 (10) ◽  
pp. 5325-5337 ◽  
Author(s):  
Lubna Maryam ◽  
Shamsi Khalid ◽  
Abid Ali ◽  
Asad U. Khan
Keyword(s):  
Amino Acid ◽  
Significant Role ◽  
Active Site ◽  
Catalytic Efficiency ◽  
Beta Lactamase ◽  
Amino Acid Residues ◽  
Catalytic Function ◽  
Close Proximity

Mutations of amino acid residues present near active site decrease the catalytic efficiency of beta lactamase enzymes.

scholarly journals IDENTIFICATION OF POTENTIAL SALMONELLA TYPHI BETA-LACTAMASE TEM 1 INHIBITORS USING PEPTIDOMIMETICS, VIRTUAL SCREENING, AND MOLECULAR DYNAMICS SIMULATIONS

2018 ◽  
Vol 10 (1) ◽  
pp. 91
Author(s):  
Rakesh K. R. Pandit ◽  
Dinesh Gupta ◽  
Tapan K. Mukherjee
Keyword(s):  
Molecular Dynamics ◽  
Antibiotic Resistance ◽  
Virtual Screening ◽  
Molecular Dynamics Simulations ◽  
Active Site ◽  
Beta Lactamase ◽  
Ramachandran Plot ◽  
Small Peptide ◽  
In Silico Docking ◽  
Dynamics Simulations

Objective: The purpose of this study was to identify a potential peptidomimetic S. typhi Beta-lactamase TEM 1 inhibitor to tackle the antibiotic resistance among S. typhi.Methods: The potential peptidomimetic inhibitor was identified by in silico docking of the small peptide WFRKQLKW with S. typhi Beta-lactamase TEM 1. The 3D coordinate geometry of the residues of small peptide interacting with the active site of the receptor was generated and mimics were identified using PEP: MMs: MIMIC server. All the identified mimics were docked at the active site of the receptor using Autodock 4.2 and the best-docked complex was selected on the basis of binding energy and number of H-bonds. The complex was then subjected to molecular dynamics simulations of 30 ns using AMBER 12 software package. The stereochemical stability of the Beta-lactamase TEM 1-WFRKQLKW complex was estimated with the help of Ramachandran plot using PROCHECK tool.Results: In the present study, a new potential peptidomimetic inhibitor (ZINC05839264) of Beta-lactamase TEM 1 has been identified based on antimicrobial peptide WFRKQLKW by virtual screening of the MMsINC database. The docking and molecular simulation studies revealed that the mimic binds more tightly to the active site of the receptor than the peptide. The Ramachandran plot also shows that the Beta-lactamase TEM 1-mimic complex is stereo chemically more stable than Beta-lactamase TEM 1-WFRKQLKW complex as more number of residues (93.6%) are falling under the core region of the plot in case of the former.Conclusion: The study shows that the peptidomimetic compound can act as a potential inhibitor of S. typhi Beta-lactamase TEM 1 and further it can be developed into more effective therapeutic to tackle the problem of antibiotic resistance.

scholarly journals Molecular Dynamics Study of Twister Ribozyme: Role of Mg2+Ions and the Hydrogen-Bonding Network in the Active Site

Biochemistry ◽  
2016 ◽  
Vol 55 (27) ◽  
pp. 3834-3846 ◽  
Author(s):  
Melek N. Ucisik ◽  
Philip C. Bevilacqua ◽  
Sharon Hammes-Schiffer
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Active Site ◽  
Hydrogen Bonding Network

Molecular dynamics study of active-site interactions with tetracoordinate transients in acetylcholinesterase and its mutants

2001 ◽  
Vol 353 (3) ◽  
pp. 645-653 ◽  
Author(s):  
Istvan J. ENYEDY ◽  
Ildiko M. KOVACH ◽  
Akos BENCSURA
Keyword(s):  
Molecular Dynamics ◽  
Glutamic Acid ◽  
Active Site ◽  
Indole Ring ◽  
Active Site Residues ◽  
Parallel Simulations ◽  
Electrostatic Stabilization ◽  
Carbenium Ion ◽  
Dynamics Simulations

The role of active-site residues in the dealkylation reaction in the PSCS diastereomer of 2-(3,3-dimethylbutyl)methylphosphonofluoridate (soman)-inhibited Torpedo californicaacetylcholinesterase (AChE) was investigated by full-scale molecular dynamics simulations using CHARMM: > 400ps equilibration was followed by 150–200ps production runs with the fully solvated tetracoordinate phosphonate adduct of the wild-type, Trp84Ala and Gly199Gln mutants of AChE. Parallel simulations were carried out with the tetrahedral intermediate formed between serine-200 Oγ of AChE and acetylcholine. We found that the NεH in histidine H+-440 is positioned to protonate the oxygen in choline and thus promote its departure. In contrast, NεH in histidine H+-440 is not aligned for a favourable proton transfer to the pinacolyl O to promote dealkylation, but electrostatic stabilization by histidine H+-440 of the developing anion on the phosphonate monoester occurs. Destabilizing interactions between residues and the alkyl fragment of the inhibitor enforce methyl migration from Cβ to Cα concerted with C—O bond breaking in soman-inhibited AChE. Tryptophan-84, phenyalanine-331 and glutamic acid-199 are within 3.7–3.9 Å (1 Å=10-10 m) from a methyl group in Cβ, 4.5–5.1 Å from Cβ and 4.8–5.8 Å from Cα, and can better stabilize the developing carbenium ion on Cβ than on Cα. The Trp84Ala mutation eliminates interactions between the incipient carbenium ion and the indole ring, but also reduces its interactions with phenylalanine-331 and aspartic acid-72. Tyrosine-130 promotes dealkylation by interacting with the indole ring of tryptophan-84. Glutamic acid-443 can influence the orientation of active-site residues through tyrosine-421, tyrosine-442 and histidine-440 in soman-inhibited AChE, and thus facilitate dealkylation.

Crystal structure of adenylate kinase from an extremophilic archaeon Aeropyrum pernix with ATP and AMP

2020 ◽  
Vol 168 (3) ◽  
pp. 223-229
Author(s):  
Yoshinori Shibanuma ◽  
Naoki Nemoto ◽  
Norifumi Yamamoto ◽  
Gen-Ichi Sampei ◽  
Gota Kawai
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Reaction Mechanism ◽  
Adenylate Kinase ◽  
Reaction Coordinate ◽  
Amino Acid Residues ◽  
Aeropyrum Pernix ◽  
Adenylate Kinases

Abstract The crystal structure of an adenylate kinase from an extremophilic archaeon Aeropyrum pernix was determined in complex with full ligands, ATP-Mg2+ and AMP, at a resolution of 2.0 Å. The protein forms a trimer as found for other adenylate kinases from archaea. Interestingly, the reacting three atoms, two phosphorus and one oxygen atoms, were located almost in line, supporting the SN2 nucleophilic substitution reaction mechanism. Based on the crystal structure obtained, the reaction coordinate was estimated by the quantum mechanics calculations combined with molecular dynamics. It was found that the reaction undergoes two energy barriers; the steps for breaking the bond between the oxygen and γ-phosphorus atoms of ATP to produce a phosphoryl fragment and creating the bond between the phosphoryl fragment and the oxygen atom of the β-phosphate group of ADP. The reaction coordinate analysis also suggested the role of amino-acid residues for the catalysis of adenylate kinase.

scholarly journals Electrostatic compared with hydrophobic interactions between bovine serum amine oxidase and its substrates

2003 ◽  
Vol 371 (2) ◽  
pp. 549-556 ◽  
Author(s):  
Maria Luisa DI PAOLO ◽  
Roberto STEVANATO ◽  
Alessandra CORAZZA ◽  
Fabio VIANELLO ◽  
Lorenzo LUNELLI ◽  
...  
Keyword(s):  
Active Site ◽  
Bovine Serum ◽  
Hydrophobic Interactions ◽  
Amine Oxidase ◽  
Amino Acid Residues ◽  
Deprotonated Form ◽  
Steady State Kinetic ◽  
Wide Range ◽  
Order Of Magnitude

A steady-state kinetic study of bovine serum amine oxidase activity was performed, over a wide range of pH values (5.4–10.2) and ionic strength (10–200mM), using various (physiological and analogue) substrates as specific probes of the active-site binding region. Relatively small changes in kcat values (approx. one order of magnitude) accompanied by marked changes in Km and kcat/Km values (approx. six orders of magnitude) were observed. This behaviour was correlated with the presence of positively charged groups or apolar chains in the substrates. In particular, it was found that the docking of the physiological polyamines, i.e. spermidine and spermine, appears to be modulated by three amino acid residues of the active site, which we have named L-H+, G-H+ and IH+, characterized by pKa values of 6.2±0.2 [Di Paolo, Scarpa, Corazza, Stevanato and Rigo (2002) Biophys. J. 83, 2231–2239], 8.2±0.3 and 7.8±0.4 respectively. The electrostatic interaction between the protonated substrates and the enzyme containing the residues L-H+, G-H+ and IH+ in the deprotonated form, the on/off role of the IH+ residue and the role of hydrophobic interactions with substrates characterized by apolar chains are discussed.

Glutamic acid-65 is an essential residue for catalysis in Proteus mirabilis glutathione S-transferase B1-1

2002 ◽  
Vol 363 (1) ◽  
pp. 189-193 ◽  
Author(s):  
Nerino ALLOCATI ◽  
Michele MASULLI ◽  
Enrico CASALONE ◽  
Silvia SANTUCCI ◽  
Bartolo FAVALORO ◽  
...  
Keyword(s):  
Proteus Mirabilis ◽  
Active Site ◽  
Structural Integrity ◽  
Catalytic Efficiency ◽  
Site Directed Mutagenesis ◽  
Amino Acid Residues ◽  
Cd Spectra ◽  
Glutathione S Transferase ◽  
Terminal Amino

The functional role of three conserved amino acid residues in Proteus mirabilis glutathione S-transferase B1-1 (PmGST B1-1) has been investigated by site-directed mutagenesis. Crystallographic analyses indicated that Glu65, Ser103 and Glu104 are in hydrogen-bonding distance of the N-terminal amino group of the γ-glutamyl moiety of the co-substrate, GSH. Glu65 was mutated to either aspartic acid or leucine, and Ser103 and Glu104 were both mutated to alanine. Glu65 mutants (Glu65→Asp and Glu65→Leu) lost all enzyme activity, and a drastic decrease in catalytic efficiency was observed for Ser103→Ala and Glu104→Ala mutants toward both 1-chloro-2,4-dinitrobenzene and GSH. On the other hand, all mutants displayed similar intrinsic fluorescence, CD spectra and thermal stability, indicating that the mutations did not affect the structural integrity of the enzyme. Taken together, these results indicate that Ser103 and Glu104 are significantly involved in the interaction with GSH at the active site of PmGST B1-1, whereas Glu65 is crucial for catalysis.

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