Molecular Dynamics Simulation and Site-Directed Mutagenesis of Alcohol Acyltransferase: A Proposed Mechanism of Catalysis

2013 ◽  
Vol 53 (10) ◽  
pp. 2689-2700 ◽  
Author(s):  
Luis Morales-Quintana ◽  
María Ximena Nuñez-Tobar ◽  
María Alejandra Moya-León ◽  
Raúl Herrera
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Site Directed Mutagenesis ◽  
Dynamics Simulation ◽  
Directed Mutagenesis ◽  
Mechanism Of Catalysis ◽  
Alcohol Acyltransferase

Molecular dynamics simulation of site-directed mutagenesis of HIV-1 Tattrans-activator

1999 ◽  
Vol 44 (8) ◽  
pp. 708-711 ◽  
Author(s):  
Yan Cui ◽  
Lunjiang Ling ◽  
Runsheng Chen ◽  
Longchuan Bai ◽  
Jiangang Yuan ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Site Directed Mutagenesis ◽  
Dynamics Simulation ◽  
Directed Mutagenesis ◽  
Hiv 1

Affinity enhancement of nanobody binding to EGFR: in silico site-directed mutagenesis and molecular dynamics simulation approaches

2016 ◽  
Vol 35 (8) ◽  
pp. 1710-1728 ◽  
Author(s):  
Alireza Farasat ◽  
Fatemeh Rahbarizadeh ◽  
Ghader Hosseinzadeh ◽  
Sharareh Sajjadi ◽  
Mehdi Kamali ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
In Silico ◽  
Site Directed Mutagenesis ◽  
Dynamics Simulation ◽  
Directed Mutagenesis

scholarly journals Characterization of suramin binding sites on the human group IIA secreted phospholipase A2 by site-directed mutagenesis and molecular dynamics simulation

2012 ◽  
Vol 519 (1) ◽  
pp. 17-22 ◽  
Author(s):  
Elisângela Aparecida Aragão ◽  
Davi Serradella Vieira ◽  
Lucimara Chioato ◽  
Tatiana Lopes Ferreira ◽  
Marcos Roberto Lourenzoni ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Phospholipase A2 ◽  
Binding Sites ◽  
Site Directed Mutagenesis ◽  
Dynamics Simulation ◽  
Directed Mutagenesis ◽  
Human Group ◽  
Secreted Phospholipase A2

scholarly journals Construction of Novel Aspartokinase Mutant A380I and Its Characterization by Molecular Dynamics Simulation

Molecules ◽  
2018 ◽  
Vol 23 (12) ◽  
pp. 3379 ◽  
Author(s):  
Caijing Han ◽  
Li Fang ◽  
Chunlei Liu ◽  
Yunna Gao ◽  
Weihong Min
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
High Throughput Screening ◽  
Model Comparison ◽  
Site Directed Mutagenesis ◽  
Dynamics Simulation ◽  
Wild Type ◽  
Open Conformation ◽  
Simulation Results ◽  
Optimal Ph

In this study, a novel monomer aspartokinase (AK) from Corynebacterium pekinense was identified, and its monomer model was constructed. Site 380 was identified by homologous sequencing and monomer model comparison as the key site which was conserved and located around the binding site of the inhibitor Lys. Furthermore, the mutant A380I with enzyme activity 11.32-fold higher than wild type AK (WT-AK), was obtained by site-directed mutagenesis and high throughput screening. In the mutant A380I, the optimal temperature was raised from 26 °C (WT-AK) to 28 °C, the optimal pH remained unchanged at 8.0, and the half-life was prolonged from 4.5 h (WT-AK) to 6.0 h, indicating enhanced thermal stability. The inhibition of A380I was weakened at various inhibitor concentrations and even activated at certain inhibitor concentrations (10 mM of Lys, 5 mM or 10 mM of Lys + Thr, 10 mM of Lys + Met, 5 mM of Lys + Thr + Met). Molecular dynamics simulation results indicated that the occupancy rate of hydrogen bond between A380I and ATP was enhanced, the effect of Lys (inhibitor) on the protein was weakened, and the angle between Ser281-Tyre358 and Asp359-Gly427 was increased after mutation, leading to an open conformation (R-state) that favored the binding of substrate.

scholarly journals Probing the importance of hydrogen bonds in the active site of the subtilisin nattokinase by site-directed mutagenesis and molecular dynamics simulation

2006 ◽  
Vol 395 (3) ◽  
pp. 509-515 ◽  
Author(s):  
Zhong-liang Zheng ◽  
Mao-qing Ye ◽  
Zhen-yu Zuo ◽  
Zhi-gang Liu ◽  
Keng-chang Tai ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Hydrogen Bonds ◽  
Transition State ◽  
Enzyme Kinetics ◽  
Structural Model ◽  
Catalytic Triad ◽  
Site Directed Mutagenesis ◽  
Dynamics Simulation ◽  
Directed Mutagenesis

Hydrogen bonds occurring in the catalytic triad (Asp32, His64 and Ser221) and the oxyanion hole (Asn155) are very important to the catalysis of peptide bond hydrolysis by serine proteases. For the subtilisin NK (nattokinase), a bacterial serine protease, construction and analysis of a three-dimensional structural model suggested that several hydrogen bonds formed by four residues function to stabilize the transition state of the hydrolysis reaction. These four residues are Ser33, Asp60, Ser62 and Thr220. In order to remove the effect of these hydrogen bonds, four mutants (Ser33→Ala33, Asp60→Ala60, Ser62→Ala62, and Thr220→Ala220) were constructed by site-directed mutagenesis. The results of enzyme kinetics indicated that removal of these hydrogen bonds increases the free-energy of the transition state (ΔΔGT). We concluded that these hydrogen bonds are more important for catalysis than for binding the substrate, because removal of these bonds mainly affects the kcat but not the Km values. A substrate, SUB1 (succinyl-Ala-Ala-Pro-Phe-p-nitroanilide), was used during enzyme kinetics experiments. In the present study we have also shown the results of FEP (free-energy perturbation) calculations with regard to the binding and catalysis reactions for these mutant subtilisins. The calculated difference in FEP also suggested that these four residues are more important for catalysis than binding of the substrate, and the simulated values compared well with the experimental values from enzyme kinetics. The results of MD (molecular dynamics) simulations further demonstrated that removal of these hydrogen bonds partially releases Asp32, His64 and Asn155 so that the stability of the transition state decreases. Another substrate, SUB2 (H-D-Val-Leu-Lys-p-nitroanilide), was used for FEP calculations and MD simulations.

Sign in / Sign up

Export Citation Format

Share Document