A Computational Approach to Enzyme Design: Predicting ω-Aminotransferase Catalytic Activity Using Docking and MM-GBSA Scoring

2014 ◽  
Vol 54 (8) ◽  
pp. 2334-2346 ◽  
Author(s):  
Sarah Sirin ◽  
Rajesh Kumar ◽  
Carlos Martinez ◽  
Michael J. Karmilowicz ◽  
Preeyantee Ghosh ◽  
...  
Keyword(s):  
Catalytic Activity ◽  
Computational Approach ◽  
Enzyme Design

Physics-based enzyme design: Predicting binding affinity and catalytic activity

2014 ◽  
Vol 82 (12) ◽  
pp. 3397-3409 ◽  
Author(s):  
Sarah Sirin ◽  
David A. Pearlman ◽  
Woody Sherman
Keyword(s):  
Catalytic Activity ◽  
Binding Affinity ◽  
Enzyme Design

scholarly journals Directed Evolution of a Glutathione Transferase for the Development of a Biosensor for Alachlor Determination

Symmetry ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 461
Author(s):  
Fereniki Perperopoulou ◽  
Maria Fragoulaki ◽  
Anastassios C. Papageorgiou ◽  
Nikolaos E. Labrou
Keyword(s):  
Catalytic Activity ◽  
Glutathione Transferase ◽  
Dna Recombination ◽  
Enzyme Reaction ◽  
Optical Biosensor ◽  
Enzyme Design ◽  
Ph Indicator ◽  
Environment Friendly ◽  
Subunit Interface ◽  
Molecular Modeling Studies

In the present work, DNA recombination of three homologous tau class glutathione transferases (GSTUs) allowed the creation of a library of tau class GmGSTUs. The library was activity screened for the identification of glutathione transferase (GST) variants with enhanced catalytic activity towards the herbicide alachlor (2-chloro-2′,6′-diethyl-N-(methoxymethyl)acetanilide). One enzyme variant (GmGSTsf) with improved catalytic activity and binding affinity for alachlor was identified and explored for the development of an optical biosensor for alachlor determination. Kinetics analysis and molecular modeling studies revealed a key mutation (Ile69Val) at the subunit interface (helix α3) that appeared to be responsible for the altered catalytic properties. The enzyme was immobilized directly on polyvinylidenefluoride membrane by crosslinking with glutaraldehyde and was placed on the inner surface of a plastic cuvette. The rate of pH changes observed as a result of the enzyme reaction was followed optometrically using a pH indicator. A calibration curve indicated that the linear concentration range for alachlor was 30–300 μM. The approach used in the present study can provide tools for the generation of novel enzymes for eco-efficient and environment-friendly analytical technologies. In addition, the outcome of this study gives an example for harnessing protein symmetry for enzyme design.

scholarly journals Computational design to improve catalytic activity of cephalosporin C acylase from Pseudomonas strain N176

RSC Advances ◽  
2017 ◽  
Vol 7 (48) ◽  
pp. 30370-30375 ◽  
Author(s):  
Ye Tian ◽  
Zhaobin Xu ◽  
Xiaoqiang Huang ◽  
Yushan Zhu
Keyword(s):  
Catalytic Activity ◽  
In Silico ◽  
Computational Design ◽  
Cephalosporin C ◽  
Enzyme Design ◽  
Catalytic Activities ◽  
Highly Efficient ◽  
Cephalosporin C Acylase

Engineering enzymes with high catalytic activities using enzyme designin silicoand a limited number of experimental evaluations is the new trend for the discovery of highly efficient biocatalysts.

scholarly journals Exploring the challenges of computational enzyme design by rebuilding the active site of a dehalogenase

2018 ◽  
Vol 116 (2) ◽  
pp. 389-394 ◽  
Author(s):  
Garima Jindal ◽  
Katerina Slanska ◽  
Veselin Kolev ◽  
Jiri Damborsky ◽  
Zbynek Prokop ◽  
...  
Keyword(s):  
Catalytic Activity ◽  
Active Site ◽  
Test Case ◽  
Wild Type ◽  
Haloalkane Dehalogenase ◽  
Enzyme Design ◽  
Wild Type Enzyme ◽  
Computational Enzyme Design ◽  
Activity Design ◽  
Computational Predictions

Rational enzyme design presents a major challenge that has not been overcome by computational approaches. One of the key challenges is the difficulty in assessing the magnitude of the maximum possible catalytic activity. In an attempt to overcome this challenge, we introduce a strategy that takes an active enzyme (assuming that its activity is close to the maximum possible activity), design mutations that reduce the catalytic activity, and then try to restore that catalysis by mutating other residues. Here we take as a test case the enzyme haloalkane dehalogenase (DhlA), with a 1,2-dichloroethane substrate. We start by demonstrating our ability to reproduce the results of single mutations. Next, we design mutations that reduce the enzyme activity and finally design double mutations that are aimed at restoring the activity. Using the computational predictions as a guide, we conduct an experimental study that confirms our prediction in one case and leads to inconclusive results in another case with 1,2-dichloroethane as substrate. Interestingly, one of our predicted double mutants catalyzes dehalogenation of 1,2-dibromoethane more efficiently than the wild-type enzyme.

Application of Modified Bloch Waves to Image Analysis of Extended Linear Defects

1974 ◽  
Vol 32 ◽  
pp. 402-403
Author(s):  
S. Nakahara ◽  
D. M. Maher
Keyword(s):  
Image Analysis ◽  
Computational Approach ◽  
Dislocation Loops ◽  
Plane Wave Expansion ◽  
Dynamical Equations ◽  
Bloch Waves ◽  
Linear Defects ◽  
Imperfect Crystal ◽  
Localized Defects ◽  
Defective Crystals

Since Head first demonstrated the advantages of computer displayed theoretical intensities from defective crystals, computer display techniques have become important in image analysis. However the computational methods employed resort largely to numerical integration of the dynamical equations of electron diffraction. As a consequence, the interpretation of the results in terms of the defect displacement field and diffracting variables is difficult to follow in detail. In contrast to this type of computational approach which is based on a plane-wave expansion of the excited waves within the crystal (i.e. Darwin representation ), Wilkens assumed scattering of modified Bloch waves by an imperfect crystal. For localized defects, the wave amplitudes can be described analytically and this formulation has been used successfully to predict the black-white symmetry of images arising from small dislocation loops.

High resolution electron microscopy of lanthanum phosphate crystals

1978 ◽  
Vol 36 (1) ◽  
pp. 274-275
Author(s):  
J. C. Wheatley ◽  
J. M. Cowley
Keyword(s):  
Electron Microscopy ◽  
Catalytic Activity ◽  
High Resolution ◽  
Petroleum Industry ◽  
High Resolution Electron Microscopy ◽  
Lanthanum Phosphate ◽  
Good Catalyst ◽  
Resolution Electron ◽  
Good Catalytic Activity ◽  
Physical And Chemical

Rare-earth phosphates are of particular interest because of their catalytic properties associated with the hydrolysis of many aromatic chlorides in the petroleum industry. Lanthanum phosphates (LaPO4) which have been doped with small amounts of copper have shown increased catalytic activity (1). However the physical and chemical characteristics of the samples leading to good catalytic activity are not known.Many catalysts are amorphous and thus do not easily lend themselves to methods of investigation which would include electron microscopy. However, the LaPO4, crystals are quite suitable samples for high resolution techniques.The samples used were obtained from William L. Kehl of Gulf Research and Development Company. The electron microscopy was carried out on a JEOL JEM-100B which had been modified for high resolution microscopy (2). Standard high resolution techniques were employed. Three different sample types were observed: 669A-1-5-7 (poor catalyst), H-L-2 (good catalyst) and 27-011 (good catalyst).

The design and catalytic performance of molybdenum active sites on an MCM-41 framework for the aerobic oxidation of 5-hydroxymethylfurfural to 2,5-diformylfuran

2019 ◽  
Vol 9 (3) ◽  
pp. 811-821 ◽  
Author(s):  
Zhao-Meng Wang ◽  
Li-Juan Liu ◽  
Bo Xiang ◽  
Yue Wang ◽  
Ya-Jing Lyu ◽  
...  
Keyword(s):  
Catalytic Activity ◽  
Active Sites ◽  
Aerobic Oxidation ◽  
Catalytic Performance ◽  
Mcm 41

The catalytic activity decreases as –(SiO)3Mo(OH)(O) > –(SiO)2Mo(O)2 > –(O)4–MoO.

Prolonged Expression of Procoagulant Activity of Human Platelets Degranulated by Thrombin

1995 ◽  
Vol 74 (03) ◽  
pp. 958-961 ◽  
Author(s):  
Raelene L Kinlough-Rathbone ◽  
Dennis W Perry
Keyword(s):  
Catalytic Activity ◽  
Thrombus Formation ◽  
Annexin V ◽  
Human Platelets ◽  
Procoagulant Activity ◽  
Prothrombinase Complex ◽  
Arterial Thrombus ◽  
Flowing Blood

SummaryPlatelets are exposed to thrombin when they take part in arterial thrombus formation, and they may return to the circulation when they are freed by fibrinolysis and dislodged by flowing blood. Thrombin causes the expression of procoagulant activity on platelets, and if this activity persists, the recirculating platelets may contribute to subsequent thrombosis. We have developed techniques to degranulate human platelets by treatment with thrombin, and recover them as single, discrete platelets that aggregate in response to both weak and strong agonists. In the present study we examined the duration of procoagulant activity on the surface of thrombin-degranulated platelets by two methods: a prothrombinase assay, and the binding of 125I-labeled annexin. Control platelets generated 0.9 ± 0.4 U thrombin per 107 platelets in 15 min. Suspensions of thrombin-degranulated platelets formed 5.4 ± 0.1 U thrombin per 107 platelets in this time. Binding of 125I-annexin V was also greater with thrombin-treated platelets than with control platelets (controls: 1.7 ±0.1 ng annexin/107 platelets; thrombin-degranulated platelets: 6.8 ± 0.2 ng annexin/107 platelets). With thrombin-degranulated platelets, increased procoagulant activity and annexin binding persisted for at least 4 h after degranulation and resuspension, indicating that the catalytic activity for the prothrombinase complex is not reversed during this time. These platelets maintained their ability to aggregate for 4 h, even in response to the weak agonist, ADP. Thus, platelets that have taken part in thrombus formation and returned to the circulation may contribute to the promotion of further thrombotic events because of the persistence of procoagulant activity on their surface.

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