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  -Glucan, water dikinase (GWD): A plastidic enzyme with redox-regulated and coordinated catalytic activity and binding affinity

2005 ◽  
Vol 102 (5) ◽  
pp. 1785-1790 ◽  
Author(s):  
R. Mikkelsen ◽  
K. E. Mutenda ◽  
A. Mant ◽  
P. Schurmann ◽  
A. Blennow
Keyword(s):  
Catalytic Activity ◽  
Binding Affinity

scholarly journals A Functional Genetic Polymorphism on Human Carbonyl Reductase 1 (CBR1 V88I) Impacts on Catalytic Activity and NADPH Binding Affinity

2007 ◽  
Vol 35 (6) ◽  
pp. 973-980 ◽  
Author(s):  
Vanessa Gonzalez-Covarrubias ◽  
Debashis Ghosh ◽  
Sukhwinder S. Lakhman ◽  
Lakshmi Pendyala ◽  
Javier G. Blanco
Keyword(s):  
Catalytic Activity ◽  
Genetic Polymorphism ◽  
Binding Affinity ◽  
Carbonyl Reductase

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.

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

scholarly journals A TET1-PSPC1-Neat1 molecular axis modulates PRC2 functions in controlling stem cell bivalency

2021 ◽  
Author(s):  
Xin Huang ◽  
Nazym Bashkenova ◽  
Yantao Hong ◽  
Diana Guallar ◽  
Zhe Hu ◽  
...  
Keyword(s):  
Stem Cells ◽  
Stem Cell ◽  
Catalytic Activity ◽  
Binding Affinity ◽  
Molecular Axis ◽  
List Type ◽  
Gene Promoters ◽  
Independent Functions ◽  
Gene Transcripts ◽  
Bivalent Gene

SUMMARYTET1 maintains hypomethylation at bivalent promoters through its catalytic activity in embryonic stem cells (ESCs). However, whether and how TET1 exerts catalytic activity-independent functions in regulating bivalent genes is not well understood. Using a proteomics approach, we mapped the TET1 interactome in mouse ESCs and identified PSPC1 as a novel TET1 partner. Genome-wide location analysis reveals that PSPC1 functionally associates with TET1 and Polycomb repressive complex-2 (PRC2) complex. We establish that PSPC1 and TET1 repress, and Neat1, the PSPC1 cognate lncRNA, activates the bivalent gene expression. In ESCs, Neat1 tethers the TET1-PSPC1 pair with PRC2 at bivalent promoters. During the ESC-to-formative epiblast-like stem cell (EpiLC) transition, PSPC1 and TET1 promote PRC2 chromatin occupancy at bivalent gene promoters while restricting Neat1 functions in facilitating PRC2 binding to bivalent gene transcripts. Our study uncovers a novel TET1-PSPC1-Neat1 molecular axis that modulates PRC2 binding affinity to chromatin and bivalent gene transcripts in controlling stem cell bivalency.In BriefTET1 is a transcriptional repressor for bivalent genes in pluripotent stem cells, but its mechanistic action on stem cell bivalency is unclear. Huang et al. use proteomics and genetic approaches to reveal that catalytic activity-independent functions of TET1, coordinated with the paraspeckle components PSPC1 and its cognate lncRNA Neat1, dynamically regulates stem cell bivalency by modulating PRC2 binding affinity to chromatin and bivalent gene transcripts in pluripotent state transition.HighlightsThe TET1 interactome identifies PSPC1 as a novel partner in ESCsTET1 and PSPC1 repress bivalent genes by promoting PRC2 chromatin occupancyNeat1 facilitates bivalent gene activation by promoting PRC2 binding to their mRNAsNeat1 bridges the TET1-PSPC1 and PRC2 complexes in regulating bivalent gene transcription

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.

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).

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