scholarly journals Structure Based Thermostability Prediction Models for Protein Single Point Mutations with Machine Learning Tools

PLoS ONE ◽  
2015 ◽  
Vol 10 (9) ◽  
pp. e0138022 ◽  
Author(s):  
Lei Jia ◽  
Ramya Yarlagadda ◽  
Charles C. Reed
2019 ◽  
Author(s):  
Nobutaka Fujieda ◽  
Miho Yuasa ◽  
Yosuke Nishikawa ◽  
Genji Kurisu ◽  
Shinobu Itoh ◽  
...  

Cupin superfamily proteins (TM1459) work as a macromolecular ligand framework with a double-stranded beta-barrel structure ligating to a Cu ion through histidine side chains. Variegating the first coordination sphere of TM1459 revealed that H52A and H54A/H58A mutants effectively catalyzed the diastereo- and enantio-selective Michael addition reaction of nitroalkanes to an α,β-unsaturated ketone. Moreover, in silico substrate docking signified C106N and F104W single-point mutations, which inverted the diastereoselectivity of H52A and further improved the stereoselectivity of H54A/H58A, respectively.


2021 ◽  
Author(s):  
Marisa L. Martino ◽  
Stephen N. Crooke ◽  
Marianne Manchester ◽  
M.G. Finn

2017 ◽  
Vol 474 (18) ◽  
pp. 3189-3205 ◽  
Author(s):  
Ashoka Chary Taviti ◽  
Tushar Kant Beuria

Cell division in bacteria is a highly controlled and regulated process. FtsZ, a bacterial cytoskeletal protein, forms a ring-like structure known as the Z-ring and recruits more than a dozen other cell division proteins. The Min system oscillates between the poles and inhibits the Z-ring formation at the poles by perturbing FtsZ assembly. This leads to an increase in the FtsZ concentration at the mid-cell and helps in Z-ring positioning. MinC, the effector protein, interferes with Z-ring formation through two different mechanisms mediated by its two domains with the help of MinD. However, the mechanism by which MinD triggers MinC activity is not yet known. We showed that MinD directly interacts with FtsZ with an affinity stronger than the reported MinC–FtsZ interaction. We determined the MinD-binding site of FtsZ using computational, mutational and biochemical analyses. Our study showed that MinD binds to the H10 helix of FtsZ. Single-point mutations at the charged residues in the H10 helix resulted in a decrease in the FtsZ affinity towards MinD. Based on our findings, we propose a novel model for MinCD–FtsZ interaction, where MinD through its direct interaction with FtsZ would trigger MinC activity to inhibit FtsZ functions.


2006 ◽  
Vol 340 (3) ◽  
pp. 792-799 ◽  
Author(s):  
Motofumi Tanaka ◽  
Motoko Nagano-Fujii ◽  
Lin Deng ◽  
Satoshi Ishido ◽  
Kiyonao Sada ◽  
...  

Author(s):  
Shradha Verma ◽  
Anuradha Chug ◽  
Amit Prakash Singh ◽  
Shubham Sharma ◽  
Puranjay Rajvanshi

With the increasing computational power, areas such as machine learning, image processing, deep learning, etc. have been extensively applied in agriculture. This chapter investigates the applications of the said areas and various prediction models in plant pathology for accurate classification, identification, and quantification of plant diseases. The authors aim to automate the plant disease identification process. To accomplish this objective, CNN has been utilized for image classification. Research shows that deep learning architectures outperform other machine learning tools significantly. To this effect, the authors have implemented and trained five CNN models, namely Inception ResNet v2, VGG16, VGG19, ResNet50, and Xception, on PlantVillage dataset for tomato leaf images. The authors analyzed 18,160 tomato leaf images spread across 10 class labels. After comparing their performance measures, ResNet50 proved to be the most accurate prediction tool. It was employed to create a mobile application to classify and identify tomato plant diseases successfully.


2007 ◽  
Vol 67 (4 suppl) ◽  
pp. 813-818 ◽  
Author(s):  
CS. Trinca ◽  
HF. Waldemarin ◽  
E. Eizirik

The Neotropical otter is one of the least known otter species, and it is considered to be threatened to various degrees throughout its geographic range. Little information exists on the ecological characteristics of this species, and no genetic study has been published about it until now, hampering the design of adequate conservation strategies for its populations. To contribute with genetic information to comprehensive conservation efforts on behalf of L. longicaudis, we characterized the molecular diversity of the 5’ portion of the mtDNA control region in samples from this species collected in Southern and Southeastern Brazil. The sequence analysis revealed a high level of haplotype diversity (h = 0.819; SE = 0.0052) and nucleotide variability ranging from 0.0039 to 0.0067. One of the sampled haplotypes was the most common in both regions and, from this sequence, several other (locally occurring) haplotypes could be derived by single point mutations. No significant genetic differentiation was observed between the Southern and Southeastern regions.


Molecules ◽  
2019 ◽  
Vol 24 (23) ◽  
pp. 4232 ◽  
Author(s):  
Stolz ◽  
Eppinger ◽  
Sosedov ◽  
Kiziak

The arylacetonitrilase from the bacterium Pseudomonas fluorescens EBC191 has been intensively studied as a model to understand the molecular basis for the substrate-, reaction-, and enantioselectivity of nitrilases. The nitrilase converts various aromatic and aliphatic nitriles to the corresponding acids and varying amounts of the corresponding amides. The enzyme has been analysed by site-specific mutagenesis and more than 50 different variants have been generated and analysed for the conversion of (R,S)-mandelonitrile and (R,S)-2-phenylpropionitrile. These comparative analyses demonstrated that single point mutations are sufficient to generate enzyme variants which hydrolyse (R,S)-mandelonitrile to (R)-mandelic acid with an enantiomeric excess (ee) of 91% or to (S)-mandelic acid with an ee-value of 47%. The conversion of (R,S)-2-phenylpropionitrile by different nitrilase variants resulted in the formation of either (S)- or (R)-2-phenylpropionic acid with ee-values up to about 80%. Furthermore, the amounts of amides that are produced from (R,S)-mandelonitrile and (R,S)-2-phenylpropionitrile could be changed by single point mutations between 2%–94% and <0.2%–73%, respectively. The present study attempted to collect and compare the results obtained during our previous work, and to obtain additional general information about the relationship of the amide forming capacity of nitrilases and the enantiomeric composition of the products.


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