scholarly journals Protein-Ligand Interactions: Discovering Potential Small-Molecule Therapies for Alzheimer's Disease and Investigating the Effect of Non-Natural Amino Acid Incorporation on Enzyme-Substrate Interactions

2015 ◽  
Author(s):  
Hann-chung Wong
Keyword(s):  
Amino Acid ◽  
Small Molecule ◽  
Natural Amino Acid ◽  
Amino Acid Incorporation ◽  
Substrate Interactions ◽  
Protein Ligand Interactions ◽  
Enzyme Substrate ◽  
Acid Incorporation ◽  
Ligand Interactions ◽  
Enzyme Substrate Interactions

scholarly journals Novel Few-shots Learning Neural Network for Predicting Carbohydrate-active Enzyme (CAZyme) Affinity Towards Fructo-oligosaccharides

2020 ◽  
Author(s):  
Shaoxun Liu ◽  
Yi Kou ◽  
Lin Chen
Keyword(s):  
Neural Network ◽  
Amino Acid ◽  
Binding Affinity ◽  
Amino Acid Sequences ◽  
Active Enzyme ◽  
Binding Interaction ◽  
Carbohydrate Active Enzyme ◽  
Protein Ligand Interactions ◽  
Enzyme Substrate ◽  
Ligand Interactions

Abstract Background: The enzymatic activity of the microbiome toward carbohydrates in the human digestive system is of enormous health significance (Zou, Y., et al., 2019; Pinard, D., et al., 2015). Predicting how carbohydrates through food intake may affect the distribution and balance of gut microbiota remains a major challenge. Understanding the enzyme-substrate specificity relationship of the carbohydrate-active enzyme (CAZyme) encoded by the vast gut microbiome will be an important step to address this question. In this study, we seek to establish an in-silico approach to studying the enzyme-substrate binding interaction. Results: We focused on the key carbohydrate-active enzyme (CAZyme) and established a novel Poisson noise-based few-shots learning neural network (pFSLNN) for predicting the binding affinity of indigestible carbohydrates. This approach achieved higher accuracy than other classic FSLNNs, and we have also formulated new algorithms for feature generation using only a few amino acid sequences. Sliding bin regression is integrated with mRMR for feature selection. Conclusion: The resulting pFSLNN is an efficient model to predict the binding affinity between CAZyme and common oligosaccharides. This model can be potentially applied to binding affinity prediction of other protein-ligand interactions based on limited amino acid sequences.

scholarly journals Transferability of N-terminal mutations of pyrrolysyl-tRNA synthetase in one species to that in another species on unnatural amino acid incorporation efficiency

Amino Acids ◽  
2020 ◽  
Author(s):  
Thomas L. Williams ◽  
Debra J. Iskandar ◽  
Alexander R. Nödling ◽  
Yurong Tan ◽  
Louis Y. P. Luk ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Genetic Code ◽  
Unnatural Amino Acids ◽  
Trna Synthetase ◽  
Unnatural Amino Acid ◽  
Amino Acid Incorporation ◽  
Acid Incorporation ◽  
Genetic Code Expansion ◽  
Incorporation Efficiency

AbstractGenetic code expansion is a powerful technique for site-specific incorporation of an unnatural amino acid into a protein of interest. This technique relies on an orthogonal aminoacyl-tRNA synthetase/tRNA pair and has enabled incorporation of over 100 different unnatural amino acids into ribosomally synthesized proteins in cells. Pyrrolysyl-tRNA synthetase (PylRS) and its cognate tRNA from Methanosarcina species are arguably the most widely used orthogonal pair. Here, we investigated whether beneficial effect in unnatural amino acid incorporation caused by N-terminal mutations in PylRS of one species is transferable to PylRS of another species. It was shown that conserved mutations on the N-terminal domain of MmPylRS improved the unnatural amino acid incorporation efficiency up to five folds. As MbPylRS shares high sequence identity to MmPylRS, and the two homologs are often used interchangeably, we examined incorporation of five unnatural amino acids by four MbPylRS variants at two temperatures. Our results indicate that the beneficial N-terminal mutations in MmPylRS did not improve unnatural amino acid incorporation efficiency by MbPylRS. Knowledge from this work contributes to our understanding of PylRS homologs which are needed to improve the technique of genetic code expansion in the future.

scholarly journals FRUCTOSE-AMINO ACIDS IN LIVER: STIMULI OF AMINO ACID INCORPORATION IN VITRO

1955 ◽  
Vol 215 (1) ◽  
pp. 111-124 ◽  
Author(s):  
Henry Borsook ◽  
Adolph Abrams ◽  
Peter H. Lowy
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Amino Acid Incorporation ◽  
Acid Incorporation
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