scholarly journals Combining simulations and experiments for the molecular engineering of multifunctional collagen mimetic peptide-based materials

Soft Matter ◽  
2021 ◽  
Author(s):  
Amber Hilderbrand ◽  
Phillip Taylor ◽  
Francesca Stanzione ◽  
Mark LaRue ◽  
Guo Chen ◽  
...  
Keyword(s):  
Amino Acid ◽  
Molecular Engineering ◽  
Complex Materials ◽  
Mimetic Peptide ◽  
Synergistic Approach ◽  
The Creation

Assembling peptides allow the creation of structurally complex materials, where amino acid selection influences resulting properties. We present a synergistic approach of experiments and simulations for examining the influence of...

scholarly journals Engineering Improves Enzymatic Synthesis of L-Tryptophan by Tryptophan Synthase from Escherichia coli

2020 ◽  
Vol 8 (4) ◽  
pp. 519
Author(s):  
Lisheng Xu ◽  
Fangkai Han ◽  
Zeng Dong ◽  
Zhaojun Wei
Keyword(s):  
Thermal Stability ◽  
Amino Acid ◽  
Directed Evolution ◽  
Amino Acid Residue ◽  
Rational Design ◽  
Molecular Engineering ◽  
Mutant Enzyme ◽  
Tryptophan Synthase ◽  
Mutant Library ◽  
Thermal Stability Of

To improve the thermostability of tryptophan synthase, the molecular modification of tryptophan synthase was carried out by rational molecular engineering. First, B-FITTER software was used to analyze the temperature factor (B-factor) of each amino acid residue in the crystal structure of tryptophan synthase. A key amino acid residue, G395, which adversely affected the thermal stability of the enzyme, was identified, and then, a mutant library was constructed by site-specific saturation mutation. A mutant (G395S) enzyme with significantly improved thermal stability was screened from the saturated mutant library. Error-prone PCR was used to conduct a directed evolution of the mutant enzyme (G395S). Compared with the parent, the mutant enzyme (G395S /A191T) had a Km of 0.21 mM and a catalytic efficiency kcat/Km of 5.38 mM−1∙s−1, which was 4.8 times higher than that of the wild-type strain. The conditions for L-tryptophan synthesis by the mutated enzyme were a L-serine concentration of 50 mmol/L, a reaction temperature of 40 °C, pH of 8, a reaction time of 12 h, and an L-tryptophan yield of 81%. The thermal stability of the enzyme can be improved by using an appropriate rational design strategy to modify the correct site. The catalytic activity of tryptophan synthase was increased by directed evolution.

scholarly journals CRISPR-TAPE: protein-centric CRISPR guide design for targeted proteome engineering

2020 ◽  
Author(s):  
DP. Anderson ◽  
HJ. Benns ◽  
EW. Tate ◽  
MA Child
Keyword(s):  
Amino Acid ◽  
Molecular Engineering ◽  
Design Tools ◽  
Design Algorithm ◽  
Homology Directed Repair ◽  
Post Hoc

AbstractRational molecular engineering of proteins with CRISPR-based approaches is challenged by the gene-centric nature of gRNA design tools. To address this, we have developed CRISPR-TAPE, a protein-centric gRNA design algorithm that allows users to target specific residues, or amino acid types within proteins. gRNA outputs can be customized to support maximal efficacy of homology-directed repair for engineering purposes, removing time consuming post-hoc curation, simplifying gRNA outputs, and reducing CPU times.

A new concept for molecular engineering of artificial enzymes: a multiscale simulation

Soft Matter ◽  
2016 ◽  
Vol 12 (3) ◽  
pp. 689-704 ◽  
Author(s):  
Pavel V. Komarov ◽  
Pavel G. Khalatur ◽  
Alexei R. Khokhlov
Keyword(s):  
Amino Acid ◽  
Multiscale Simulation ◽  
Molecular Engineering ◽  
Artificial Enzymes ◽  
Amino Acid Residues ◽  
Protein Amino Acid ◽  
Functional Analog ◽  
First Time

We have designed, for the first time, a functional analog of chymotrypsin from synthetic monomers imitating protein amino acid residues.

scholarly journals Construction of a chimeric human gene encoding renalase with a modified N-terminus

2020 ◽  
Vol 3 (3) ◽  
pp. e00137
Author(s):  
V.I. Fedchenko ◽  
A.A. Kaloshin ◽  
N.I. Kozlova ◽  
A.T. Kopylov ◽  
A.E. Medvedev
Keyword(s):  
Amino Acid ◽  
Human Gene ◽  
Amino Acid Sequences ◽  
Protective Effects ◽  
Gene Encoding ◽  
Approaches To Studying ◽  
Receptor Proteins ◽  
N Terminus ◽  
The Creation

Renalase (RNLS) is a recently discovered protein that plays different roles inside and outside cells. Extracellular RNLS exhibits protective effects on the cell, acting on its receptor proteins, while intracellular RNLS acts as FAD-dependent oxidoreductase (EC 1.6.3.5). The ratio of the intracellular and extracellular forms of this protein, as well as the mechanisms and factors responsible for its transport from the cell, remain unknown. One of the approaches to studying these issues can be the creation of chimeric forms of this protein with modified fragments of its amino acid sequences. This work describes a method for constructing a chimeric human RNLS gene encoding RNLS without its N-terminal peptid

scholarly journals Coupling biocatalysis with high-energy flow reactions for the synthesis of carbamates and β-amino acid derivatives

2021 ◽  
Vol 17 ◽  
pp. 379-384
Author(s):  
Alexander Leslie ◽  
Thomas S Moody ◽  
Megan Smyth ◽  
Scott Wharry ◽  
Marcus Baumann
Keyword(s):  
Amino Acid ◽  
Energy Flow ◽  
Building Blocks ◽  
High Energy ◽  
High Yield ◽  
Addition Reactions ◽  
Flow Process ◽  
The Creation ◽  
Immobilized Calb ◽  
Yield And Purity

A continuous flow process is presented that couples a Curtius rearrangement step with a biocatalytic impurity tagging strategy to produce a series of valuable Cbz-carbamate products. Immobilized CALB was exploited as a robust hydrolase to transform residual benzyl alcohol into easily separable benzyl butyrate. The resulting telescoped flow process was effectively applied across a series of acid substrates rendering the desired carbamate structures in high yield and purity. The derivatization of these products via complementary flow-based Michael addition reactions furthermore demonstrated the creation of β-amino acid species. This strategy thus highlights the applicability of this work towards the creation of important chemical building blocks for the pharmaceutical and speciality chemical industries.

The incorporation of a non-natural amino acid (aza-tryptophan) may help to crystallize a protein and to solve its crystal structure. Application to bacteriophage λ lysozyme.

1999 ◽  
Vol 55 (2) ◽  
pp. 430-435 ◽  
Author(s):  
Christine Evrard ◽  
Jacques Fastrez ◽  
Jean-Paul Declercq
Keyword(s):  
Crystal Structure ◽  
Amino Acid ◽  
Binding Sites ◽  
Heavy Atom ◽  
Natural Amino Acid ◽  
Bacteriophage Λ ◽  
Wild Type ◽  
Tryptophan Residues ◽  
Crystallographic Symmetry ◽  
The Creation

Until now, wild-type bacteriophage λ lysozyme had been impossible to crystallize. This difficulty could be overcome by the replacement of the four tryptophan residues by aza-tryptophans. Analysis of the intermolecular and intramolecular contacts in this modification allows understanding of the differences in behaviour between the native and modified molecules. Furthermore, this mutation was very useful for the creation of new heavy-atom binding sites and for the solution of the non-crystallographic symmetry, which is extremely important for phase improvement. This procedure seems to be generally applicable, at least in the search for new possibilities for heavy-atom binding sites.

scholarly journals Bomb Carbon as a Tracer of Dietary Carbon Sources in Omnivorous Mammals

Radiocarbon ◽  
2001 ◽  
Vol 43 (2B) ◽  
pp. 711-721 ◽  
Author(s):  
Nancy Beavan-Athfield ◽  
Rodger J Sparks
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Essential Amino Acid ◽  
Carbon Sources ◽  
Essential Amino Acids ◽  
Metabolic Effects ◽  
C Value ◽  
The Creation ◽  
Carbon Contribution

We have isolated amino acid groups from modern bone hydrolysates and compared their relative Δ14C value to assess the carbon contribution of diet to the overall radiocarbon signal in bone. We find that both essential and non-essential amino acids may produce widely varying 14C, relative to other amino acid groups in the hydrolysate and to the original whole bone protein. We hypothesize that the 14C variations in non-essential amino acids may be due to metabolic effects that utilize essential amino acid carbon skeletons in the creation of non-essential amino acids.

scholarly journals Rational molecular engineering of l-amino acid deaminase for production of α-ketoisovaleric acid from l-valine by Escherichia coli

RSC Advances ◽  
2017 ◽  
Vol 7 (11) ◽  
pp. 6615-6621 ◽  
Author(s):  
Ruoxi Li ◽  
Hossain Gazi Sakir ◽  
Jianghua Li ◽  
Hyun-dong Shin ◽  
Guocheng Du ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Molecular Engineering

The targeted modification of enzymatic efficiency can drive an increased production of desired metabolites.

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