A Simple Protocol for the Modular Assembly of “Millipede” Artificial Enzymes

Motherwell, William B.; Atkinson, Catherine E.; Aliev, Abil E.; Wong, Stephanie Y. F.; Warrington, Brian H.

doi:10.1002/ange.200352370

Cited by 2 publications

(1 citation statement)

References 30 publications

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“…To explore potentially effective strategies for mimicking natural enzymes [30][31][32][33][34], Huang and co-workers [1] studied the self-assembly of a synthetic amphiphilic short peptide, Bpeptide 1^(Fmoc-Phe-Phe-His-CONH 2 ), into peptide nanotubes. The imidazolyl group of the histidine was found to act as a catalyst for the hydrolysis of p-nitrophenyl acetate (PNPA) with high catalytic activity, thereby mimicking the action of native hydrolase enzymes [35][36][37].…”

Section: Introductionmentioning

confidence: 99%

Molecular dynamics simulation and conformational analysis of some catalytically active peptides

Honarparvar

Skelton

2015

J Mol Model

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The design of stable and inexpensive artificial enzymes with potent catalytic activity is a growing field in peptide science. The first step in this design process is to understand the key factors that can affect the conformational preference of an enzyme and correlate them with its catalytic activity. In this work, molecular dynamics simulations in explicit water of two catalytically active peptides (peptide 1: Fmoc-Phe1-Phe2-His-CONH2; peptide 2: Fmoc-Phe1-Phe2-Arg-CONH2) were performed at temperatures of 300, 400, and 500 K. Conformational analysis of these peptides using Ramachandran plots identified the secondary structures of the amino acid residues involved (Phe1, Phe2, His, Arg) and confirmed their conformational flexibility in solution. Furthermore, Ramachandran maps revealed the intrinsic preference of the constituent residues of these compounds for a helical conformation. Long-range interaction distances and radius of gyration (R g) values obtained during 20 ns MD simulations confirmed their tendency to form folded conformations. Results showed a decrease in side-chain (Phe1, Phe2, His ring, and Arg) contacts as the temperature was raised from 300 to 400 K and then to 500 K. Finally, the radial distribution functions (RDF) of the water molecules around the nitrogen atoms in the catalytically active His and Arg residues of peptide 1 and peptide 2 revealed that the strongest water-peptide interaction occurred with the arginine nitrogen atoms in peptide 2. Our results highlight differences in the secondary structures of the two peptides that can be explained by the different arrangement of water molecules around the nitrogen atoms of Arg in peptide 2 as compared to the arrangement of water molecules around the nitrogen atoms of His in peptide 1. The results of this work thus provide detailed insight into peptide conformations which can be exploited in the future design of peptide analogs.

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Section: Introductionmentioning

confidence: 99%

Molecular dynamics simulation and conformational analysis of some catalytically active peptides

Honarparvar

Skelton

2015

J Mol Model

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Some Recent Advances in the Design and Use of Molecular Balances for the Experimental Quantification of Intramolecular Noncovalent Interactions of π Systems

Aliev

Motherwell

2019

Chemistry A European J

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Herein, various molecular balances used for comparing the strengths of intramolecular noncovalent interactions are reviewed. Our overview indicates that considerable quantitative insight into the strength of noncovalent interactions can be gained through the careful design of molecular balances. Many exciting opportunities certainly exist for the design of further new balances to quantify and dissect the relative strengths of noncovalent interactions as a function of solvation and the importance of the many factors that contribute to overall molecular recognition. However, even simple model molecules can show a multiplicity of intramolecular noncovalent interactions acting in a combined fashion. It is therefore essential to undertake a detailed computational analysis to identify all possible noncovalent interactions present in a selected molecular balance prior to a quantitative experimental assessment of the strength of a particular noncovalent interaction. It is also argued that the words “torsion” and “molecular balance” seem to have become inextricably linked and, in consequence, even top pan and seesaw balances have been mistakenly referred to in these terms.

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A Simple Protocol for the Modular Assembly of “Millipede” Artificial Enzymes

Cited by 2 publications

References 30 publications

Molecular dynamics simulation and conformational analysis of some catalytically active peptides

Molecular dynamics simulation and conformational analysis of some catalytically active peptides

Some Recent Advances in the Design and Use of Molecular Balances for the Experimental Quantification of Intramolecular Noncovalent Interactions of π Systems

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