Effect of Secondary Structure and Side Chain Length of Hydrophobic Amino Acid Residues on the Antimicrobial Activity and Toxicity of 14‐Residue‐Long de novo AMPs

ChemMedChem ◽  
2020 ◽  
Author(s):  
Gopal Pandit ◽  
Nabarupa Chowdhury ◽  
Sk. Abdul Mohid ◽  
Anil P. Bidkar ◽  
Anirban Bhunia ◽  
...  
Keyword(s):  
Antimicrobial Activity ◽  
Amino Acid ◽  
Secondary Structure ◽  
Chain Length ◽  
De Novo ◽  
Side Chain ◽  
Amino Acid Residues ◽  
Hydrophobic Amino Acid ◽  
Side Chain Length

scholarly journals Development of Antimicrobial Stapled Peptides Based on Magainin 2 Sequence

Molecules ◽  
2021 ◽  
Vol 26 (2) ◽  
pp. 444
Author(s):  
Motoharu Hirano ◽  
Chihiro Saito ◽  
Hidetomo Yokoo ◽  
Chihiro Goto ◽  
Ryuji Kawano ◽  
...  
Keyword(s):  
Antimicrobial Activity ◽  
Amino Acid ◽  
Hemolytic Activity ◽  
Helical Structure ◽  
Antimicrobial Activities ◽  
Side Chain ◽  
Membrane Disruption ◽  
Amino Acid Residues ◽  
Electrophysiological Measurements ◽  
Cell Membrane Disruption

Magainin 2 (Mag2), which was isolated from the skin of the African clawed frog, is a representative antimicrobial peptide (AMP) that exerts antimicrobial activity via microbial membrane disruption. It has been reported that the helicity and amphipathicity of Mag2 play important roles in its antimicrobial activity. We investigated and recently reported that 17 amino acid residues of Mag2 are required for its antimicrobial activity, and accordingly developed antimicrobial foldamers containing α,α-disubstituted amino acid residues. In this study, we further designed and synthesized a set of Mag2 derivatives bearing the hydrocarbon stapling side chain for helix stabilization. The preferred secondary structures, antimicrobial activities, and cell-membrane disruption activities of the synthesized peptides were evaluated. Our analyses revealed that hydrocarbon stapling strongly stabilized the helical structure of the peptides and enhanced their antimicrobial activity. Moreover, peptide 2 stapling between the first and fifth position from the N-terminus showed higher antimicrobial activity than that of Mag2 against both gram-positive and gram-negative bacteria without exerting significant hemolytic activity. To investigate the modes of action of tested peptides 2 and 8 in antimicrobial and hemolytic activity, electrophysiological measurements were performed.

Effect of charged amino acid side chain length on lateral cross-strand interactions between carboxylate- and guanidinium-containing residues in a β-hairpin

Amino Acids ◽  
2015 ◽  
Vol 47 (5) ◽  
pp. 885-898 ◽  
Author(s):  
Hsiou-Ting Kuo ◽  
Shing-Lung Liu ◽  
Wen-Chieh Chiu ◽  
Chun-Jen Fang ◽  
Hsien-Chen Chang ◽  
...  
Keyword(s):  
Amino Acid ◽  
Chain Length ◽  
Side Chain ◽  
Amino Acid Side Chain ◽  
Side Chain Length

scholarly journals Extent of N-terminal methionine excision from Escherichia coli proteins is governed by the side-chain length of the penultimate amino acid.

1989 ◽  
Vol 86 (21) ◽  
pp. 8247-8251 ◽  
Author(s):  
P. H. Hirel ◽  
M. J. Schmitter ◽  
P. Dessen ◽  
G. Fayat ◽  
S. Blanquet
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Chain Length ◽  
Side Chain ◽  
Side Chain Length

Effects of Arginine Deimination and Citrulline Side‐Chain Length on Peptide Secondary Structure Formation

ChemBioChem ◽  
2019 ◽  
Vol 20 (16) ◽  
pp. 2118-2124
Author(s):  
Po‐Yi Wu ◽  
Chin‐Yi Chen ◽  
Jhe‐Hao Li ◽  
Jin‐Kai Lin ◽  
Ting‐Hsuan Chen ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Structure Formation ◽  
Chain Length ◽  
Side Chain ◽  
Side Chain Length ◽  
Secondary Structure Formation ◽  
Peptide Secondary Structure

Effect of Charged Amino Acid Side Chain Length at Non-Hydrogen Bonded Strand Positions on β-Hairpin Stability

Biochemistry ◽  
2013 ◽  
Vol 52 (44) ◽  
pp. 7785-7797 ◽  
Author(s):  
Li-Hung Kuo ◽  
Jhe-Hao Li ◽  
Hsiou-Ting Kuo ◽  
Cheng-Yun Hung ◽  
Hsin-Yun Tsai ◽  
...  
Keyword(s):  
Amino Acid ◽  
Chain Length ◽  
Side Chain ◽  
Amino Acid Side Chain ◽  
Side Chain Length ◽  
Hydrogen Bonded

Effect of the basic amino-acid side chain length and the penultimate residue on the hydrolysis of benzoyldipeptides by carboxypeptidase B

1978 ◽  
Vol 56 (5) ◽  
pp. 315-318 ◽  
Author(s):  
Graham J. Moore ◽  
N. Leo Benoiton
Keyword(s):  
Amino Acid ◽  
Chain Length ◽  
Basic Amino Acid ◽  
Side Chain ◽  
Amino Acid Side Chain ◽  
Carboxypeptidase B ◽  
Side Chain Length ◽  
C Terminus ◽  
Guanidino Group ◽  
Hydrolysis Of

The kinetic parameters Km and kcat/Km have been determined for the carboxypeptidase B (CPB, EC 3.4.12.3) catalyzed hydrolysis of benzoylglycyl-DL-homolysine and benzoylglycyl-L-homoarginine. Plots of these data and those for Bz-Gly-Orn and Bz-Gly-Arg (Wolff, E. C., Schirmer, E. W. &Folk, J. E. (1962) J. Biol. Chem. 237, 3094–3099) and Bz-Gly-Lys versus the length of the side chain of the basic amino acid indicate that unlike trypsin (EC 3.4.21.4) (Seely, J. H. &Benoiton, N. L. (1970) Can. J. Biochem. 48, 1122–1131) CPB has a higher binding affinity for a guanidino group than for an amino group at the side chain of the substrate C-terminus. On the other hand, CPB is similar to trypsin (ibid) in that the best substrate would have a side chain length between those of lysine and arginine.Studies with Bz-MeGly-Lys and Bz-Ala-Lys showed that the former is very slowly hydrolyzed by CPB but that the latter is a good substrate, with a high affinity for the enzyme, indicative of considerable participation of the Cα-methyl group of alanine in the binding of the substrate to the enzyme.

Exploring the impact of the side-chain length on peptide/RNA binding events

2017 ◽  
Vol 19 (28) ◽  
pp. 18452-18460
Author(s):  
Lola Sbicca ◽  
Alejandro López González ◽  
Alexandra Gresika ◽  
Audrey Di Giorgio ◽  
Jordi Teixido Closa ◽  
...  
Keyword(s):  
Amino Acid ◽  
Chain Length ◽  
Rna Binding ◽  
Side Chain ◽  
Amino Acid Side Chain ◽  
Side Chain Length ◽  
Tar Rna ◽  
The Impact ◽  
Hiv 1

The impact of the amino-acid side-chain length on peptide–RNA binding events has been investigated using HIV-1 Tat derived peptides as ligands and the HIV-1 TAR RNA element as an RNA model.

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