Elucidating NH2-I3V3A3G3K3-COOH and NH2-K3G3A3V3I3-COOH polypeptide membranes: A classical molecular dynamics study

Andrade, Douglas X. de; Oliveira, Leonardo Bruno Assis; Colherinhas, Guilherme

doi:10.1016/j.molliq.2019.02.006

Cited by 24 publications

(5 citation statements)

References 54 publications

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“…These atoms have the same chemical environment in the compound and little interaction with the solvent, which characterizes this homogeneity in the magnetic signal. Our results show that the sequence of carbon atoms ( CHCHCH 3 is due to the intensity of these higher excited states, which contribute to a new band that overlaps that calculated with the first 10 states.…”

Section: Nuclear Magnetic Resonancementioning

confidence: 54%

“…In recent years, there has been an increase in interest for biological molecules especially amino acids, which has had great appeal for the manufacture of new nanomaterials and applications. In this regard, the determination of spectroscopic properties and the possible dependence of these properties on amino acid chain growth becomes an important point for applications of these new nanomaterials whether in the membranes research [1][2][3][4] or self-assemble properties [5][6][7][8] , energy storage 9 or even pharmaceutical applications [10][11][12] . In this article, we focus on the amino acid Isoleucine (ILE) which has a characteristic hydrophobic structure and has a high β-sheet formation potential compared to the other amino acids.…”

Section: Introductionmentioning

confidence: 99%

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Molecular dynamic simulations, GIAO‐NMR and TD‐DFT spectroscopy analyze for zwitterionic isoleucine (ILE)_N, 1 ≤ N ≤ 6, in water solution

et al. 2020

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In this article, we investigate the effects of the isoleucine (ILE) N amino acid chain growth, N = 1.0.6, the ILE conformational effect as well as the solvent presence on the electrical and magnetic spectroscopic properties when these compounds are in aqueous solution. Computational molecular dynamics simulations were performed to include the solvent medium and generate uncorrelated configurations involving solute-solvent structures. The charge point model for solvent was used to obtain the results for quantum mechanical calculation, in special DFT calculations, for (ILE) N structures. Our results for the magnetic shielding constant obtained via GIAO-DFT-NMR calculations show that there is evidence of a magnetic behavior that characterizes the number of peptide bonds and, therefore, how the N isoleucine polypeptide chain is composed. TD-DFT results also show an absorption band shift to larger wavelengths indicating a dependence on N growth.

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Section: Nuclear Magnetic Resonancementioning

confidence: 54%

Section: Introductionmentioning

confidence: 99%

Molecular dynamic simulations, GIAO‐NMR and TD‐DFT spectroscopy analyze for zwitterionic isoleucine (ILE)_N, 1 ≤ N ≤ 6, in water solution

et al. 2020

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“…4f). Among them, the thickness is determined based on the difference between the interface of the water density profile and the PIS-A-1 membrane 27 . Consequently, appropriately increasing the number of polar and basic residues in the sequence to form a larger hydrophilic channel is one of the feasible strategies to improve the antibacterial activity of PIS-A-1.…”

Section: Pis-a-1 Structure Depends On Environment Hydrophobicitymentioning

confidence: 99%

“…All systems were calculated under the NPT ensemble with semi-isotropic coupling at 1 bar on both XY and Z directions using the Nose-hoover and Parrinello-Rahman coupling methods. Nonbonding interactions were measured with an integration time-step of 2 fs and a cutoff scheme of 1.2 nm 27 . Furthermore, long-range electrostatic interactions were measured using the Particle Mesh Ewald method with a Fourier spacing of 0.1 nm.…”

Section: Simulationsmentioning

confidence: 99%

An optimized antimicrobial peptide analog acts as an antibiotic adjuvant to reverse methicillin-resistant Staphylococcus aureus

Chen

Wang

2022

npj Sci Food

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The misuse of antibiotics in animal protein production has driven the emergence of a range of drug-resistant pathogens, which threaten existing public health security. Consequently, there is an urgent need to develop novel antimicrobials and new infection treatment options to address the challenges posed by the dramatic spread of antibiotic resistance. Piscidins, a class of fish-specific antimicrobial peptides (AMPs), are regarded as promising therapies for biomedical applications. Progress towards potential analogs from the piscidin family has been hampered by unenforceable structural optimization strategies. Here, we leverage a strategy of bioinformatics analysis combined with molecular dynamics (MD) simulation to identify specific functional hotspots in piscidins and rationally design related analogues. As expected, this approach yields a potent and non-toxic PIS-A-1 that can be used as an antibiotic adjuvant to reverse methicillin-resistant Staphylococcus aureus (MRSA) pathogens. Remarkably, the structural optimization scheme and application strategy proposed here will contribute richer therapeutic options for the safe production of animal protein.

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“…Among the architectures found in the peptide scenario, ,,,,,− the nanomembranes stand out. In addition to having several applications, ,− understanding the nanomembranes’ self-organization can help in the formation of more complex architectures .…”

Section: Introductionmentioning

confidence: 99%

Polar Zipper on a Peptide Nanomembrane: A Characterization by Potential of Mean Force

Andrade

Colherinhas

2022

J. Phys. Chem. B

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In this work, nanomembranes formed by the I3 XGK (X = Q, S, or N) polar peptides are studied to characterize the average force and energy required to separate two neighboring β-sheets laterally joined by polar zippers. The results presented are obtained using a methodology (state of the art) involving the pulling umbrella method to generate the samples (umbrella sampling) and the potential of mean force (PMF) to evaluate the energetic variation evolved in the process of separating the polar zipper. It was observed that the maximum force required to separate the regions linked by polar zippers is 1.48 kJ/mol nm for the I3 NGK nanomembrane and 1.22 kJ/mol nm [1.30 kJ/mol nm] for the I3 QGK [I3 SGK] nanomembranes, emphasizing that polar zippers play an important role in the interaction that interconnects β-sheets in broad and robust two-dimensional structures (tapes and membranes), offering an agile route to the construction of distinct nanomaterials from β-sheets. Also, negative values were obtained for energy as a function of the reaction coordinate for the regions where the formation of polar zippers occurs, showing that the lateral union of neighboring β-sheets is energetically favorable, with a value up to −3.0 kJ/mol, in the case of I3 NGK nanomembranes.

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Elucidating NH2-I3V3A3G3K3-COOH and NH2-K3G3A3V3I3-COOH polypeptide membranes: A classical molecular dynamics study

Cited by 24 publications

References 54 publications

Molecular dynamic simulations, GIAO‐NMR and TD‐DFT spectroscopy analyze for zwitterionic isoleucine (ILE)_N, 1 ≤ N ≤ 6, in water solution

Molecular dynamic simulations, GIAO‐NMR and TD‐DFT spectroscopy analyze for zwitterionic isoleucine (ILE)_N, 1 ≤ N ≤ 6, in water solution

An optimized antimicrobial peptide analog acts as an antibiotic adjuvant to reverse methicillin-resistant Staphylococcus aureus

Polar Zipper on a Peptide Nanomembrane: A Characterization by Potential of Mean Force

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Elucidating NH2-I3V3A3G3K3-COOH and NH2-K3G3A3V3I3-COOH polypeptide membranes: A classical molecular dynamics study

Cited by 24 publications

References 54 publications

Molecular dynamic simulations, GIAO‐NMR and TD‐DFT spectroscopy analyze for zwitterionic isoleucine (ILE)N, 1 ≤ N ≤ 6, in water solution

Molecular dynamic simulations, GIAO‐NMR and TD‐DFT spectroscopy analyze for zwitterionic isoleucine (ILE)N, 1 ≤ N ≤ 6, in water solution

An optimized antimicrobial peptide analog acts as an antibiotic adjuvant to reverse methicillin-resistant Staphylococcus aureus

Polar Zipper on a Peptide Nanomembrane: A Characterization by Potential of Mean Force

Contact Info

Product

Resources

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Molecular dynamic simulations, GIAO‐NMR and TD‐DFT spectroscopy analyze for zwitterionic isoleucine (ILE)_N, 1 ≤ N ≤ 6, in water solution

Molecular dynamic simulations, GIAO‐NMR and TD‐DFT spectroscopy analyze for zwitterionic isoleucine (ILE)_N, 1 ≤ N ≤ 6, in water solution