The influence of polar and non-polar interactions on the self-assembly of peptide nanomembranes and their applications: An atomistic study using classical molecular dynamics

Andrade, Douglas X. de; Colherinhas, Guilherme

doi:10.1016/j.molliq.2020.114263

Cited by 15 publications

(15 citation statements)

References 52 publications

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“…These nanomembranes were solvated in water (modeled with TIP3P water model 50 ) and simulated for 110 ns, following the protocol reported in reference 48. MD simulations results show that the I 3 XGK nanomembranes are very stable mainly due to the formation of numerous HBs between the peptides, 48 forming a network consistent with the previous work. 6,7,51 As shown in Figure 2, in polar nanomembranes, the formation of polar zippers occurs, laterally linking the neighboring β-sheets.…”

Section: Methodssupporting

confidence: 88%

“…Furthermore, from the monomer, a dimer was formed in order to position the polar residues facing the same side, while on the other side there would be nonpolar residues. 48 Thus, in a dimer, there would be a predominantly polar region and a predominantly nonpolar region. These dimers were then positioned to form nanomembranes with regions where they would form polar zippers and others where they would have purely nonpolar interactions.…”

Section: Methodsmentioning

confidence: 99%

“…More recently, Wang et al, 40 carried out experimental and computational studies demonstrating the formation of polar zippers between neighboring β-sheets in Ac-I 3 XGK (X = Q, S, N) polypeptide rather than between β-strands within a sheet. Afterward, Andrade and Colherinhas 48 performed a theoretical characterization of polar zippers on I 3 XGK membranes, using completely atomistic molecular dynamics (MD).…”

Section: Introductionmentioning

confidence: 99%

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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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Section: Methodssupporting

confidence: 88%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

Andrade

Colherinhas

2022

J. Phys. Chem. B

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“…The R group of nonpolar amino acids is hydrophobic. It is known that peptides have a polycationic and hydrophobic nature and that these properties are important to the initial interaction between AMPs and bacterial cell membrane ( Hancock et al, 1995 ; Wu et al, 1999 ; Andrade and Colherinhas, 2020 ).…”

Section: Amino Acid Substitutions and Their Effect On Antimicrobial A...mentioning

confidence: 99%

Antimicrobial Peptide Analogs From Scorpions: Modifications and Structure-Activity

Amorim-Carmo

Parente

Souza

et al. 2022

Front. Mol. Biosci.

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The rapid development of multidrug-resistant pathogens against conventional antibiotics is a global public health problem. The irrational use of antibiotics has promoted therapeutic limitations against different infections, making research of new molecules that can be applied to treat infections necessary. Antimicrobial peptides (AMPs) are a class of promising antibiotic molecules as they present broad action spectrum, potent activity, and do not easily induce resistance. Several AMPs from scorpion venoms have been described as a potential source for the development of new drugs; however, some limitations to their application are also observed. Here, we describe strategies used in several approaches to optimize scorpion AMPs, addressing their primary sequence, biotechnological potential, and characteristics that should be considered when developing an AMP derived from scorpion venoms. In addition, this review may contribute towards improving the understanding of rationally designing new molecules, targeting functional AMPs that may have a therapeutic application.

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“…[45] The addition of MD simulations of PbA-bilayer interactions is applicable in determining the interactions of nanoassemblies with biological membranes. [46,47] In this work, we have designed eight new peptide bolaamphiphiles with a wide variety of structures and explored their early stage (100 ns) self-assembly process using MD simulations in varying conditions. Examining early-stage self-assembly is crucial as it provides critical information regarding initial interactions between the molecules that drive the self-assembly process.…”

Section: Introductionmentioning

confidence: 99%

Investigation of Self‐Assembly of Symmetric and Asymmetric Peptide Bolaamphiphiles by COSMO‐RS and Atomistic Simulations and Their Interactions with POPC Bilayers

Lebedenko

Banerjee

2021

Macro Theory & Simulations

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In this work, eight new peptide bolaamphiphiles (PbAs) are designed containing polar (serine or threonine) and nonpolar amino acid head groups (tryptophan or tyrosine) connected by varying aliphatic carbon chains of different lengths and saturation. The physicochemical properties of the bolaamphiphiles are examined by COSMO-RS to determine sigma profiles, potential, and sigma surfaces. Self-assembly is studied using atomistic molecular dynamic simulations under protonated and deprotonated conditions. To mimic physiological conditions, simulations are also carried out in the presence of sodium chloride and the impact of salt on the self-assembly process is also studied. In general, hydrophobic PbAs are found to form higher-order supramolecular structures while PbAs connected by shorter chains or hydrophilic head groups form globular, more compact structures. Self-assembly is more favorable when the PbAs are protonated. Membrane interactions are then studied using MD simulations and the results indicate that the hydrophobic PbAs interact more favorably with the POPC membrane surfaces. These simulations provide insights about the intricate interactions and properties of the PbAs and shed light on the ability to form fine-tuned structures at the nanoscale. This study may lead to the development of novel PbAs for potential applications in a wide variety of biological applications.

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The influence of polar and non-polar interactions on the self-assembly of peptide nanomembranes and their applications: An atomistic study using classical molecular dynamics

Cited by 15 publications

References 52 publications

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

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

Antimicrobial Peptide Analogs From Scorpions: Modifications and Structure-Activity

Investigation of Self‐Assembly of Symmetric and Asymmetric Peptide Bolaamphiphiles by COSMO‐RS and Atomistic Simulations and Their Interactions with POPC Bilayers

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