scholarly journals Experimental and Computational Investigation of the Structure of Peptide Monolayers on Gold Nanoparticles

2016 ◽  
Author(s):  
Elena Colangelo ◽  
Qiubo Chen ◽  
Adam M. Davidson ◽  
David Paramelle ◽  
Michael B. Sullivan ◽  
...  
Keyword(s):  
Gold Nanoparticles ◽  
Secondary Structure ◽  
Small Molecules ◽  
Self Assembly ◽  
Gold Surface ◽  
Biochemical Properties ◽  
Computational Investigation ◽  
Predictive Tool ◽  
Dynamics Simulations ◽  
Β Sheet

ABSTRACTThe self-assembly and self-organization of small molecules at the surface of nanoparticles constitute a potential route towards the preparation of advanced protein-like nanosystems. However, their structural characterization, critical to the design of bio-nanomaterials with well-defined biophysical and biochemical properties, remains highly challenging. Here, a computational model for peptide-capped gold nanoparticles is developed using experimentally characterized CALNN-and CFGAILSS-capped gold nanoparticles as a benchmark. The structure of CALNN and CFGAILSS monolayers is investigated by both structural biology techniques and molecular dynamics simulations. The calculations reproduce the experimentally observed dependence of the monolayer secondary structure on peptide capping density and on nanoparticle size, thus giving us confidence in the model. Furthermore, the computational results reveal a number of new features of peptide-capped monolayers, including the importance of sulfur movement for the formation of secondary structure motifs, the presence of water close to the gold surface even in tightly packed peptide monolayers, and the existence of extended 2D parallel β-sheet domains in CFGAILSS monolayers. The model developed here provides a predictive tool that may assist in the design of further bio-nanomaterials.

Time evolution of β-lactoglobulin corona formation on gold nanoparticles and impact on allergy

2020 ◽  
Author(s):  
Xiaoning Zhang ◽  
Meifeng Li ◽  
Yuanping Lv ◽  
Xiaoling Sun ◽  
Yao Han ◽  
...  
Keyword(s):  
Gold Nanoparticles ◽  
Secondary Structure ◽  
Time Evolution ◽  
Electrostatic Force ◽  
Protein Corona ◽  
Raw Milk ◽  
Covalent Bonds ◽  
Corona Formation ◽  
Β Lactoglobulin ◽  
Β Sheet

Abstract Gold nanoparticles (AuNPs) are modified immediately by the adsorption of β-lactoglobulin (βlg) when designed as colorimetric probe in raw milk, leading to the formation of a protein corona. This adsorption results mainly from a fast electrostatic force and a slow formation of Au-S covalent bonds, which is a precondition for the use of AuNPs in biodetection. The proteins corona influences the structure and bioactivity of adsorbed protein, such as the allergy. In this study, the mechanism of βlg adsorbed on AuNPs was investigated in terms of stoichiometry, binding affinity (Ka), time evolution of Au-S bond, and general secondary structure changes to address the desensitization of AuNPs. The results show that about 3,600 βlg are adsorbed on a single AuNPs, and the Ka is 2.9 ± 0.7 × 10 6 M -1 . The formation of Au-S bonds takes about 9 h, which is the time needed for complete changes in secondary structure and the IgE combining capacity. The structure of allergenic epitopes assigned to β-sheet was destroyed by the formation of Au-S bond, then induced to the decrease allergy. Furthermore, Fourier transform infrared spectroscopy confirmed a decrease in β-sheet contents after conjugated with AuNPs.

Evaluation of the effects of phenylalanine and carboxylate on the rheological behaviors of small molecule hydrogelators containing naphthalene

2012 ◽  
Vol 1418 ◽  
Author(s):  
Junfeng Shi ◽  
Yue Pan ◽  
Yuan Gao ◽  
Bing Xu
Keyword(s):  
Small Molecules ◽  
Rheological Properties ◽  
Self Assembly ◽  
Cysteine Residue ◽  
Molecular Structures ◽  
Carboxylic Group ◽  
Aromatic Interactions ◽  
Carboxylate Groups ◽  
Transmission Electron ◽  
Β Sheet

ABSTRACTBy systematically altering the number and position of phenylalanine and carboxylate groups on a series of hydrogelators containing a naphthalene motif, we evaluated the correlation of molecular structures, self-assembly, and the rheological properties of the hydrogels. The storage moduli of the hydrogels decrease with the increase of the number of phenylalanine or with the insertion of a cysteine residue, and the effect of the carboxylic group on the rheological properties depends on the backbone of the hydrogelators. Transmission electron microscopy shows that these hydrogelators self-assemble in water to form nanofibers and result in threedimensional networks. Circular dichroism experiment indicates the hydrogelators self-assemble to form β-sheet-like structure within the nanofibers. This work suggests that control of the synergy of hydrogen bonding and aromatic-aromatic interactions may offer a feasible way to modulate the rheological properties of molecular hydrogels consisting of small molecules.

scholarly journals Anatomy of a selectively coassembled β-sheet peptide nanofiber

2020 ◽  
Vol 117 (9) ◽  
pp. 4710-4717 ◽  
Author(s):  
Qing Shao ◽  
Kong M. Wong ◽  
Dillon T. Seroski ◽  
Yiming Wang ◽  
Renjie Liu ◽  
...  
Keyword(s):  
Self Assembly ◽  
Molecular Level ◽  
Form And Function ◽  
Transmission Electron ◽  
Peptide Pair ◽  
High Concentrations ◽  
Dynamics Simulations ◽  
And Function ◽  
20 Nm ◽  
Β Sheet

Peptide self-assembly, wherein molecule A associates with other A molecules to form fibrillar β-sheet structures, is common in nature and widely used to fabricate synthetic biomaterials. Selective coassembly of peptide pairs A and B with complementary partial charges is gaining interest due to its potential for expanding the form and function of biomaterials that can be realized. It has been hypothesized that charge-complementary peptides organize into alternating ABAB-type arrangements within assembled β-sheets, but no direct molecular-level evidence exists to support this interpretation. We report a computational and experimental approach to characterize molecular-level organization of the established peptide pair, CATCH. Discontinuous molecular dynamics simulations predict that CATCH(+) and CATCH(−) peptides coassemble but do not self-assemble. Two-layer β-sheet amyloid structures predominate, but off-pathway β-barrel oligomers are also predicted. At low concentration, transmission electron microscopy and dynamic light scattering identified nonfibrillar ∼20-nm oligomers, while at high concentrations elongated fibers predominated. Thioflavin T fluorimetry estimates rapid and near-stoichiometric coassembly of CATCH(+) and CATCH(−) at concentrations ≥100 μM. Natural abundance13C NMR and isotope-edited Fourier transform infrared spectroscopy indicate that CATCH(+) and CATCH(−) coassemble into two-component nanofibers instead of self-sorting. However,13C–13C dipolar recoupling solid-state NMR measurements also identify nonnegligible AA and BB interactions among a majority of AB pairs. Collectively, these results demonstrate that strictly alternating arrangements of β-strands predominate in coassembled CATCH structures, but deviations from perfect alternation occur. Off-pathway β-barrel oligomers are also suggested to occur in coassembled β-strand peptide systems.

scholarly journals The influence of molecular mobility on the properties of networks of gold nanoparticles and organic ligands

2014 ◽  
Vol 5 ◽  
pp. 1664-1674 ◽  
Author(s):  
Edwin J Devid ◽  
Paulo N Martinho ◽  
M Venkata Kamalakar ◽  
Úna Prendergast ◽  
Christian Kübel ◽  
...  
Keyword(s):  
Gold Nanoparticles ◽  
Self Assembly ◽  
Microcontact Printing ◽  
Single Layer ◽  
Gold Surface ◽  
Tunnel Barrier ◽  
Dynamic Changes ◽  
Aromatic Molecules ◽  
Capping Ligands ◽  
Molecular Layers

We prepare and investigate two-dimensional (2D) single-layer arrays and multilayered networks of gold nanoparticles derivatized with conjugated hetero-aromatic molecules, i.e., S-(4-{[2,6-bipyrazol-1-yl)pyrid-4-yl]ethynyl}phenyl)thiolate (herein S-BPP), as capping ligands. These structures are fabricated by a combination of self-assembly and microcontact printing techniques, and are characterized by electron microscopy, UV–visible spectroscopy and Raman spectroscopy. Selective binding of the S-BPP molecules to the gold nanoparticles through Au–S bonds is found, with no evidence for the formation of N–Au bonds between the pyridine or pyrazole groups of BPP and the gold surface. Subtle, but significant shifts with temperature of specific Raman S-BPP modes are also observed. We attribute these to dynamic changes in the orientation and/or increased mobility of the molecules on the gold nanoparticle facets. As for their conductance, the temperature-dependence for S-BPP networks differs significantly from standard alkanethiol-capped networks, especially above 220 K. Relating the latter two observations, we propose that dynamic changes in the molecular layers effectively lower the molecular tunnel barrier for BPP-based arrays at higher temperatures.

scholarly journals Disclosing the Interaction of Gold Nanoparticles with Aβ(1–40) Monomers through Replica Exchange Molecular Dynamics Simulations

2020 ◽  
Vol 22 (1) ◽  
pp. 26
Author(s):  
Francesco Tavanti ◽  
Alfonso Pedone ◽  
Maria Cristina Menziani
Keyword(s):  
Gold Nanoparticles ◽  
Electrostatic Interactions ◽  
Amyloid Fibrils ◽  
Specific Binding ◽  
Cognitive Impairments ◽  
Amyloid Β ◽  
Gold Surface ◽  
Replica Exchange ◽  
Replica Exchange Molecular Dynamics ◽  
Dynamics Simulations

Amyloid-β aggregation is one of the principal causes of amyloidogenic diseases that lead to the loss of neuronal cells and to cognitive impairments. The use of gold nanoparticles treating amyloidogenic diseases is a promising approach, because the chemistry of the gold surface can be tuned in order to have a specific binding, obtaining effective tools to control the aggregation. In this paper, we show, by means of Replica Exchange Solute Tempering Molecular Simulations, how electrostatic interactions drive the absorption of Amyloid-β monomers onto citrates-capped gold nanoparticles. Importantly, upon binding, amyloid monomers show a reduced propensity in forming β-sheets secondary structures that are characteristics of mature amyloid fibrils.

scholarly journals Modification of Gold Surface with Gold Nanoparticles and Cyclohexyl Dithiocarbamate as a Selective Sensor for Cysteine

2013 ◽  
Vol 2013 ◽  
pp. 1-5 ◽  
Author(s):  
Ehab AlShamaileh ◽  
Haytham Saadeh ◽  
Valerie Favry
Keyword(s):  
Gold Nanoparticles ◽  
Cyclic Voltammetry ◽  
Modified Electrode ◽  
Self Assembly ◽  
Gold Surface ◽  
The Self ◽  
Self Assembled Monolayer ◽  
Chemically Modified ◽  
Modified Surface ◽  
Selective Sensor

The self-assembly of cyclohexylamine dithiocarbamate (C6DTC) on gold (Au) and gold nanoparticles (AuNPs) was studied electrochemically using cyclic voltammetry (CV). Cyclic voltammetry was used to study the systemFe(CN)63-/Fe(CN)64-at the electrode surface of (C6DTC/Au) and (C6DTC/AuNPs). The application of the resulting chemically modified surface as a selective sensor for cysteine, among other amino acids, was investigated. Linear oxidative desorption technique was used to characterize the modified electrode that consists of the self-assembled monolayer of cyclohexylamine dithiocarbamate on gold nanoparticles deposited on Au electrode (C6DTC/AuNPs/Au). The results showed an enhancement in the oxidation peak of cysteine on the modified electrode and hence a greater sensitivity.

Mechanistic Study of Self-Assembling Peptide RADA16-I in Formation of Nanofibers and Hydrogels

2009 ◽  
Vol 1 (1) ◽  
Author(s):  
Hangyu Zhang ◽  
Hanlin Luo ◽  
Xiaojun Zhao
Keyword(s):  
Self Assembly ◽  
Physiological Condition ◽  
Biochemical Properties ◽  
Low Ph ◽  
Repulsive Force ◽  
Mechanistic Study ◽  
Peptide Backbone ◽  
Self Assembling ◽  
Phosphate Buffered Saline ◽  
Β Sheet

The biophysical and biochemical properties of RADA16-I, the representative of a class of self-assembling peptides, were studied to elucidate the molecular mechanism of nanofiber and hydrogel formations. We found that self-assembly occurs in the solution at low pH (pH 4), rather than the popular belief that it occurs in the physiological environment. Actually, the peptide lost its β-sheet structure and formed irregular aggregates in the condition around pH 7. Our results demonstrated that the extended conformation of peptide backbone caused by the electrostatic repulsive force in acid solution is crucial for the peptide to self-assemble into nanofibers. Importantly, we have proposed a mechanism for the peptide to form nanofiber hydrogel in the physiological condition, which is not propitious for nanofiber formation. Hypothetically, it is by virtue of the tendency of fibers to collapse and form irregular aggregates at pH 7 that we could obtain stable hydrogels by introducing phosphate buffered saline into the system.

Sequence Specificity Despite Intrinsic Disorder: How a Disease-Associated Val/Met Polymorphism Shifts Tertiary Interactions in a Long Disordered Protein

2019 ◽  
Author(s):  
Ruchi Lohia ◽  
Reza Salari ◽  
Grace Brannigan
Keyword(s):  
Secondary Structure ◽  
Electrostatic Interactions ◽  
Intrinsically Disordered Proteins ◽  
Disordered Proteins ◽  
Sequence Specificity ◽  
Intrinsically Disordered ◽  
Specific Effects ◽  
Heterogeneous Polymer ◽  
Non Local ◽  
Dynamics Simulations

<div>The role of electrostatic interactions and mutations that change charge states in intrinsically disordered proteins (IDPs) is well-established, but many disease-associated mutations in IDPs are charge-neutral. The Val66Met single nucleotide polymorphism (SNP) encodes a hydrophobic-to-hydrophobic mutation at the midpoint of the prodomain of precursor brain-derived neurotrophic factor (BDNF), one of the earliest SNPs to be associated with neuropsychiatric disorders, for which the underlying molecular mechanism is unknown. Here we report on over 250 μs of fully-atomistic, explicit solvent, temperature replica exchange molecular dynamics simulations of the 91 residue BDNF prodomain, for both the V66 and M66 sequence.</div><div>The simulations were able to correctly reproduce the location of both local and non-local secondary changes due to the Val66Met mutation when compared with NMR spectroscopy. We find that the local structure change is mediated via entropic and sequence specific effects. We show that the highly disordered prodomain can be meaningfully divided into domains based on sequence alone. Monte Carlo simulations of a self-excluding heterogeneous polymer, with monomers representing each domain, suggest the sequence would be effectively segmented by the long, highly disordered polyampholyte near the sequence midpoint. This is qualitatively consistent with observed interdomain contacts within the BDNF prodomain, although contacts between the two segments are enriched relative to the self-excluding polymer. The Val66Met mutation increases interactions across the boundary between the two segments, due in part to a specific Met-Met interaction with a Methionine in the other segment. This effect propagates to cause the non-local change in secondary structure around the second methionine, previously observed in NMR. The effect is not mediated simply via changes in inter-domain contacts but is also dependent on secondary structure formation around residue 66, indicating a mechanism for secondary structure coupling in disordered proteins. </div>

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