Structure Determination of Hen Egg-White Lysozyme Aggregates Adsorbed to Lipid/Water and Air/Water Interfaces

Strazdaitė, Simona; Navakauskas, E; Kirschner, Johannes; Šneideris, Tomas; Niaura, Gediminas

doi:10.1021/acs.langmuir.9b03826

Cited by 27 publications

(25 citation statements)

References 65 publications

(125 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Note that both force fields predicted a slightly larger fraction of β -sheet structure. Because the formation of β -sheet was argued to increase the possibility of protein aggregation [ 6 , 83 , 84 ], both force fields should be used with caution in simulations of concentrated systems crowded by proteins. Note that no significant changes were observed in the protein secondary structures for all of the simulated systems ( Table S6 ).…”

Section: Resultsmentioning

confidence: 99%

Atomistic Simulation of Lysozyme in Solutions Crowded by Tetraethylene Glycol: Force Field Dependence

Liu

Qiu

et al. 2022

Molecules

View full text Add to dashboard Cite

The behavior of biomolecules in crowded environments remains largely unknown due to the accuracy of simulation models and the limited experimental data for comparison. Here we chose a small crowder of tetraethylene glycol (PEG-4) to investigate the self-crowding of PEG-4 solutions and molecular crowding effects on the structure and diffusion of lysozyme at varied concentrations from dilute water to pure PEG-4 liquid. Two Amber-like force fields of Amber14SB and a99SB-disp were examined with TIP3P (fast diffusivity and low viscosity) and a99SB-disp (slow diffusivity and high viscosity) water models, respectively. Compared to the Amber14SB protein simulations, the a99SB-disp model yields more coordinated water and less PEG-4 molecules, less intramolecular hydrogen bonds (HBs), more protein–water HBs, and less protein–PEG HBs as well as stronger interactions and more hydrophilic and less hydrophobic contacts with solvent molecules. The a99SB-disp model offers comparable protein–solvent interactions in concentrated PEG-4 solutions to that in pure water. The PEG-4 crowding leads to a slow-down in the diffusivity of water, PEG-4, and protein, and the decline in the diffusion from atomistic simulations is close to or faster than the hard sphere model that neglects attractive interactions. Despite these differences, the overall structure of lysozyme appears to be maintained well at different PEG-4 concentrations for both force fields, except a slightly large deviation at 370 K at low concentrations with the a99SB-disp model. This is mainly attributed to the strong intramolecular interactions of the protein in the Amber14SB force field and to the large viscosity of the a99SB-disp water model. The results indicate that the protein force fields and the viscosity of crowder solutions affect the simulation of biomolecules under crowding conditions.

show abstract

Section: Resultsmentioning

confidence: 99%

Atomistic Simulation of Lysozyme in Solutions Crowded by Tetraethylene Glycol: Force Field Dependence

Liu

Qiu

et al. 2022

Molecules

View full text Add to dashboard Cite

show abstract

“…ThT fluorescence signals were observed in domains which corresponded to the optical signatures observed under bright field, indicating that α-synuclein at the POPC-decorated LC-aqueous interface formed β-sheet structures (Figure 3). We also carried out control experiments, for example, lysozyme (amyloid protein containing β-sheet structures) [27] and bovine serum albumin (BSA) (non-amyloidogenic protein without β-sheet structures) [22a] at a concentration of 1 μM were incubated onto the POPC-decorated LC-aqueous interface, respectively. Lysozyme induced elongated and branched pattern, while BSA triggered ellipsoidal domains in LCs (Figure S2).…”

Section: Characterization Of α-Synuclein Conformation At the Popc-decorated Lc-aqueous Interfacementioning

confidence: 99%

Combination of liquid crystal and deep learning reveals distinct signatures of Parkinson's disease‐related wild‐type α‐synuclein and six pathogenic mutants

Yang

Zhao

et al. 2021

Chemistry An Asian Journal

View full text Add to dashboard Cite

α-Synuclein is a central player in Parkinson's disease (PD) pathology. Various point mutations in α-synuclein have been identified to alter the protein-phospholipid binding behavior and cause PD. Therefore, exploration of α-synucleinphospholipid interaction is important for understanding the PD pathogenesis and helping the early diagnosis of PD. Herein, a phospholipid-decorated liquid crystal (LC)-aqueous interface is constructed to investigate the binding between α-synucleins (wild-type and six familial mutant A30P, E46K, H50Q, G51D, A53E and A53T) and phospholipid. The application of deep learning analyzes and reveals distinct LC signatures generated by the binding of α-synuclein and phospholipid. This system allows for the identification of single point mutant α-synucleins with an average accuracy of 98.3 � 1.3% in a fast and efficient manner. We propose that this analytical methodology provides a new platform to understand α-synuclein-lipid interactions, and can be potentially developed for easy identification of α-synuclein mutations in common clinic.

show abstract

“…son's disease [6]. SFG spectroscopy is able to provide detailed molecular level information of the interfacial aggregation of biomolecules and the adsorption of aggregated peptides and proteins at biological interfaces [1,5].…”

Section: Structure Determination Of Biomolecules At Interfacesmentioning

confidence: 99%

“…Schematic illustration of the SFG experiment (left image). The SFG spectra (right image) of hen eggwhite lysozyme oligomers adsorbed to a DOPG/D 2 O interface taken with SSP (S-SFG, S-532 nm, and P-IR) polarization combination at different pD values (adapted from[5]).…”

mentioning

confidence: 99%

SFG vibrational spectroscopy for the investigation of interfaces

Januskevicius

Kananavičius²,

Umhofer³

et al. 2021

PhotonicsViews

View full text Add to dashboard Cite

show abstract

Structure Determination of Hen Egg-White Lysozyme Aggregates Adsorbed to Lipid/Water and Air/Water Interfaces

Cited by 27 publications

References 65 publications

Atomistic Simulation of Lysozyme in Solutions Crowded by Tetraethylene Glycol: Force Field Dependence

Atomistic Simulation of Lysozyme in Solutions Crowded by Tetraethylene Glycol: Force Field Dependence

Combination of liquid crystal and deep learning reveals distinct signatures of Parkinson's disease‐related wild‐type α‐synuclein and six pathogenic mutants

SFG vibrational spectroscopy for the investigation of interfaces

Contact Info

Product

Resources

About