Monitoring structural changes in intrinsically disordered proteins using QCM-D: application to the bacterial cell division protein ZipA

Mateos-Gil, Pablo; Tsortos, Achilleas; Vélez, Marisela; Gizeli, Electra

doi:10.1039/c6cc02127a

Cited by 22 publications

(30 citation statements)

References 42 publications

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“…Experiments with adsorbed discrete particles such as liposomes and viruses made use of a different approach, providing estimations of the size of the nanoentities involved [9]. A model developed by Tsortos et al [7,21,22] allowed quantitative evaluation of the size and shape of tethered biomolecules (DNA and proteins) [23,24]; here, the hydrodynamic quantities of the intrinsic viscosity [η] and the radius R h were explicitly taken into account and were linked to the acoustic ratio D/ f [21].…”

Section: Introductionmentioning

confidence: 99%

Hydrodynamics of Quartz-Crystal-Microbalance DNA Sensors Based on Liposome Amplifiers

et al. 2020

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The quartz-crystal microbalance (QCM) has become an important technique for the detection of biomolecules and their interactions. Acoustic sensing of DNA requires hybridizing the oligonucleotide chain with a nanoparticle that acts as an acoustic amplifier. In this device, the amplifier remains suspended in the liquid, nanometers away from the surface. The hydrodynamics of nonadsorbed nanoparticles in QCM sensing devices has, however, been overlooked in the literature. Here, we show that the acoustic response (shifts in frequency, f , and dissipation, D) of the amplifier-target complex is determined by the hydrodynamic wall stress. Our study focuses on an alternative type of DNA sensor based on liposome-DNA complexes and provides a theoretical analysis backed up by experiments with 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine liposomes. The target DNA strands are attached on one side to surface-adsorbed neutravidin through a biotin linker, while the other side is anchored to a liposome acting as an amplifier. A range of liposome radii and double-stranded-DNA contour lengths are studied, covering sizes up to the wave penetration depth (δ ∼ 100 nm). Simulations, based on the immersed boundary method and an elastic-network model, are in excellent agreement with the experiments. We derive an analytical expression for the acoustic impedance, which reflects strong signal amplification as the liposome gets closer to the wall. This enhancement is due to hydrodynamic reflection: the ambient flow induces a stress on the liposome surface, which propagates back to the resonator. For this reason, acoustic signals are extremely sensitive to the distribution of the liposome-wall distance (which we determine from the mechanical properties of double-stranded-DNA chains). Our approach helps in deciphering the role of hydrodynamics in acoustic sensing and reveals the role of parameters hitherto largely unexplored. A practical consequence may be improvements in the design of biosensors and detection schemes.

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Section: Introductionmentioning

confidence: 99%

Hydrodynamics of Quartz-Crystal-Microbalance DNA Sensors Based on Liposome Amplifiers

et al. 2020

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“…It is also worth highlighting that this initial layer is not affected by the UV treatment, as can be deduced from the similar values obtained for the acoustic ratios at t = 1 min and t = 5 min (SM3-1). Apart from providing information about the kinetics of protein adsorption, D vs F plots are also useful in elucidating the structural properties of proteinaceous films [31][32][33] as well as in providing qualitative information about their viscoelastic properties [3,31]. D vs F show that for each type of surface US and SS have a similar profile: i) for the untreated surfaces (Fig.…”

Section: Discussionmentioning

confidence: 99%

Real-time formation of salivary films onto polymeric materials for dental applications: Differences between unstimulated and stimulated saliva

Weber

Barrantes

2017

Colloids and Surfaces B: Biointerfaces

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The formation of salivary films onto oral prostheses materials is of central importance for understanding their performance and interaction with oral tissue and flora. The aim of this work was to study and compare the salivary films formed from unstimulated and stimulated whole saliva on two common polymeric materials, polycarbonate and poly(methyl methacrylate). Irradiating these materials with UV light is a simple way to modify their wettability, roughness and ζ-potential. Therefore, the effect of UV exposure of polycarbonate and poly(methyl methacrylate) on saliva adsorption was also investigated. For this purpose a quartz crystal microbalance with dissipation and SDS-PAGE have been combined in order to associate the thicknesses and viscoelastic properties of the salivary films with their protein composition. SDS-PAGE results suggest that a larger diversity of proteins is involved in the formation of stimulated saliva pellicles. Furthermore, according to QCM-D, pellicles formed from stimulated saliva are thinner and stiffer than the ones formed from unstimulated saliva if the polymeric materials have not been exposed to UV light although both types of saliva form a biphasic layer. For UV-treated materials, the same is applied to polycarbonate but not to poly(methyl methacrylate) where stimulated saliva yields thicker and softer films than unstimulated saliva being the adsorption process of a multiphasic nature. These results highlight the importance of choosing the appropriate sample depending on the type of study to be performed.

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“…3B) to FtsZ polymerization with ZipA-bound FtsZ polymers emanating into the solution phase (3D polymerization) whilst the constant effective thickness up to 0.5 µM represented a two dimensional FtsZ film. We cannot however rule out that the higher density of filaments on the surface imposes a rearrangement of the nonstructured region of sZipA that could cause the extension of the flexible domain into the solution and thus make a (likely minor) contribution to the effective thickness increase 35 . The 3D thickness growth was found to be well described by a conventional Hill equation.…”

Section: Quantification Of Ftsz Surface Densities and Identification Of Ftsz Polymer Growth Regimesmentioning

confidence: 96%

“…The region that can be folded, according to 9 ). The relatively high associated dissipation shift (D ≈ 5 × 10 -6 ) can be ascribed to the presence of the flexible linker that connects the globular FtsZ binding domain to the SLB 34,35 and provides compliance to the protein film. Only a minor fraction of sZipA was released upon rinsing with buffer (Fig.…”

Section: Preparation Of Model Membranesmentioning

confidence: 99%

Reversible Membrane Tethering by ZipA Determines FtsZ Polymerization in Two and Three Dimensions

et al. 2019

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In most bacteria, the early step of septum formation implies the association of soluble FtsZ polymers to the cytoplasmic membrane. ZipA, together with FtsA, provide membrane tethering to FtsZ in Escherichia coli, forming a dynamic proto-ring that serves as an assembly scaffold for the remaining elements of the divisome. Despite their importance for bacterial cell division, multivalent interactions between proto-ring elements at membrane surfaces remain poorly characterized in quantitative terms. Here we measured the binding of FtsZ to ZipA incorporated in supported lipid bilayers at controlled densities by using a combination of biophysical surface-sensitive techniques (quartz crystal microbalance and spectroscopic ellipsometry) and analyzed how ZipA density and FtsZ concentration control the state of assembly of FtsZ. We find that ZipA attachment enables FtsZ-GMPCPP (where GMPCPP is a GTP analogue with reduced hydrolysis) to assemble in

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Monitoring structural changes in intrinsically disordered proteins using QCM-D: application to the bacterial cell division protein ZipA

Cited by 22 publications

References 42 publications

Hydrodynamics of Quartz-Crystal-Microbalance DNA Sensors Based on Liposome Amplifiers

Hydrodynamics of Quartz-Crystal-Microbalance DNA Sensors Based on Liposome Amplifiers

Real-time formation of salivary films onto polymeric materials for dental applications: Differences between unstimulated and stimulated saliva

Reversible Membrane Tethering by ZipA Determines FtsZ Polymerization in Two and Three Dimensions

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