European Biophysics Journal最新文献

At the 25th International Analytical Ultracentrifugation Workshop and Symposium, we described the recent implementation of the UltraScan SOlution MOdeler AlphaFold (US-SOMO-AF) database, containing hydrodynamic, structural, CD calculations, and other ancillary information, performed on the entire AF v2 database of predicted protein structures, containing more than 1,000,000 entries. The scope of the US-SOMO-AF database was that of providing direct access to pre-calculated physicochemical parameters for rapid assessment against their experimentally determined counterparts to test the compatibility in solution of predicted AlphaFold structures. In the meantime, the AlphaFold consortium has extended its database of predicted structures to an astonishing > 200 million entries, making it quite impractical for their coverage in the US-SOMO-AF database. Therefore, we have created the US-SOMO-Web site, allowing the rapid calculations of all the properties, as present in the US-SOMO-AF database, on user-supplied PDB and mmCIF structures, as well as allowing direct processing of the latest AlphaFold models. Major features on the website are described, along with current limitations and potential future developments.

Previous work with Atomic Force Microscope (AFM) nanoindentation, on longitudinal and cross-sections of the human hair fibre, allowed for the derivation of a model for the mechanical behaviour of human hair, called the Anisotropic Index. Expanding that research further, and by applying this model, the nanomechanical behaviour of hairs from patients with the disease Trichothiodystrophy (TTD) has been examined and structural insights, gained from combining the AFM results with Differential Scanning Calorimetry (DSC) experiments and tensile measurements, suggests that TTD-affected hairs have a relatively increased amount of Keratin Intermediate Filaments, contained in compartments of differing crosslinking extent. The associated calculations of axial and transverse Young’s Moduli deliver values in good agreement with the measured fibre mechanics. Furthermore, comparing these findings with the results previously obtained from the study of hairs from patients with the disease Monilethrix, it is shown that the Anisotropic Index correlates well with the known deficiencies in both hair types obtained from such patients and allows for discerning between the Control hair and from those affected by the two diseases. AFM nanoindentation along and across the fibre axis and the Anisotropic Index thus appear to reveal structural details of hair not otherwise acquirable, whilst DSC may offer a quick and simple method for distinguishing between different severities of TTD.

In applications of bio-inspired nanoparticles (NPs), their composition is often optimised by including ionizable lipids. I use a generic statistical model to describe the charge and potential distributions in lipid nanoparticles (LNPs) containing such lipids. The LNP structure is considered to contain the biophase regions separated by narrow interphase boundaries with water. Ionizable lipids are uniformly distributed at the biophase–water boundaries. The potential is there described at the mean-filed level combining the Langmuir–Stern equation for ionizable lipids and the Poisson–Boltzmann equation for other charges in water. The latter equation is used outside a LNP as well. With physiologically reasonable parameters, the model predicts the scale of the potential in a LNP to be rather low, smaller or about (k_textrm{B}T/e), and to change primarily near the LNP-solution interface or, more precisely, inside an NP near this interface because the charge of ionizable lipids becomes rapidly neutralized along the coordinate towards the center of a LNP. The extent of dissociation-mediated neutralization of ionizable lipids along this coordinate increases but only slightly. Thus, the neutralization is primarily due to the negative and positive ions related to the ionic strength in solution and located inside a LNP.

Although the magnetosensitivity to weak magnetic fields, such as the geomagnetic field, which was exhibited by radical pairs that are potentially responsible for avian navigation, has been previously investigated by spin dynamics simulations, understanding this behavior for proposed radical pairs in other species is limited. These include, for example, radical pairs formed in the single-cell green alga Chlamydomonas reinhardtii (CraCRY) and in Columba livia (ClCRY4). In addition, the radical pair of FADH^• with the one-electron reduced cyclobutane thymine dimer that was shown to be sensitive to weak magnetic fields has been of interest. In this work, we investigated the directional magnetosensitivity of these radical pairs to a weak magnetic field by spin dynamics simulations. We find significant reduction in the magnetosensitivity by inclusion of dipolar and exchange interactions, which can be mitigated by a scavenging radical, as demonstrated for the [FAD^•− TyrD^•] radical pair in CraCRY, but not for the [FADH^• T□T^•−] radical pair because of the large exchange coupling. The directional magnetosensitivity of the ClCRY4 [FAD^•− TyrE^•] radical pair can survive this adverse effect even without the scavenging reaction, possibly motivating further experimental exploration.

Proper interpretation of analytical ultracentrifugation (AUC) data for purified proteins requires ancillary information and calculations to account for factors such as buoyancy, buffer viscosity, hydration, and temperature. The utility program SEDNTERP has been widely used by the AUC community for this purpose since its introduction in the mid-1990s. Recent extensions to this program (1) allow it to incorporate data from diffusion as well as AUC experiments; and (2) allow it to calculate the refractive index of buffer solutions (based on the solute composition of the buffer), as well as the specific refractive increment (dn/dc) of proteins based on their composition. These two extensions should be quite useful to the light scattering community as well as helpful for AUC users. The latest version also adds new terms to the partial specific volume calculations which should improve the accuracy, particularly for smaller proteins and peptides, and can calculate the viscosity of buffers containing heavy isotopes of water. It also uses newer, more accurate equations for the density of water and for the hydrodynamic properties of rods and disks. This article will summarize and review all the equations used in the current program version and the scientific background behind them. It will tabulate the values used to calculate the partial specific volume and dn/dc, as well as the polynomial coefficients used in calculating the buffer density and viscosity (most of which have not been previously published), as well as the new ones used in calculating the buffer refractive index.

From the discovery of the first membrane-interacting polymer, styrene maleic-acid (SMA), there has been a rapid development of membrane solubilising polymers. These new polymers can solubilise membranes under a wide range of conditions and produce varied sizes of nanoparticles, yet there has been a lack of broad comparison between the common polymer types and solubilising conditions. Here, we present a comparative study on the three most common commercial polymers: SMA 3:1, SMA 2:1, and DIBMA. Additionally, this work presents, for the first time, a comparative characterisation of polymethacrylate copolymer (PMA). Absorbance and dynamic light scattering measurements were used to evaluate solubilisation across key buffer conditions in a simple, adaptable assay format that looked at pH, salinity, and divalent cation concentration. Lipid-polymer nanoparticles formed from SMA variants were found to be the most susceptible to buffer effects, with nanoparticles from either zwitterionic DMPC or POPC:POPG (3:1) bilayers only forming in low to moderate salinity (< 600 mM NaCl) and above pH 6. DIBMA-lipid nanoparticles could be formed above a pH of 5 and were stable in up to 4 M NaCl. Similarly, PMA-lipid nanoparticles were stable in all NaCl concentrations tested (up to 4 M) and a broad pH range (3–10). However, for both DIBMA and PMA nanoparticles there is a severe penalty observed for bilayer solubilisation in non-optimal conditions or when using a charged membrane. Additionally, lipid fluidity of the DMPC-polymer nanoparticles was analysed through cw-EPR, showing no cooperative gel-fluid transition as would be expected for native-like lipid membranes.

A method for removing time- and radially invariant noise from sedimentation velocity and sedimentation equilibrium experiments performed in an analytical ultracentrifuge is presented. The method averages repeat radial incident light measurements as a function of the photomultiplier response at different wavelengths to remove the majority of the time-invariant noise contributions from intensity data measurements. The results of this method are compared to traditional absorbance data generated with a buffer reference and the Beckman Optima AUC data acquisition program, and with the standard UltraScan refinement workflow. The method avoids the amplification of stochastic noise inherent in the absorbance scan subtraction traditionally employed in sedimentation velocity and equilibrium data. In addition, the collection of intensity data frees up the reference channel for additional samples, doubling the capacity of the instrument. In comparison to absorbance data, the residual mean square deviation of a fitted sedimentation velocity experiment without additional noise correction by UltraScan was improved by a factor of 4.5 when using the new method. This improvement benefits sedimentation equilibrium experiments as well as analytical buoyant density equilibrium experiments where routine time-invariant noise correction calculations cannot be performed.

The gating mechanism of acid-sensitive ion channels (ASICs) remains unclear, despite the availability of atomic-scale structures in various functional states. The collapse of the acidic pocket and structural changes in the low-palm region are assumed to trigger activation. For the acidic pocket, protonation of some residues can minimize repulsion in the collapsed conformation. The relationship between low-palm rearrangements and gating is unknown. In this work, we performed a Monte Carlo energy optimization of known ASIC1a structures and determined the residue–residue interactions in different functional states. For rearrangements in the acidic pocket, our results are consistent with previously proposed mechanisms, although significant complexity was revealed for the residue–residue interactions. The data support the proposal of a gating mechanism in the low-palm region, in which residues E80 and E417 share a proton to activate the channel.

Hydration of biological macromolecules is important for their stability and function. Historically, attempts have been made to describe the degree of macromolecular hydration using a single parameter over a narrow range of values. Here, we describe a method to calculate two types of hydration: surface shell water and entrained water. A consideration of these two types of hydration helps to explain the “hydration problem” in hydrodynamics. The combination of these two types of hydration allows accurate calculation of hydrodynamic volume and related macromolecular properties such as sedimentation and diffusion coefficients, intrinsic viscosities, and the concentration-dependent non-ideality identified with sedimentation velocity experiments.

Morphogenesis, tissue regeneration, and cancer invasion involve transitions in tissue morphology. These transitions, caused by collective cell migration (CCM), have been interpreted as active wetting/de-wetting transitions. This phenomenon is considered based on a model system as wetting of a cell aggregate on a rigid substrate, which includes cell aggregate movement and isotropic/anisotropic spreading of a cell monolayer around the aggregate depending on the substrate rigidity and aggregate size. This model system accounts for the transition between 3D epithelial aggregate and 2D cell monolayer as a product of: (1) tissue surface tension, (2) surface tension of substrate matrix, (3) cell–matrix interfacial tension, (4) interfacial tension gradient, (5) viscoelasticity caused by CCM, and (6) viscoelasticity of substrate matrix. These physical parameters depend on the cell contractility and state of cell–cell and cell–matrix adhesion contacts, as well as the stretching/compression of cellular systems caused by CCM. Despite extensive research devoted to study cell wetting, we still do not understand the interplay among these physical parameters which induces an oscillatory trend of cell rearrangement. This review focuses on these physical parameters in governing the cell rearrangement in the context of epithelial aggregate wetting/de-wetting, and on modeling approaches aimed at reproducing and understanding these biological systems. In this context, we not only review previously published biophysical models for cell rearrangement caused by CCM, but also propose new extensions of those models to point out the interrelation between cell–matrix interfacial tension and epithelial viscoelasticity and the role of the interfacial tension gradient in cell spreading.