European Biophysics Journal最新文献

Lithium has been the treatment of choice for patients with bipolar disorder. However, lithium overdose happens more frequently since it has a very narrow therapeutic range in blood, necessitating investigation of its adverse effects on blood cells. The possible changes that lithium exposure may have on functional and morphological characteristics of human red blood cells (RBCs) have been studied ex vivo using single-cell Raman spectroscopy, optical trapping, and membrane fluorescent probe. The Raman spectroscopy was performed with excitation at 532 nm light, which also results in simultaneous photoreduction of intracellular hemoglobin (Hb). The level of photoreduction of lithium-exposed RBCs was observed to decline with lithium concentration, indicating irreversible oxygenation of intracellular Hb from lithium exposure. The lithium exposure may also have an effect on RBC membrane, which was investigated via optical stretching in a laser trap and the results suggest lower membrane fluidity for the lithium-exposed RBCs. The membrane fluidity of RBCs was further studied using the Prodan generalized polarization method and the results verify the reduction of membrane fluidity upon lithium exposure.

Multi-wavelength analytical ultracentrifugation (MW-AUC) is a recently developed technique that has proven to be a promising tool to investigate mixtures of molecules containing multiple chromophores. It provides an orthogonal separation approach by distinguishing molecules based on their spectral and hydrodynamic properties. Existing software implementations do not permit the user to assess the integrity of the spectral decomposition. To address this shortcoming, we developed a new spectral decomposition residual visualization module, which monitors the accuracy of the spectral decomposition. This module assists the user by providing visual and statistical feedback from the decomposition. The software has been integrated into the UltraScan software suite and an example of a mixture containing thyroglobulin and DNA is presented for illustration purposes.

The study of mechanical properties of tissues can be considered as biomarkers for early detection of cancer and help in new treatments. In this study, the Young’s modulus of MCF-7 breast cancer tissue was extracted using atomic force microscopy (AFM) by measuring the interaction force of the sample and performing a simulation. The force–indentation depth diagram was plotted by averaging the experimental results. In this paper, the modulus of elasticity of breast cancer tissue has been extracted with complex models such as DMT, MD, BCP, and SUN. By comparing the experimental and theoretical results and by changing the amount of hypothetical Young’s modulus in the spherical contact models, the Young’s modulus of the cancer tissue is considered to be between 300 and 400 Pa. The geometry of the cell was also assumed to be spherical according to the images obtained by atomic force microscopy.

The structure of DNA double helix is stabilized by water molecules and metal counterions that form the ion-hydration shell around the macromolecule. Understanding the role of the ion-hydration shell in the physical mechanisms of the biological functioning of DNA requires detailed studies of its structure and dynamics at the atomistic level. In the present work, the study of collective vibrations of water molecules around the DNA double helix was performed within the framework of classical all-atom molecular dynamics methods. Calculating the vibrational density of states, the vibrations of water molecules in the low-frequency spectra ranged from (sim)30 to (sim)300 (hbox {cm}^{-1}) were analyzed for the case of different regions of the DNA double helix (minor groove, major groove, and phosphate groups). The analysis revealed significant differences in the collective vibrations behavior of water molecules in the DNA hydration shell, compared to the vibrations of bulk water. All low-frequency modes of the DNA ion-hydration shell are shifted by about 15–20 (hbox {cm}^{-1}) towards higher frequencies, which is more significant for water molecules in the minor groove region of the double helix. The interactions of water molecules with the atoms of the macromolecule induce intensity decrease of the mode of hydrogen-bond symmetrical stretching near 150 (hbox {cm}^{-1}), leading to the disappearance of this mode in the DNA spectra. The obtained results can provide an interpretation of the experimental data for DNA low-frequency spectra and may be important for the understanding of the processes of indirect protein–nucleic recognition.

Outer membrane proteins (OMPs) must exist as an unfolded ensemble while interacting with a chaperone network in the periplasm of Gram-negative bacteria. Here, we developed a method to model unfolded OMP (uOMP) conformational ensembles using the experimental properties of two well-studied OMPs. The overall sizes and shapes of the unfolded ensembles in the absence of a denaturant were experimentally defined by measuring the sedimentation coefficient as a function of urea concentration. We used these data to model a full range of unfolded conformations by parameterizing a targeted coarse-grained simulation protocol. The ensemble members were further refined by short molecular dynamics simulations to reflect proper torsion angles. The final conformational ensembles have polymer properties different from unfolded soluble and intrinsically disordered proteins and reveal inherent differences in the unfolded states that necessitate further investigation. Building these uOMP ensembles advances the understanding of OMP biogenesis and provides essential information for interpreting structures of uOMP-chaperone complexes.

The ability to simulate sedimentation velocity (SV) analytical ultracentrifugation (AUC) experiments has proved to be a valuable tool for research planning, hypothesis testing, and pedagogy. Several options for SV data simulation exist, but they often lack interactivity and require up-front calculations on the part of the user. This work introduces SViMULATE, a program designed to make AUC experimental simulation quick, straightforward, and interactive. SViMULATE takes user-provided parameters and outputs simulated AUC data in a format suitable for subsequent analyses, if desired. The user is not burdened by the necessity to calculate hydrodynamic parameters for simulated macromolecules, as the program can compute these properties on the fly. It also frees the user of decisions regarding simulation stop time. SViMULATE features a graphical view of the species that are under simulation, and there is no limit on their number. Additionally, the program emulates data from different experimental modalities and data-acquisition systems, including the realistic simulation of noise for the absorbance optical system. The executable is available for immediate download.

There is a long tradition in the Biophysics community of using simulations as a means to understand macromolecular behavior in various physicochemical methods. This allows a rigorous means to interpret observations in terms of fundamental principles, including chemical equilibrium, reaction kinetics, transport processes and thermodynamics. Here we simulate data for the Gilbert Theory for self-association, a fundamental analytical ultracentrifuge (AUC) technique to understand the shape of sedimentation velocity reaction boundaries that involve reversible monomer–Nmer interactions. Simulating monomer–dimer through monomer–hexamer systems as a function of concentration about the equilibrium constant allows a visual means to differentiate reaction stoichiometry by determining end points and inflection positions. Including intermediates (eg A₁-A₂-A₃-A₄-A₅-A₆) in the simulations reveals the smoothing of the reaction boundary and the removal of sharp inflections between monomers and polymers. The addition of cooperativity restores sharp boundaries or peaks to the observation and allows more discrimination in the selection of possible fitting models. Thermodynamic nonideality adds additional features when applied across wide ranges of concentration that might be appropriate for high-concentration therapeutic monoclonal antibody (mAb) solutions. This presentation serves as a tutorial for using modern AUC analysis software like SEDANAL for selecting potential fitting models.

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.