European Biophysics Journal最新文献

This paper has been prepared to commemorate the 70th anniversary of the Institute of Biophysics of the Czech Academy of Sciences (IBP CAS), which has a long-standing tradition in researching the biological effects of ionizing radiation (IR). Radiobiology has recently gained renewed importance due to several compelling factors. The demand for a better understanding of the biological effects of both low and high doses of various types of ionizing radiation, along with improved radiation protection, is increasing—particularly in the context of critical ongoing human activities such as medical diagnostics, radiotherapy, and the operation of nuclear power plants. This demand also extends to newly emerging scenarios, including the development of hadron and FLASH radiotherapy, as well as mixed radiation field exposures related to planned manned missions to Mars. Unfortunately, there is also an urgent need to address the heightened risk of nuclear materials and weapons misuse by terrorists or even rogue states. Additionally, nuclear energy is currently the only viable alternative that can provide efficient, sustainable, and ecological coverage for the dramatically increasing current and future energy demands. Understanding the risks of IR exposure necessitates exploring how different types of IR interact with living organisms at the most fundamental level of complexity, specifically at the level of molecules and their complexes. The rising interest in radiobiology is, therefore, also driven by new experimental opportunities that enable research at previously unimaginable levels of detail and complexity. In this manuscript, we will address the important questions in radiobiology, focusing specifically on the mechanisms of radiation-induced DNA damage and repair within the context of chromatin architecture. We will emphasize the differing effects of photon and high-LET particle radiation on chromatin and DNA. Both forms of IR are encountered on Earth but are particularly significant in space.

Band-forming experiments allow the study of a wide variety of systems by overlaying two solutions with different densities in an analytical ultracentrifuge. Despite their potential benefits over other methods, these experiments are rarely used because all available fitting software encounters systematic errors, failing to account for the evolving gradient in density and viscosity due to diffusive mixing between the two layers. We develop and experimentally validate a predictive model for the purely diffusive mixing of two solutions in a cylindrical system. Capturing the space- and time-dependent evolution of density and viscosity in band-forming experiments, the model enhances their interpretation and underscores the need for analysis software to account for these dynamic changes.

Knowledge of the hydrophobicity of amino acids is essential to understanding the structure and function of proteins. One of the most useful tools for this purpose has been the use of hydrophobicity scales. In these scales, each amino acid is attributed with a numerical value that characterizes its hydrophobic or hydrophilic behavior in a protein. These values depend on the particular methodologies used to obtain them. In the present work, we present a way to infer a hydrophobicity scale for all the amino acids from their partial atomic charge from the uniCHARMM force field. All amino acids are more or less soluble in water as they need to be easily bioavailable in the cell medium. It is during the folding process of a polypeptide chain, that an amino acid goes from a soluble state to be part of a folded protein within a cohesive hydrophobic core. In the present work, we have implemented a model and a formula that considers hydrophilicity as the ability of the atoms of amino acids to interact with water, being proportional to the accessibility to the solvent and its partial charge, depending on its sign. On the other hand, hydrophobicity is considered to be more intense the lower the charge on the atom and also proportional to the accessibility of the atom. This procedure improves the accuracy of protein hydrophobicity calculations down to the atomic level.

Nucleic acids, molecules essential for all life, can adopt many alternative structures besides the well-known right-handed double helix, some of which have been reported to exist and function in vivo. One of the most appropriate methods for structural studies of nucleic acids is circular dichroism spectroscopy, utilizing structure-induced chirality due to the asymmetric winding of absorbing nucleobases. Using electronic CD and absorption spectroscopies in combination with melting experiments, we analyzed a conformational equilibrium between DNA double helix and two alternative conformations of nucleic acids, cytosine i-motifs and guanine quadruplexes, as a function of the primary structure of model G/C-rich sequences, containing blocks of G and C runs in particular DNA strands. This paper is a part of special issue dedicated to 70th anniversary of the Biophysical Institute of the Czech Academy of Sciences, where circular dichroism spectroscopy of nucleic acids has been used successfully and impactfully for many years.

The thiamine (vitamin B1) biosynthesis pathway is essential for most prokaryotes and some eukaryotes, including yeasts and plants. The 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate kinase (HMPP kinase), encoded by the thiD gene, catalyzes two phosphorylation reactions involving intermediates in this pathway, ultimately producing thiamine pyrophosphate, the active form of thiamine. Here, we present the crystal structure of HMPP kinase from Thermus thermophilus HB8 (TtHMPPK), resolved at a resolution of 2.05 Å. The asymmetric unit of the TtHMPPK structure includes one protomer, though it functions as a homodimer in its active form, like the HMPP kinase from Salmonella typhimurium. The TtHMPPK protomer is an α/β protein featuring nine β-sheets flanked by eight structurally conserved α-helices, which are characteristic of the ribokinase family. The structure reveals a Rossmann β–α–β motif, commonly found in nucleotide-binding proteins. Structural analysis of TtHMPPK, compared to the Salmonella typhimurium HMPP kinase, indicates that Ala16, Thr40, Gln42, Ala78, and Val105 are active site residues involved in catalysis. The structural studies suggest that TtHMPPK belongs to the ribokinase superfamily and exhibits structural similarities with an enzyme containing a Rossmann-like structural motif (RLM). This Rossmann fold enables HMPP kinase to catalyze the phosphorylation of HMPP, a critical step in thiamine production.

Graphical abstract

Comparing experimental and calculated hydrodynamic properties of (bio)-macromolecules, such as the translational diffusion coefficient (D_{t(20,w)}^{0}) and the intrinsic viscosity [η], is a useful strategy for the validation of predicted and/or solved atomic-level structures. Bead modeling is a prominent methodology, with several computational tools available. The program GRPY (Generalized Rotne–Prager–Yamakawa) allows the hydrodynamic calculations to be performed at the one-atom one-bead scale, allowing overlaps, but it is computer intensive with CPU requirements depending on the number of beads N as ~ N³. The program ZENO, based on the electrostatics–hydrodynamics analogy and using a Monte Carlo numerical path integration, can compute (D_{t(20,w)}^{0}) and [η] directly on bead models, and it is almost independent of the target size. Since bead models are a very efficient way to include the hydration effect when dealing with bio-macromolecules, we present here an in-depth comparison between GRPY and ZENO, both as implemented in the US-SOMO suite. Relatively low but systematic differences (0.2–2%, increasing with model size) appear when using bead models of proteins at the residue- or atomic-level scales. When comparing the results provided on a restricted set of bead models by two other computationally intensive methods having other drawbacks, the very accurate but not handling overlaps HYDROMULTIPOLE, and the boundary elements BEST requiring extrapolation, GRPY was found to fare better than ZENO. While efforts are in progress to directly improve the ZENO performance, a heuristic correction based on the results for a series of protein bead models is proposed, allowing for a better consistency with GRPY.