Biophysical reviews最新文献

This editorial for Volume 16, Issue 3 of Biophysical Reviews highlights the three-dimensional structural and dynamic information encoded in DNA sequences and introduces the topics covered in this special issue of the journal on Multiscale Simulations of DNA from Electrons to Nucleosomes. Biophysical Reviews is the official journal of the International Union for Pure and Applied Biophysics (IUPAB 2024). The international scope of the articles in the issue exemplifies the goals of IUPAB to organize worldwide advancements, co-operation, communication, and education in biophysics.

DNA carries more than the list of biochemical instructions that drive the basic functions of living systems. The sequence of base pairs includes a multitude of structural and energetic signals that determine the degree to which the long, threadlike molecule moves and how it responds to proteins and other molecules involved in its processing and packaging. The arrangements of successive base pairs in high-resolution protein-DNA crystal structures provide useful benchmarks for atomic-level simulations of double-helical DNA as well as information potentially useful in interpreting the properties of specific DNA sequences. The set of currently available structures has enough examples to characterize the conformational preferences of the DNA base-pair steps within the context of their immediate neighbors, i.e., in the context of tetramers, and reveals surprising effects of certain neighbors on local chain properties. The proteins in contact with DNA present various microenvironments that sense and/or induce the observed spatial forms. The cumulative buildup of amino-acid atoms in different protein-DNA complexes produces a binding cloud around the double helix with subtle sequence-dependent features. While the microenvironment presented by each protein to DNA is highly unique, the overall composition of amino-acid atoms within close range of DNA in a broad collection of structures is fairly uniform. The buildup of protein atoms of different types around the DNA provides new information for the improvement of nucleic acid force fields and fresh ideas for the exploration of the properties of DNA in solution.

Predicting the structure and dynamics of RNA molecules still proves challenging because of the relative scarcity of experimental RNA structures on which to train models and the very sensitive nature of RNA towards its environment. In the last decade, several atomistic force fields specifically designed for RNA have been proposed and are commonly used for simulations. However, it is not necessarily clear which force field is the most suitable for a given RNA molecule. In this contribution, we propose the use of the computational energy landscape framework to explore the energy landscape of RNA systems as it can bring complementary information to the more standard approaches of enhanced sampling simulations based on molecular dynamics. We apply the EL framework to the study of a small RNA pseudoknot, the Aquifex aeolicus tmRNA pseudoknot PK1, and we compare the results of five different RNA force fields currently available in the AMBER simulation software, in implicit solvent. With this computational approach, we can not only compare the predicted 'native' states for the different force fields, but the method enables us to study metastable states as well. As a result, our comparison not only looks at structural features of low energy folded structures, but provides insight into folding pathways and higher energy excited states, opening to the possibility of assessing the validity of force fields also based on kinetics and experiments providing information on metastable and unfolded states.

Supplementary information: The online version contains supplementary material available at 10.1007/s12551-024-01202-9.

This Editorial for Volume 16 Issue 2 first describes the issue contents before describing some upcoming events within Biophysical Reviews and concludies with an announcement on the transition of Chief Editors thanks to the outgoing Chief Editor.

Water oxidation in photosystem II (PSII) is performed by the oxygen-evolving complex Mn₄CaO₅ which can be extracted from PSII and then reconstructed using exogenous cations Mn(II) and Ca²⁺. The binding efficiency of other cations to the Mn-binding sites in Mn-depleted PSII was investigated without any positive results. At the same time, a study of the Fe cations interaction with Mn-binding sites showed that it binds at a level comparable with the binding of Mn cations. Binding of Fe(II) cations first requires its light-dependent oxidation. In general, the interaction of Fe(II) with Mn-depleted PSII has a number of features similar to the two-quantum model of photoactivation of the complex with the release of oxygen. Interestingly, incubation of Ca-depleted PSII with Fe(II) cations under certain conditions is accompanied by the formation of a chimeric cluster Mn/Fe in the oxygen-evolving complex. PSII with the cluster 2Mn2Fe was found to be capable of water oxidation, but only to the H₂O₂ intermediate. However, the cluster 3Mn1Fe can oxidize water to O₂ with an efficiency about 25% of the original in the absence of extrinsic proteins PsbQ and PsbP. In the presence of these proteins, the efficiency of O₂ evolution can reach 80% of the original when adding exogenous Ca²⁺. In this review, we summarized information on the formation of chimeric Mn-Fe clusters in the oxygen-evolving complex. The data cited may be useful for detailing the mechanism of water oxidation.

Microbes thrive in diverse porous environments-from soil and riverbeds to human lungs and cancer tissues-spanning multiple scales and conditions. Short- to long-term fluctuations in local factors induce spatio-temporal heterogeneities, often leading to physiologically stressful settings. How microbes respond and adapt to such biophysical constraints is an active field of research where considerable insight has been gained over the last decades. With a focus on bacteria, here we review recent advances in self-organization and dispersal in inorganic and organic porous settings, highlighting the role of active interactions and feedback that mediates microbial survival and fitness. We discuss open questions and opportunities for using integrative approaches to advance our understanding of the biophysical strategies which microbes employ at various scales to make porous settings habitable.

Cellular DNA is constantly exposed to endogenous or exogenous factors that can induce lesions. Several types of lesions have been described that can result from UV/ionizing irradiations, oxidative stress, or free radicals, among others. In order to overcome the deleterious effects of such damages, i.e., mutagenicity or cytotoxicity, cells possess a highly complex DNA repair machinery, involving repair enzymes targeting specific types of lesions through dedicated cellular pathways. In addition, DNA is highly compacted in the nucleus, the first level of compaction consisting of ~ 147 DNA base pairs wrapped around a core of histones, the so-called nucleosome core particle. In this complex environment, the DNA structure is highly constrained, and fine-tuned mechanisms involving remodeling processes are required to expose the DNA to repair enzymes and to facilitate the damage removal. However, these nucleosome-specific mechanisms remain poorly understood, and computational methods emerged only recently as powerful tools to investigate DNA damages in such complex systems as the nucleosome. In this mini-review, we summarize the latest advances brought out by computational approaches in the field, opening new exciting perspectives for the study of DNA damage and repair in the nucleosome context.