Biophysical reviews最新文献_第7页

Structure-based prediction of protein-nucleic acid binding using graph neural networks. 利用图神经网络进行基于结构的蛋白质-核酸结合预测。

IF 4.9

Biophysical reviews Pub Date : 2024-06-26 eCollection Date: 2024-06-01 DOI: 10.1007/s12551-024-01201-w

Jared M Sagendorf, Raktim Mitra, Jiawei Huang, Xiaojiang S Chen, Remo Rohs

{"title":"Structure-based prediction of protein-nucleic acid binding using graph neural networks.","authors":"Jared M Sagendorf, Raktim Mitra, Jiawei Huang, Xiaojiang S Chen, Remo Rohs","doi":"10.1007/s12551-024-01201-w","DOIUrl":"10.1007/s12551-024-01201-w","url":null,"abstract":"Protein-nucleic acid (PNA) binding plays critical roles in the transcription, translation, regulation, and three-dimensional organization of the genome. Structural models of proteins bound to nucleic acids (NA) provide insights into the chemical, electrostatic, and geometric properties of the protein structure that give rise to NA binding but are scarce relative to models of unbound proteins. We developed a deep learning approach for predicting PNA binding given the unbound structure of a protein that we call PNAbind. Our method utilizes graph neural networks to encode the spatial distribution of physicochemical and geometric properties of protein structures that are predictive of NA binding. Using global physicochemical encodings, our models predict the overall binding function of a protein, and using local encodings, they predict the location of individual NA binding residues. Our models can discriminate between specificity for DNA or RNA binding, and we show that predictions made on computationally derived protein structures can be used to gain mechanistic understanding of chemical and structural features that determine NA recognition. Binding site predictions were validated against benchmark datasets, achieving AUROC scores in the range of 0.92-0.95. We applied our models to the HIV-1 restriction factor APOBEC3G and showed that our model predictions are consistent with and help explain experimental RNA binding data.Supplementary information: The online version contains supplementary material available at 10.1007/s12551-024-01201-w.","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"16 3","pages":"297-314"},"PeriodicalIF":4.9,"publicationDate":"2024-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11427629/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142341545","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

DNA simulation benchmarks revealed with the accumulation of high-resolution structures. 随着高分辨率结构的积累而揭示的 DNA 模拟基准。

IF 4.9

Biophysical reviews Pub Date : 2024-06-18 eCollection Date: 2024-06-01 DOI: 10.1007/s12551-024-01198-2

Wilma K Olson, Robert T Young, Luke Czapla

{"title":"DNA simulation benchmarks revealed with the accumulation of high-resolution structures.","authors":"Wilma K Olson, Robert T Young, Luke Czapla","doi":"10.1007/s12551-024-01198-2","DOIUrl":"10.1007/s12551-024-01198-2","url":null,"abstract":"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.","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"16 3","pages":"275-284"},"PeriodicalIF":4.9,"publicationDate":"2024-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11297015/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141888436","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Assessing RNA atomistic force fields via energy landscape explorations in implicit solvent. 通过隐含溶剂中的能量景观探索评估 RNA 原子力场

IF 4.9

Biophysical reviews Pub Date : 2024-06-17 eCollection Date: 2024-06-01 DOI: 10.1007/s12551-024-01202-9

Konstantin Röder, Samuela Pasquali

{"title":"Assessing RNA atomistic force fields via energy landscape explorations in implicit solvent.","authors":"Konstantin Röder, Samuela Pasquali","doi":"10.1007/s12551-024-01202-9","DOIUrl":"10.1007/s12551-024-01202-9","url":null,"abstract":"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.","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"16 3","pages":"285-295"},"PeriodicalIF":4.9,"publicationDate":"2024-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11297004/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141888434","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Biophysical Reviews: a transition in the journal. 生物物理评论》：杂志的转型。

IF 4.9

Biophysical reviews Pub Date : 2024-05-02 eCollection Date: 2024-04-01 DOI: 10.1007/s12551-024-01191-9

Damien Hall, Wilma K Olson

引用次数: 0

Current analysis of cations substitution in the oxygen-evolving complex of photosystem II. 光系统 II 氧发生复合体中阳离子置换的电流分析。

Biophysical reviews Pub Date : 2024-04-30 eCollection Date: 2024-04-01 DOI: 10.1007/s12551-024-01186-6

Boris Semin, Aleksey Loktyushkin, Elena Lovyagina

{"title":"Current analysis of cations substitution in the oxygen-evolving complex of photosystem II.","authors":"Boris Semin, Aleksey Loktyushkin, Elena Lovyagina","doi":"10.1007/s12551-024-01186-6","DOIUrl":"10.1007/s12551-024-01186-6","url":null,"abstract":"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.","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"16 2","pages":"237-247"},"PeriodicalIF":0.0,"publicationDate":"2024-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11078907/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140911173","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Microbes in porous environments: from active interactions to emergent feedback. 多孔环境中的微生物：从主动互动到突发反馈。

Biophysical reviews Pub Date : 2024-04-19 eCollection Date: 2024-04-01 DOI: 10.1007/s12551-024-01185-7

Chenyu Jin, Anupam Sengupta

引用次数: 0

DNA damage and repair in the nucleosome: insights from computational methods. 核小体中的 DNA 损伤和修复：计算方法的启示。

IF 4.9

Biophysical reviews Pub Date : 2024-03-12 eCollection Date: 2024-06-01 DOI: 10.1007/s12551-024-01183-9

Natacha Gillet, Elise Dumont, Emmanuelle Bignon

{"title":"DNA damage and repair in the nucleosome: insights from computational methods.","authors":"Natacha Gillet, Elise Dumont, Emmanuelle Bignon","doi":"10.1007/s12551-024-01183-9","DOIUrl":"10.1007/s12551-024-01183-9","url":null,"abstract":"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.","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"16 3","pages":"345-356"},"PeriodicalIF":4.9,"publicationDate":"2024-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11297232/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141888435","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Biophysical Reviews: peering into 2024. 生物物理评论》：展望 2024 年。

IF 4.9

Biophysical reviews Pub Date : 2024-02-20 eCollection Date: 2024-02-01 DOI: 10.1007/s12551-024-01182-w

Damien Hall

引用次数: 0

Biophysical reviews Special issue call: The 21st IUPAB Congress 2024 Kyoto Japan. 生物物理评论特刊征集：第 21 届 IUPAB 大会 2024 日本京都。

IF 4.9

Biophysical reviews Pub Date : 2024-02-19 eCollection Date: 2024-02-01 DOI: 10.1007/s12551-024-01181-x

Wilma K Olson, Damien Hall

引用次数: 0

Special Mini-Issue: Quantitative methods to decipher cellular heterogeneity - from single-cell to spatial omic methods. 小型特刊：解读细胞异质性的定量方法--从单细胞到空间 omic 方法。