Proteins-Structure Function and Bioinformatics最新文献_第5页

A geometrical framework for thinking about proteins. 一个思考蛋白质的几何框架。

IF 3.2 4区生物学

Proteins-Structure Function and Bioinformatics Pub Date : 2025-01-01 Epub Date: 2023-08-10 DOI: 10.1002/prot.26567

Jayanth R Banavar, Achille Giacometti, Trinh X Hoang, Amos Maritan, Tatjana Škrbić

引用次数: 0

A spectrophotometric trimethylamine monooxygenase assay. 分光光度法测定三甲胺单加氧酶。

IF 3.2 4区生物学

Proteins-Structure Function and Bioinformatics Pub Date : 2025-01-01 Epub Date: 2023-09-29 DOI: 10.1002/prot.26597

Shiwangi Maurya, Abhishek Singh, Gurunath Ramanathan

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The alteration of structural network upon transient association between proteins studied using graph theory. 利用图论研究蛋白质间瞬时缔合时结构网络的改变。

IF 3.2 4区生物学

Proteins-Structure Function and Bioinformatics Pub Date : 2025-01-01 Epub Date: 2023-10-30 DOI: 10.1002/prot.26606

Vasam Manjveekar Prabantu, Himani Tandon, Sankaran Sandhya, Ramanathan Sowdhamini, Narayanaswamy Srinivasan

{"title":"The alteration of structural network upon transient association between proteins studied using graph theory.","authors":"Vasam Manjveekar Prabantu, Himani Tandon, Sankaran Sandhya, Ramanathan Sowdhamini, Narayanaswamy Srinivasan","doi":"10.1002/prot.26606","DOIUrl":"10.1002/prot.26606","url":null,"abstract":"Proteins such as enzymes perform their function by predominant non-covalent bond interactions between transiently interacting units. There is an impact on the overall structural topology of the protein, albeit transient nature of such interactions, that enable proteins to deactivate or activate. This aspect of the alteration of the structural topology is studied by employing protein structural networks, which are node-edge representative models of protein structure, reported as a robust tool for capturing interactions between residues. Several methods have been optimized to collect meaningful, functionally relevant information by studying alteration of structural networks. In this article, different methods of comparing protein structural networks are employed, along with spectral decomposition of graphs to study the subtle impact of protein-protein interactions. A detailed analysis of the structural network of interacting partners is performed across a dataset of around 900 pairs of bound complexes and corresponding unbound protein structures. The variation in network parameters at, around, and far away from the interface are analyzed. Finally, we present interesting case studies, where an allosteric mechanism of structural impact is understood from communication-path detection methods. The results of this analysis are beneficial in understanding protein stability, for future engineering, and docking studies.","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":"217-225"},"PeriodicalIF":3.2,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71415408","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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Challenges in bridging the gap between protein structure prediction and functional interpretation. 弥合蛋白质结构预测和功能解释之间差距的挑战。

IF 3.2 4区生物学

Proteins-Structure Function and Bioinformatics Pub Date : 2025-01-01 Epub Date: 2023-10-18 DOI: 10.1002/prot.26614

Mihaly Varadi, Maxim Tsenkov, Sameer Velankar

{"title":"Challenges in bridging the gap between protein structure prediction and functional interpretation.","authors":"Mihaly Varadi, Maxim Tsenkov, Sameer Velankar","doi":"10.1002/prot.26614","DOIUrl":"10.1002/prot.26614","url":null,"abstract":"The rapid evolution of protein structure prediction tools has significantly broadened access to protein structural data. Although predicted structure models have the potential to accelerate and impact fundamental and translational research significantly, it is essential to note that they are not validated and cannot be considered the ground truth. Thus, challenges persist, particularly in capturing protein dynamics, predicting multi-chain structures, interpreting protein function, and assessing model quality. Interdisciplinary collaborations are crucial to overcoming these obstacles. Databases like the AlphaFold Protein Structure Database, the ESM Metagenomic Atlas, and initiatives like the 3D-Beacons Network provide FAIR access to these data, enabling their interpretation and application across a broader scientific community. Whilst substantial advancements have been made in protein structure prediction, further progress is required to address the remaining challenges. Developing training materials, nurturing collaborations, and ensuring open data sharing will be paramount in this pursuit. The continued evolution of these tools and methodologies will deepen our understanding of protein function and accelerate disease pathogenesis and drug development discoveries.","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":"400-410"},"PeriodicalIF":3.2,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11623436/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41241249","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Surface exposed and charged residues drive thermostability in fungi. 表面暴露和带电的残留物驱动真菌的热稳定性。

IF 3.2 4区生物学

Proteins-Structure Function and Bioinformatics Pub Date : 2025-01-01 Epub Date: 2023-11-01 DOI: 10.1002/prot.26623

Shricharan Senthilkumar, Sankar Mahesh, Subachandran Jaisankar, Ragothaman M Yennamalli

{"title":"Surface exposed and charged residues drive thermostability in fungi.","authors":"Shricharan Senthilkumar, Sankar Mahesh, Subachandran Jaisankar, Ragothaman M Yennamalli","doi":"10.1002/prot.26623","DOIUrl":"10.1002/prot.26623","url":null,"abstract":"Fungi, though mesophilic, include thermophilic and thermostable species, as well. The thermostability of proteins observed in these fungi is most likely to be attributed to several molecular factors, such as the presence of salt bridges and hydrogen bond interactions between side chains. These factors cannot be generalized for all fungi. Factors impacting thermostability can guide how fungal thermophilic proteins gain thermostability. We curated a dataset of proteins for 14 thermophilic fungi and their evolutionarily closer mesophiles. Additionally, the proteome of Chaetomium thermophilum and its evolutionarily related mesophile Chaetomium globosum was analyzed. Using eggNOG, we categorized the proteomes into clusters of orthologous groups (COGs). While the individual count of proteins is over-represented in mesophiles (for COGs S, G, L, and Q), there are certain features that are significantly enriched in thermophiles (such as charged residues, exposed residues, polar residues, etc.). Since fungi are known to be cellulolytic and chitinolytic by nature, we selected 37 existing carbohydrate-active enzymes (CAZyme) families in Eurotiales, Mucorales, and Sordariales. We looked at closely similar sequences and their modeled structures for further comparison. Comparing solvent accessibilities of thermophilic and mesophilic proteins, exposed and intermediate residues are observed higher in thermophiles whereas buried residues are observed higher in mesophiles. For specific five CAZYme families (GH7, GH11, GH18, GH45, and CBM1) we looked at position-specific substitutions between thermophiles and mesophiles. We also found that there are relatively more intramolecular interactions in thermophiles compared to mesophiles. Thus, we found factors such as surface exposed residues and charged residues that are highly likely to impart thermostability in fungi, and this study sets the stage for further studies in the area of fungal thermostability.","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":"226-240"},"PeriodicalIF":3.2,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71429555","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

II. Geometrical framework for thinking about globular proteins: The power of poking. 2。思考球形蛋白质的几何框架：戳的力量。

IF 3.2 4区生物学

Proteins-Structure Function and Bioinformatics Pub Date : 2025-01-01 Epub Date: 2023-08-21 DOI: 10.1002/prot.26566

Tatjana Škrbić, Achille Giacometti, Trinh X Hoang, Amos Maritan, Jayanth R Banavar

引用次数: 0

Empowering canonical biochemicals with cross-linked novelty: Recursions in applications of protein cross-links. 用交联的新颖性赋予典型生化物质以力量：蛋白质交联应用中的递归。

IF 3.2 4区生物学

Proteins-Structure Function and Bioinformatics Pub Date : 2025-01-01 Epub Date: 2023-08-17 DOI: 10.1002/prot.26571

Jinam Ravindra Bora, Radhakrishnan Mahalakshmi

{"title":"Empowering canonical biochemicals with cross-linked novelty: Recursions in applications of protein cross-links.","authors":"Jinam Ravindra Bora, Radhakrishnan Mahalakshmi","doi":"10.1002/prot.26571","DOIUrl":"10.1002/prot.26571","url":null,"abstract":"Diversity in the biochemical workhorses of the cell-that is, proteins-is achieved by the innumerable permutations offered primarily by the 20 canonical L-amino acids prevalent in all biological systems. Yet, proteins are known to additionally undergo unusual modifications for specialized functions. Of the various post-translational modifications known to occur in proteins, the recently identified non-disulfide cross-links are unique, residue-specific covalent modifications that confer additional structural stability and unique functional characteristics to these biomolecules. We review an exclusive class of amino acid cross-links encompassing aromatic and sulfur-containing side chains, which not only confer superior biochemical characteristics to the protein but also possess additional spectroscopic features that can be exploited as novel chromophores. Studies of their in vivo reaction mechanism have facilitated their specialized in vitro applications in hydrogels and protein anchoring in monolayer chips. Furthering the discovery of unique canonical cross-links through new chemical, structural, and bioinformatics tools will catalyze the development of protein-specific hyperstable nanostructures, superfoods, and biotherapeutics.","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":"11-25"},"PeriodicalIF":3.2,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7616502/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10005507","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

CSM-Potential2: A comprehensive deep learning platform for the analysis of protein interacting interfaces. CSM-P潜势2：一个用于分析蛋白质相互作用界面的综合深度学习平台。

IF 3.2 4区生物学

Proteins-Structure Function and Bioinformatics Pub Date : 2025-01-01 Epub Date: 2023-10-23 DOI: 10.1002/prot.26615

Carlos H M Rodrigues, David B Ascher

{"title":"CSM-Potential2: A comprehensive deep learning platform for the analysis of protein interacting interfaces.","authors":"Carlos H M Rodrigues, David B Ascher","doi":"10.1002/prot.26615","DOIUrl":"10.1002/prot.26615","url":null,"abstract":"Proteins are molecular machinery that participate in virtually all essential biological functions within the cell, which are tightly related to their 3D structure. The importance of understanding protein structure-function relationship is highlighted by the exponential growth of experimental structures, which has been greatly expanded by recent breakthroughs in protein structure prediction, most notably RosettaFold, and AlphaFold2. These advances have prompted the development of several computational approaches that leverage these data sources to explore potential biological interactions. However, most methods are generally limited to analysis of single types of interactions, such as protein-protein or protein-ligand interactions, and their complexity limits the usability to expert users. Here we report CSM-Potential2, a deep learning platform for the analysis of binding interfaces on protein structures. In addition to prediction of protein-protein interactions binding sites and classification of biological ligands, our new platform incorporates prediction of interactions with nucleic acids at the residue level and allows for ligand transplantation based on sequence and structure similarity to experimentally determined structures. We anticipate our platform to be a valuable resource that provides easy access to a range of state-of-the-art methods to expert and non-expert users for the study of biological interactions. Our tool is freely available as an easy-to-use web server and API available at https://biosig.lab.uq.edu.au/csm_potential.","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":"209-216"},"PeriodicalIF":3.2,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11623435/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49694306","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

On the pathway of the formation of secondary structures in proteins. 关于蛋白质二级结构形成的途径。

IF 3.2 4区生物学

Proteins-Structure Function and Bioinformatics Pub Date : 2025-01-01 Epub Date: 2023-09-23 DOI: 10.1002/prot.26591

Pinak Chakrabarti

{"title":"On the pathway of the formation of secondary structures in proteins.","authors":"Pinak Chakrabarti","doi":"10.1002/prot.26591","DOIUrl":"10.1002/prot.26591","url":null,"abstract":"Protein structures are typically made up of well-defined modules, called secondary structures. A hierarchical model of protein folding may start with the formation of five-membered non-covalently-linked ring motifs involving O⋅⋅⋅C=O and N-H···N interactions connecting two consecutive peptide groups. Some of these interactions lead to polyproline II structure, which are known to occur in the unfolded state of proteins. These interactions constitute different types of γ-turns, providing the sharpest reversal of the chain direction. Occurring transiently in the unfolded state, and in tandem, they can lead to β-turns. One of the β-turns (type I) is predisposed (from a consideration of residue usage) to form the N-terminal of an α-helix, which then propagates toward its C-terminal direction. O⋅⋅⋅C=O interactions encompass four distinct types of conformational features, and one of them has very similar backbone torsion angles as the polyproline II (PPII) conformation and can thus contribute to the formation of PPII helix. An adjustment from these angles can also drive the formation of β-strand. N-H···N interactions can also constitute capping interaction at helix termini and can link a PPII helix to an α-helix. Thus, the polypeptide backbone is endowed with all the features that can initiate the formation of secondary structural elements, and the γ-turn motifs (resulting from O⋅⋅⋅C=O and N-H···N interactions) are the basic units the protein structures are made up of.","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":"396-399"},"PeriodicalIF":3.2,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41173530","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Atomic visualization of flipped-back conformations of high mannose glycans interacting with cargo lectins: An MD simulation perspective. 高甘露糖聚糖与货物凝集素相互作用的反翻构象的原子可视化：MD模拟视角。

IF 3.2 4区生物学

Proteins-Structure Function and Bioinformatics Pub Date : 2025-01-01 Epub Date: 2023-07-19 DOI: 10.1002/prot.26556

Nisha Grandhi Jayaprakash, Dheeraj Kumar Sarkar, Avadhesha Surolia

{"title":"Atomic visualization of flipped-back conformations of high mannose glycans interacting with cargo lectins: An MD simulation perspective.","authors":"Nisha Grandhi Jayaprakash, Dheeraj Kumar Sarkar, Avadhesha Surolia","doi":"10.1002/prot.26556","DOIUrl":"10.1002/prot.26556","url":null,"abstract":"Protein-carbohydrate interactions play a crucial role in mediating several biomolecular recognition events. We attempt to unravel its intricacies by understanding how carbohydrate-binding proteins interpret the glycan code. We aim to decipher lectin-mediated recognition in the endoplasmic reticulum (ER), which plays a crucial role in ER-mediated quality control (ER-QC). The ER-QC functions in three phases-protein folding, transport, and degradation. Altered protein QC leads to ER-related storage disorders. Cargo transport proteins-Ergic53 and Vip36-necessary for maintaining cellular homeostasis-are our primary focus. They recognize monoglucosylated/high mannose N-glycans on the folded glycoproteins. This article reports on the first dynamic investigation of the ER cargo lectins in complex with the high mannose glycans using an advanced sampling technique-replica exchange molecular dynamics to decipher the inherent conformational heterogeneity and the binding mechanism. The study involves simulations for the proteins complexed with three high mannose glycans-Man8B, Man9, and mono-glucosylated glycan. The recognition process is captured using MD simulations to achieve mechanistic insights and characterize the dynamics of glycans in their native and bound states via dihedral angle analysis. Results indicate that the flipped conformation of the glycans was crucial in differentiating their interaction with the proteins. Similar conformers of the glycans are preferred for Ergic53 and Vip36 in their glycan recognition events. Ergic53 preferred Man8B while it was Man9 for Vip36, in coherence with the previous experimental reports. These simulations provide a computational microscopic purview of the mechanism at both spatial and temporal scales. The results correlate with the published experimental data on the specificities of these lectins.","PeriodicalId":56271,"journal":{"name":"Proteins-Structure Function and Bioinformatics","volume":" ","pages":"112-133"},"PeriodicalIF":3.2,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9834745","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0