大鼠肠道脂肪酸结合蛋白的结构特性及其动态变化:对内在紊乱的洞察。

IF 1 4区 生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Protein and Peptide Letters Pub Date : 2024-01-01 DOI:10.2174/0109298665313811240530055004
Oyku Irem Balli, Sule Irem Caglayan, Vladimir N Uverksy, Orkid Coskuner-Weber
{"title":"大鼠肠道脂肪酸结合蛋白的结构特性及其动态变化:对内在紊乱的洞察。","authors":"Oyku Irem Balli, Sule Irem Caglayan, Vladimir N Uverksy, Orkid Coskuner-Weber","doi":"10.2174/0109298665313811240530055004","DOIUrl":null,"url":null,"abstract":"<p><strong>Background: </strong>The rat intestinal fatty acid-binding protein (I-FABP) is expressed in the small intestine and is involved in the absorption and transport of dietary fatty acids. It is used as a marker for intestinal injury and is associated with various gastrointestinal disorders. I-FABP has been studied extensively using conventional experimental and computational techniques. However, the detection of intrinsically disordered regions requires the application of special sampling molecular dynamics simulations along with certain bioinformatics because conventional computational and experimental studies face challenges in identifying the features of intrinsic disorder.</p><p><strong>Methods: </strong>Replica exchange molecular dynamics simulations were conducted along with bioinformatics studies to gain deeper insights into the structural properties of I-FABP. Specifically, the C<i>α</i> and H<i>α</i> chemical shift values werecalculated, and the findings were compared to the experiments. Furthermore, secondary and tertiary structure properties were also calculated, and the protein was clustered using k-means clustering. The end-to-end distance and radius of gyration values were reported for the protein in an aqueous solution medium. In addition, its disorder tendency was studied using various bioinformatics tools.</p><p><strong>Results and conclusion: </strong>It was reported that I-FABP is a flexible protein with regions that demonstrate intrinsic disorder characteristics. This flexibility and intrinsic disorder characteristics of IFABP may be related to its nature in ligand binding processes.</p>","PeriodicalId":20736,"journal":{"name":"Protein and Peptide Letters","volume":null,"pages":null},"PeriodicalIF":1.0000,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Structural Properties of Rat Intestinal Fatty Acid-Binding Protein with its Dynamics: Insights into Intrinsic Disorder.\",\"authors\":\"Oyku Irem Balli, Sule Irem Caglayan, Vladimir N Uverksy, Orkid Coskuner-Weber\",\"doi\":\"10.2174/0109298665313811240530055004\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><strong>Background: </strong>The rat intestinal fatty acid-binding protein (I-FABP) is expressed in the small intestine and is involved in the absorption and transport of dietary fatty acids. It is used as a marker for intestinal injury and is associated with various gastrointestinal disorders. I-FABP has been studied extensively using conventional experimental and computational techniques. However, the detection of intrinsically disordered regions requires the application of special sampling molecular dynamics simulations along with certain bioinformatics because conventional computational and experimental studies face challenges in identifying the features of intrinsic disorder.</p><p><strong>Methods: </strong>Replica exchange molecular dynamics simulations were conducted along with bioinformatics studies to gain deeper insights into the structural properties of I-FABP. Specifically, the C<i>α</i> and H<i>α</i> chemical shift values werecalculated, and the findings were compared to the experiments. Furthermore, secondary and tertiary structure properties were also calculated, and the protein was clustered using k-means clustering. The end-to-end distance and radius of gyration values were reported for the protein in an aqueous solution medium. In addition, its disorder tendency was studied using various bioinformatics tools.</p><p><strong>Results and conclusion: </strong>It was reported that I-FABP is a flexible protein with regions that demonstrate intrinsic disorder characteristics. This flexibility and intrinsic disorder characteristics of IFABP may be related to its nature in ligand binding processes.</p>\",\"PeriodicalId\":20736,\"journal\":{\"name\":\"Protein and Peptide Letters\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":1.0000,\"publicationDate\":\"2024-01-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Protein and Peptide Letters\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.2174/0109298665313811240530055004\",\"RegionNum\":4,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q4\",\"JCRName\":\"BIOCHEMISTRY & MOLECULAR BIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Protein and Peptide Letters","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.2174/0109298665313811240530055004","RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q4","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}
引用次数: 0

摘要

背景:大鼠肠脂肪酸结合蛋白(I-FABP)在小肠中表达,参与膳食脂肪酸的吸收和转运。它被用作肠道损伤的标志物,并与各种胃肠道疾病相关。人们利用传统的实验和计算技术对 I-FABP 进行了广泛的研究。然而,由于传统的计算和实验研究在确定内在无序区特征方面面临挑战,因此检测内在无序区需要应用特殊取样分子动力学模拟和一定的生物信息学:方法:为了更深入地了解 I-FABP 的结构特性,我们在进行生物信息学研究的同时进行了复制交换分子动力学模拟。具体而言,计算了 Cα 和 Hα 化学位移值,并将结果与实验结果进行了比较。此外,还计算了二级和三级结构的属性,并使用 K-means 聚类方法对蛋白质进行了聚类。报告了该蛋白质在水溶液介质中的端到端距离和回旋半径值。此外,还利用各种生物信息学工具研究了其紊乱趋势:结果和结论:据报道,I-FABP 是一种柔性蛋白质,其区域显示出固有的无序特征。I-FABP的这种柔性和内在无序特性可能与其在配体结合过程中的性质有关。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
查看原文
分享 分享
微信好友 朋友圈 QQ好友 复制链接
本刊更多论文
Structural Properties of Rat Intestinal Fatty Acid-Binding Protein with its Dynamics: Insights into Intrinsic Disorder.

Background: The rat intestinal fatty acid-binding protein (I-FABP) is expressed in the small intestine and is involved in the absorption and transport of dietary fatty acids. It is used as a marker for intestinal injury and is associated with various gastrointestinal disorders. I-FABP has been studied extensively using conventional experimental and computational techniques. However, the detection of intrinsically disordered regions requires the application of special sampling molecular dynamics simulations along with certain bioinformatics because conventional computational and experimental studies face challenges in identifying the features of intrinsic disorder.

Methods: Replica exchange molecular dynamics simulations were conducted along with bioinformatics studies to gain deeper insights into the structural properties of I-FABP. Specifically, the Cα and Hα chemical shift values werecalculated, and the findings were compared to the experiments. Furthermore, secondary and tertiary structure properties were also calculated, and the protein was clustered using k-means clustering. The end-to-end distance and radius of gyration values were reported for the protein in an aqueous solution medium. In addition, its disorder tendency was studied using various bioinformatics tools.

Results and conclusion: It was reported that I-FABP is a flexible protein with regions that demonstrate intrinsic disorder characteristics. This flexibility and intrinsic disorder characteristics of IFABP may be related to its nature in ligand binding processes.

求助全文
通过发布文献求助,成功后即可免费获取论文全文。 去求助
来源期刊
Protein and Peptide Letters
Protein and Peptide Letters 生物-生化与分子生物学
CiteScore
2.90
自引率
0.00%
发文量
98
审稿时长
2 months
期刊介绍: Protein & Peptide Letters publishes letters, original research papers, mini-reviews and guest edited issues in all important aspects of protein and peptide research, including structural studies, advances in recombinant expression, function, synthesis, enzymology, immunology, molecular modeling, and drug design. Manuscripts must have a significant element of novelty, timeliness and urgency that merit rapid publication. Reports of crystallization and preliminary structure determination of biologically important proteins are considered only if they include significant new approaches or deal with proteins of immediate importance, and preliminary structure determinations of biologically important proteins. Purely theoretical/review papers should provide new insight into the principles of protein/peptide structure and function. Manuscripts describing computational work should include some experimental data to provide confirmation of the results of calculations. Protein & Peptide Letters focuses on: Structure Studies Advances in Recombinant Expression Drug Design Chemical Synthesis Function Pharmacology Enzymology Conformational Analysis Immunology Biotechnology Protein Engineering Protein Folding Sequencing Molecular Recognition Purification and Analysis
期刊最新文献
Immunoproteomics: A Review of Techniques, Applications, and Advancements. SGSM2 in Uveal Melanoma: Implications for Survival, Immune Infiltration, and Drug Sensitivity. Exploring the Regulatory Interaction of Differentially Expressed Proteins in Cleft Palate Induced by Retinoic Acid. Immunoproteomics: Approach to Diagnostic and Vaccine Development. Characterization of Luciferase from Photorhabdus kayaii and its Application for In vivo Imaging Studies in Mice.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
0
微信
客服QQ
Book学术公众号 扫码关注我们
反馈
×
意见反馈
请填写您的意见或建议
请填写您的手机或邮箱
已复制链接
已复制链接
快去分享给好友吧!
我知道了
×
扫码分享
扫码分享
Book学术官方微信
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术
文献互助 智能选刊 最新文献 互助须知 联系我们:info@booksci.cn
Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。
Copyright © 2023 Book学术 All rights reserved.
ghs 京公网安备 11010802042870号 京ICP备2023020795号-1