IIBR Informatics: Tools and databases for proteome-wide modeling and analysis of alpha-helix association in membrane, from folding intermediates to structural interactomes

单次通过(即定位)跨膜(TM)蛋白是真核膜蛋白中含量最丰富、功能最多样但被研究最少的一类蛋白。结合受体、酶、黏附蛋白和转录调节因子在许多重要过程中发挥关键作用，包括细胞生长、增殖、分化、迁移、通讯、凋亡和恶性转化。为了执行它们的生物学功能，这些蛋白质通过它们的TMα-螺旋和水溶性域形成二聚体或更大的复合体。α-螺旋复合体在膜中的高度柔韧性和结构异质性阻碍了它们的结晶，需要发展计算方法来获得TM复合体的三维(3D)结构和多态组织。目前的项目旨在开发和应用新的计算方法来解决比对蛋白质的TM异二聚体的建模问题，使蛋白质组学能够对其结构进行广泛的研究。开发的方法、工具和补充数据库将推进从头算蛋白质结构预测方法，这将使在生物物理、结构和进化生物学、药物化学和生物信息学领域工作或学习的广大研究人员、教师和学生受益。通过其更广泛的影响，该项目提供了一个机会，培训本科生和研究生使用新的计算机语言和网络技术开发生物信息学资源。开发的工具箱将用于研究生级别的药物化学课程和基于网络的研讨会。此外，该项目将支持俄克拉荷马城一所公立学校的生物教育，该学校的少数民族学生比例较高。该项目将产生一个由两个数据库和五个网络工具组成的新型计算基础设施。将新开发三种方法和网络工具：(1)用于识别和建模TM异二聚体的TMMatch；(2)用于检测和分析膜蛋白三维结构中稳定的双螺旋折叠单元的TMPold；以及(3)用于可视化膜上蛋白质相互作用网络的1TMnet。这些网络工具将与现有的PPM和FMAP辅助网络服务器一起纳入两个改进的数据库，用于对膜中的阿尔法螺旋进行建模和定位。扩大的膜组数据库收集了6种生物的定位蛋白质，将包括由TM Match模拟的所有TM二聚体的3D结构和由1TMnet(https://membranome.org/)识别的蛋白质网络。升级后的OPM数据库保存了所有已知的位于膜中的3D结构的膜蛋白，将包括由TMPold和TM Match在完整膜蛋白(https://opm.phar.umich.edu/).)中检测到的稳定的双螺旋折叠单元的结构拟议的工具箱将允许创建一个科学工作流程，从蛋白质组范围的比特蛋白TM二聚体建模到确定它们与不同细胞和生物体中的各种生物途径相关的相互作用网络。来自代表所有生命王国的六个选定物种的比对蛋白质相互作用图的比较将促进我们对单程膜蛋白在进化过程中生物复杂性增加的了解。易于使用的公共网络工具将有利于学术和与健康相关的研究。TMP折叠网工具将能够计算确定稳定的α-螺旋折叠中间体，从而为从头计算模拟多通道膜蛋白的结构和分析其折叠路径铺平道路。TMMatch网络服务器将能够分析TM二聚体中与疾病相关的突变的结构影响，并将帮助设计和优化用于治疗目的的TMα-螺旋复合体。该奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

Single-pass (i.e. bitopic) transmembrane (TM) proteins are the most abundant and functionally diverse, but the least explored class of eukaryotic membrane proteins. Bitopic receptors, enzymes, adhesion proteins, and transcription regulators play key roles in many vital processes, including cell growth, proliferation, differentiation, migration, communication, apoptosis, and malignant transformation. To perform their biological functions, these proteins form dimers or larger complexes via their TM alpha-helices and water-soluble domains. The high flexibility and structural heterogeneity of alpha-helical complexes in membranes impede their crystallization and require development of computational approaches as a viable alternative to obtain three-dimensional (3D) structures and multistate organization of TM complexes. The current project aims to develop and apply new computational methods to solve the problem of modeling TM heterodimers of bitopic proteins, enabling proteome-wide studies of their structures. The developed methodology, tools, and complementary databases will advance ab initio protein structure prediction methods, which will benefit a broad community of researchers, teachers, and students who work or study in the fields of biophysics, structural and evolutionary biology, medicinal chemistry, and bioinformatics. Through its broader impacts, this project offers an opportunity to train undergraduate and graduate computer science students in developing bioinformatics resources using new computer languages and web technologies. The developed toolbox will be used in the curriculum for a graduate-level medicinal chemistry course and web-based workshops. Further, the project will support the biology education in an Oklahoma City public school with a high percentage of underrepresented minority students. The project will generate a novel computational infrastructure composed of two databases and five web tools. Three methods and web tools will be newly developed: (1) TMmatch for the identification and modeling of TM heterodimers; (2) TMPfold for the detection and analysis of stable two-helical folding units in 3D structures of membrane proteins; and (3) 1TMnet for the visualization of protein interaction networks in membranes. These web tools will be included in two improved databases together with the existing PPM and FMAP auxiliary web servers for modeling and positioning of alpha-helices in membranes. The expanded Membranome database, which collects bitopic proteins from six organisms, will incorporate 3D structures of all TM dimers modeled by TMmatch and protein networks identified by 1TMnet (https://membranome.org/ ). The upgraded OPM database, which holds all membrane proteins with known 3D structures positioned in membranes, will include structures of stable two-helical folding units detected by TMPfold and TMmatch in integral membrane proteins (https://opm.phar.umich.edu/). The proposed toolbox will allow for the creation of a scientific workflow from proteome-wide modeling of bitopic protein TM dimers to identification of their interaction networks associated with various biological pathways in different cells and organisms. The comparison of interaction maps of bitopic proteins from six selected species representing all kingdoms of life will advance our knowledge of increased biocomplexity of single-pass membrane proteins during evolution. The easy-to use public web tools will be beneficial for academic and health-related research. The TMPfold web tool will enable computational determination of stable alpha-helical folding intermediates, thus paving the way to ab-initio modeling of structures of multi-pass membrane proteins and analysis of their folding pathways. The TMmatch web server will enable analysis of structural effects of disease-related mutations in TM dimers and will help in the design and optimization of TM alpha-helical complexes for therapeutic purposes.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.