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

单通（即双位）跨膜蛋白是最丰富和功能多样的真核生物膜蛋白，但也是探索最少的一类。双视受体、酶、粘附蛋白和转录调节因子在细胞生长、增殖、分化、迁移、通讯、凋亡和恶性转化等许多重要过程中发挥着关键作用。为了发挥其生物学功能，这些蛋白质通过其TM α -螺旋和水溶性结构域形成二聚体或更大的复合物。膜中α -螺旋配合物的高柔韧性和结构非均质性阻碍了它们的结晶，需要开发计算方法作为获得TM配合物的三维（3D）结构和多态组织的可行替代方法。目前的项目旨在开发和应用新的计算方法来解决双位蛋白的TM异二聚体的建模问题，从而实现对其结构的蛋白质组级研究。开发的方法、工具和补充数据库将推进从头计算蛋白质结构预测方法，这将使在生物物理学、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泛的研究人员、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，培训计算机科学专业的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水平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，该学校的少数族裔学生比例很高。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。将开发3种新方法和网络工具：(1)TMmatch用于TM异二聚体的识别和建模；(2) TMPfold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；(3) 1TMnet用于膜内蛋白质相互作用网络的可视化。这些网络工具将与现有的PPM和FMAP辅助网络服务器一起包含在两个改进的数据库中，用于对膜中的α -螺旋进行建模和定位。扩展后的膜组数据库收集了来自六种生物的双位蛋白，将整合TMmatch建模的所有TM二聚体的3D结构和1TMnet （https://membranome.org/）鉴定的蛋白质网络。升级后的OPM数据库包含了所有已知位于膜上的3D结构的膜蛋白，将包括通过TMPfold和TMmatch在完整膜蛋白中检测到的稳定的双螺旋折叠单元结构（https://opm.phar.umich.edu/）。提出的工具箱将允许创建一个科学的工作流程，从双位蛋白TM二聚体的蛋白质组范围建模到鉴定它们与不同细胞和生物体中各种生物途径相关的相互作用网络。比较来自6个代表所有生命王国的选定物种的双位蛋白的相互作用图将促进我们对进化过程中单遍膜蛋白增加的生物复杂性的认识。易于使用的公共网络工具将有利于学术和健康相关的研究。TMPfold网络工具将能够计算确定稳定的α -螺旋折叠中间体，从而为多通道膜蛋白结构的从头计算建模和折叠途径的分析铺平道路。TMmatch web服务器将能够分析TM二聚体中疾病相关突变的结构效应，并将有助于设计和优化用于治疗目的的TM α -螺旋复合物。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值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.