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

Regents Of The University Of Michigan - Ann Arbor, Ann Arbor MI

Investigators

Abstract

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.