Kentaro Shimizu1, Wei Cao2, Gull Saad3, Michiru Shoji4, Tohru Terada5. 1. Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan. Electronic address: shimizu@bi.a.u-tokyo.ac.jp. 2. Faculty of Information Networking for Innovation and Design, Toyo University, Tokyo, Japan. Electronic address: cao@iniad.org. 3. Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan. Electronic address: saad.gul@gmail.com. 4. Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan. Electronic address: michiru0110@bi.a.u-tokyo.ac.jp. 5. Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan. Electronic address: tterada@iu.a.u-tokyo.a.lc.jp.
Abstract
BACKGROUND: Membrane proteins play important roles in cell survival and cell communication, as they function as transporters, receptors, anchors and enzymes. They are also potential targets for drugs that block receptors or inhibit enzymes related to diseases. Although the number of known structures of membrane proteins is still small relative to the size of the proteome as a whole, many new membrane protein structures have been determined recently. SCOPE OF THE ARTICLE: We compared and analyzed the widely used membrane protein databases, mpstruc, Orientations of Proteins in Membranes (OPM), and PDBTM, as well as the extended dataset of mpstruc based on sequence similarity, the PDB structures whose classification field indicates that they are "membrane proteins" and the proteins with Structural Classification of Proteins (SCOP) class-f domains. We evaluated the relationships between these databases or datasets based on the overlap in their contents and the degree of consistency in the structural, topological, and functional classifications and in the transmembrane domain assignment. MAJOR CONCLUSIONS: The membrane databases differ from each other in their coverage, and in the criteria that they use for annotation and classification. To ensure the efficient use of these databases, it is important to understand their differences and similarities. The establishment of more detailed and consistent annotations for the sequence, structure, membrane association, and function of membrane proteins is still required. GENERAL SIGNIFICANCE: Considering the recent growth of experimentally determined structures, a broad survey and cumulative analysis of the sum of knowledge as presented in the membrane protein structure databases can be helpful to elucidate structures and functions of membrane proteins. We also aim to provide a framework for future research and classification of membrane proteins.
BACKGROUND: Membrane proteins play important roles in cell survival and cell communication, as they function as transporters, receptors, anchors and enzymes. They are also potential targets for drugs that block receptors or inhibit enzymes related to diseases. Although the number of known structures of membrane proteins is still small relative to the size of the proteome as a whole, many new membrane protein structures have been determined recently. SCOPE OF THE ARTICLE: We compared and analyzed the widely used membrane protein databases, mpstruc, Orientations of Proteins in Membranes (OPM), and PDBTM, as well as the extended dataset of mpstruc based on sequence similarity, the PDB structures whose classification field indicates that they are "membrane proteins" and the proteins with Structural Classification of Proteins (SCOP) class-f domains. We evaluated the relationships between these databases or datasets based on the overlap in their contents and the degree of consistency in the structural, topological, and functional classifications and in the transmembrane domain assignment. MAJOR CONCLUSIONS: The membrane databases differ from each other in their coverage, and in the criteria that they use for annotation and classification. To ensure the efficient use of these databases, it is important to understand their differences and similarities. The establishment of more detailed and consistent annotations for the sequence, structure, membrane association, and function of membrane proteins is still required. GENERAL SIGNIFICANCE: Considering the recent growth of experimentally determined structures, a broad survey and cumulative analysis of the sum of knowledge as presented in the membrane protein structure databases can be helpful to elucidate structures and functions of membrane proteins. We also aim to provide a framework for future research and classification of membrane proteins.
Authors: Irena Roterman; Katarzyna Stapor; Krzysztof Gądek; Tomasz Gubała; Piotr Nowakowski; Piotr Fabian; Leszek Konieczny Journal: Membranes (Basel) Date: 2021-12-30