Biomaterial Database

Prediction of the exposure status of transmembrane beta barrel residues from protein sequence. 2011

Sikander Hayat, and Peter Walter, and Yungki Park, and Volkhard Helms

Center for Bioinformatics, Saarland University, Germany. s.hayat@bioinformatik.uni-saarland.de

We present BTMX (Beta barrel TransMembrane eXposure), a computational method to predict the exposure status (i.e. exposed to the bilayer or hidden in the protein structure) of transmembrane residues in transmembrane beta barrel proteins (TMBs). BTMX predicts the exposure status of known TM residues with an accuracy of 84.2% over 2,225 residues and provides a confidence score for all predictions. Predictions made are in concert with the fact that hydrophobic residues tend to be more exposed to the bilayer. The biological relevance of the input parameters is also discussed. The highest prediction accuracy is obtained when a sliding window comprising three residues with similar C(α)-C(β) vector orientations is employed. The prediction accuracy of the BTMX method on a separate unseen non-redundant test dataset is 78.1%. By employing out-pointing residues that are exposed to the bilayer, we have identified various physico-chemical properties that show statistically significant differences between the beta strands located at the oligomeric interfaces compared to the non-oligomeric strands. The BTMX web server generates colored, annotated snake-plots as part of the prediction results and is available under the BTMX tab at http://service.bioinformatik.uni-saarland.de/tmx-site/. Exposure status prediction of TMB residues may be useful in 3D structure prediction of TMBs.

UI	MeSH Term	Description	Entries
D008565	Membrane Proteins	Proteins which are found in membranes including cellular and intracellular membranes. They consist of two types, peripheral and integral proteins. They include most membrane-associated enzymes, antigenic proteins, transport proteins, and drug, hormone, and lectin receptors.	Cell Membrane Protein,Cell Membrane Proteins,Cell Surface Protein,Cell Surface Proteins,Integral Membrane Proteins,Membrane-Associated Protein,Surface Protein,Surface Proteins,Integral Membrane Protein,Membrane Protein,Membrane-Associated Proteins,Membrane Associated Protein,Membrane Associated Proteins,Membrane Protein, Cell,Membrane Protein, Integral,Membrane Proteins, Integral,Protein, Cell Membrane,Protein, Cell Surface,Protein, Integral Membrane,Protein, Membrane,Protein, Membrane-Associated,Protein, Surface,Proteins, Cell Membrane,Proteins, Cell Surface,Proteins, Integral Membrane,Proteins, Membrane,Proteins, Membrane-Associated,Proteins, Surface,Surface Protein, Cell
D008958	Models, Molecular	Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.	Molecular Models,Model, Molecular,Molecular Model
D003198	Computer Simulation	Computer-based representation of physical systems and phenomena such as chemical processes.	Computational Modeling,Computational Modelling,Computer Models,In silico Modeling,In silico Models,In silico Simulation,Models, Computer,Computerized Models,Computer Model,Computer Simulations,Computerized Model,In silico Model,Model, Computer,Model, Computerized,Model, In silico,Modeling, Computational,Modeling, In silico,Modelling, Computational,Simulation, Computer,Simulation, In silico,Simulations, Computer
D000595	Amino Acid Sequence	The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.	Protein Structure, Primary,Amino Acid Sequences,Sequence, Amino Acid,Sequences, Amino Acid,Primary Protein Structure,Primary Protein Structures,Protein Structures, Primary,Structure, Primary Protein,Structures, Primary Protein
D001185	Artificial Intelligence	Theory and development of COMPUTER SYSTEMS which perform tasks that normally require human intelligence. Such tasks may include speech recognition, LEARNING; VISUAL PERCEPTION; MATHEMATICAL COMPUTING; reasoning, PROBLEM SOLVING, DECISION-MAKING, and translation of language.	AI (Artificial Intelligence),Computer Reasoning,Computer Vision Systems,Knowledge Acquisition (Computer),Knowledge Representation (Computer),Machine Intelligence,Computational Intelligence,Acquisition, Knowledge (Computer),Computer Vision System,Intelligence, Artificial,Intelligence, Computational,Intelligence, Machine,Knowledge Representations (Computer),Reasoning, Computer,Representation, Knowledge (Computer),System, Computer Vision,Systems, Computer Vision,Vision System, Computer,Vision Systems, Computer
D016001	Confidence Intervals	A range of values for a variable of interest, e.g., a rate, constructed so that this range has a specified probability of including the true value of the variable.	Confidence Interval,Interval, Confidence,Intervals, Confidence
D017433	Protein Structure, Secondary	The level of protein structure in which regular hydrogen-bond interactions within contiguous stretches of polypeptide chain give rise to ALPHA-HELICES; BETA-STRANDS (which align to form BETA-SHEETS), or other types of coils. This is the first folding level of protein conformation.	Secondary Protein Structure,Protein Structures, Secondary,Secondary Protein Structures,Structure, Secondary Protein,Structures, Secondary Protein
D017510	Protein Folding	Processes involved in the formation of TERTIARY PROTEIN STRUCTURE.	Protein Folding, Globular,Folding, Globular Protein,Folding, Protein,Foldings, Globular Protein,Foldings, Protein,Globular Protein Folding,Globular Protein Foldings,Protein Foldings,Protein Foldings, Globular
D057927	Hydrophobic and Hydrophilic Interactions	The thermodynamic interaction between a substance and WATER.	Hydrophilic Interactions,Hydrophilic and Hydrophobic Interactions,Hydrophilicity,Hydrophobic Interactions,Hydrophobicity,Hydrophilic Interaction,Hydrophilicities,Hydrophobic Interaction,Hydrophobicities,Interaction, Hydrophilic,Interaction, Hydrophobic,Interactions, Hydrophilic,Interactions, Hydrophobic
D019295	Computational Biology	A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.	Bioinformatics,Molecular Biology, Computational,Bio-Informatics,Biology, Computational,Computational Molecular Biology,Bio Informatics,Bio-Informatic,Bioinformatic,Biologies, Computational Molecular,Biology, Computational Molecular,Computational Molecular Biologies,Molecular Biologies, Computational