TRAC: A Platform for Structure-Function Studies of NSS-Proteins Integrates Information from Bioinformatics and Biomedical Literature

Abstract

To enable rigorous and reliable modeling of functional mechanisms of membrane proteins, the computational modeling and simulation approaches must take advantage, to the fullest extent possible, of the wealth of data obtained experimentally. This type of information makes it possible not only to construct rigorous molecular models and quantitative representations of function, but also to test, verify and refine them continuously. Among the proteins in the cell membrane, the family of Neurotransmitter: Sodium Symporter (NSS) exhibits highly complex mechanisms that involve multiple molecular states in the substrate and ion transport cycle. Due to their high biological and medical importance, experimental data for these systems is abundant, and efficient management of information from the literature and other relevant data sources promises to be very rewarding. We have developed an information management system (IMS) for data concerning the NSS proteins to enable retrieval, structured organization, and query of information available in the literature. The IMS supports the interplay between computational approaches and experimental studies of structure, function and physiological mechanisms of the NSS, and is of special utility in the integration of data of different types and various sources, and of the mechanistic understanding emerging from separate functional studies of individual members of the family.