G - Domain prediction across the diversity of G protein families
G proteins, also known as guanine nucleotide-binding proteins, are a family of proteins that act as molecular switche inside cells, and are involved in transmitting signals from a variety of stimuli outside a cell to its interior. There activity is regulated by factors that control their ability to bind to and hydrolyze guanosine triphosphate (GTP) to guanosine diphosphate (GDP). GTP-binding (G) proteins constitute a class of P-loop (phosphate-binding loop) proteins that work as molecular switches between the GDP-bound OFF and the GTP-bound ON state. The common principle is the 160 - 180 residue G domain with an ἀ, β topology that is responsible for nucleotide-dependent conformational changes and drives many biological functions. Although the G domain uses a universally conserved switching mechanism, its structure, function, and GTPase reaction are modified for many different pathways and processes. The G domain comprises of five adjacent consensus motifs called G boxes, which are separated by amino acid spacers of different lengths. The project deals with the development of a software implementing the Spacers and Mismatch Algorithm (SMA). SMA can predict G domains in a given G protein sequence, based on user-specified constraints for approximate G-box patterns and inter-box gaps in each G protein family. The parameters can be customized as more G proteins will be discovered and characterized structurally. The SMA had even predicted the family-specific G box motifs including the less characterized G5 motif as well as G domain boundaries with higher precision. Thus, the software will contain placeholders for user input and will implement the Spacers and Mismatch Algorithm, at the backend, and will provide the user with the results. Overall, this will function as a framework for the algorithm with taking into consideration, user-friendly mode of appearance.
Keywords: G proteins, G domain, G box, Software, Spacers and Mismatch Algorithm