Abstract
Guanine nucleotide binding proteins are characterized by a structurally and mechanistically conserved GTP-binding domain, indispensable for binding GTP. The G domain comprises of five adjacent consensus motifs called G boxes, which are separated by amino acid spacers of different lengths. Several G proteins, discovered over time, are characterized by diverse function and sequence. This sequence diversity is also observed in the G box motifs (specifically the G5 box) as well as the inter-G box spacer length. The Spacers and Mismatch Algorithm (SMA) introduced in this study, 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 SMA parameters can be customized as more G proteins are discovered and characterized structurally. Family-specific G box motifs including the less characterized G5 motif as well as G domain boundaries were predicted with higher precision. Overall, our analysis suggests the possible classification of G protein families based on family-specific G box sequences and lengths of inter-G box spacers.
Significance Statement It is difficult to define the boundaries of a G domain as well as predict G boxes and important GTP-binding residues of a G protein, if structural information is not available. Sequence alignment and phylogenetic methods are often unsuccessful, given the sequence diversity across G protein families. SMA is a unique method which uses approximate pattern matching as well as inter-motif separation constraints to predict the locations of G-boxes. It is able to predict all G boxes including the less characterized G5 motif which marks the carboxy-terminal boundary of a G domain. Thus, SMA can be used to predict G domain boundaries within a large multi-domain protein as long as the user-specified constraints are satisfied.This is your blog post. Great looking images make your blog posts more visually compelling for your audience, so choose media that really wows. Adding fun and compelling videos is another great way to engage your audience and keep them coming back for more. Want to spice up your post with a gallery? It’s never been easier to customize your content and captivate your readers.
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