Structure-function Analysis of Inflammatory Bowel Disease Associated Proteins and Moonlighting Proteins

Proteins are fundamental functional and structural components of life. The central dogma describes how DNA sequences encode protein sequences, and a protein’s sequence generally corresponds to a specific three-dimensional structure and function. In this set of projects, we studied examples where a protein’s sequence enables it to have more than one function and examples where genetic changes in the DNA sequence lead to changes in the protein sequence and structure that are associated with disease. Moonlighting proteins have two or more physiologically relevant distinct functions performed by a single polypeptide chain. MoonProt is a comprehensive open access database storing expert curated annotations for moonlighting proteins. In the latest release, we expanded the number of annotated proteins to 370 and modified several dozen protein annotations with additional or updated information, including more links to protein structures in the Protein Data Bank, compared with the previous release. The most common types of moonlighting proteins include enzymes, chaperones, DNA binding proteins, and transcription factors. The new entries in version 2.0 include more examples from humans and several model organisms, more proteins involved in disease, and proteins with different combinations of functions. Inflammatory bowel disease (IBD) is a group of autoimmune diseases affecting the gastrointestinal tract, including Crohn’s disease (CD) and ulcerative colitis (UC). With a growing number of protein structures available, computer-based analysis of the effects of the amino acid substitutions on the three-dimensional structure can be used to provide more insight as to how these changes lead to disease predisposition. A list of single amino acid substitutions associated with CD and/or UC was collected from GWAS (Genome Wide Association Study) and NGS (Next Generation Sequencing) clinical platforms, and used to develop insights about protein structural changes leading to pathogenesis of inflammatory bowel diseases. In this study, more than 200 single amino acid polymorphisms within 109 proteins were identified. Changes in a variety of biochemical and biophysical properties of the amino acids including polarity, volume, and hydrophobicity and characteristics about the location of the substitution within the sequence and structure, including local secondary structure, hydrogen bonding of the sidechain, crystallographic B (thermal) factor, and conservation, were studied. The sites of the inflammatory bowel disease-associated mutations are not highly conserved, and almost all the mutations are located on the surface of the protein, which are results that differ from previous studies of disease-associated mutations in general. This study can be helpful for selecting proteins for further biochemical and biophysical analysis and for aiding in the development of improved clinical diagnostic methods and therapeutics for Crohn’s disease and ulcerative colitis.