Abstract
Purpose:
Conserved protein domains are independently folding fragments of polypeptide sequences, existing in humans and ancient species, and demonstrating a distinct functional behavior. DNA sequence variation in protein coding regions may alter the structure and function of conserved domains by yielding peptide, disulfide bond, hydrogen bond, and electrostatic changes. In this work we examine the putative consequences of DNA coding variants on the 3-D structure of complement proteins as these changes may relate to advanced age-related macular degeneration (AAMD).
Methods:
We used extant findings from large-scale genotyping projects on the molecular genetics of AMD (including ~80,000 people) and data from the 1000 Genomes Pilot, ENCODE Project, and Conserved Domains Database to identify AAMD-associated DNA sequence variants resident in genomic regions encoding conserved complement protein domains. We report findings for SUSHI repeats (short complement-like repeats, SCR) here. Amino acid sequences of 54 SUSHI modules from C2, CFB, CFH, F13B, CFHR1, CFHR2, CFHR3, CFHR4 (AAMD-associated genes) complement protein sequences were aligned using Promals3D to show the conserved sequence pattern. 3-D structure of SUSHI domains was modeled by homology in order to place AAMD-associated residue substitutions within a consensus sequence and evaluate the severity of the changes.
Results:
AAMD-associated (P <= 5.0 x 10E-8) SNPs encoding SUSHI domains yielded residue changes in CFH (V61I, Y402H, R1210C), CFHR4 (N210S), F13B (R115H), and CFB (R32Q) proteins. In the aligned consensus sequence, identity was > 94% across proteins for two sets of cysteine residues forming disulfide bonds essential for maintaining the domain native fold and integrity. Conserved proline (85%) and tryptophan (87%) residues were proximal to the 4 cysteines, as were the AMD-associated residues.
Conclusions:
The orientation of SUSHI modules relative to each other is critical for function of protein binding and catalytic domains. SUSHI repeats in mature complement proteins, encoded in part by AAMD-associated DNA sequence variants, share evolutionarily conserved cysteine residues essential for maintaining protein native folds. These residues are proximal to AAMD-associated amino acids. Our findings may be used to guide development of small therapeutic molecules designed to precisely and accurately target AMD-susceptibility loci in genes and proteins.
Keywords: 412 age-related macular degeneration •
660 proteins encoded by disease genes •
539 genetics