LRR Conservation Mapping to Predict Functional Sites within Protein Leucine-Rich Repeat Domains

Computational prediction of protein functional sites can be a critical first step for analysis of large or complex proteins. Contemporary methods often require several homologous sequences and/or a known protein structure, but these resources are not available for many proteins. Leucine-rich repeats (LRRs) are ligand interaction domains found in numerous proteins across all taxonomic kingdoms, including immune system receptors in plants and animals. We devised Repeat Conservation Mapping (RCM), a computational method that predicts functional sites of LRR domains. RCM utilizes two or more homologous sequences and a generic representation of the LRR structure to identify conserved or diversified patches of amino acids on the predicted surface of the LRR. RCM was validated using solved LRR+ligand structures from multiple taxa, identifying ligand interaction sites. RCM was then used for de novo dissection of two plant microbe-associated molecular pattern (MAMP) receptors, EF-TU RECEPTOR (EFR) and FLAGELLIN-SENSING 2 (FLS2). In vivo testing of Arabidopsis thaliana EFR and FLS2 receptors mutagenized at sites identified by RCM demonstrated previously unknown functional sites. The RCM predictions for EFR, FLS2 and a third plant LRR protein, PGIP, compared favorably to predictions from ODA (optimal docking area), Consurf, and PAML (positive selection) analyses, but RCM also made valid functional site predictions not available from these other bioinformatic approaches. RCM analyses can be conducted with any LRR-containing proteins at www.plantpath.wisc.edu/RCM, and the approach should be modifiable for use with other types of repeat protein domains

The predictors of foot ulceration in patients with rheumatoid arthritis

This study was conducted to determine the predictors of foot ulceration occurring in patients with rheumatoid arthritis (RA) without diabetes. A multi-centre case control study was undertaken; participants were recruited from eight sites (UK). Cases were adults diagnosed with RA (without diabetes) and the presence of a validated foot ulcer, defined as a full thickness skin defect occurring in isolation on / below the midline of the malleoli and requiring > 14 days to heal. Controls met the same criteria but were ulcer naive. Clinical examination included loss of sensation (10g monofilament); ankle-brachial pressure index (ABPI); forefoot deformity (Platto); plantar pressures (PressureStat); RA disease activity (36 swollen/tender joint counts) and the presence of vasculitis. History taking included past ulceration/foot surgery; current medication and smoking status. Participants completed the Health Assessment Questionnaire (HAQ) and Foot Impact Scale. A total of 83 cases with 112 current ulcers and 190 ulcer naïve controls participated. Cases were significantly older (mean age 71 years; 95 % confidence interval [CI], 69-73 vs. 62 years, 60-64) and had longer RA disease duration (mean 22 years; 19-25 vs. 15, 13-17). Univariate analysis showed that risk of ulceration increases with loss of sensation; abnormality of ABPI and foot deformity. Plantar pressures and joint counts were not significant predictors. HAQ score and history of foot surgery were strongly associated with ulceration (odds ratio [OR] = 1.704, 95 % CI 1.274-2.280 and OR = 2.256, 95 % CI 1.294-3.932). Three cases and two controls presented with suspected cutaneous vasculitis. In logistic regression modelling, ABPI (OR = 0.04; 95 % CI, 0.01-0.28) forefoot deformity (OR = 1.14; 95 % CI, 1.08-1.21) and loss of sensation (OR = 1.22; 95 % CI, 1.10-1.36) predicted risk of ulceration. In patients with RA, ABPI, forefoot deformity and loss of sensation predict risk of ulceration but, in contrast with diabetes, raised plantar pressures do not predict risk