Computational protocol: A molecular model of the full-length human NOD-like receptor family CARD domain containing 5 (NLRC5) protein

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Protocol publication

[…] Structural data were downloaded from Protein Data Bank [] while protein sequences and sequence annotation data were derived from UniProt database []. Multiple sequence alignments were performed using Clustal W (1.83) and Clustal X (2.0.12) programs []. The LRRML conformational LRR database (v0.6) [], the LRRfinder2.0 webserver [] and the LRR Conservation Mapping Program [] were used for the analyses of LRRs of NLRC5 protein. [...] Secondary structure predictions were performed using the PredictProtein server []. Modeller 7v7 software was used to prepare the homology models []. Molecular dynamics calculations were performed by Sybyl program package (Tripos Inc., St. Louis, MO, USA) using the following parameters: AMBER7_FF99 force field, 1 fs step size, 6 Å non-bonded cutoff, dielectric constant was set to 4 and only the SH-LRR linker region of human NLRC5 (Thr653-Gln687) was allowed to move. The molecule was gradually cooled from 300 to 10 K temperature (temperature was set to 300, 250, 200, 150, 100 and 10 K in the consecutive steps) and 1000 fs-long runs were performed on every temperature value. Energy minimizations were performed by Sybyl without any fixed atoms using the following parameters: AMBER7_FF99 force field, 100–100 Powell iterations were applied using 6, 7 and 8 Å non-bonded cutoff values in the consecutive steps and the dielectric constant was set to 4, 3 and 1, respectively, followed by further 10.000 iterations using the parameters of the last previous run. Calculations and molecular visualizations of the structural models were performed using the Sybyl program package run on Silicon Graphics Fuel workstations (Silicon Graphics International, Fremont, CA, USA). POLYVIEW-3D (available at: http://polyview.cchmc.org/polyview3d.html) was used to prepare surface representation []. […]

Pipeline specifications

Software tools Clustal W, LRRfinder, PP, MODELLER, POLYVIEW-3D
Application Protein structure analysis
Organisms Homo sapiens