Fig. 6: Analyses on the structure changes of CRABPâ…ˇ protein induced by mutation or ligand binding.
From: Measuring and locating the changes in protein structure using MELO
Apart from the most common conformations (39 conformations of identical sequences deposited by different research groups), holo-CRABPⅡ (HC), which bound retinoic acids, two conformations were collected from PDB: apo-CRABPⅡ (AC) without retinoic acid and mutant CRABPⅡ (MC) with the R35D and K36D mutation. a evaluating outcome for three groups of structure pairs (HC vs HC, MC vs HC, and AC vs HC) based on VSSmeasur (x-axis) and SPSmeasur (y-axis) of MELO. Great shifts among protein segments between MC and HC were captured by MELO (0.21 <VSSmeasur < 0.30 & 0.58 <SPSmeasur < 0.61). Both the variations in secondary structures and shifts among protein segments between AC and HC were discovered by MELO (0.50 <VSSmeasur < 0.53 & 0.55 <SPSmeasur < 0.59). No significant change in structure was observed among 39 conformations of HC by MELO (0.01 <VSSmeasur < 0.21 & 0.03 <SPSmeasur < 0.26), which illustrated the stability and accuracy of MELO in differentiating changed structure and the unchanged one. b violin plots for comparing three methods by analyzing their abilities to discern the structure change among three conformations of CRABPⅡ. MELO was able to identify the extensive shift among protein segments between MC and HC, and reveal the variations in secondary structure and shifts among protein segments between AC and HC. TM-score could not identify structure change not only between MC and HC but also between AC and HC, and LDDT was not useful enough to identify the corresponding structure changes. c assessing structure change between mutant CRABPⅡ (MC, PDB:7OXW) and holo-CRABPⅡ (HC, PDB:6HKR) based on different methods. Only MELO could capture the shifts among segments (VSSmeasur = 0.25 & SPSmeasur = 0.59). d evaluating the structure change between apo-CRABPⅡ (AC, PDB:1BLR) and holo-CRABPⅡ (HC, PDB:6HKR) using different methods. Only MELO could detect the variations in secondary structure and shifts among protein segments (VSSmeasur = 0.53 & SPSmeasur = 0.58.
