Factors correlating with significant differences between X-ray structures of myoglobin

Abstract

Validation of general ideas about the origins of conformational differences in proteins is critical in order to arrive at meaningful functional insights. Here, principal component analysis (PCA) and distance difference matrices are used to validate some such ideas about the conformational differences between 291 myoglobin structures from sperm whale, horse and pig. Almost all of the horse and pig structures form compact PCA clusters with only minor coordinate differences and outliers that are easily explained. The 222 whale structures form a few dense clusters with multiple outliers. A few whale outliers with a prominent distortion of the GH loop are very similar to the cluster of horse structures, which all have a similar GH-loop distortion apparently owing to intermolecular crystal lattice hydrogen bonds to the GH loop from residues near the distal histidine His64. The variations of the GH-loop coordinates in the whale structures are likely to be owing to the observed alternative intermolecular crystal lattice bond, with the change to the GH loop distorting bonds correlated with the binding of specific `unusual' ligands. Such an alternative intermolecular bond is not observed in horse myoglobins, obliterating any correlation with the ligands. Intermolecular bonds do not usually cause significant coordinate differences and cannot be validated as their universal cause. Most of the native-like whale myoglobin structure outliers can be correlated with a few specific factors. However, these factors do not always lead to coordinate differences beyond the previously determined uncertainty thresholds. The binding of unusual ligands by myoglobin, leading to crystal-induced distortions, suggests that some of the conformational differences between the apo and holo structures might not be `functionally important' but rather artifacts caused by the binding of `unusual' substrate analogs. The causes of P6 symmetry in myoglobin crystals and the relationship between crystal and solution structures are also discussed.

Crystal structures of native cytochrome c 6 from Thermosynechococcus elongatus in two different space groups and implications for its oligomerization

“…The structure and position of the heme group are widely conserved, with a minor difference in the position of the attached carboxy groups in the model derived by NMR coloured light blue. additives can alter molecular interactions and could lead to different packing symmetries (Kondrashov et al, 2008;Rashin et al, 2014) despite the use of an identical precipitant solution.…”

Apolipoprotein CII Amyloidosis Associated With p.Lys41Thr Mutation

“…We computed an alignment-free median residue−residue distance matrix within each trajectory. 22 , 23 , 24 The distance difference matrix quantifies the median pairwise proximity of residues to each other. Simulations were analyzed using custom scripts, the Bio3D R package and Visual Molecular Dynamics (VMD).…”

Polymorphisms in STING affect human innate immune responses to poxviruses

“…Trajectories were then evaluated using multiple metrics, including C-alpha Root Mean Squared Deviation (RMSD), Root Mean Squared Fluctuation (RMSF), Principal Component (PC) analysis, alignment-free distance difference matrix (Holm and Sander, 1993;Grant et al, 2006;Rashin et al, 2014), and distance monitors across the ligand binding site. We quantified variance of atomic C α -C α ( Figure 7A) distances using median absolute difference (MAD).…”