PMC

Structure stability analysis of the p.P247L, p.L443P, p.R606H, p.H327T, p.S637T, p.R749H, p.E377A, p.V69M, p.G709R, p.P432L mutations on the partial tertiary structure of CPT1Aprotein (Uniprot: AF-P50416-F1). Structure stability analysis of the p.F352L mutation on the partial tertiary structure of CPT2 protein (Uniprot: AF-P23786-F1). A: The wildtype amino-acid residue at 247 site, 443 site, 606 site, 327 site, 637 site, 749 site, 377 site, 69 site, 709 site, 432 site and 352 site (CPT2 protein) colored green has no contact with the amino-acid residue nearby. (A) base on this model, after amino-acid was substituted by the Leucine amino acid residue at this site, five atoms clash and contacts were found in this region. (B) After amino-acid was substituted by the Proline amino acid residue at this site, five atoms clash and contacts were found in this region. (C) After amino-acid was substituted by the Histidine amino acid residue at this site, three atoms clash and contacts were found in this region. (D) After amino-acid was substituted by the Threonine amino acid residue at this site, no atom clash and contacts were found in this region. (E) After amino-acid was substituted by the Threonine amino acid residue at this site, one atoms clash and contacts were found in this region. (F) After amino-acid was substituted by the Histidine amino acid residue at this site, three atom clash and contacts were found in this region. (G) After amino-acid was substituted by the Aspartic acid residue at this site, 0 atoms clash and contacts were found in this region. H After amino-acid was substituted by the Methionine amino acid residue at this site, seven atoms clash and contacts were found in this region. (I) After amino-acid was substituted by the Argnine amino acid residue at this site, 37 atoms clash and contacts were found in this region. (J) After amino-acid was substituted by the Leucine amino acid residue at this site, 0 atoms clash and contacts were found in this region (K) After amino-acid was substituted by the Leucine amino acid residue at this site, one atoms clash and contacts were found in this region. Amino acid change marked with red arrows. Atoms clash and contacts are shown in yellow lines. The Structure stability analysis of novel mutations were performed by Chimera version 1.15.

(A): residue to residue contact of light chain of FXa and daboxin P (B): residue to residue contact of heavy chain of FXa and daboxin P. The residue to residue contact area of the interacting amino acid residues for the chains has been considered above 8 Ų for the design of the contact map.

Description of structural properties. (A) Visualization of solvent accessibility. (B) Visualization of local packing density. Each colored red particle represents a residue in the protein. In A, the lower red particle represents a surface residue. The red and white molecules indicate solvent molecules (e.g., water) that are contacting the red amino acid. This residue has a larger solvent accessibility because there is a larger proportion of the residue surface exposed to solvent. The upper red particle represents a core residue. This residue is not in contact with any solvent molecules and thus has low solvent accessibility. Relative solvent accessibility is obtained by normalizing the solvent accessibility of a given residue by the maximum amount of solvent accessibility for that amino acid. In B, the arrows pointing towards each residue indicate contacts between the red focal residue and its neighboring residues. The upper red residue represents a residue that has many neighbors (represented by the arrows) and thus has a high weighted contact number. The lower red residue is a surface amino acid with few neighbors and thus has a lower weighted contact number.

Comparison of the residue contact networks in the rhodopsin cycle. a, Residue contact networks of the structural intermediates of the rhodopsin cycle. In the residue contact networks, amino acid residues are denoted as nodes and the presence of contacts between pairs of residues are denoted as edges. ‘Contact fingerprinting’ and key residue contact changes in the binding pocket are displayed. For every residue contact within the ensemble, the presence or absence of an equivalent residue contact between equivalent positions across the rest of the states was recorded. This information is represented as an array of filled (contact present) and empty (contact absent) cells, which are referred to here as ‘contact fingerprints’. b, Inactive state only contacts map to the retinal binding pocket and the G protein-coupling region. Active state only contacts map to the region linking the two regions. A key structural change in the binding pocket involving aromatic contacts between Phe293 and Phe294 is shown in stick representation. (a-b) inactive states are shown in grey and active states are shown in green.