Hydrophobic core packing in the Arx1 protein. A) Ribbon representation of the ctArx1 structure. ctArx1 crystallized readily, whereas cgArx1 did not. Adaptive (destabilizing) and neutral (non-destabilizing) amino acids are highlighted in red and blue, respectively. The positions of amino acids, which differ between the cg and ctArx1 proteins, are marked in yellow. The positions of the ctArx1 specific cysteines, C249 and C335, and the prolines, P135 and P182, are indicated by stars and triangles respectively. The N- and C-termini of ctArx1 are indicated by ‘N’ and ‘C’. B) Mutation of a hydrophobic patch leads to reduced thermostability of ctArx1. Two ctArx1 mutant proteins containing mutations within the hydrophobic patch described in (C,D,E) are tested for their thermostability in comparison to wild-type ctArx1 at the indicated temperatures and at a protein concentration of 8 mg/ml. ctArx1-destab7 contains the five destabilizing mutations of ctArx1-destab (Figure 4B) and two mutated hydrophobic residues (F146L, W357L), ctArx1-destab3 contains F146L, W357L, and the destabilizing mutation R350K. C) A closed hydrophobic stretch of exchanged amino acids in ctArx1 increases the contact between secondary structure elements and close a surface groove in ctArx1. Val128, Phe146, Trp357 and Phe362 of ctArx1 are highlighted in yellow. D) The corresponding modeled amino acid residues of cgArx1, Leu128, Leu147, Leu358 and Leu363, are highlighted in magenta. In both panels the volumes of the residues are indicated with small dots. E) The adaption of ctArx1 to thermophily is achieved in part by the increase of hydrophobic density and polar/electrostatic contacts with the core of the protein’s scaffold. The adaptive amino acid Arg350 (Lys) is highlighted in red. Hydrophobic animo acids, which differ between the cg and ctArx1 proteins, are marked in yellow. Amino acid side chain interactions are indicated by black, dashed lines.
van Noort et al. BMC Evolutionary Biology 2013 13:7 doi:10.1186/1471-2148-13-7