Packing Is a Key Selection Factor in the Evolution of Protein Hydrophobic Cores

Abstract

The energy derived from optimized van der Waals interactions in closely packed, folded proteins has been proposed to be of similar energetic magnitude to hydrophobicity in stabilizing the native state. If packing is this energetically important, it should influence the evolution of protein core sequences. To test this hypothesis, the occurrence of various amino acid side chains in the major hydrophobic core of staphylococcal nuclease and 42 homologous proteins was determined. Most such positions in this protein family are usually isoleucine, leucine, or valine. Previously we have constructed and measured the stabilities of 12 single, 44 double, 64 triple, and 32 quadruple mutants, representing all possible permutations of these three side chains at two overlapping sets of four positions in the core of staphylococcal nuclease. The stabilities and interaction energies of those mutants with various combinations of the most common, or consensus, sequence were compared to the stabilities of all other mutants. Mutants which had the consensus side-chain combinations were not necessarily the most stable, but usually were found to have the best interaction energies. In other words, these proteins were far more stable than would be predicted from simply summing the observed energetic effects of the component single mutations, apparently reflecting particularly favorable packing interactions that are possible for the most common side chains. An additional 12 mutants which tested possible alternate explanations of the results were constructed. The stabilities and interaction energies of these mutants also support the conclusion that packing is a crucial determinant guiding the sequence evolution of protein cores.

The Contribution of Polar Group Burial to Protein Stability Is Strongly Context-dependent

“…We have emphasized previously the importance of van der Waals interactions in the tightly packed interior of a protein to the contribution of polar group burial to stability (4). Recently, several groups have pointed out that the enhanced van der Waals interactions resulting from the tight packing of groups in the interior of folded proteins are also of crucial importance to the hydrophobic effect (24,40,41).…”

Local complexity of amino acid interactions in a protein core

“…The quality of packing has been reported as uniformly high throughout the core of proteins (1), with mean side chain volumes slightly smaller than those observed in amino acid crystals (2,3). The efficient packing of residues is often as important as the hydrophobic effect in determining the thermodynamic stability of the folded state (4)(5)(6)(7)(8) and may represent a key component of the overall evolutionary pressure guiding sequence variation of a protein fold (9,10). Also, optimal packing of the core has been used as a design principle in creating artificial proteins, often with improved stability (11,12).…”

Aromatic Anchor at an Invariant Hormone-Receptor Interface

“…Such invariance is particularly striking given the following: (i) the essentially native activities of Gly B24 and Met B24 analogs; (ii) the divergence generally observed among hydrophobic cores of globular proteins over this time scale (85); and (iii) the corresponding plasticity of core packing in model systems as revealed by random combinatorial mutagenesis (86). In light of the clinical association between Ser B24 (16) and a monogenic form of DM (15) linked to endoreticular stress in pancreatic ␤-cells (67), we speculate that Phe B24 confers a uniquely favorable combination of foldability, avoidance of misfolding, native assembly, stability, receptor binding and hormonal signaling.…”