Factors contributing to decreased protein stability when aspartic acid residues are in β‐sheet regions

Asp residues are significantly under represented in β‐sheet regions of proteins, especially in the middle of β‐strands, as found by a number of studies using statistical, modeling, or experimental methods. To further understand the reasons for this under representation of Asp, we prepared and analyzed mutants of a β‐domain. Two Gln residues of the immunoglobulin light‐chain variable domain (VL) of protein Len were replaced with Asp, and then the effects of these changes on protein stability and protein structure were studied. The replacement of Q38D, located at the end of a β‐strand, and that of Q89D, located in the middle of a β‐strand, reduced the stability of the parent immunoglobulin VL domain by 2.0 kcal/mol and 5.3 kcal/mol, respectively. Because the Q89D mutant of the wild‐type VL‐Len domain was too unstable to be expressed as a soluble protein, we prepared the Q89D mutant in a triple mutant background, VL‐Len M4L/Y27dD/T94H, which was 4.2 kcal/mol more stable than the wild‐type VL‐Len domain. The structures of mutants VL‐Len Q38D and VL‐Len Q89D/M4L/Y27dD/T94H were determined by X‐ray diffraction at 1.6 Å resolution. We found no major perturbances in the structures of these Q→D mutant proteins relative to structures of the parent proteins. The observed stability changes have to be accounted for by cumulative effects of the following several factors: (1) by changes in main‐chain dihedral angles and in side‐chain rotomers, (2) by close contacts between some atoms, and, most significantly, (3) by the unfavorable electrostatic interactions between the Asp side chain and the carbonyls of the main chain. We show that the Asn side chain, which is of similar size but neutral, is less destabilizing. The detrimental effect of Asp within a β‐sheet of an immunoglobulin‐type domain can have very serious consequences. A somatic mutation of a β‐strand residue to Asp could prevent the expression of the domain both in vitro and in vivo, or it could contribute to the pathogenic potential of the protein in vivo.