Effect of a specific hydrogen bond (N138ND2–Q106O) on conformational integrity, stability, and activity of staphylococcal nuclease

Protein conformational disorder and enzyme catalysis

Though lacking a well-defined three-dimensional structure, intrinsically unstructured proteins are ubiquitous in nature. These molecules play crucial roles in many cellular processes, especially signaling and regulation. Surprisingly, even enzyme catalysis can tolerate substantial disorder. This observation contravenes conventional wisdom but is relevant to an understanding of how protein dynamics modulates enzyme function. This chapter reviews properties and characteristics of disordered proteins, emphasizing examples of enzymes that lack defined structures, and considers implications of structural disorder for catalytic efficiency and evolution.

Probing the subtle conformational state of N138ND2–Q106O hydrogen bonding deletion mutant (Asn138Asp) of staphylococcal nuclease using time of flight mass spectrometry with limited proteolysis

Recent studies indicate that the N138ND2-Q106O hydrogen bonding deletion in staphylococcal nuclease significantly alters the conformational integrity and stability of the nuclease. To find out the structural basis of the changes, mass spectrometry and limited proteolysis methods were combined to probe the subtle conformational changes in the SNaseN138D mutant and SNaseN138D-Ca2+-pdTp complex. The results reveal that the N138ND2-Q106O hydrogen bonding deletion makes the C-terminal part of alpha-helix 1 and alpha-helix 2 in the C-terminal subdomain of SNaseN138D unfold to some extent, but does not have much effect on the N-terminal part of alpha-helix 1, alpha-helix 3, and the N-terminal beta-barrel subdomain of SNaseN138D. Binding of ligands makes the alpha-helices 1 and 2 more resistant to protease Glu-C attack and converts the partially unfolded state to a native-like state. This study also demonstrates how mass spectrometry can be combined with limited proteolysis to observe conformational changes induced by ligand binding.

The effects of amino acid replacements of glycine 20 on conformational stability and catalysis of staphylococcal nuclease

Staphylococcal nuclease (SNase) is a well-established model for protein folding studies. Its three-dimensional structure has been determined. The enzyme, Ca2+, and DNA or RNA substrate form a ternary complex. Glycine 20 is the second position of the first beta-turn of SNase, which may serve as the folding initiation site for the SNase polypeptide. To study the role of Gly20 in the conformational stability and catalysis of SNase, three mutants, in which Gly20 was replaced by alanine, valine, or isoleucine, were constructed and studied by using circular dichroism spectra, intrinsic and ANS-binding fluorescence spectra, stability and activity assays. The mutations have little effect on the conformational integrity of the mutants. However, the catalytic activity is reduced drastically by the mutations, and the stability of the protein is progressively decreased in the order G20A<G20V<G20I. Kinetic analysis indicates that the mutant enzymes G20A and G20V show almost 20-fold higher KmCa values than the wild-type enzyme, and the value for G20I is more than 50-fold higher. KACa values indicate more than 17.5-fold weaker binding of Ca2+ to the G20A and G20V mutants, and more than 39-fold weaker to the G20I mutant, compared to wild-type SNase. The above results suggest that the substitutions at Gly20 cause significantly weaker binding of Ca2+ in both the binary enzyme-Ca2+ complex and the ternary complex. However, there is little difference in the values of KmDNA and KSDNA between the mutants and the wild-type enzyme, suggesting that the substitutions at Gly20 have little effect on the binding of DNA substrates to the enzyme. Consistent with the changes in KmCa and KACa, the mutant enzymes G20A, G20V and G20I show about 10(3)-, 10(4)- and 10(5)-fold lower KCat values than the wild-type enzyme, respectively. These results suggest that Gly20 plays an important role in maintaining a suitable conformation at the active site of the enzyme.