Local stability identification and the role of a key aromatic amino acid residue in staphylococcal nuclease refolding

Characterization of a nontypeable Haemophilus influenzae thermonuclease

Nontypeable Haemophilus influenzae (NTHi) has been shown to form biofilms, comprised of extracellular DNA (eDNA), in the middle ear and bronchus during clinical infections. Studies in our laboratory have shown that NTHi possesses a homolog of Staphylococcus aureus thermonuclease (staphylococcal thermonuclease), NTHi nuclease (NTHi Nuc, HI_1296). This enzyme had similar size, heat stability, and divalent cation requirements to those of the staphylococcal homolog as determined by light scattering and circular dichroism spectroscopy. Small angle X-ray scattering (SAXS) analysis suggested an overall shape and substrate-binding site comparable to those of staphylococcal nuclease. However, NTHi Nuc was approximately 25-fold more active in fluorescence resonance energy transfer (FRET) activity assay than staphylococcal thermonuclease. Homology modeling implicates shorter NTHi Nuc loops near the active site for this enhanced activity.

Efficiency optimisation of proteins on a chip

This study elucidates that the protein reorientation on a chip can be changed by an external electric field (EEF) and optimised for achieving strong effective binding between proteins. Protein A and its binding protein immunoglobulin G (IgG) were used as an example, in addition to an anticancer peptide (CB1a) and its antibody (anti-CB1a). The binding forces (BFs) were measured by atomic force microscopy (AFM) with EEFs applied at different angles (EEF°). The optimal angle (OA) of the EEF (OAEEF°) corresponding to the maximum binding force (BFmax) was obtained. The results showed that the BFmax values between IgG/Protein A and anti-CB1a/CB1a were 6424.2 ± 195.3 pN (OAEEF° = 45°) and 729.1 ± 33.2 pN (OAEEF° = 22.5°), respectively. Without an EEF, the BF values were only 730.0 ± 113.9 pN and 337.3 ± 35.0 pN, respectively. Based on these observations, we concluded that the efficient optimisation of protein-protein interaction on a chip is essential. This finding is applicable to the industrial fabrication of all protein chips.

Conformational consequences of ionization of Lys, Asp, and Glu buried at position 66 in staphylococcal nuclease

The pK(a) values measured previously for the internal Lys-66, Asp-66, and Glu-66 in variants of a highly stable form of staphylococcal nuclease are shifted by as many as 5 pK(a) units relative to normal pK(a) values in water. These shifts cannot be reproduced with continuum electrostatics calculations with static structures unless the protein is treated with high dielectric constants near 10. These high apparent dielectric constants are inconsistent with the highly hydrophobic microenvironments of the ionizable moieties in crystal structures. To examine the origins of these high apparent dielectric constants, we showed that the pK(a) values of these internal residues are sensitive to the global stability of the protein; the shifts tend to be smaller in less stable forms of nuclease. This implies that the apparent dielectric constants reported by these internal ionizable groups are high because they reflect conformational reorganization coupled to their ionization. To detect this directly, acid-base titrations monitored with Trp fluorescence and near-UV and far-UV CD spectroscopy were performed on variants with Lys-66, Glu-66, or Asp-66 in background proteins with different stabilities. Conformational reorganization coupled to the ionization of the internal groups was spectroscopically detectable, especially in the less stable background proteins. The data show that to improve the accuracy of structure-based pK(a) calculations of internal groups the calculations will have to treat explicitly all structural reorganization coupled to ionization. The data also suggest a novel approach to mapping the folding free energy landscape of proteins by using internal ionizable groups to stabilize partially unfolded states.

Importance of the C-terminal loop L137-S141 for the folding and folding stability of staphylococcal nuclease

The role of the C-terminal loop L137-S141 in the folding and folding stability of staphylococcal nuclease (SNase) was investigated by deletion mutation. The C-terminal truncated SNase fragments, SNase137, SNase139, SNase140, and SNase141 containing residues 1-137, 1-139, 1-140, and 1-141, respectively, were adopted in this study. Folding states of these four SNase fragments were analyzed by circular dichroism and fluorescence measurements. The solution structure of SNase140 was determined and compared to those of SNase141 and native SNase using the heteronuclear NMR method. The results showed that folding of the four SNase fragments is correlated with the folding of helix alpha3. With the chain length extending from L137 and I139 to S141, folding of the fragments progressively approached to the tertiary folding of native SNase, and the folding stability was enhanced. These observations revealed that the C-terminal loop L137-S141 has profound effect not only on the folding of helix alpha3 but also on the stabilizing folding of both the alpha- and beta-subdomains of SNase. Analysis indicates that stabilizing folding of the SNase and SNase fragments depends to a large extent on the hydrophobic packing interactions in both the C-terminal local structural region surrounding W140 including the loop L137-S141 and the N-terminal local structural region of the "beta-barrel" hydrophobic core.

Nonlocal interactions are responsible for tertiary structure formation in staphylococcal nuclease

Rapid molecular collapse mediated by nonlocal interactions is believed to be a crucial event for protein folding. To investigate the role of nonlocal interactions in tertiary structure formation, we performed a nonlocal interaction substitution mutation analysis on staphylococcal nuclease (SNase). Y54 and I139 of wild-type (WT) SNase and Delta140-149 were substituted by cysteine to form intramolecular disulfide bonds, respectively called WT-SS and Delta140-149-SS. Under physiological conditions, the reduced form of Delta140-149-SS appears to assume a denatured structure; in contrast, the oxidized form of Delta140-149-SS forms a native-like structure. From this result, we conclude that the C-terminal region participates in a nonlocal interaction that is indispensable for the native structure. Although the oxidized form of WT-SS assumes a more compact denatured structure under acidic conditions than the WT, the kinetic measurements reveal that the refolding reactions of both the reduced and oxidized forms of WT-SS are similar to those of the WT, suggesting that an intact nonlocal interaction is established within the dead time (22 ms). On the basis of these results, we propose that the native nonlocal contact established at the early stage of the folding process facilitates further secondary structure formation.