Mechanism of formation of the C‐terminal β‐hairpin of the B3 domain of the immunoglobulin binding protein G from Streptococcus. I. Importance of hydrophobic interactions in stabilization of β‐hairpin structure

Abstract

We previously studied a 16-amino acid-residue fragment of the C-terminal β-hairpin (residues 46-61), ], of the B3 domain of the immunoglobulin binding protein G from Streptoccocus, and found that hydrophobic interactions and the turn region play an important role in stabilizing the structure. Based on these results, we carried out systematic structural studies of peptides derived from the sequence of IG(46-61) by systematically shortening the peptide by one residue at a time from both the C and the N terminus. To determine the structure and stability of two resulting 12-and 14-amino acid residue peptides, IG(48-59) and IG(47-60), respectively, we carried out CD, NMR and calorimetric studies of these peptides in pure water. Our results show that IG(48-59) possesses organized three-dimensional structure stabilized by hydrophobic interactions (Tyr50 -Phe57 and Trp48 -Val59) at T = 283 and 305 K. At T = 313 K, the structure breaks down because of increased chain entropy, but the turn region is preserved in the same position observed for the structure of the whole protein. The breakdown of structure occurs near the melting temperature of this peptide (T m = 310 K) measured by Differential Scanning Calorimetry (DSC). The melting temperature of IG(47-60) determined by DSC is T m = 330 K and its structure is similar to that of the native β-hairpin at all (lower) temperatures examined (283 -313 K). Both of these truncated sequences are conserved in all known amino acid sequences of the B domains of the immunoglobulin binding protein G from bacteria. Thus, this study contributes to an understanding of the mechanism of folding of this whole family of proteins, and provides information about the mechanism of formation and stabilization of a β-hairpin structural element.

Thermodynamics of protein folding using a modified Wako-Saitô-Muñoz-Eaton model

“…Using this approach, as the backbone H-bond interactions were defined solely as enthalpic constraints, our results show that backbone H-bonds only have a minor effect on the sigmoidal behavior (cooperative behavior) because of their small free energy contribution. This result is consistent with Scheraga and his coworkers, who pointed out that no clear evidence supports the presence of backbone H-bonds in non-turn regions [8,66,67,[80][81][82][83][84]. In other words, the backbone H-bond interaction may not contribute as much as expected in the cooperative formation of β-hairpins but may play only a structural as well as energetic constraint in modulation of the cooperative system [see Fig.…”

Mechanism of formation of the C‐terminal β‐hairpin of the B3 domain of the immunoglobulin‐binding protein G from Streptococcus. IV. Implication for the mechanism of folding of the parent protein

“…We found that, even for peptides of different length, which share a common 6-residue fragment, the following conformational properties remain unchanged: (i) we found that the 6-residue sequence corresponding to the turn region in the structure of the β-hairpin always possesses a structure very similar to that observed in the structure of the native protein, regardless of the peptide length used in our study. Moreover, we performed our study over a relatively wide range of temperatures (283 - 323 K), and found that the conformational properties of the turn region are not temperature dependent;22,33-35 (ii) our previous study22,33-35 also showed that, regardless of the peptide length, the general shape of the investigated peptide resembles a β-hairpin-like structure, which is stabilized by long-range hydrophobic interactions between nonpolar residues. We did not find any evidence that hydrogen bonds participate in the structure stabilization (some hydrogen bonds are observed within the turn region, but they have only very local character) as was suggested in earlier studies 32…”

“…As in our previous studies22,33-35 we used the DSC method to determine thermal stability41 and possible tendency to aggregation of the peptide 42. The DSC experiment can detect oligomerization/aggregation processes in a wide range of temperatures, using a very small amount of an investigated compound, and can show if the process of aggregation/oligomerization is reversible with changes of temperature.…”

“…Usually peptide fragment length was determined by the length of the corresponding regular secondary structure elements present in the structure of complete proteins 20,24-32. In our previous studies, we addressed this problem by studying peptides of different lengths from 6 up to 20 residues corresponding to the C-terminal β-hairpin from the B3 domain of protein G 22,33-35. We found that, even for peptides of different length, which share a common 6-residue fragment, the following conformational properties remain unchanged: (i) we found that the 6-residue sequence corresponding to the turn region in the structure of the β-hairpin always possesses a structure very similar to that observed in the structure of the native protein, regardless of the peptide length used in our study.…”

Investigations of copper(II) complexation by fragments of the FBP28 protein using isothermal titration (ITC) and differential scanning calorimetry (DSC)

“…The b-hairpin from the FBP28 protein is known to initiate the folding of this protein [8]. This is an independently forming region whose folding is not induced by a b-hairpin and is consequently an excellent object by which to study the factors that influence b-hairpin formation.…”