Mechanism of formation of the C‐terminal β‐hairpin of the B3 domain of the immunoglobulin binding protein G from Streptococcus. II. Interplay of local backbone conformational dynamics and long‐range hydrophobic interactions in hairpin formation

Abstract

Two peptides, corresponding to the turn region of the C-terminal β-hairpin of the B3 domain of the immunoglobulin binding protein G from Streptoccocus, consisting of residues 51-56 ] and 50-57 ], respectively, were studied by CD and NMR spectroscopy at various temperatures and by differential scanning calorimetry. Our results show that the part of the sequence corresponding to the β-turn in the native structure (DDATKT) of the B3 domain forms bent conformations similar to those observed in the native protein. The formation of a turn is observed for both peptides in a broad range of temperatures (T = 283-323 K), which confirms the conclusion drawn from our previous studies of longer sequences from the C-terminal β-hairpin of the B3 domain of the immunoglobulin binding protein G (16, 14 and 12 residues), that the DDATKT sequence forms a nucleation site for formation of the β-hairpin structure of peptides corresponding to the C-terminal part of all the B domains of the immunoglobulin binding protein G. We also show and discuss the role of long-range hydrophobic interactions as well as local conformational properties of polypeptide chains in the mechanism of formation of the β-hairpin structure.

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

“…In our study of the 20-residue peptide, we observed a similar situation of long-range interactions between hydrophobic residues located far from the turn region and an absence of H N (i) – H N (i+1) interactions within the turn region35. The hydrophobic interaction (between Val47 and Val59) observed in the IG(28-61) fragment at 313 K is a non-native one, as was often observed for shorter β-hairpin fragments studied in our previous work [between the “1 st pair” (Tyr50 – Phe57)22,33,34 and the “2 nd pair” (Trp48 – Val59) of hydrophobic residues] 22,35. This means that hydrophobic interactions, as well as any long-range interactions, which stabilize the C-terminal β-hairpin structure, are very dynamic and their pattern is very sensitive to the length of the peptide under investigation.…”

“…On the other hand, for the 20-residue peptide studied in our previous work35, we showed that none of the amide protons possessed small temperature coefficients. The results of NMR measurements of peptides of different length show that amide protons with low temperature coefficients are always observed in the turn region22,33-34; however, in some cases, the presence of the turn structure (detected by ROE connectivities) was not associated with low-temperature-coefficient amide protons35. Such an observation could lead to the conclusion that possible hydrogen bonds in the turn region are rather induced by the general shape of the polypeptide chain in the turn region, but are not the interaction that creates the turn of the polypeptide chain22,22-35.…”

“…Our previous studies showed that, for peptides with length 6, 8, 12, 14, and 16 residues, respectively (all of them based on the sequence of the C-terminal β-hairpin of the B3 domain of protein G), the six-residue fragment Asp51 - Thr56 (corresponding to the turn sequence in the structure of the native protein) is conformationally very rigid and has a bent shape very similar to that observed in the structure of the native protein 22,33,34. The conformational feature of this six-residue fragment remains unchanged in the range of temperatures T = 283 - 313 K for peptides of various length (from 6 to 16 residues).…”

“…The conformational feature of this six-residue fragment remains unchanged in the range of temperatures T = 283 - 313 K for peptides of various length (from 6 to 16 residues). Because of its unusual conformational properties, this six-residue peptide could be a nucleation center for the folding of the whole B3 domain protein G 22,33,34. However, when we studied a longer 20-residue peptide,35 based on the sequence of the C-terminal β-hairpin of the B3 domain of protein G, we found that the unusual conformational rigidity of the turn region is observed only at low temperature (T = 283 K).…”