Conformational studies of the C‐terminal 16‐amino‐acid‐residue fragment of the B3 domain of the immunoglobulin binding protein G from Streptococcus

Abstract

The structure and stability of the 16-amino-acid-residue fragment [IG(46–61)] corresponding to the C-terminal β-hairpin of the B3 domain of the immunoglobulin binding protein G from Streptococcus was investigated by means of CD and NMR spectroscopy and by differential scanning calorimetry. The CD and 2D NMR experiments were carried out (i) in water at different temperatures and (ii) at one temperature (305 K), with only CD, at different TFE concentrations. Our results show that the IG(46–61) peptide possesses organized three-dimensional structure at all investigated temperatures. The three-dimensional structure of the IG(46–61) peptide resembles the general shape of a β-hairpin that is also observed for this peptide in the experimental structure of the B3 domain in the whole G protein; the structure is stabilized by hydrophobic interactions between nonpolar side chains. Our study shows that the melting temperature of the IG(46–61) peptide is about 320 K which supports the hypothesis that the investigated peptide can serve as a folding initiation site of the B3 domain of the immunoglobulin binding protein G.

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

“…These features make each of the B domains an ideal system for studying protein folding and stability 27,30–33. In our previous work,34 we showed that the 16-amino-acid-residue fragment, corresponding to the C-terminal β-hairpin of the B3 domain of the immunoglobulin binding protein G from Streptoccocus , resembled the general shape of a β-hairpin structure observed for this peptide in the structure of the whole protein, at all temperatures investigated. However, we found that the structure was stabilized by hydrophobic interactions between side chains and not by the hydrogen bonds suggested in previous studies 8,35…”

Molecular Dynamics Insight into the Diverse Thermodynamic Behavior of a Beta‐Hairpin Peptide

“…5,11,[19][20][21] Several well-folded b-hairpins were designed based on those criteria; for example, Fesinmeyer et al 22 designed GB1-m3, which is a GB1-variant with an approximately 86% hairpin population. It is because of the availability of stable b-hairpins that experimental 5,6,9,11,12,18,[23][24][25][26][27] and computational 10,17,[28][29][30] approaches have been able to reveal many fundamental properties of b-hairpins, such as their thermodynamic properties (e.g., free energy change), melting temperature, and folding timescale. The rapid folding timescale of b-hairpins 27 (~ms) suggests that the formation of these structures is associated with the early stage of protein folding, perhaps providing a nucleation site to initiate subsequent folding events surrounding the center (the site).…”

“…It is well known that CD measures the exciton couplets that arise from the through-space interaction of a chromophore's excited states and that the exciton effect gives either an average coupling behavior over the whole system (e.g., peptide bonds) or a local coupling result (e.g., a trp-trp pair), depending on the molar ellipticities at different selected wavelengths. 23,24,31 The NMR spectrum provides the chemical shift for almost all of the protons in the system; however, only a few proton species can be used as local probes to trace the folding-unfolding behavior of proteins, 5,6,32 e.g., the e-aromatic proton of the tyrosine residue. 23 DSC measures the heat absorbed during unfolding, which is a global property of proteins.…”

“…23,24,31 The NMR spectrum provides the chemical shift for almost all of the protons in the system; however, only a few proton species can be used as local probes to trace the folding-unfolding behavior of proteins, 5,6,32 e.g., the e-aromatic proton of the tyrosine residue. 23 DSC measures the heat absorbed during unfolding, which is a global property of proteins. 23,24 The experimental techniques mentioned all reflect their probe-dependent characteristics; several provide local properties, whereas others provide global properties or even more complicated local-global interplay.…”

“…23 DSC measures the heat absorbed during unfolding, which is a global property of proteins. 23,24 The experimental techniques mentioned all reflect their probe-dependent characteristics; several provide local properties, whereas others provide global properties or even more complicated local-global interplay. The probe-dependent issue has been investigated via multi-probe spectroscopy, primarily for the identification of downhill folding.…”