Sakurai K , Goto Y PNAS 2007;104:15346-15351
description
Transcript of Sakurai K , Goto Y PNAS 2007;104:15346-15351
![Page 1: Sakurai K , Goto Y PNAS 2007;104:15346-15351](https://reader036.fdocuments.us/reader036/viewer/2022062500/5681552d550346895dc306c8/html5/thumbnails/1.jpg)
Sakurai K , Goto Y PNAS 2007;104:15346-15351Zeinab
Mokhtari
24 May 2011
![Page 2: Sakurai K , Goto Y PNAS 2007;104:15346-15351](https://reader036.fdocuments.us/reader036/viewer/2022062500/5681552d550346895dc306c8/html5/thumbnails/2.jpg)
![Page 3: Sakurai K , Goto Y PNAS 2007;104:15346-15351](https://reader036.fdocuments.us/reader036/viewer/2022062500/5681552d550346895dc306c8/html5/thumbnails/3.jpg)
![Page 4: Sakurai K , Goto Y PNAS 2007;104:15346-15351](https://reader036.fdocuments.us/reader036/viewer/2022062500/5681552d550346895dc306c8/html5/thumbnails/4.jpg)
![Page 5: Sakurai K , Goto Y PNAS 2007;104:15346-15351](https://reader036.fdocuments.us/reader036/viewer/2022062500/5681552d550346895dc306c8/html5/thumbnails/5.jpg)
The analysis of conventional spectroscopic data, such as fluorescence or CD data, can not determine which residues are responsible for the change of stability.
pH conformation of proteins structure and function
Heteronuclear NMR spectra, such as the heteronuclear sequential quantum correlation (HSQC) spectrum, monitoring the behavior of essentially all residues, has the potential to address the contributions of individual residues.
![Page 6: Sakurai K , Goto Y PNAS 2007;104:15346-15351](https://reader036.fdocuments.us/reader036/viewer/2022062500/5681552d550346895dc306c8/html5/thumbnails/6.jpg)
Bovine-lactoglobulin (β-LG) : consists of 162 amino acid residues (18 kDa) and contains two tryptophan residues, Trp-19 and Trp-61
Predominantly β-sheet protein consisting of nine β-strands (A–I), of which the A–H strands form an up-and-down β-barrel, and one major α-helix at the C terminus of the molecule.
![Page 7: Sakurai K , Goto Y PNAS 2007;104:15346-15351](https://reader036.fdocuments.us/reader036/viewer/2022062500/5681552d550346895dc306c8/html5/thumbnails/7.jpg)
Experimental design.
A number of pH-induced structural transitions as well as changes in the association state and stability, between pH 2 and 8.
pKa,M-Q = 3pKa,Q-N = 5pKa,N-R = 7
a four-state mechanism
A monomeric form with a high stability at acidic pH
A monomeric form with a high stability at acidic pH
Dimerization with little alteration in structure at around pH=3
Dimerization with little alteration in structure at around pH=3
conversion from the acidic Q state to the native (N) dimeric state between pH 4.5 and 6 (changes in compactness)
conversion from the acidic Q state to the native (N) dimeric state between pH 4.5 and 6 (changes in compactness)
Tanford transition : a conformational change of the EF loop (residues 85–90), which might be caused by the cleavage of hydrogen bonds between the F and G strands (pH=7)
Tanford transition : a conformational change of the EF loop (residues 85–90), which might be caused by the cleavage of hydrogen bonds between the F and G strands (pH=7)
![Page 8: Sakurai K , Goto Y PNAS 2007;104:15346-15351](https://reader036.fdocuments.us/reader036/viewer/2022062500/5681552d550346895dc306c8/html5/thumbnails/8.jpg)
pH titration and hydrogen/deuterium (H/D) exchange experiments monitored by HSQC to relate the pH-dependent stability with the conformational behavior at the residue level
PCA to correlate pH-dependent HSQC spectra with pH-dependent conformational transitions
![Page 9: Sakurai K , Goto Y PNAS 2007;104:15346-15351](https://reader036.fdocuments.us/reader036/viewer/2022062500/5681552d550346895dc306c8/html5/thumbnails/9.jpg)
HSQC spectra at pH 2.4–8.1 to examine the four-state conformational transitions
It is evident that chemical shifts of many signals change with pH. For these residues, we observed no evident change of peak intensity, suggesting the fast exchange between conformational states. On the other hand, some residues showed a decrease in peak intensity above pH 6 without changing the chemical shift, suggesting a contribution of slow conformational change.
![Page 10: Sakurai K , Goto Y PNAS 2007;104:15346-15351](https://reader036.fdocuments.us/reader036/viewer/2022062500/5681552d550346895dc306c8/html5/thumbnails/10.jpg)
Gln-5Gln-5
From pH 2 to pH 5, the signal of Gln-5 moves toward the top right of the spectrum whereas, from pH 5 to pH 8, it moves downwards.
Individual residues show their own transitions, whose midpoints do not necessarily converge to common pKa values, indicating that the four-state transition is not a result of highly cooperative transitions throughout the molecule.
The pH-dependent conformational change of β-LG might be a result of collective conformational changes of many residues.
Individual residues show their own transitions, whose midpoints do not necessarily converge to common pKa values, indicating that the four-state transition is not a result of highly cooperative transitions throughout the molecule.
The pH-dependent conformational change of β-LG might be a result of collective conformational changes of many residues.
![Page 11: Sakurai K , Goto Y PNAS 2007;104:15346-15351](https://reader036.fdocuments.us/reader036/viewer/2022062500/5681552d550346895dc306c8/html5/thumbnails/11.jpg)
SVDSVD
![Page 12: Sakurai K , Goto Y PNAS 2007;104:15346-15351](https://reader036.fdocuments.us/reader036/viewer/2022062500/5681552d550346895dc306c8/html5/thumbnails/12.jpg)
3dominant PCs3dominant PCs
![Page 13: Sakurai K , Goto Y PNAS 2007;104:15346-15351](https://reader036.fdocuments.us/reader036/viewer/2022062500/5681552d550346895dc306c8/html5/thumbnails/13.jpg)
Although we also performed the following fitting with the first four PCs, no apparent improvement was detected, consistent with the profile that the amplitude of PC4 was small over the pH range studied.
![Page 14: Sakurai K , Goto Y PNAS 2007;104:15346-15351](https://reader036.fdocuments.us/reader036/viewer/2022062500/5681552d550346895dc306c8/html5/thumbnails/14.jpg)
S1 S⇄ 2 S⇄ 3 S⇄ 4
The relations between these species :
acid dissociation
constantfractions of species i, fSi , as a function of pH
PCs described with the fractions for each species :
3-dimensional vector containing the first, second, and third PCs
a 3-dimensional vector describing the corresponding species
![Page 15: Sakurai K , Goto Y PNAS 2007;104:15346-15351](https://reader036.fdocuments.us/reader036/viewer/2022062500/5681552d550346895dc306c8/html5/thumbnails/15.jpg)
![Page 16: Sakurai K , Goto Y PNAS 2007;104:15346-15351](https://reader036.fdocuments.us/reader036/viewer/2022062500/5681552d550346895dc306c8/html5/thumbnails/16.jpg)
For NMR chemical shifts, this means the fast exchange between different conformational states.
PCA assumed a linear combination of the basis spectra.
![Page 17: Sakurai K , Goto Y PNAS 2007;104:15346-15351](https://reader036.fdocuments.us/reader036/viewer/2022062500/5681552d550346895dc306c8/html5/thumbnails/17.jpg)
Thanks