5. Proline cis–trans isomerization is a slow event that can occur in
the denatured state of proteins. In these cases, refolding timecourse typically displays slow phase(s) that are directly associated with proline cis–trans isomerization.
References
1. Fersht A (1999) Structure and mechanism in
protein science. Freeman W.H. and Co,
New York
2. Fersht AR, Matouschek A, Serrano L (1992)
The folding of an enzyme. I. Theory of protein
engineering analysis of stability and pathway of
protein folding. J Mol Biol 224:771–782
3. Doyle DA, Lee A, Lewis J, Kim E, Sheng M,
MacKinnon R (1996) Crystal structures of a
complexed and peptide-free membrane
protein-binding domain: molecular basis of
peptide
recognition
by
PDZ.
Cell
85:1067–1076
4. Calosci N, Chi CN, Richter B, Camilloni C,
Engstrom Å, Eklund L, Travaglini-AllocatelliC, Gianni S, Vendruscolo M, Jemth P (2008)
Comparison of successive transition states for
folding reveals alternative early folding pathways of two homologous proteins. Proc Natl
Acad Sci U S A 105:19241–19246
5. Chi CN, Gianni S, Calosci N, TravagliniAllocatelli C, Engstrom Å, Jemth P (2007) A
conserved folding mechanism for PDZ
domains. FEBS Lett 581:1109–1113
6. Gianni S, Ivarsson Y, De Simone A, TravagliniAllocatelli C, Brunori M, Vendruscolo M
(2010) Structural characterization of a misfolded intermediate populated during the folding process of a PDZ domain. Nat Struct Mol
Biol 17:1431–1437
7. Hultqvist G, Pedersen SW, Chi CN,
Strømgaard K, Gianni S, Jemth P (2012) An
expanded view of the protein folding landscape
of PDZ domains. Biochem Biophys Res Commum 421:550–553
8. Ivarsson
Y,
Travaglini-Allocatelli
C,
Brunori M, Gianni S (2008) Folding and
misfolding in a naturally occurring circularly
permuted PDZ domain. J Biol Chem
283:8954–8960
9. Ivarsson Y, Travaglini-Allocatelli C, Jemth P,
Malatesta F, Brunori M, Gianni S (2007) An
on-pathway intermediate in the folding of a
PDZ domain. J Biol Chem 282:8568–8572
10. Jemth P, Gianni S (2007) PDZ domains: folding and binding. Biochemistry 46:8701–8708
11. Gianni S, Geierhaas CD, Calosci N, Jemth P,
Vuister
GW,
Travaglini-Allocatelli
C,
Vendruscolo M, Brunori M (2007) A PDZ
domain recapitulates a unifying mechanism
for protein folding. Proc Natl Acad Sci U S A
104:128–133
12. Di Silvio E, Brunori M, Gianni S (2015) Frustration sculpts the early stages of protein folding.
Angew
Chem
Int
Ed
Engl
54:10867–10869
13. Fersht AR, Sato S (2004) Phi-value analysis and
the nature of protein-folding transition states.
Proc Natl Acad Sci U S A 101:7976–7981
14. Myers JK, Pace CN, Scholtz JM (1995) Denaturant m values and heat capacity changes: relation to changes in accessible surface areas of
protein unfolding. Protein Sci 4:2138–2148
15. Jackson SE, Fersht AR (1991) Folding of chymotrypsin inhibitor 2. 1. Evidence for a
two-state
transition.
Biochemistry
30:10428–10435
16. Parker MJ, Spencer J, Clarke AR (1995) An
integrated kinetic analysis of intermediates
and transition states in protein folding reactions. J Mol Biol 253(5):771–786
156
Candice Gautier and Stefano Gianni
the denatured state of proteins. In these cases, refolding timecourse typically displays slow phase(s) that are directly associated with proline cis–trans isomerization.
References
1. Fersht A (1999) Structure and mechanism in
protein science. Freeman W.H. and Co,
New York
2. Fersht AR, Matouschek A, Serrano L (1992)
The folding of an enzyme. I. Theory of protein
engineering analysis of stability and pathway of
protein folding. J Mol Biol 224:771–782
3. Doyle DA, Lee A, Lewis J, Kim E, Sheng M,
MacKinnon R (1996) Crystal structures of a
complexed and peptide-free membrane
protein-binding domain: molecular basis of
peptide
recognition
by
PDZ.
Cell
85:1067–1076
4. Calosci N, Chi CN, Richter B, Camilloni C,
Engstrom Å, Eklund L, Travaglini-AllocatelliC, Gianni S, Vendruscolo M, Jemth P (2008)
Comparison of successive transition states for
folding reveals alternative early folding pathways of two homologous proteins. Proc Natl
Acad Sci U S A 105:19241–19246
5. Chi CN, Gianni S, Calosci N, TravagliniAllocatelli C, Engstrom Å, Jemth P (2007) A
conserved folding mechanism for PDZ
domains. FEBS Lett 581:1109–1113
6. Gianni S, Ivarsson Y, De Simone A, TravagliniAllocatelli C, Brunori M, Vendruscolo M
(2010) Structural characterization of a misfolded intermediate populated during the folding process of a PDZ domain. Nat Struct Mol
Biol 17:1431–1437
7. Hultqvist G, Pedersen SW, Chi CN,
Strømgaard K, Gianni S, Jemth P (2012) An
expanded view of the protein folding landscape
of PDZ domains. Biochem Biophys Res Commum 421:550–553
8. Ivarsson
Y,
Travaglini-Allocatelli
C,
Brunori M, Gianni S (2008) Folding and
misfolding in a naturally occurring circularly
permuted PDZ domain. J Biol Chem
283:8954–8960
9. Ivarsson Y, Travaglini-Allocatelli C, Jemth P,
Malatesta F, Brunori M, Gianni S (2007) An
on-pathway intermediate in the folding of a
PDZ domain. J Biol Chem 282:8568–8572
10. Jemth P, Gianni S (2007) PDZ domains: folding and binding. Biochemistry 46:8701–8708
11. Gianni S, Geierhaas CD, Calosci N, Jemth P,
Vuister
GW,
Travaglini-Allocatelli
C,
Vendruscolo M, Brunori M (2007) A PDZ
domain recapitulates a unifying mechanism
for protein folding. Proc Natl Acad Sci U S A
104:128–133
12. Di Silvio E, Brunori M, Gianni S (2015) Frustration sculpts the early stages of protein folding.
Angew
Chem
Int
Ed
Engl
54:10867–10869
13. Fersht AR, Sato S (2004) Phi-value analysis and
the nature of protein-folding transition states.
Proc Natl Acad Sci U S A 101:7976–7981
14. Myers JK, Pace CN, Scholtz JM (1995) Denaturant m values and heat capacity changes: relation to changes in accessible surface areas of
protein unfolding. Protein Sci 4:2138–2148
15. Jackson SE, Fersht AR (1991) Folding of chymotrypsin inhibitor 2. 1. Evidence for a
two-state
transition.
Biochemistry
30:10428–10435
16. Parker MJ, Spencer J, Clarke AR (1995) An
integrated kinetic analysis of intermediates
and transition states in protein folding reactions. J Mol Biol 253(5):771–786
156
Candice Gautier and Stefano Gianni