 |
PDBsum entry 1qkx
|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
| |
|
DOI no:
|
Protein Sci
9:2322-2328
(2000)
|
|
PubMed id:
|
|
|
|
|
|
| |
|
Thermodynamic and structural characterization of Asn and Ala residues in the disallowed II' region of the Ramachandran plot.
|
|
M.C.Vega,
J.C.Martínez,
L.Serrano.
|
|
|
|
|
| |
ABSTRACT
|
|
|
|
| |
|
|
Residue Asn47 at position L1 of a type II' beta-turn of the alpha-spectrin SH3
domain is located in a disallowed region of the Ramachandran plot (phi = 56 +/-
12, psi = -118 +/- 17). Therefore, it is expected that replacement of Asn47 by
Gly should result in a considerable stabilization of the protein. Thermodynamic
analysis of the N47G and N47A mutants shows that the change in free energy is
small (approximately 0.7 kcal/mol; approximately 3 kJ/mol) and comparable to
that found when mutating a Gly to Ala in a alpha-helix or beta-sheet. X-ray
structural analysis of these mutants shows that the conformation of the
beta-turn does not change upon mutation and, therefore, that there is no
relaxation of the structure, nor is there any gain or loss of interactions that
could explain the small energy change. Our results indicate that the energetic
definition of II' region of the Ramachandran plot (phi = 60 +/- 30, psi = -115
+/- 15) should be revised for at least Ala and Asn in structure validation and
protein design.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
 |
 |
|
Literature references that cite this PDB file's key reference
|
|
|
| |
PubMed id
|
|
Reference
|
|
|
|
|
|
A.Cámara-Artigas,
M.Andújar-Sánchez,
E.Ortiz-Salmerón,
C.Cuadri,
and
S.Casares
(2009).
The effect of a proline residue on the rate of growth and the space group of alpha-spectrin SH3-domain crystals.
|
| |
Acta Crystallogr D Biol Crystallogr,
65,
1247-1252.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
E.S.Cobos,
A.M.Candel,
and
J.C.Martinez
(2008).
An error analysis for two-state protein-folding kinetic parameters and phi-values: progress toward precision by exploring pH dependencies on Leffler plots.
|
| |
Biophys J,
94,
4393-4404.
|
|
|
|
|
|
|
S.Casares,
O.López-Mayorga,
M.C.Vega,
A.Cámara-Artigas,
and
F.Conejero-Lara
(2007).
Cooperative propagation of local stability changes from low-stability and high-stability regions in a SH3 domain.
|
| |
Proteins,
67,
531-547.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
S.R.Trevino,
S.Schaefer,
J.M.Scholtz,
and
C.N.Pace
(2007).
Increasing protein conformational stability by optimizing beta-turn sequence.
|
| |
J Mol Biol,
373,
211-218.
|
|
|
|
|
|
|
N.Srinivasan
(2006).
Computational Biology and Bioinformatics: a tinge of Indian spice.
|
| |
Bioinformation,
1,
105-109.
|
|
|
|
|
|
|
V.Chevelkov,
K.Faelber,
A.Diehl,
U.Heinemann,
H.Oschkinat,
and
B.Reif
(2005).
Detection of dynamic water molecules in a microcrystalline sample of the SH3 domain of alpha-spectrin by MAS solid-state NMR.
|
| |
J Biomol NMR,
31,
295-310.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
L.Spagnolo,
S.Ventura,
and
L.Serrano
(2003).
Folding specificity induced by loop stiffness.
|
| |
Protein Sci,
12,
1473-1482.
|
|
|
|
|
|
|
S.Ventura,
M.C.Vega,
E.Lacroix,
I.Angrand,
L.Spagnolo,
and
L.Serrano
(2002).
Conformational strain in the hydrophobic core and its implications for protein folding and design.
|
| |
Nat Struct Biol,
9,
485-493.
|
|
|
PDB codes:
|
|
|
|
|
|
|
The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
|
|
Links
