 |
PDBsum entry 1s1o
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
De novo protein
|
PDB id
|
|
|
|
1s1o
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
PDB id:
|
|
|
|
| Name: |
|
De novo protein
|
|
|
Title:
|
|
Nmr structure of a d,l alternating pentadecamer of norleucine: double antiparallel beta-helix
|
|
Structure:
|
|
Boc-l-nle-(d-nle-l-nle)5-d-nle(methyl)-l-nle-d-nle-l-nle methyl ester. Chain: a, b. Engineered: yes
|
|
Source:
|
|
Synthetic: yes. Other_details: the peptide was chemimcally synthesized.
|
|
NMR struc:
|
|
5 models
|
|
|
Authors:
|
|
E.Navarro,E.Fennude,B.Celda
|
|
Key ref:
|
|
E.Navarro
et al.
(2002).
Solution structure of a D,L-alternating oligonorleucine as a model of double-stranded antiparallel beta-helix.
Biopolymers,
64,
198-209.
PubMed id:
|
|
|
Date:
|
|
|
07-Jan-04
|
Release date:
|
24-Feb-04
|
|
|
|
|
|
|
|
Headers
|
|
|
|
References
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
| |
|
|
Biopolymers
64:198-209
(2002)
|
|
PubMed id:
|
|
|
|
|
|
| |
|
Solution structure of a D,L-alternating oligonorleucine as a model of double-stranded antiparallel beta-helix.
|
|
E.Navarro,
E.Fenude,
B.Celda.
|
|
|
|
|
| |
ABSTRACT
|
|
|
|
| |
|
|
Conformational characteristics of alternating D,L linear peptides are of
particular interest because of their capacity to form transmembrane channels
with different transport properties, as some natural antibiotics do. Single- and
double-stranded beta-helical structures are common for alternating D,L peptides.
The stability of the beta-helix depends on several structural factors, such as
the backbone peptide length, type and position of side chains, and nature of
terminal groups. The NMR and molecular dynamics solution conformation of a
synthetic alternating D,L-oligopeptide with 15 norleucines (XVMe) has been used
as a model to get insight in to the conformational features of double-stranded
beta-helix structures. The NH chemical shift values (delta(NH)) and long-range
nuclear Overhauser effects (NOE) cross peaks, in particular interstrand
connectivities, clearly point to an antiparallel double-stranded beta-helix for
the XVMe major conformation in solution. An extensive set of distances (from NOE
cross peaks) and H-bonds (from delta(NH)) has been included in the molecular
dynamics calculations. The experimental NMR data and theoretical calculations
clearly indicate that the most probable conformation of XVMe in solution is a
double-strand antiparallel beta(5.6) increasing decreasing-helix structure.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
 |
 |
|
Literature references that cite this PDB file's key reference
|
|
|
| |
PubMed id
|
|
Reference
|
|
|
|
|
|
H.González-Díaz,
M.A.Dea-Ayuela,
L.G.Pérez-Montoto,
F.J.Prado-Prado,
G.Agüero-Chapín,
F.Bolas-Fernández,
R.I.Vazquez-Padrón,
and
F.M.Ubeira
(2010).
QSAR for RNases and theoretic-experimental study of molecular diversity on peptide mass fingerprints of a new Leishmania infantum protein.
|
| |
Mol Divers,
14,
349-369.
|
|
|
|
|
|
|
P.E.Schneggenburger,
A.Beerlink,
B.Worbs,
T.Salditt,
and
U.Diederichsen
(2009).
A novel heavy-atom label for side-specific peptide iodination: synthesis, membrane incorporation and X-ray reflectivity.
|
| |
Chemphyschem,
10,
1567-1576.
|
|
|
|
|
|
|
H.González-Díaz,
Y.González-Díaz,
L.Santana,
F.M.Ubeira,
and
E.Uriarte
(2008).
Proteomics, networks and connectivity indices.
|
| |
Proteomics,
8,
750-778.
|
|
|
|
|
|
|
A.Küsel,
Z.Khattari,
P.E.Schneggenburger,
A.Banerjee,
T.Salditt,
and
U.Diederichsen
(2007).
Conformation and Interaction of a D,L-alternating peptide with a bilayer membrane: x-ray reflectivity, CD, and FTIR spectroscopy.
|
| |
Chemphyschem,
8,
2336-2343.
|
|
|
|
|
|
|
H.González-Díaz,
L.Saíz-Urra,
R.Molina,
Y.González-Díaz,
and
A.Sánchez-González
(2007).
Computational chemistry approach to protein kinase recognition using 3D stochastic van der Waals spectral moments.
|
| |
J Comput Chem,
28,
1042-1048.
|
|
|
|
|
|
|
S.Chowdhury,
G.Schatte,
and
H.B.Kraatz
(2006).
Rational design of bioorganometallic foldamers: a potential model for parallel beta-helical peptides.
|
| |
Angew Chem Int Ed Engl,
45,
6882-6884.
|
|
|
|
|
|
|
C.Baldauf,
R.Günther,
and
H.J.Hofmann
(2005).
Side-chain control of folding of the homologous alpha-, beta-, and gamma-peptides into "mixed" helices (beta-helices).
|
| |
Biopolymers,
80,
675-687.
|
|
|
|
|
|
|
H.González-Díaz,
and
E.Uriarte
(2005).
Biopolymer stochastic moments. I. Modeling human rhinovirus cellular recognition with protein surface electrostatic moments.
|
| |
Biopolymers,
77,
296-303.
|
|
|
|
|
|
|
E.Navarro,
E.Fenude,
and
B.Celda
(2004).
Conformational and structural analysis of the equilibrium between single- and double-strand beta-helix of a D,L-alternating oligonorleucine.
|
| |
Biopolymers,
73,
229-241.
|
|
|
PDB code:
|
|
|
|
|
|
|
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
