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PDBsum entry 1e8l
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* Residue conservation analysis
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Enzyme class:
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E.C.3.2.1.17
- lysozyme.
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Reaction:
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Hydrolysis of the 1,4-beta-linkages between N-acetyl-D-glucosamine and N-acetylmuramic acid in peptidoglycan heteropolymers of the prokaryotes cell walls.
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Protein Sci
10:677-688
(2001)
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PubMed id:
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A refined solution structure of hen lysozyme determined using residual dipolar coupling data.
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H.Schwalbe,
S.B.Grimshaw,
A.Spencer,
M.Buck,
J.Boyd,
C.M.Dobson,
C.Redfield,
L.J.Smith.
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ABSTRACT
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A high resolution NMR structure of hen lysozyme has been determined using 209
residual 1H-15N dipolar coupling restraints from measurements made in two
different dilute liquid crystalline phases (bicelles) in conjunction with a data
set of 1632 NOE distance restraints, 110 torsion angle restraints, and 60
hydrogen bond restraints. The ensemble of 50 low-energy calculated structures
has an average backbone RMSD of 0.50+/-0.13A to the mean structure and of
1.49+/-0.10A to the crystal structure of hen lysozyme. To assess the importance
of the dipolar coupling data in the structure determination, the final
structures are compared with an ensemble calculated using an identical protocol
but excluding the dipolar coupling restraints. The comparison shows that
structures calculated with the dipolar coupling data are more similar to the
crystal structure than those calculated without, and have better stereochemical
quality. The structures also show improved quality factors when compared with
additional dipolar coupling data that were not included in the structure
calculations, with orientation-dependent 15N chemical shift changes measured in
the bicelle solutions, and with T1/T2 values obtained from 15N relaxation
measurements. Analysis of the ensemble of NMR structures and comparisons with
crystal structures, 15N relaxation data, and molecular dynamics simulations of
hen lysozyme provides a detailed description of the solution structure of this
protein and insights into its dynamical behavior.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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H.Webb,
B.M.Tynan-Connolly,
G.M.Lee,
D.Farrell,
F.O'Meara,
C.R.Søndergaard,
K.Teilum,
C.Hewage,
L.P.McIntosh,
and
J.E.Nielsen
(2011).
Remeasuring HEWL pK(a) values by NMR spectroscopy: Methods, analysis, accuracy, and implications for theoretical pK(a) calculations.
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Proteins,
79,
685-702.
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M.V.Fedorov,
J.M.Goodman,
D.Nerukh,
and
S.Schumm
(2011).
Self-assembly of trehalose molecules on a lysozyme surface: the broken glass hypothesis.
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Phys Chem Chem Phys,
13,
2294-2299.
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V.A.Higman,
J.Boyd,
L.J.Smith,
and
C.Redfield
(2011).
Residual dipolar couplings: are multiple independent alignments always possible?
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J Biomol NMR,
49,
53-60.
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B.A.Mazzeo,
S.Chandra,
B.L.Mellor,
and
J.Arellano
(2010).
Temperature-stable parallel-plate dielectric cell for broadband liquid impedance measurements.
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Rev Sci Instrum,
81,
125103.
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D.Stratmann,
E.Guittet,
and
C.van Heijenoort
(2010).
Robust structure-based resonance assignment for functional protein studies by NMR.
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J Biomol NMR,
46,
157-173.
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J.E.Kohn,
P.V.Afonine,
J.Z.Ruscio,
P.D.Adams,
and
T.Head-Gordon
(2010).
Evidence of functional protein dynamics from X-ray crystallographic ensembles.
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PLoS Comput Biol,
6,
0.
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K.Lindorff-Larsen,
S.Piana,
K.Palmo,
P.Maragakis,
J.L.Klepeis,
R.O.Dror,
and
D.E.Shaw
(2010).
Improved side-chain torsion potentials for the Amber ff99SB protein force field.
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Proteins,
78,
1950-1958.
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K.N.Woods
(2010).
Solvent-induced backbone fluctuations and the collective librational dynamics of lysozyme studied by terahertz spectroscopy.
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Phys Rev E Stat Nonlin Soft Matter Phys,
81,
031915.
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C.David,
S.Foley,
and
M.Enescu
(2009).
Protein S-S bridge reduction: a Raman and computational study of lysozyme interaction with TCEP.
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Phys Chem Chem Phys,
11,
2532-2542.
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J.A.Vila,
Y.A.Arnautova,
O.A.Martin,
and
H.A.Scheraga
(2009).
Quantum-mechanics-derived 13Calpha chemical shift server (CheShift) for protein structure validation.
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Proc Natl Acad Sci U S A,
106,
16972-16977.
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K.Berlin,
D.P.O'Leary,
and
D.Fushman
(2009).
Improvement and analysis of computational methods for prediction of residual dipolar couplings.
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J Magn Reson,
201,
25-33.
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A.N.Koller,
H.Schwalbe,
and
H.Gohlke
(2008).
Starting structure dependence of NMR order parameters derived from MD simulations: implications for judging force-field quality.
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Biophys J,
95,
L04-L06.
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G.Nodet,
D.Abergel,
and
G.Bodenhausen
(2008).
Predicting NMR relaxation rates in anisotropically tumbling proteins through networks of coupled rotators.
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Chemphyschem,
9,
625-633.
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R.Das,
and
D.Baker
(2008).
Macromolecular modeling with rosetta.
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Annu Rev Biochem,
77,
363-382.
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A.Pastore,
S.Salvadori,
and
P.A.Temussi
(2007).
Peptides and proteins in a confined environment: NMR spectra at natural isotopic abundance.
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J Pept Sci,
13,
342-347.
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M.Christen,
B.Keller,
and
W.F.van Gunsteren
(2007).
Biomolecular structure refinement based on adaptive restraints using local-elevation simulation.
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J Biomol NMR,
39,
265-273.
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B.Zagrovic,
and
W.F.van Gunsteren
(2006).
Comparing atomistic simulation data with the NMR experiment: how much can NOEs actually tell us?
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Proteins,
63,
210-218.
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M.A.da Silva,
I.A.Farhat,
E.P.Arêas,
and
J.R.Mitchell
(2006).
Solvent-induced lysozyme gels: effects of system composition and temperature on structural and dynamic characteristics.
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Biopolymers,
83,
443-454.
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N.Powers,
and
J.H.Jensen
(2006).
Chemically accurate protein structures: validation of protein NMR structures by comparison of measured and predicted pKa values.
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J Biomol NMR,
35,
39-51.
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R.B.Best,
K.Lindorff-Larsen,
M.A.DePristo,
and
M.Vendruscolo
(2006).
Relation between native ensembles and experimental structures of proteins.
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Proc Natl Acad Sci U S A,
103,
10901-10906.
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W.F.van Gunsteren,
D.Bakowies,
R.Baron,
I.Chandrasekhar,
M.Christen,
X.Daura,
P.Gee,
D.P.Geerke,
A.Glättli,
P.H.Hünenberger,
M.A.Kastenholz,
C.Oostenbrink,
M.Schenk,
D.Trzesniak,
N.F.van der Vegt,
and
H.B.Yu
(2006).
Biomolecular modeling: Goals, problems, perspectives.
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Angew Chem Int Ed Engl,
45,
4064-4092.
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C.Oostenbrink,
T.A.Soares,
N.F.van der Vegt,
and
W.F.van Gunsteren
(2005).
Validation of the 53A6 GROMOS force field.
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Eur Biophys J,
34,
273-284.
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C.Schlörb,
K.Ackermann,
C.Richter,
J.Wirmer,
and
H.Schwalbe
(2005).
Heterologous expression of hen egg white lysozyme and resonance assignment of tryptophan side chains in its non-native states.
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J Biomol NMR,
33,
95.
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E.S.Collins,
J.Wirmer,
K.Hirai,
H.Tachibana,
S.Segawa,
C.M.Dobson,
and
H.Schwalbe
(2005).
Characterisation of disulfide-bond dynamics in non-native states of lysozyme and its disulfide deletion mutants by NMR.
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Chembiochem,
6,
1619-1627.
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K.Simon,
J.Xu,
C.Kim,
and
N.R.Skrynnikov
(2005).
Estimating the accuracy of protein structures using residual dipolar couplings.
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J Biomol NMR,
33,
83-93.
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C.J.Langmead,
A.Yan,
R.Lilien,
L.Wang,
and
B.R.Donald
(2004).
A polynomial-time nuclear vector replacement algorithm for automated NMR resonance assignments.
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J Comput Biol,
11,
277-298.
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D.Zheng,
J.M.Aramini,
and
G.T.Montelione
(2004).
Validation of helical tilt angles in the solution NMR structure of the Z domain of Staphylococcal protein A by combined analysis of residual dipolar coupling and NOE data.
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Protein Sci,
13,
549-554.
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PDB code:
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T.A.Soares,
X.Daura,
C.Oostenbrink,
L.J.Smith,
and
W.F.van Gunsteren
(2004).
Validation of the GROMOS force-field parameter set 45Alpha3 against nuclear magnetic resonance data of hen egg lysozyme.
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J Biomol NMR,
30,
407-422.
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V.A.Higman,
J.Boyd,
L.J.Smith,
and
C.Redfield
(2004).
Asparagine and glutamine side-chain conformation in solution and crystal: a comparison for hen egg-white lysozyme using residual dipolar couplings.
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J Biomol NMR,
30,
327-346.
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Y.Qu,
J.T.Guo,
V.Olman,
and
Y.Xu
(2004).
Protein structure prediction using sparse dipolar coupling data.
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Nucleic Acids Res,
32,
551-561.
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A.Leitner,
and
W.Lindner
(2003).
Probing of arginine residues in peptides and proteins using selective tagging and electrospray ionization mass spectrometry.
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J Mass Spectrom,
38,
891-899.
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B.Jiménez,
L.Poggi,
and
M.Piccioli
(2003).
Monitoring the early steps of unfolding of dicalcium and mono-Ce3+-substituted forms of P43M calbindin D9k.
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Biochemistry,
42,
13066-13073.
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PDB code:
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E.García-Hernández,
R.A.Zubillaga,
E.A.Chavelas-Adame,
E.Vázquez-Contreras,
A.Rojo-Domínguez,
and
M.Costas
(2003).
Structural energetics of protein-carbohydrate interactions: Insights derived from the study of lysozyme binding to its natural saccharide inhibitors.
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Protein Sci,
12,
135-142.
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J.E.Nielsen,
and
J.A.McCammon
(2003).
On the evaluation and optimization of protein X-ray structures for pKa calculations.
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Protein Sci,
12,
313-326.
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R.E.Georgescu,
E.G.Alexov,
and
M.R.Gunner
(2002).
Combining conformational flexibility and continuum electrostatics for calculating pK(a)s in proteins.
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Biophys J,
83,
1731-1748.
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J.H.Prestegard,
and
A.I.Kishore
(2001).
Partial alignment of biomolecules: an aid to NMR characterization.
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Curr Opin Chem Biol,
5,
584-590.
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J.R.Tolman
(2001).
Dipolar couplings as a probe of molecular dynamics and structure in solution.
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Curr Opin Struct Biol,
11,
532-539.
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S.D.Maleknia,
and
K.Downard
(2001).
Radical approaches to probe protein structure, folding, and interactions by mass spectrometry.
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Mass Spectrom Rev,
20,
388-401.
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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.
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Links
