Related ArticlesNMR-detected hydrogen exchange and molecular dynamics simulations provide structural insight into fibril formation of prion protein fragment 106-126.
Proc Natl Acad Sci U S A. 2003 Dec 9;100(25):14790-5
Authors: Kuwata K, Matumoto T, Cheng H, Nagayama K, James TL, Roder H
PrP106-126, a peptide corresponding to residues 107-127 of the human prion protein, induces neuronal cell death by apoptosis and causes proliferation and hypertrophy of glia, reproducing the main neuropathological features of prion-related transmissible spongiform encephalopathies, such as bovine spongiform encephalopathy and Creutzfeldt-Jakob disease. Although PrP106-126 has been shown to form amyloid-like fibrils in vitro, their structural properties have not been elucidated. Here, we investigate the conformational characteristics of a fibril-forming fragment of the mouse prion protein, MoPrP106-126, by using electron microscopy, CD spectroscopy, NMR-detected hydrogen-deuterium exchange measurements, and molecular dynamics simulations. The fibrils contain approximately 50% beta-sheet structure, and strong amide exchange protection is limited to the central portion of the peptide spanning the palindromic sequence VAGAAAAGAV. Molecular dynamics simulations indicate that MoPrP106-126 in water assumes a stable structure consisting of two four-stranded parallel beta-sheets that are tightly packed against each other by methyl-methyl interactions. Fibril formation involving polyalanine stacking is consistent with the experimental observations.
Structural characterization of recombinant human myoglobin isoforms by (1)H and (129)Xe NMR and molecular dynamics simulations.
Structural characterization of recombinant human myoglobin isoforms by (1)H and (129)Xe NMR and molecular dynamics simulations.
Structural characterization of recombinant human myoglobin isoforms by (1)H and (129)Xe NMR and molecular dynamics simulations.
Biochim Biophys Acta. 2011 Jul 13;
Authors: Gussoni M, Scorciapino MA, Vezzoli A, Anedda R, Greco F, Ceccarelli M, Casu M
Myoglobin (Mb), the main cytosolic oxygen storage/deliver protein, is also known to interact with different small ligands exerting other fundamental physiological roles. In...
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Structure and Dynamics of the A?21–30 Peptide from the Interplay of NMR Experiments and Molecular Simulations
Structure and Dynamics of the A?21–30 Peptide from the Interplay of NMR Experiments and Molecular Simulations
Nicolas L. Fawzi, Aaron H. Phillips, Jory Z. Ruscio, Michaeleen Doucleff, David E. Wemmer and Teresa Head-Gordon
Journal of the American Chemical Society
DOI: 10.1021/ja204315n
http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA
http://feeds.feedburner.com/~r/acs/jacsat/~4/bEQEah_ik60
[NMR paper] Molecular dynamics simulations of photoactive yellow protein (PYP) in three states of
Molecular dynamics simulations of photoactive yellow protein (PYP) in three states of its photocycle: a comparison with X-ray and NMR data and analysis of the effects of Glu46 deprotonation and mutation.
Related Articles Molecular dynamics simulations of photoactive yellow protein (PYP) in three states of its photocycle: a comparison with X-ray and NMR data and analysis of the effects of Glu46 deprotonation and mutation.
Eur Biophys J. 2002 Dec;31(7):504-20
Authors: Antes I, Thiel W, van Gunsteren WF
Photoactive yellow protein (PYP) is a...
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[NMR paper] The solution conformations of amino acids from molecular dynamics simulations of Gly-
The solution conformations of amino acids from molecular dynamics simulations of Gly-X-Gly peptides: comparison with NMR parameters.
Related Articles The solution conformations of amino acids from molecular dynamics simulations of Gly-X-Gly peptides: comparison with NMR parameters.
Biochem Cell Biol. 1998;76(2-3):164-70
Authors: van der Spoel D
The conformations that amino acids can adopt in the random coil state are of fundamental interest in the context of protein folding research and studies of protein-peptide interactions. To date, no...
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11-17-2010 11:06 PM
Constraining Binding Hot Spots: NMR and Molecular Dynamics Simulations Provide a Stru
Constraining Binding Hot Spots: NMR and Molecular Dynamics Simulations Provide a Structural Explanation for Enthalpy-Entropy Compensation in SH2-Ligand Binding.
Related Articles Constraining Binding Hot Spots: NMR and Molecular Dynamics Simulations Provide a Structural Explanation for Enthalpy-Entropy Compensation in SH2-Ligand Binding.
J Am Chem Soc. 2010 Aug 18;132(32):11058-70
Authors: Ward JM, Gorenstein NM, Tian J, Martin SF, Post CB
NMR spectroscopy and molecular dynamics (MD) simulations were used to probe the structure and dynamics...
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Using NMR Chemical Shifts as Structural Restraints in Molecular Dynamics Simulations
Using NMR Chemical Shifts as Structural Restraints in Molecular Dynamics Simulations of Proteins.
Related Articles Using NMR Chemical Shifts as Structural Restraints in Molecular Dynamics Simulations of Proteins.
Structure. 2010 Aug 11;18(8):923-933
Authors: Robustelli P, Kohlhoff K, Cavalli A, Vendruscolo M
We introduce a procedure to determine the structures of proteins by incorporating NMR chemical shifts as structural restraints in molecular dynamics simulations. In this approach, the chemical shifts are expressed as differentiable...
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Constraining Binding Hot Spots: NMR and Molecular Dynamics Simulations Provide a Stru
Constraining Binding Hot Spots: NMR and Molecular Dynamics Simulations Provide a Structural Explanation for Enthalpy−Entropy Compensation in SH2−Ligand Binding
Joshua M. Ward<sup>†</sup>, Nina M. Gorenstein<sup>†</sup>, Jianhua Tian<sup>‡</sup>, Stephen F. Martin<sup>‡</sup> and Carol Beth Post*<sup>†</sup>
Department of Medicinal Chemistry, Markey Center for Structural Biology, and Purdue Cancer Center, Purdue University, West Lafayette, Indiana 47907, and Department of Chemistry and Biochemistry and The Institute of Cellular and Molecular Biology, The University of Texas,...