The outer membrane protein Ail (attachment invasion locus) is a virulence factor of Yersinia pestis that mediates cell invasion, cell attachment and complement resistance. Here we describe its three-dimensional backbone structure determined in decyl-phosphocholine (DePC) micelles by NMR spectroscopy. The NMR structure was calculated using the membrane function of the implicit solvation potential, eefxPot, which we have developed to facilitate NMR structure calculations in a physically realistic environment. We show that the eefxPot force field guides the protein towards its native fold. The resulting structures provide information about the membrane-embedded global position of Ail, and have higher accuracy, higher precision and improved conformational properties, compared to the structures calculated with the standard repulsive potential.
[NMR paper] Correction: Fragment density functional theory calculation of NMR chemical shifts for proteins with implicit solvation.
Correction: Fragment density functional theory calculation of NMR chemical shifts for proteins with implicit solvation.
Related Articles Correction: Fragment density functional theory calculation of NMR chemical shifts for proteins with implicit solvation.
Phys Chem Chem Phys. 2015 Apr 21;
Authors: Zhu T, He X, Zhang JZ
Abstract
Correction for 'Fragment density functional theory calculation of NMR chemical shifts for proteins with implicit solvation' by Tong Zhu et al., Phys. Chem. Chem. Phys., 2012, 14, 7837-7845.
nmrlearner
Journal club
0
04-22-2015 03:33 PM
NMR-Restrained Structure Calculations of Membrane Proteins in Implicit Lipid Bilayer Membranes
NMR-Restrained Structure Calculations of Membrane Proteins in Implicit Lipid Bilayer Membranes
Publication date: 27 January 2015
Source:Biophysical Journal, Volume 108, Issue 2, Supplement 1</br>
Author(s): Ye Tian , Charles Schwieters , Stanley Opella , Francesca Marassi</br>
</br></br>
</br></br>
More...
nmrlearner
Journal club
0
01-28-2015 05:28 PM
[NMR paper] Solid-state NMR of the Yersinia pestis outer membrane protein Ail in lipid bilayer nanodiscs sedimented by ultracentrifugation.
Solid-state NMR of the Yersinia pestis outer membrane protein Ail in lipid bilayer nanodiscs sedimented by ultracentrifugation.
Solid-state NMR of the Yersinia pestis outer membrane protein Ail in lipid bilayer nanodiscs sedimented by ultracentrifugation.
J Biomol NMR. 2015 Jan 13;
Authors: Ding Y, Fujimoto LM, Yao Y, Marassi FM
Abstract
Solid-state NMR studies of sedimented soluble proteins has been developed recently as an attractive approach for overcoming the size limitations of solution NMR spectroscopy while bypassing the...
nmrlearner
Journal club
0
01-13-2015 02:31 PM
Solid-state NMR of the Yersinia pestis outer membrane protein Ail in lipid bilayer nanodiscs sedimented by ultracentrifugation
Solid-state NMR of the Yersinia pestis outer membrane protein Ail in lipid bilayer nanodiscs sedimented by ultracentrifugation
Abstract
Solid-state NMR studies of sedimented soluble proteins has been developed recently as an attractive approach for overcoming the size limitations of solution NMR spectroscopy while bypassing the need for sample crystallization or precipitation (Bertini et al. Proc Natl Acad Sci USA 108(26):10396â??10399, 2011). Inspired by the potential benefits of this method, we have investigated the ability to sediment lipid bilayer...
nmrlearner
Journal club
0
01-12-2015 11:31 PM
NMR-Restrained Protein Structure Calculations in Implicit Environment
NMR-Restrained Protein Structure Calculations in Implicit Environment
Publication date: 28 January 2014
Source:Biophysical Journal, Volume 106, Issue 2, Supplement 1</br>
Author(s): Ye Tian , Charles Schwieters , Stanley J. Opella , Francesca M. Marassi</br>
</br></br>
</br></br>
More...
nmrlearner
Journal club
0
01-29-2014 12:50 AM
[NMR paper] Protein heteronuclear NMR assignments using mean-field simulated annealing.
Protein heteronuclear NMR assignments using mean-field simulated annealing.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Protein heteronuclear NMR assignments using mean-field simulated annealing.
J Magn Reson. 1997 Mar;125(1):34-42
Authors: Buchler NE, Zuiderweg ER, Wang H, Goldstein RA
A computational method for the assignment of the NMR spectra of larger (21 kDa) proteins using a set of six of the most sensitive heteronuclear multidimensional nuclear magnetic...
nmrlearner
Journal club
0
08-22-2010 03:03 PM
[NMR paper] Simulated annealing with restrained molecular dynamics using a flexible restraint pot
Simulated annealing with restrained molecular dynamics using a flexible restraint potential: theory and evaluation with simulated NMR constraints.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles Simulated annealing with restrained molecular dynamics using a flexible restraint potential: theory and evaluation with simulated NMR constraints.
...
nmrlearner
Journal club
0
08-22-2010 02:27 PM
[NMR paper] Simulated annealing with restrained molecular dynamics using CONGEN: energy refinemen
Simulated annealing with restrained molecular dynamics using CONGEN: energy refinement of the NMR solution structures of epidermal and type-alpha transforming growth factors.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Simulated annealing with restrained molecular dynamics using CONGEN: energy refinement of the NMR solution structures of epidermal and type-alpha...
Backbone structure of Yersinia pestis Ail determined in micelles by NMR-restrained simulated annealing with implicit membrane solvation
Linear Mode
