BioNMR
NMR aggregator & online community since 2003
BioNMR    
Learn or help to learn NMR - get free NMR books!
 

Go Back   BioNMR > Educational resources > Journal club
Advanced Search



Jobs Groups Conferences Literature Pulse sequences Software forums Programs Sample preps Web resources BioNMR issues


Webservers
NMR processing:
MDD
NMR assignment:
Backbone:
Autoassign
MARS
UNIO Match
PINE
Side-chains:
UNIO ATNOS-Ascan
NOEs:
UNIO ATNOS-Candid
UNIO Candid
ASDP
Structure from NMR restraints:
Ab initio:
GeNMR
Cyana
XPLOR-NIH
ASDP
UNIO ATNOS-Candid
UNIO Candid
Fragment-based:
BMRB CS-Rosetta
Rosetta-NMR (Robetta)
Template-based:
GeNMR
I-TASSER
Refinement:
Amber
Structure from chemical shifts:
Fragment-based:
WeNMR CS-Rosetta
BMRB CS-Rosetta
Homology-based:
CS23D
Simshift
Torsion angles from chemical shifts:
Preditor
TALOS
Promega- Proline
Secondary structure from chemical shifts:
CSI (via RCI server)
TALOS
MICS caps, β-turns
d2D
PECAN
Flexibility from chemical shifts:
RCI
Interactions from chemical shifts:
HADDOCK
Chemical shifts re-referencing:
Shiftcor
UNIO Shiftinspector
LACS
CheckShift
RefDB
NMR model quality:
NOEs, other restraints:
PROSESS
PSVS
RPF scores
iCing
Chemical shifts:
PROSESS
CheShift2
Vasco
iCing
RDCs:
DC
Anisofit
Pseudocontact shifts:
Anisofit
Protein geomtery:
Resolution-by-Proxy
PROSESS
What-If
iCing
PSVS
MolProbity
SAVES2 or SAVES4
Vadar
Prosa
ProQ
MetaMQAPII
PSQS
Eval123D
STAN
Ramachandran Plot
Rampage
ERRAT
Verify_3D
Harmony
Quality Control Check
NMR spectrum prediction:
FANDAS
MestReS
V-NMR
Flexibility from structure:
Backbone S2
Methyl S2
B-factor
Molecular dynamics:
Gromacs
Amber
Antechamber
Chemical shifts prediction:
From structure:
Shiftx2
Sparta+
Camshift
CH3shift- Methyl
ArShift- Aromatic
ShiftS
Proshift
PPM
CheShift-2- Cα
From sequence:
Shifty
Camcoil
Poulsen_rc_CS
Disordered proteins:
MAXOCC
Format conversion & validation:
CCPN
From NMR-STAR 3.1
Validate NMR-STAR 3.1
NMR sample preparation:
Protein disorder:
DisMeta
Protein solubility:
camLILA
ccSOL
Camfold
camGroEL
Zyggregator
Isotope labeling:
UPLABEL
Solid-state NMR:
sedNMR


Reply
Thread Tools Search this Thread Rate Thread Display Modes
  #1  
Unread 08-06-2015, 10:24 AM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 17,256
Points: 193,617, Level: 100
Points: 193,617, Level: 100 Points: 193,617, Level: 100 Points: 193,617, Level: 100
Level up: 0%, 0 Points needed
Level up: 0% Level up: 0% Level up: 0%
Activity: 50.7%
Activity: 50.7% Activity: 50.7% Activity: 50.7%
Last Achievements
Award-Showcase
NMR Credits: 0
NMR Points: 193,617
Downloads: 0
Uploads: 0
Default A Practical Implicit Membrane Potential for NMR Structure Calculations of Membrane Proteins.

A Practical Implicit Membrane Potential for NMR Structure Calculations of Membrane Proteins.

A Practical Implicit Membrane Potential for NMR Structure Calculations of Membrane Proteins.

Biophys J. 2015 Aug 4;109(3):574-585

Authors: Tian Y, Schwieters CD, Opella SJ, Marassi FM

Abstract
The highly anisotropic environment of the lipid bilayer membrane imposes significant constraints on the structures and functions of membrane proteins. However, NMR structure calculations typically use a simple repulsive potential that neglects the effects of solvation and electrostatics, because explicit atomic representation of the solvent and lipid molecules is computationally expensive and impractical for routine NMR-restrained calculations that start from completely extended polypeptide templates. Here, we describe the extension of a previously described implicit solvation potential, eefxPot, to include a membrane model for NMR-restrained calculations of membrane protein structures in XPLOR-NIH. The key components of eefxPot are an energy term for solvation free energy that works together with other nonbonded energy functions, a dedicated force field for conformational and nonbonded protein interaction parameters, and a membrane function that modulates the solvation free energy and dielectric screening as a function of the atomic distance from the membrane center, relative to the membrane thickness. Initial results obtained for membrane proteins with structures determined experimentally in lipid bilayer membranes show that eefxPot affords significant improvements in structural quality, accuracy, and precision. Calculations with eefxPot are straightforward to implement and can be used to both fold and refine structures, as well as to run unrestrained molecular-dynamics simulations. The potential is entirely compatible with the full range of experimental restraints measured by various techniques. Overall, it provides a useful and practical way to calculate membrane protein structures in a physically realistic environment.


PMID: 26244739 [PubMed - as supplied by publisher]



More...
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
A Practical Implicit Membrane Potential for NMR Structure Calculations of Membrane Proteins
A Practical Implicit Membrane Potential for NMR Structure Calculations of Membrane Proteins Publication date: 4 August 2015 Source:Biophysical Journal, Volume 109, Issue 3</br> Author(s): Ye Tian, Charles*D. Schwieters, Stanley*J. Opella, Francesca*M. Marassi</br> The highly anisotropic environment of the lipid bilayer membrane imposes significant constraints on the structures and functions of membrane proteins. However, NMR structure calculations typically use a simple repulsive potential that neglects the effects of solvation and electrostatics, because...
nmrlearner Journal club 0 08-05-2015 08:21 PM
[NMR paper] Backbone structure of Yersinia pestis Ail determined in micelles by NMR-restrained simulated annealing with implicit membrane solvation.
Backbone structure of Yersinia pestis Ail determined in micelles by NMR-restrained simulated annealing with implicit membrane solvation. Backbone structure of Yersinia pestis Ail determined in micelles by NMR-restrained simulated annealing with implicit membrane solvation. J Biomol NMR. 2015 Jul 5; Authors: Marassi FM, Ding Y, Schwieters CD, Tian Y, Yao Y Abstract The outer membrane protein Ail (attachment invasion locus) is a virulence factor of Yersinia pestis that mediates cell invasion, cell attachment and complement...
nmrlearner Journal club 0 07-06-2015 04:35 PM
Backbone structure of Yersinia pestis Ail determined in micelles by NMR-restrained simulated annealing with implicit membrane solvation
Backbone structure of Yersinia pestis Ail determined in micelles by NMR-restrained simulated annealing with implicit membrane solvation Abstract 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,...
nmrlearner Journal club 0 07-05-2015 02:07 AM
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] A practical implicit solvent potential for NMR structure calculation.
A practical implicit solvent potential for NMR structure calculation. Related Articles A practical implicit solvent potential for NMR structure calculation. J Magn Reson. 2014 Apr 2;243C:54-64 Authors: Tian Y, Schwieters CD, Opella SJ, Marassi FM Abstract The benefits of protein structure refinement in water are well documented. However, performing structure refinement with explicit atomic representation of the solvent molecules is computationally expensive and impractical for NMR-restrained structure calculations that start from...
nmrlearner Journal club 0 04-22-2014 03:54 PM
[NMR paper] A Practical Implicit Solvent Potential for NMR Structure Calculation
A Practical Implicit Solvent Potential for NMR Structure Calculation Publication date: Available online 2 April 2014 Source:Journal of Magnetic Resonance</br> Author(s): Ye Tian , Charles D. Schwieters , Stanley J. Opella , Francesca M. Marassi</br> The benefits of protein structure refinement in water are well documented. However, performing structure refinement with explicit atomic representation of the solvent molecules is computationally expensive and impractical for NMR-restrained structure calculations that start from completely extended polypeptide...
nmrlearner Journal club 0 04-02-2014 11:54 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] Membrane protein structure: the contribution and potential of novel solid state NMR a
Membrane protein structure: the contribution and potential of novel solid state NMR approaches. Related Articles Membrane protein structure: the contribution and potential of novel solid state NMR approaches. Mol Membr Biol. 1995 Jul-Sep;12(3):233-46 Authors: Watts A, Ulrich AS, Middleton DA Alternative methods for describing molecular detail for large integral membrane proteins are required in the absence of routine crystallographic approaches. Novel solid state NMR methods, devised for the study of large molecular assemblies, are now finding...
nmrlearner Journal club 0 08-22-2010 03:41 AM


Thread Tools Search this Thread
Search this Thread:

Advanced Search
Display Modes Rate This Thread
Rate This Thread:

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is On
Trackbacks are Off
Pingbacks are Off
Refbacks are Off



BioNMR advertisements to pay for website hosting and domain registration. Nobody does it for us.



Powered by vBulletin® Version 3.7.3
Copyright ©2000 - 2017, Jelsoft Enterprises Ltd.
Copyright, BioNMR.com, 2003-2013
Search Engine Friendly URLs by vBSEO 3.6.0

All times are GMT. The time now is 05:03 AM.


Map