Related ArticlesAn Exhaustive Search Algorithm to Aid NMR-Based Structure Determination of Rotationally Symmetric Transmembrane Oligomers.
Sci Rep. 2017 Dec 12;7(1):17373
Authors: Yang J, Piai A, Shen HB, Chou JJ
Abstract
Nuclear magnetic resonance (NMR) has been an important source of structural restraints for solving structures of oligomeric transmembrane domains (TMDs) of cell surface receptors and viral membrane proteins. In NMR studies, oligomers are assembled using inter-protomer distance restraints. But, for oligomers that are higher than dimer, these distance restraints all have two-fold directional ambiguity, and resolving such ambiguity often requires time-consuming trial-and-error calculations using restrained molecular dynamics (MD) with simulated annealing (SA). We report an Exhaustive Search algorithm for Symmetric Oligomer (ExSSO), which can perform near-complete search of the symmetric conformational space in a very short time. In this approach, the predetermined protomer model is subject to full angular and spatial search within the symmetry space. This approach, which can be applied to any rotationally symmetric oligomers, was validated using the structures of the Fas death receptor, the HIV-1 gp41 fusion protein, the influenza proton channel, and the MCU pore. The algorithm is able to generate approximate oligomer solutions quickly as initial inputs for further refinement using the MD/SA method.
[NMR paper] The AUDANA algorithm for automated protein 3D structure determination from NMR NOE data.
The AUDANA algorithm for automated protein 3D structure determination from NMR NOE data.
The AUDANA algorithm for automated protein 3D structure determination from NMR NOE data.
J Biomol NMR. 2016 May 12;
Authors: Lee W, Petit CM, Cornilescu G, Stark JL, Markley JL
Abstract
We introduce AUDANA (Automated Database-Assisted NOE Assignment), an algorithm for determining three-dimensional structures of proteins from NMR data that automates the assignment of 3D-NOE spectra, generates distance constraints, and conducts iterative high...
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The AUDANA algorithm for automated protein 3D structure determination from NMR NOE data
The AUDANA algorithm for automated protein 3D structure determination from NMR NOE data
Abstract
We introduce AUDANA (Automated Database-Assisted NOE Assignment), an algorithm for determining three-dimensional structures of proteins from NMR data that automates the assignment of 3D-NOE spectra, generates distance constraints, and conducts iterative high temperature molecular dynamics and simulated annealing. The protein sequence, chemical shift assignments, and NOE spectra are the only required inputs. Distance constraints generated automatically from...
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05-13-2016 09:30 AM
[NMR paper] Structure Determination of Membrane Proteins in Their Native Phospholipid Bilayer Environment by Rotationally Aligned Solid-State NMR Spectroscopy.
Structure Determination of Membrane Proteins in Their Native Phospholipid Bilayer Environment by Rotationally Aligned Solid-State NMR Spectroscopy.
Structure Determination of Membrane Proteins in Their Native Phospholipid Bilayer Environment by Rotationally Aligned Solid-State NMR Spectroscopy.
Acc Chem Res. 2013 Jul 5;
Authors: Opella SJ
Abstract
One of the most important topics in experimental structural biology is determining the structures of membrane proteins. These structures represent one-third of all of the information...
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07-09-2013 02:47 PM
NMR Structural Inference of Symmetric Homo-Oligomers.
NMR Structural Inference of Symmetric Homo-Oligomers.
NMR Structural Inference of Symmetric Homo-Oligomers.
J Comput Biol. 2011 Jun 30;
Authors: Chandola H, Yan AK, Potluri S, Donald BR, Bailey-Kellogg C
Abstract Symmetric homo-oligomers represent a majority of proteins, and determining their structures helps elucidate important biological processes, including ion transport, signal transduction, and transcriptional regulation. In order to account for the noise and sparsity in the distance restraints used in Nuclear Magnetic Resonance (NMR)...
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Determination of the Structures of Symmetric Protein Oligomers from NMR Chemical Shifts and Residual Dipolar Couplings.
Determination of the Structures of Symmetric Protein Oligomers from NMR Chemical Shifts and Residual Dipolar Couplings.
Determination of the Structures of Symmetric Protein Oligomers from NMR Chemical Shifts and Residual Dipolar Couplings.
J Am Chem Soc. 2011 Apr 5;
Authors: Sgourakis NG, Lange OF, Dimaio F, Andre? I, Fitzkee NC, Rossi P, Montelione GT, Bax A, Baker D
Symmetric protein dimers, trimers, and higher-order cyclic oligomers play key roles in many biological processes. However, structural studies of oligomeric systems by solution NMR...
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Determination of the Structures of Symmetric Protein Oligomers from NMR Chemical Shifts and Residual Dipolar Couplings
Determination of the Structures of Symmetric Protein Oligomers from NMR Chemical Shifts and Residual Dipolar Couplings
Nikolaos G. Sgourakis, Oliver F. Lange, Frank DiMaio, Ingemar Andre?, Nicholas C. Fitzkee, Paolo Rossi, Gaetano T. Montelione, Ad Bax and David Baker
http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja111318m/aop/images/medium/ja-2010-11318m_0008.gif
Journal of the American Chemical Society
DOI: 10.1021/ja111318m
http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA...
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[NMR paper] NMR structure determination of a membrane protein with two transmembrane helices in m
NMR structure determination of a membrane protein with two transmembrane helices in micelles: MerF of the bacterial mercury detoxification system.
Related Articles NMR structure determination of a membrane protein with two transmembrane helices in micelles: MerF of the bacterial mercury detoxification system.
Biochemistry. 2005 Apr 5;44(13):5196-206
Authors: Howell SC, Mesleh MF, Opella SJ
The three-dimensional backbone structure of a membrane protein with two transmembrane helices in micelles was determined using solution NMR methods that...
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[NMR paper] A calculation strategy for the structure determination of symmetric dimers by 1H NMR.
A calculation strategy for the structure determination of symmetric dimers by 1H NMR.
Related Articles A calculation strategy for the structure determination of symmetric dimers by 1H NMR.
Proteins. 1993 Nov;17(3):297-309
Authors: Nilges M
The structure determination of symmetric dimers by NMR is impeded by the ambiguity of inter- and intramonomer NOE crosspeaks. In this paper, a calculation strategy is presented that allows the calculation of dimer structures without resolving the ambiguity by additional experiments (like asymmetric...
An Exhaustive Search Algorithm to Aid NMR-Based Structure Determination of Rotationally Symmetric Transmembrane Oligomers.
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