Abstract
Recent advances in G-protein-coupled receptor structural biology have provided only limited insight into the active conformations of these key signaling molecules. A paper from Nygaard et*al. reveals the dynamic nature of GPCRs along the activation pathway by complementing NMR experiments with ultralong-timescale molecular dynamics simulations.
PPM: a side-chain and backbone chemical shift predictor for the assessment of protein conformational ensembles
PPM: a side-chain and backbone chemical shift predictor for the assessment of protein conformational ensembles
Abstract The combination of the wide availability of protein backbone and side-chain NMR chemical shifts with advances in understanding of their relationship to protein structure makes these parameters useful for the assessment of structural-dynamic protein models. A new chemical shift predictor (PPM) is introduced, which is solely based on physicalâ??chemical contributions to the chemical shifts for both the protein backbone and methyl-bearing amino-acid side chains. To...
nmrlearner
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09-15-2012 09:04 AM
[NMR paper] Measuring pK(a) values in protein folding transition state ensembles by NMR spectrosc
Measuring pK(a) values in protein folding transition state ensembles by NMR spectroscopy.
Related Articles Measuring pK(a) values in protein folding transition state ensembles by NMR spectroscopy.
J Am Chem Soc. 2005 Jun 29;127(25):8904-5
Authors: Tollinger M, Kay LE, Forman-Kay JD
Protein folding kinetic data have been obtained for the marginally stable N-terminal SH3 domain of the Drosophila protein drk as a function of pH in order to investigate the electrostatic properties of Asp8 in the folding transition state ensemble. The slow exchange...
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11-25-2010 08:21 PM
[NMR paper] Principal components analysis of protein structure ensembles calculated using NMR dat
Principal components analysis of protein structure ensembles calculated using NMR data.
Related Articles Principal components analysis of protein structure ensembles calculated using NMR data.
J Biomol NMR. 2001 May;20(1):61-70
Authors: Howe PW
One important problem when calculating structures of biomolecules from NMR data is distinguishing converged structures from outlier structures. This paper describes how Principal Components Analysis (PCA) has the potential to classify calculated structures automatically, according to correlated...
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11-19-2010 08:32 PM
[NMR paper] Defining protein ensembles with native-state NH exchange: kinetics of interconversion
Defining protein ensembles with native-state NH exchange: kinetics of interconversion and cooperative units from combined NMR and MS analysis.
Related Articles Defining protein ensembles with native-state NH exchange: kinetics of interconversion and cooperative units from combined NMR and MS analysis.
J Mol Biol. 1999 Jan 22;285(3):1265-75
Authors: Arrington CB, Teesch LM, Robertson AD
Previous studies of native-state peptide hydrogen atom (NH) exchange in turkey ovomucoid third domain (OMTKY3) yielded the thermodynamics and kinetics of...
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11-18-2010 07:05 PM
[NMR paper] NMR characterization of partially folded and unfolded conformational ensembles of pro
NMR characterization of partially folded and unfolded conformational ensembles of proteins.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_120x27.gif Related Articles NMR characterization of partially folded and unfolded conformational ensembles of proteins.
Biopolymers. 1999;51(3):191-207
Authors: Barbar E
Studies of unfolded and partially folded proteins provide important insight into the initiation and process of protein folding. This review focuses on the...
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08-21-2010 04:03 PM
Mapping of protein structural ensembles by chemical shifts
Abstract Applying the chemical shift prediction programs SHIFTX and SHIFTS to a data base of protein structures with known chemical shifts we show that the averaged chemical shifts predicted from the structural ensembles explain better the experimental data than the lowest energy structures. This is in agreement with the fact that proteins in solution occur in multiple conformational states in fast exchange on the chemical shift time scale. However, in contrast to the real conditions in solution at ambient temperatures, the standard NMR structural calculation methods as well chemical shift...
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08-14-2010 04:19 AM
Structure-based protein NMR assignments using native structural ensembles
Structure-based protein NMR assignments using native structural ensembles
Mehmet Serkan Apaydın, Vincent Conitzer and Bruce Randall Donald
Journal of Biomolecular NMR; 2008; 40(4); pp 263-276
Abstract:
An important step in NMR protein structure determination is the assignment of resonances and NOEs to corresponding nuclei. Structure-based assignment (SBA) uses a model structure (“template”) for the target protein to expedite this process. Nuclear vector replacement (NVR) is an SBA framework that combines multiple sources of NMR data (chemical shifts, RDCs, sparse NOEs, amide exchange...
matthias
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08-14-2008 12:54 AM
Programs for alignment of protein NMR ensembles
If you need to align models in your NMR ensemble, you can use the following programs to do so. MolMol
- Official website
- Linux binaries from Patrick Finerty website
- BioXRay distribution
SuperPose server
Suppose
Conformational Ensembles in GPCR Activation.
Linear Mode
