Related ArticlesRapid assessment of protein structural stability and fold validation via NMR.
Methods Enzymol. 2005;394:142-75
Authors: Hoffmann B, Eichmüller C, Steinhauser O, Konrat R
In structural proteomics, it is necessary to efficiently screen in a high-throughput manner for the presence of stable structures in proteins that can be subjected to subsequent structure determination by X-ray or NMR spectroscopy. Here we illustrate that the (1)H chemical distribution in a protein as detected by (1)H NMR spectroscopy can be used to probe protein structural stability (e.g., the presence of stable protein structures) of proteins in solution. Based on experimental data obtained on well-structured proteins and proteins that exist in a molten globule state or a partially folded alpha-helical state, a well-defined threshold exists that can be used as a quantitative benchmark for protein structural stability (e.g., foldedness) in solution. Additionally, in this chapter we describe a largely automated strategy for rapid fold validation and structure-based backbone signal assignment. Our methodology is based on a limited number of NMR experiments (e.g., HNCA and 3D NOESY-HSQC) and performs a Monte Carlo-type optimization. The novel feature of the method is the opportunity to screen for structural fragments (e.g., template scanning). The performance of this new validation tool is demonstrated with applications to a diverse set of proteins.
Rapid measurement of residual dipolar couplings for fast fold elucidation of proteins
Rapid measurement of residual dipolar couplings for fast fold elucidation of proteins
Abstract It has been demonstrated that protein folds can be determined using appropriate computational protocols with NMR chemical shifts as the sole source of experimental restraints. While such approaches are very promising they still suffer from low convergence resulting in long computation times to achieve accurate results. Here we present a suite of time- and sensitivity optimized NMR experiments for rapid measurement of up to six RDCs per residue. Including such an RDC data set, measured in less...
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09-17-2011 10:20 AM
NMR as a Unique Tool in Assessment and Complex Determination of Weak Protein-Protein Interactions.
NMR as a Unique Tool in Assessment and Complex Determination of Weak Protein-Protein Interactions.
NMR as a Unique Tool in Assessment and Complex Determination of Weak Protein-Protein Interactions.
Top Curr Chem. 2011 Aug 2;
Authors: Vinogradova O, Qin J
Protein-protein interactions are crucial for a wide variety of biological processes. These interactions range from high affinity (K (d) < nM) to very low affinity (K (d) > mM). While much is known about the nature of high affinity protein complexes, our knowledge about structural characteristics...
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08-03-2011 12:00 PM
[NMR paper] The fumarate sensor DcuS: progress in rapid protein fold elucidation by combining pro
The fumarate sensor DcuS: progress in rapid protein fold elucidation by combining protein structure prediction methods with NMR spectroscopy.
Related Articles The fumarate sensor DcuS: progress in rapid protein fold elucidation by combining protein structure prediction methods with NMR spectroscopy.
J Magn Reson. 2005 Apr;173(2):310-6
Authors: Meiler J, Baker D
We illustrate how moderate resolution protein structures can be rapidly obtained by interlinking computational prediction methodologies with un- or partially assigned NMR data. To...
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11-25-2010 08:21 PM
[NMR paper] NMR structural studies reveal a novel protein fold for MerB, the organomercurial lyas
NMR structural studies reveal a novel protein fold for MerB, the organomercurial lyase involved in the bacterial mercury resistance system.
Related Articles NMR structural studies reveal a novel protein fold for MerB, the organomercurial lyase involved in the bacterial mercury resistance system.
Biochemistry. 2004 Jul 6;43(26):8322-32
Authors: Di Lello P, Benison GC, Valafar H, Pitts KE, Summers AO, Legault P, Omichinski JG
Mercury resistant bacteria have developed a system of two enzymes (MerA and MerB), which allows them to efficiently...
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11-24-2010 09:51 PM
[NMR paper] Rapid protein fold determination using unassigned NMR data.
Rapid protein fold determination using unassigned NMR data.
Related Articles Rapid protein fold determination using unassigned NMR data.
Proc Natl Acad Sci U S A. 2003 Dec 23;100(26):15404-9
Authors: Meiler J, Baker D
Experimental structure determination by x-ray crystallography and NMR spectroscopy is slow and time-consuming compared with the rate at which new protein sequences are being identified. NMR spectroscopy has the advantage of rapidly providing the structurally relevant information in the form of unassigned chemical shifts (CSs),...
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11-24-2010 09:16 PM
[NMR paper] Two structural subdomains of barstar detected by rapid mixing NMR measurement of amid
Two structural subdomains of barstar detected by rapid mixing NMR measurement of amide hydrogen exchange.
Related Articles Two structural subdomains of barstar detected by rapid mixing NMR measurement of amide hydrogen exchange.
Proteins. 1998 Feb 15;30(3):295-308
Authors: Bhuyan AK, Udgaonkar JB
Equilibrium amide hydrogen exchange studies of barstar have been carried out at pH 6.7, 32 degrees C using one- and two-dimensional nuclear magnetic resonance. An unusually large fraction of the backbone amide hydrogens of barstar exchange too fast to...
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11-17-2010 11:06 PM
CABS-NMR-De novo tool for rapid global fold determination from chemical shifts, resid
CABS-NMR-De novo tool for rapid global fold determination from chemical shifts, residual dipolar couplings and sparse methyl-methyl noes.
CABS-NMR-De novo tool for rapid global fold determination from chemical shifts, residual dipolar couplings and sparse methyl-methyl noes.
J Comput Chem. 2010 Aug 30;
Authors: Latek D, Kolinski A
Recent development of nuclear magnetic resonance (NMR) techniques provided new types of structural restraints that can be successfully used in fast and low-cost global protein fold determination. Here, we present...
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09-02-2010 03:58 PM
[NMR paper] Assessment by 1H NMR spectroscopy of the structural behaviour of human parathyroid-ho
Assessment by 1H NMR spectroscopy of the structural behaviour of human parathyroid-hormone-related protein(1-34) and its close relationship with the N-terminal fragments of human parathyroid hormone in solution.
Related Articles Assessment by 1H NMR spectroscopy of the structural behaviour of human parathyroid-hormone-related protein(1-34) and its close relationship with the N-terminal fragments of human parathyroid hormone in solution.
Biol Chem. 1997 Dec;378(12):1501-8
Authors: Gronwald W, Schomburg D, Tegge W, Wray V
Human...
Rapid assessment of protein structural stability and fold validation via NMR.
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