Recent advances in molecular modeling of protein structures are changing the field of structural biology. AlphaFold-2 (AF2), an AI system developed by DeepMind, Inc., utilizes attention-based deep learning to predict models of protein structures with high accuracy relative to structures determined by X-ray crystallography and cryo-electron microscopy (cryoEM). Comparing AF2 models to structures determined using solution NMR data, both high similarities and distinct differences have been...
[NMR paper] Assessment of Prediction Methods for Protein Structures Determined by NMR in CASP14: Impact of AlphaFold2
Assessment of Prediction Methods for Protein Structures Determined by NMR in CASP14: Impact of AlphaFold2
NMR studies can provide unique information about protein conformations in solution. In CASP14, three reference structures provided by solution NMR methods were available (T1027, T1029, and T1055), as well as a fourth data set of NMR-derived contacts for an integral membrane protein (T1088). For the three targets with NMR-based structures, the best prediction results ranged from very good (GDT_TS = 0.90, for T1055) to poor (GDT_TS = 0.47, for T1029). We explored the basis of these...
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[NMR paper] Comparative Assessment of NMR Probes for the Experimental Description of Protein Folding Pathways with High-Pressure NMR
Comparative Assessment of NMR Probes for the Experimental Description of Protein Folding Pathways with High-Pressure NMR
Multidimensional NMR intrinsically provides multiple probes that can be used for deciphering the folding pathways of proteins: NH amide and C?H? groups are strategically located on the backbone of the protein, while CH(3) groups, on the side-chain of methylated residues, are involved in important stabilizing interactions in the hydrophobic core. Combined with high hydrostatic pressure, these observables provide a powerful tool to explore the conformational landscapes of...
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A Community Resource of Experimental Data for NMR – X-ray Crystal Structure Pairs
A Community Resource of Experimental Data for NMR – X-ray Crystal Structure Pairs
ABSTRACT
We have developed an on-line NMR/X-ray Structure Pair Data Repository. The NIGMS Protein Structure Initiative (PSI) has provided many valuable reagents, 3D structures, and technologies for structural biology. The Northeast Structural Genomics Consortium was one of several PSI centers. NESG used both X-ray crystallography and NMR spectroscopy for protein structure determination. A key goal of the PSI was to provide experimental structures for at least one representative of each of hundreds of...
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08-22-2015 11:20 AM
Blind Testing of Routine, Fully Automated Determination of Protein Structures from NMR Data
Blind Testing of Routine, Fully Automated Determination of Protein Structures from NMR Data
8 February 2012
Publication year: 2012
Source:Structure, Volume 20, Issue 2</br>
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The protocols currently used for protein structure determination by nuclear magnetic resonance (NMR) depend on the determination of a large number of upper distance limits for proton-proton pairs. Typically, this task is performed manually by an experienced researcher rather than automatically by using a specific computer program. To assess whether it is indeed possible to generate in a fully...
High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data
High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data
Abstract X-ray diffraction and nuclear magnetic resonance spectroscopy (NMR) are the staple methods for revealing atomic structures of proteins. Since crystals of biomolecular assemblies and membrane proteins often diffract weakly and such large systems encroach upon the molecular tumbling limit of solution NMR, new methods are essential to extend structures of such systems to high resolution. Here we present a method that incorporates solid-state NMR restraints alongside...
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09-26-2011 06:42 AM
High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data.
High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data.
High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data.
J Biomol NMR. 2011 Sep 22;
Authors: Tang M, Sperling LJ, Berthold DA, Schwieters CD, Nesbitt AE, Nieuwkoop AJ, Gennis RB, Rienstra CM
Abstract
X-ray diffraction and nuclear magnetic resonance spectroscopy (NMR) are the staple methods for revealing atomic structures of proteins. Since crystals of biomolecular...
Blind Assessment of Monomeric AlphaFold2 Protein Structure Models with Experimental NMR Data
Linear Mode
