scholarly journals High Accuracy Protein Structures from Minimal Sparse Paramagnetic Solid‐State NMR Restraints

2019 ◽  
Vol 131 (20) ◽  
pp. 6636-6640
Author(s):  
Alberto Perez ◽  
Kari Gaalswyk ◽  
Christopher P. Jaroniec ◽  
Justin L. MacCallum
Keyword(s):  
Solid State ◽  
Solid State Nmr ◽  
Protein Structures ◽  
High Accuracy ◽  
Nmr Restraints

High accuracy protein structures from minimal sparse paramagnetic solid-state NMR restraints

2018 ◽  
Author(s):  
Alberto Perez ◽  
Kari Gaalswyk ◽  
Christopher P. Jaroniec ◽  
Justin L. MacCallum
Keyword(s):  
Solid State ◽  
Solid State Nmr ◽  
Protein Structures ◽  
High Accuracy ◽  
Atomistic Simulations ◽  
Quantitative Mapping ◽  
Model Protein ◽  
Experimental Approaches ◽  
Nmr Restraints ◽  
Protein Gb1

AbstractThere is a pressing need for new computational tools to integrate data from diverse experimental approaches in structural biology. We present a strategy that combines sparse paramagnetic solid-state NMR restraints with physics-based atomistic simulations. Our approach explicitly accounts for uncertainty in the interpretation of experimental data through the use of a semi-quantitative mapping between the data and the restraint energy that is calibrated by extensive simulations. We apply our approach to solid-state NMR data for the model protein GB1 labeled with Cu2+-EDTA at six different sites. We are able to determine the structure to ca. 1 Å accuracy within a single day of computation on a modest GPU cluster. We further show that in 4 of 6 cases, the data from only a single paramagnetic tag are sufficient to fold the protein to high accuracy.

scholarly journals High Accuracy Protein Structures from Minimal Sparse Paramagnetic Solid‐State NMR Restraints

2019 ◽  
Vol 58 (20) ◽  
pp. 6564-6568 ◽  
Author(s):  
Alberto Perez ◽  
Kari Gaalswyk ◽  
Christopher P. Jaroniec ◽  
Justin L. MacCallum
Keyword(s):  
Solid State ◽  
Solid State Nmr ◽  
Protein Structures ◽  
High Accuracy ◽  
Nmr Restraints

Protein structure by solid-state NMR spectroscopy

1987 ◽  
Vol 19 (1-2) ◽  
pp. 7-49 ◽  
Author(s):  
S. J. Opella ◽  
P. L. Stewart ◽  
K. G. Valentine
Keyword(s):  
Solid State ◽  
Nmr Spectroscopy ◽  
Solid State Nmr ◽  
Structural Information ◽  
Biological Systems ◽  
Genetic Regulation ◽  
Protein Structures ◽  
Crystalline Solid ◽  
Solid State Nmr Spectroscopy ◽  
Nmr Methods

The three-dimensional structures of proteins are among the most valuable contributions of biophysics to the understanding of biological systems (Dickerson & Geis, 1969; Creighton, 1983). Protein structures are utilized in the description and interpretation of a wide variety of biological phenomena, including genetic regulation, enzyme mechanisms, antibody recognition, cellular energetics, and macroscopic mechanical and structural properties of molecular assemblies. Virtually all of the information currently available about the structures of proteins at atomic resolution has been obtained from diffraction studies of single crystals of proteins (Wyckoff et al, 1985). However, recently developed NMR methods are capable of determining the structures of proteins and are now being applied to a variety of systems, including proteins in solution and other non-crystalline environments that are not amenable for X-ray diffraction studies. Solid-state NMR methods are useful for proteins that undergo limited overall reorientation by virtue of their being in the crystalline solid state or integral parts of supramolecular structures that do not reorient rapidly in solution. For reviews of applications of solid-state NMR spectroscopy to biological systems see Torchia and VanderHart (1979), Griffin (1981), Oldfield et al. (1982), Opella (1982), Torchia (1982), Gauesh (1984), Torchia (1984) and Opella (1986). This review describes how solid-state NMR can be used to obtain structural information about proteins. Methods applicable to samples with macroscopic orientation are emphasized.

scholarly journals Exploring Protein Structures by DNP-Enhanced Methyl Solid-State NMR Spectroscopy

2019 ◽  
Vol 141 (50) ◽  
pp. 19888-19901 ◽  
Author(s):  
Jiafei Mao ◽  
Victoria Aladin ◽  
Xinsheng Jin ◽  
Alexander J. Leeder ◽  
Lynda J. Brown ◽  
...  
Keyword(s):  
Solid State ◽  
Nmr Spectroscopy ◽  
Solid State Nmr ◽  
Protein Structures ◽  
Solid State Nmr Spectroscopy

scholarly journals Solid-State NMR Studies of the Succinate-Acetate Permease from Citrobacter Koseri in Liposomes and Native Nanodiscs

Life ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 908
Author(s):  
Xing-Qi Dong ◽  
Jing-Yu Lin ◽  
Peng-Fei Wang ◽  
Yi Li ◽  
Jian Wang ◽  
...  
Keyword(s):  
Solid State ◽  
Chemical Shift ◽  
Solid State Nmr ◽  
Protein Structures ◽  
Anion Channel ◽  
Transmembrane Domains ◽  
Helical Structures ◽  
Nmr Studies ◽  
Two Samples ◽  
Lipid Environment

The succinate-acetate permease (SatP) is an anion channel with six transmembrane domains. It forms different oligomers, especially hexamers in the detergent as well as in the membrane. Solid-state NMR studies of SatP were carried out successfully on SatP complexes by reconstructing the protein into liposomes or retaining the protein in the native membrane of E. Coli., where it was expressed. The comparison of 13C-13C 2D correlation spectra between the two samples showed great similarity, opening the possibility to further study the acetate transport mechanism of SatP in its native membrane environment. Solid-state NMR studies also revealed small chemical shift differences of SatP in the two different membrane systems, indicating the importance of the lipid environment in determining the membrane protein structures and dynamics. Combining different 2D SSNMR spectra, chemical shift assignments were made on some sites, consistent with the helical structures in the transmembrane domains. In the end, we pointed out the limitation in the sensitivity for membrane proteins with such a size, and also indicated possible ways to overcome it.

scholarly journals 3D Structure Determination of the Crh Protein from Highly Ambiguous Solid-State NMR Restraints

2008 ◽  
Vol 130 (11) ◽  
pp. 3579-3589 ◽  
Author(s):  
Antoine Loquet ◽  
Benjamin Bardiaux ◽  
Carole Gardiennet ◽  
Christophe Blanchet ◽  
Marc Baldus ◽  
...  
Keyword(s):  
Solid State ◽  
Structure Determination ◽  
Solid State Nmr ◽  
3D Structure ◽  
Nmr Restraints ◽  
3D Structure Determination

scholarly journals A refinement protocol to determine structure, topology, and depth of insertion of membrane proteins using hybrid solution and solid-state NMR restraints

2009 ◽  
Vol 44 (4) ◽  
pp. 195-205 ◽  
Author(s):  
Lei Shi ◽  
Nathaniel J. Traaseth ◽  
Raffaello Verardi ◽  
Alessandro Cembran ◽  
Jiali Gao ◽  
...  
Keyword(s):  
Solid State ◽  
Membrane Proteins ◽  
Solid State Nmr ◽  
Structure Topology ◽  
Hybrid Solution ◽  
Nmr Restraints
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