Understanding the Molecular Dynamics Associated with Polymorphic Transitions ofdl-Norvaline with Solid-State NMR Methods

2011 ◽  
Vol 115 (12) ◽  
pp. 2814-2823 ◽  
Author(s):  
Pingping Ren ◽  
Detlef Reichert ◽  
Qinghua He ◽  
Limin Zhang ◽  
Huiru Tang
Keyword(s):  
Molecular Dynamics ◽  
Solid State ◽  
Solid State Nmr ◽  
Polymorphic Transitions ◽  
Nmr Methods

Solid state NMR of membrane proteins: methods and applications

2021 ◽  
Author(s):  
Vivien Yeh ◽  
Boyan B. Bonev
Keyword(s):  
Solid State ◽  
High Resolution ◽  
Membrane Proteins ◽  
Solid State Nmr ◽  
Lipid Membrane ◽  
Cell Function ◽  
Membrane Lipid ◽  
Pharmacological Intervention ◽  
Nmr Methods ◽  
Informative Approach

Membranes of cells are active barriers, in which membrane proteins perform essential remodelling, transport and recognition functions that are vital to cells. Membrane proteins are key regulatory components of cells and represent essential targets for the modulation of cell function and pharmacological intervention. However, novel folds, low molarity and the need for lipid membrane support present serious challenges to the characterisation of their structure and interactions. We describe the use of solid state NMR as a versatile and informative approach for membrane and membrane protein studies, which uniquely provides information on structure, interactions and dynamics of membrane proteins. High resolution approaches are discussed in conjunction with applications of NMR methods to studies of membrane lipid and protein structure and interactions. Signal enhancement in high resolution NMR spectra through DNP is discussed as a tool for whole cell and interaction studies.

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.

Lipid Dynamics Studied by Calculation of 31P Solid-State NMR Spectra Using Ensembles from Molecular Dynamics Simulations

2014 ◽  
Vol 118 (19) ◽  
pp. 5119-5129 ◽  
Author(s):  
Sara K. Hansen ◽  
Mikkel Vestergaard ◽  
Lea Thøgersen ◽  
Birgit Schiøtt ◽  
Niels Chr. Nielsen ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Solid State ◽  
Molecular Dynamics Simulations ◽  
Solid State Nmr ◽  
Nmr Spectra ◽  
Lipid Dynamics ◽  
Dynamics Simulations

scholarly journals The Dynamics of the Neuropeptide Y Receptor Type 1 Investigated by Solid-State NMR and Molecular Dynamics Simulation

Molecules ◽  
2020 ◽  
Vol 25 (23) ◽  
pp. 5489
Author(s):  
Alexander Vogel ◽  
Mathias Bosse ◽  
Marcel Gauglitz ◽  
Sarah Wistuba ◽  
Peter Schmidt ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Solid State ◽  
Neuropeptide Y ◽  
Solid State Nmr ◽  
Bound State ◽  
Receptor Activation ◽  
Order Parameters ◽  
Dynamics Simulation ◽  
15N Nmr

We report data on the structural dynamics of the neuropeptide Y (NPY) G-protein-coupled receptor (GPCR) type 1 (Y1R), a typical representative of class A peptide ligand GPCRs, using a combination of solid-state NMR and molecular dynamics (MD) simulation. First, the equilibrium dynamics of Y1R were studied using 15N-NMR and quantitative determination of 1H-13C order parameters through the measurement of dipolar couplings in separated-local-field NMR experiments. Order parameters reporting the amplitudes of the molecular motions of the C-H bond vectors of Y1R in DMPC membranes are 0.57 for the Cα sites and lower in the side chains (0.37 for the CH2 and 0.18 for the CH3 groups). Different NMR excitation schemes identify relatively rigid and also dynamic segments of the molecule. In monounsaturated membranes composed of longer lipid chains, Y1R is more rigid, attributed to a higher hydrophobic thickness of the lipid membrane. The presence of an antagonist or NPY has little influence on the amplitude of motions, whereas the addition of agonist and arrestin led to a pronounced rigidization. To investigate Y1R dynamics with site resolution, we conducted extensive all-atom MD simulations of the apo and antagonist-bound state. In each state, three replicas with a length of 20 μs (with one exception, where the trajectory length was 10 μs) were conducted. In these simulations, order parameters of each residue were determined and showed high values in the transmembrane helices, whereas the loops and termini exhibit much lower order. The extracellular helix segments undergo larger amplitude motions than their intracellular counterparts, whereas the opposite is observed for the loops, Helix 8, and termini. Only minor differences in order were observed between the apo and antagonist-bound state, whereas the time scale of the motions is shorter for the apo state. Although these relatively fast motions occurring with correlation times of ns up to a few µs have no direct relevance for receptor activation, it is believed that they represent the prerequisite for larger conformational transitions in proteins.

scholarly journals Solid-State NMR Techniques for the Structural Characterization of Cyclic Aggregates Based on Borane–Phosphane Frustrated Lewis Pairs

Molecules ◽  
2020 ◽  
Vol 25 (6) ◽  
pp. 1400 ◽  
Author(s):  
Robert Knitsch ◽  
Melanie Brinkkötter ◽  
Thomas Wiegand ◽  
Gerald Kehr ◽  
Gerhard Erker ◽  
...  
Keyword(s):  
Solid State ◽  
Structural Characterization ◽  
Solid State Nmr ◽  
Magic Angle ◽  
Frustrated Lewis Pairs ◽  
Wide Range ◽  
Nmr Techniques ◽  
Nmr Methods ◽  
Lewis Pairs

Modern solid-state NMR techniques offer a wide range of opportunities for the structural characterization of frustrated Lewis pairs (FLPs), their aggregates, and the products of cooperative addition reactions at their two Lewis centers. This information is extremely valuable for materials that elude structural characterization by X-ray diffraction because of their nanocrystalline or amorphous character, (pseudo-)polymorphism, or other types of disordering phenomena inherent in the solid state. Aside from simple chemical shift measurements using single-pulse or cross-polarization/magic-angle spinning NMR detection techniques, the availability of advanced multidimensional and double-resonance NMR methods greatly deepened the informational content of these experiments. In particular, methods quantifying the magnetic dipole–dipole interaction strengths and indirect spin–spin interactions prove useful for the measurement of intermolecular association, connectivity, assessment of FLP–ligand distributions, and the stereochemistry of adducts. The present review illustrates several important solid-state NMR methods with some insightful applications to open questions in FLP chemistry, with a particular focus on supramolecular associates.

Sign in / Sign up

Export Citation Format

Share Document