Determination of local ligand conformations in slowly tumbling proteins by homonuclear 2D and 3D NMR: application to heme propionates in leghemoglobin

1993 ◽  
Vol 115 (14) ◽  
pp. 6238-6246 ◽  
Author(s):  
Dimitrios Morikis ◽  
Rafael Bruschweiler ◽  
Peter E. Wright
Keyword(s):  
3D Nmr ◽  
2D And 3D

scholarly journals Structure of Nanobody Nb23

Molecules ◽  
2021 ◽  
Vol 26 (12) ◽  
pp. 3567
Author(s):  
Mathias Percipalle ◽  
Yamanappa Hunashal ◽  
Jan Steyaert ◽  
Federico Fogolari ◽  
Gennaro Esposito
Keyword(s):  
Nmr Spectroscopy ◽  
Chemical Shift ◽  
Solution Structure ◽  
Chemical Shifts ◽  
Molecular Size ◽  
Side Chain ◽  
3D Nmr ◽  
Target Antigen ◽  
Internuclear Distances ◽  
2D And 3D

Background: Nanobodies, or VHHs, are derived from heavy chain-only antibodies (hcAbs) found in camelids. They overcome some of the inherent limitations of monoclonal antibodies (mAbs) and derivatives thereof, due to their smaller molecular size and higher stability, and thus present an alternative to mAbs for therapeutic use. Two nanobodies, Nb23 and Nb24, have been shown to similarly inhibit the self-aggregation of very amyloidogenic variants of β2-microglobulin. Here, the structure of Nb23 was modeled with the Chemical-Shift (CS)-Rosetta server using chemical shift assignments from nuclear magnetic resonance (NMR) spectroscopy experiments, and used as prior knowledge in PONDEROSA restrained modeling based on experimentally assessed internuclear distances. Further validation was comparatively obtained with the results of molecular dynamics trajectories calculated from the resulting best energy-minimized Nb23 conformers. Methods: 2D and 3D NMR spectroscopy experiments were carried out to determine the assignment of the backbone and side chain hydrogen, nitrogen and carbon resonances to extract chemical shifts and interproton separations for restrained modeling. Results: The solution structure of isolated Nb23 nanobody was determined. Conclusions: The structural analysis indicated that isolated Nb23 has a dynamic CDR3 loop distributed over different orientations with respect to Nb24, which could determine differences in target antigen affinity or complex lability.

Local symmetry in 2D and 3D NMR spectra

1989 ◽  
Vol 85 (2) ◽  
pp. 337-358 ◽  
Author(s):  
S Boentges ◽  
B.U Meier ◽  
C Griesinger ◽  
R.R Ernst
Keyword(s):  
Nmr Spectra ◽  
Local Symmetry ◽  
3D Nmr ◽  
2D And 3D

scholarly journals Subsurface investigations of landslides using geophysical methods : geoelectrical applications in the Swabian Alb (Germany)

2006 ◽  
Vol 61 (3) ◽  
pp. 201-208 ◽  
Author(s):  
R. Bell ◽  
J.-E. Kruse ◽  
A. Garcia ◽  
T. Glade ◽  
A. Hördt
Keyword(s):  
Soil Moisture ◽  
Geophysical Methods ◽  
Economic Damage ◽  
The World ◽  
Subsurface Investigation ◽  
3D Information ◽  
Moisture Conditions ◽  
2D And 3D ◽  
2D Resistivity

Abstract. Landslides occur frequently all over the world, causing at times considerable economic damage, injuries and even death. In order to improve hazard assessment, common landslide types of a given region need to be investigated in detail. While traditional techniques of subsurface investigation are expensive and only provide point information, geophysical methods are suitable tools for gathering 2D and 3D information on the subsurface quickly, reliably and cost-effectively. In this study, the suitability and limitations of 2D resistivity for the determination of landslide extent, structure and soil moisture conditions are presented. For this purpose, two identical profiles were taken during a two-month period. Significant differences in electrical resistivity (>1000 Ωm) due to varying soil moisture conditions were observed. Using various inversion parameters, it was possible to model two distinct subsurface images. Regrettably, the sliding plane could not be detected reliably, possibly due to the homogeniety of the landslide material and underlying bedrock.

Homonuclear three-dimensional proton NMR spectroscopy of pike parvalbumin. Comparison of short- and medium-range NOEs from 2D and 3D NMR

1990 ◽  
Vol 112 (13) ◽  
pp. 5024-5030 ◽  
Author(s):  
Andre Padilla ◽  
Geerten W. Vuister ◽  
Rolf Boelens ◽  
Gerard J. Kleywegt ◽  
Adrien Cave ◽  
...  
Keyword(s):  
Nmr Spectroscopy ◽  
Three Dimensional ◽  
Proton Nmr ◽  
3D Nmr ◽  
Proton Nmr Spectroscopy ◽  
Medium Range ◽  
2D And 3D

A novel local radial basis function collocation method for multi-dimensional piezoelectric problems

2021 ◽  
pp. 1045389X2110572
Author(s):  
Amir Noorizadegan ◽  
Der Liang Young ◽  
Chuin-Shan Chen
Keyword(s):  
Radial Basis Function ◽  
Collocation Method ◽  
Basis Function ◽  
Shape Parameter ◽  
Piezoelectric Medium ◽  
The Finite Element Method ◽  
Mechanical Field ◽  
Radial Basis ◽  
2D And 3D

The local radial basis function collocation method (LRBFCM), a strong-form formulation of the meshless numerical method, is proposed for solving piezoelectric medium problems. The proposed numerical algorithm is based on the local Kansa method using variable shape parameter. We introduce a novel technique for the determination of shape parameter in the LRBFCM, which leads to greater accuracy, and simplicity. The implemented algorithm is first verified with a 2D Poisson equation. Then, we employed LRBFCM in a numerical simulation for 2D and 3D piezoelectric problems involving mutual coupling of the electric field and elastodynamic equations for mechanical field. The presented meshless method is verified using corresponding results obtained from the finite element method and moving least squares meshless local Petrov–Galerkin method. In particular, the 2D piezoelectric problem is verified with an exact solution.

Characterization of 3D Surface Texture Directionality Using Multi-Scale Curvature Tensor Analysis

2017 ◽  
Author(s):  
Tomasz Bartkowiak
Keyword(s):  
Curvature Tensor ◽  
Surface Texture ◽  
Sampling Interval ◽  
Tensor Analysis ◽  
Principal Curvatures ◽  
Multi Scale ◽  
Principal Directions ◽  
2D And 3D ◽  
3D Surface Texture

Anisotropy of surface texture can in many practical cases significantly affect the interaction between the surface and phenomena that influence or are influenced by the topography. Tribological contacts in sheet forming, wetting behavior or dental wear are good examples. This article introduces and exemplifies a method for quantification and visualization of anisotropy using the newly developed 3D multi-scale curvature tensor analysis. Examples of a milled steel surface, which exhibited an evident anisotropy, and a ruby contact probe surface, which was the example of isotropic surface, were measured by the confocal microscope. They were presented in the paper to support the proposed approach. In the method, the curvature tensor T is calculated using three proximate unit vectors normal to the surface. The multi-scale effect is achieved by changing the size of the sampling interval for the estimation of the normals. Normals are estimated from regular meshes by applying a covariance matrix method. Estimation of curvature tensor allows determination of two directions around which surface bends the most and the least (principal directions) and the bending radii (principal curvatures). The direction of the normal plane, where the curvature took its maximum, could be plotted for each analyzed region and scale. In addition, 2D and 3D distribution graphs could be provided to visualize anisotropic or isotropic characteristics. This helps to determine the dominant texture direction or directions for each scale. In contrast to commonly used surface isotropy/anisotropy determination techniques such as Fourier transform or autocorrelation, the presented method provides the analysis in 3D and for every region at each scale. Thus, different aspects of the studied surfaces could clearly be seen at different scales.

Shape Design From Exemplar Sketches Using Graph-Based Sketch Analysis

2012 ◽  
Vol 134 (11) ◽  
Author(s):  
Günay Orbay ◽  
Levent Burak Kara
Keyword(s):  
Design Space ◽  
Deformation Analysis ◽  
Functional Requirements ◽  
Shape Information ◽  
Interactive Editing ◽  
Geometric Deformation ◽  
A New Technique ◽  
Shape Characteristics ◽  
2D And 3D

We describe a new technique that works from a set of concept sketches to support the exploration and engineering of products. Our approach allows the capture and reuse of geometric shape information contained in concept sketches, as a means to generate solutions that can concurrently satisfy aesthetic and functional requirements. At the heart of our approach is a graph-based representation of sketches that allows the determination of topological and geometric similarities in the input sketches. This analysis, when combined with a geometric deformation analysis, results in a design space from which new shapes can be synthesized, or a developing design can be optimized to satisfy prescribed objectives. Moreover, it facilitates a sketch-based, interactive editing of existing designs that preserves the shape characteristics captured in the design space. A key advantage of the proposed method is that shape features common to all sketches as well as those unique to each sketch can be separately identified, thus allowing a mixing of different sketches to generate a topologically and geometrically rich set of conceptual alternatives. We demonstrate our technique with 2D and 3D examples.

scholarly journals Determination of relative tensor orientations by γ-encoded chemical shift anisotropy/heteronuclear dipolar coupling 3D NMR spectroscopy in biological solids

2010 ◽  
Vol 12 (45) ◽  
pp. 14873 ◽  
Author(s):  
Guangjin Hou ◽  
Sivakumar Paramasivam ◽  
In-Ja L. Byeon ◽  
Angela M. Gronenborn ◽  
Tatyana Polenova
Keyword(s):  
Nmr Spectroscopy ◽  
Chemical Shift ◽  
Dipolar Coupling ◽  
Chemical Shift Anisotropy ◽  
3D Nmr ◽  
Biological Solids

Structure and Metabolic-Flow Analysis of Molecular Complexity in a 13 C-Labeled Tree by 2D and 3D NMR

2016 ◽  
Vol 55 (20) ◽  
pp. 6000-6003 ◽  
Author(s):  
Takanori Komatsu ◽  
Risa Ohishi ◽  
Amiu Shino ◽  
Jun Kikuchi
Keyword(s):  
Flow Analysis ◽  
3D Nmr ◽  
Molecular Complexity ◽  
2D And 3D ◽  
Labeled Tree
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