scholarly journals Using Complementary NMR Data Sets To Detect Inconsistencies and Model Flaws in the Structure Determination of Human Interleukin-4

2017 ◽  
Vol 121 (29) ◽  
pp. 7055-7063 ◽  
Author(s):  
Lorna J. Smith ◽  
Wilfred F. van Gunsteren ◽  
Niels Hansen
Keyword(s):  
Structure Determination ◽  
Interleukin 4 ◽  
Data Sets ◽  
Nmr Data

Structure determination using poorly diffracting membrane-protein crystals: the H+-ATPase and Na+,K+-ATPase case history

2010 ◽  
Vol 66 (3) ◽  
pp. 309-313 ◽  
Author(s):  
Bjørn P. Pedersen ◽  
J. Preben Morth ◽  
Poul Nissen
Keyword(s):  
Structure Determination ◽  
Heavy Atom ◽  
Real Space ◽  
Search Model ◽  
Data Sets ◽  
Molecular Replacement ◽  
Maximum Resolution ◽  
Phase Combination ◽  
Site Identification

An approach is presented for the structure determination of membrane proteins on the basis of poorly diffracting crystals which exploits molecular replacement for heavy-atom site identification at 6–9 Å maximum resolution and improvement of the heavy-atom-derived phases by multi-crystal averaging using quasi-isomorphous data sets. The multi-crystal averaging procedure allows real-space density averaging followed by phase combination between non-isomorphous native data sets to exploit crystal-to-crystal nonisomorphism despite the crystals belonging to the same space group. This approach has been used in the structure determination of H+-ATPase and Na+,K+-ATPase using Ca2+-ATPase models and its successful application to the Mhp1 symporter using LeuT as a search model is demonstrated.

The use of Mo Kα radiation in the assignment of the absolute configuration of light-atom molecules; the importance of high-resolution data

2014 ◽  
Vol 70 (4) ◽  
pp. 660-668 ◽  
Author(s):  
Eduardo C. Escudero-Adán ◽  
Jordi Benet-Buchholz ◽  
Pablo Ballester
Keyword(s):  
High Resolution ◽  
Crystal Structures ◽  
Structure Determination ◽  
Great Majority ◽  
Data Sets ◽  
Light Atom ◽  
High Resolution Data ◽  
The Absolute ◽  
Absolute Structure

Recent studies have confirmed the usefulness of the Hooft and Parsons methodologies for determination of the absolute crystal structures of enantiopure light-atom compounds using CuKα radiation. While many single-crystal diffractometers used for small-molecule structure determination are equipped with molybdenum anodes, use of data from such instruments for the absolute structure determination of light-atom crystal structures is rarely documented and has often been found to be unsuccessful. The Hooft and Parsons methodologies have been applied to 44 data sets obtained from single crystals containing light-atom molecules of known chirality using Mo Kαradiation. Several factors influencing the calculation of accurate and precise values for the Hooft and Parsons parameters obtained from these data sets have been identified, the inclusion of high-resolution diffraction data being particularly important. The correct absolute structure was obtained in all cases, with the standard uncertainties of the final absolute structure parameters below 0.1 for the great majority.

scholarly journals Simultaneous Assignment and Structure Determination of Proteins From Sparsely Labeled NMR Datasets

2021 ◽  
Vol 8 ◽  
Author(s):  
Arup Mondal ◽  
Alberto Perez
Keyword(s):  
Bayesian Approach ◽  
Structure Determination ◽  
Structure Prediction ◽  
Critical Assessment ◽  
Limited Data ◽  
Computational Tools ◽  
Nmr Data

Sparsely labeled NMR samples provide opportunities to study larger biomolecular assemblies than is traditionally done by NMR. This requires new computational tools that can handle the sparsity and ambiguity in the NMR datasets. The MELD (modeling employing limited data) Bayesian approach was assessed to be the best performing in predicting structures from sparsely labeled NMR data in the 13th edition of the Critical Assessment of Structure Prediction (CASP) event—and limitations of the methodology were also noted. In this report, we evaluate the nature and difficulty in modeling unassigned sparsely labeled NMR datasets and report on an improved methodological pipeline leading to higher-accuracy predictions. We benchmark our methodology against the NMR datasets provided by CASP 13.

Reaktion von 1.4-Dienen mit Metallkomplexen, I Darstellung und Röntgenstrukturanalyse eines π-enyl-Komplexes der Zusammensetzung (C8H13PdCl)2/ Reaction of 1,4-Dienes with Metal Complexes, I Synthesis and X-ray Structure Determination of a π-enyl Complex of Composition (C8H18PdCl)2

1976 ◽  
Vol 31 (4) ◽  
pp. 455-462 ◽  
Author(s):  
Peter Feldhaus ◽  
Richard Ratka ◽  
Hermann Schmid ◽  
Manfred L. Ziegler
Keyword(s):  
Metal Complexes ◽  
Structure Determination ◽  
Three Dimensional ◽  
Fourier Methods ◽  
X Ray ◽  
H Nmr ◽  
Nmr Data ◽  
Cell Dimensions ◽  
Unit Cell Dimensions

Reaction of (C6H5CN)2PdCl2 and 1,3-dimethylenecyclohexane led to an exocyclic π-enyl complex of formula (C8H13PdCl)2-bis(η3-2-methylene-6-methylcyclohexyl)(di-µ-chloro)-dipalladium. IR and 1H NMR data are in agreement with this formulation.The compound is monoclinic, with unit cell dimensions α = 499.97 ± 0.08, b =1342.26 ± 0.19, c =1379.60 ± 0.20 pm, β = 99.43 ± 0.02°, space group C5h2-P21/C, Ζ = 2, dX-ray = 1.83 g/cm3.The structure was determined from three-dimensional X-ray data by Patterson and Fourier methods. Least squares refinement by use of 1045 independent reflections has reached R1 = 5.6%.

Bis(4-picoline-κN)gold(I) dibromidoaurate(I) and bis(4-picoline-κN)gold(I) dichloridoaurate(I): space-group ambiguity?

2013 ◽  
Vol 69 (7) ◽  
pp. 709-711 ◽  
Author(s):  
Cindy Döring ◽  
Peter G. Jones
Keyword(s):  
Phase Transformation ◽  
Hydrogen Bonds ◽  
Structure Determination ◽  
Monoclinic Space Group ◽  
Data Sets ◽  
Asymmetric Unit ◽  
Space Group ◽  
Monoclinic Cell ◽  
Rule Out

Bis(4-picoline-κN)gold(I) dibromidoaurate(I), [Au(C6H7N)2][AuBr2], (I), crystallizes in the monoclinic space groupP21/n, with two half cations and one general anion in the asymmetric unit. The cations, located on centres of inversion, assemble to form chains parallel to theaaxis, but there are no significant contacts between the cations. Cohesion is provided by flanking anions, which are connected to the cations by short Au...Au contacts and C—H...Br hydrogen bonds, and to each other by Br...Br contacts. The corresponding chloride derivative, [Au(C6H7N)2][AuCl2], (II), is isotypic. A previous structure determination of (II), reported in the space groupP\overline{1} with very similar axis lengths to those of (I) [Linet al.(2008).Inorg. Chem.47, 2543–2551], might be identical to the structure presented here, except that its γ angle of 88.79 (7)° seems to rule out a monoclinic cell. No phase transformation of (II) could be detected on the basis of data sets recorded at 100, 200 and 295 K.

Potential Anticancer Agents, XI. X-Ray Structure Determination of Acantholide [1]

1979 ◽  
Vol 34 (9-10) ◽  
pp. 677-682 ◽  
Author(s):  
H. Lotter ◽  
H. Wagner ◽  
A. A. Saleh ◽  
G. A. Cordell ◽  
N. R. Famsworth
Keyword(s):  
Solid State ◽  
Antitumor Activity ◽  
Sesquiterpene Lactone ◽  
Anticancer Agents ◽  
Structure Determination ◽  
Direct Methods ◽  
X Ray ◽  
Activity Evaluation ◽  
Nmr Data

Abstract The X-ray structure of acantholide, a melampolide sesquiterpene lactone from Acanthosper­mum glabratum (D C .) Willd. was determined by the aid of direct methods. The compound was cy­totoxic but displayed no antitumor activity. Evaluation of the X-ray and NMR data indicated that the same conformation exists in the solid state as in solution.

scholarly journals Structure determination of an integral membrane protein at room temperature from crystalsin situ

2015 ◽  
Vol 71 (6) ◽  
pp. 1228-1237 ◽  
Author(s):  
Danny Axford ◽  
James Foadi ◽  
Nien-Jen Hu ◽  
Hassanul Ghani Choudhury ◽  
So Iwata ◽  
...  
Keyword(s):  
Membrane Protein ◽  
Structure Determination ◽  
Room Temperature ◽  
Protein Structures ◽  
Integral Membrane Protein ◽  
Data Sets ◽  
X Ray Diffraction ◽  
Haemophilus Influenza

The structure determination of an integral membrane protein using synchrotron X-ray diffraction data collected at room temperature directly in vapour-diffusion crystallization plates (in situ) is demonstrated. Exposing the crystalsin situeliminates manual sample handling and, since it is performed at room temperature, removes the complication of cryoprotection and potential structural anomalies induced by sample cryocooling. Essential to the method is the ability to limit radiation damage by recording a small amount of data per sample from many samples and subsequently assembling the resulting data sets using specialized software. The validity of this procedure is established by the structure determination ofHaemophilus influenzaTehA at 2.3 Å resolution. The method presented offers an effective protocol for the fast and efficient determination of membrane-protein structures at room temperature using third-generation synchrotron beamlines.

scholarly journals Extending the applicability of P3D for structure determination of small molecules

2021 ◽  
Vol 2 (1) ◽  
pp. 105-116
Author(s):  
Alain Ibáñez de Opakua ◽  
Markus Zweckstetter
Keyword(s):  
Nuclear Magnetic Resonance ◽  
Magnetic Resonance ◽  
Small Molecules ◽  
Structure Determination ◽  
Structural Characteristics ◽  
Discrimination Power ◽  
Nmr Parameters ◽  
Structural Assignment ◽  
Nmr Data

Abstract. The application of anisotropic nuclear magnetic resonance (NMR) parameters for the correct structural assignment of small molecules requires the use of partially ordered media. Previously we demonstrated that the use of P3D simulations using poly(γ-benzyl-L-glutamate) (PBLG) as an alignment medium allows for the determination of the correct diastereomer from extremely sparse NMR data. Through the analysis of the structural characteristics of small molecules in different alignment media, here we show that when steric or electrostatic factors dominate the alignment, P3D-PBLG retains its diastereomer discrimination power. We also demonstrate that P3D simulations can define the different conformations of a flexible small molecule from sparse NMR data.

scholarly journals REDCRAFT: A computational platform using residual dipolar coupling NMR data for determining structures of perdeuterated proteins in solution

2021 ◽  
Vol 17 (2) ◽  
pp. e1008060
Author(s):  
Casey A. Cole ◽  
Nourhan S. Daigham ◽  
Gaohua Liu ◽  
Gaetano T. Montelione ◽  
Homayoun Valafar
Keyword(s):  
Nmr Spectroscopy ◽  
Structure Determination ◽  
Residual Dipolar Couplings ◽  
Dipolar Coupling ◽  
Nuclear Overhauser Effect ◽  
Critical Role ◽  
Protein Structures ◽  
Perdeuterated Proteins ◽  
Nmr Data

Nuclear Magnetic Resonance (NMR) spectroscopy is one of the three primary experimental means of characterizing macromolecular structures, including protein structures. Structure determination by solution NMR spectroscopy has traditionally relied heavily on distance restraints derived from nuclear Overhauser effect (NOE) measurements. While structure determination of proteins from NOE-based restraints is well understood and broadly used, structure determination from Residual Dipolar Couplings (RDCs) is relatively less well developed. Here, we describe the new features of the protein structure modeling program REDCRAFT and focus on the new Adaptive Decimation (AD) feature. The AD plays a critical role in improving the robustness of REDCRAFT to missing or noisy data, while allowing structure determination of larger proteins from less data. In this report we demonstrate the successful application of REDCRAFT in structure determination of proteins ranging in size from 50 to 145 residues using experimentally collected data, and of larger proteins (145 to 573 residues) using simulated RDC data. In both cases, REDCRAFT uses only RDC data that can be collected from perdeuterated proteins. Finally, we compare the accuracy of structure determination from RDCs alone with traditional NOE-based methods for the structurally novel PF.2048.1 protein. The RDC-based structure of PF.2048.1 exhibited 1.0 Å BB-RMSD with respect to a high-quality NOE-based structure. Although optimal strategies would include using RDC data together with chemical shift, NOE, and other NMR data, these studies provide proof-of-principle for robust structure determination of largely-perdeuterated proteins from RDC data alone using REDCRAFT.

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