scholarly journals Integrated X-ray crystallography, optical and computational methods in studies of structure and luminescence of new synthesized complexes of lanthanides with ligands derived from 2,6-diformylpyridine

Polyhedron ◽  
2011 ◽  
Vol 30 (5) ◽  
pp. 851-859 ◽  
Author(s):  
Gelson Manzoni de Oliveira ◽  
Aline Machado ◽  
Geraldo Wachholz Gomes ◽  
Jorge H.S.K. Monteiro ◽  
Marian R. Davolos ◽  
...  
Keyword(s):  
Computational Methods ◽  
X Ray ◽  
X Ray Crystallography

scholarly journals Role of Computational Methods in Going beyond X-ray Crystallography to Explore Protein Structure and Dynamics

2018 ◽  
Vol 19 (11) ◽  
pp. 3401 ◽  
Author(s):  
Ashutosh Srivastava ◽  
Tetsuro Nagai ◽  
Arpita Srivastava ◽  
Osamu Miyashita ◽  
Florence Tama
Keyword(s):  
Protein Dynamics ◽  
Computational Methods ◽  
Protein Structures ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
X Ray ◽  
X Ray Crystallography ◽  
Insight Into

Protein structural biology came a long way since the determination of the first three-dimensional structure of myoglobin about six decades ago. Across this period, X-ray crystallography was the most important experimental method for gaining atomic-resolution insight into protein structures. However, as the role of dynamics gained importance in the function of proteins, the limitations of X-ray crystallography in not being able to capture dynamics came to the forefront. Computational methods proved to be immensely successful in understanding protein dynamics in solution, and they continue to improve in terms of both the scale and the types of systems that can be studied. In this review, we briefly discuss the limitations of X-ray crystallography in studying protein dynamics, and then provide an overview of different computational methods that are instrumental in understanding the dynamics of proteins and biomacromolecular complexes.

scholarly journals Diamagnetic cobalt(III)tris(o-ethylxanthate) and nickel(II)bis(o-ethylxanthate)

2017 ◽  
Vol 16 (2) ◽  
pp. 138-146 ◽  
Author(s):  
Filip Varga ◽  
Ján Titiš ◽  
Cyril Rajnák ◽  
Ján Moncoľ ◽  
Roman Boča
Keyword(s):  
Ir Spectroscopy ◽  
Single Crystal ◽  
Computational Methods ◽  
Magnetic Measurements ◽  
X Ray ◽  
X Ray Crystallography ◽  
Ethyl Xanthate

Abstract Diamagnetic [Co(xanth)3] and [Ni(xanth)2] complexes have been prepared by reaction of Co(II) and Ni(II) salts with potassium O-ethyl xanthate (Kxanth). The isolated Co(III) and Ni(II) complexes have been characterized by single-crystal X-ray crystallography, UV-VIS and IR spectroscopy, computational methods, and magnetic measurements.

scholarly journals Principles and characteristics of biological assemblies in experimentally determined protein structures

2019 ◽  
Author(s):  
Qifang Xu ◽  
Roland L. Dunbrack
Keyword(s):  
Physical Properties ◽  
Computational Methods ◽  
Structural Information ◽  
Protein Structures ◽  
Sequence Conservation ◽  
Homologous Proteins ◽  
X Ray ◽  
Biologically Relevant ◽  
X Ray Crystallography

AbstractMore than half of all structures in the PDB are assemblies of two or more proteins, including both homooligomers and heterooligomers. Structural information on these assemblies comes from X-ray crystallography, NMR, and cryo-EM spectroscopy. The correct assembly in an X-ray structure is often ambiguous, and computational methods have been developed to identify the most likely biologically relevant assembly based on physical properties of assemblies and sequence conservation in interfaces. Taking advantage of the large number of structures now available, some of the most recent methods have relied on similarity of interfaces and assemblies across structures of homologous proteins.

scholarly journals Temperature artifacts in protein structures bias ligand-binding predictions

2021 ◽  
Author(s):  
Shanshan YC Bradford ◽  
Lea El Khoury ◽  
Yunhui Ge ◽  
Meghan Osato ◽  
David L. Mobley ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Computational Methods ◽  
Protein Function ◽  
Gold Standard ◽  
Protein Structures ◽  
X Ray ◽  
Conformational Ensembles ◽  
X Ray Crystallography ◽  
Methods Development ◽  
Ligand Discovery

X-ray crystallography is the gold standard to resolve conformational ensembles that are significant for protein function, ligand discovery, and computational methods development. However, relevant conformational states may be missed at...

scholarly journals Reaction Mechanism of Glutamate Carboxypeptidase II Revealed by Mutagenesis, X-ray Crystallography, and Computational Methods

Biochemistry ◽  
2009 ◽  
Vol 48 (19) ◽  
pp. 4126-4138 ◽  
Author(s):  
Vojtěch Klusák ◽  
Cyril Bařinka ◽  
Anna Plechanovová ◽  
Petra Mlčochová ◽  
Jan Konvalinka ◽  
...  
Keyword(s):  
Reaction Mechanism ◽  
Computational Methods ◽  
Glutamate Carboxypeptidase Ii ◽  
X Ray ◽  
X Ray Crystallography ◽  
Glutamate Carboxypeptidase

Investigating Saccharomyces cerevisiae alkene reductase OYE 3 by substrate profiling, X-ray crystallography and computational methods

2018 ◽  
Vol 8 (19) ◽  
pp. 5003-5016 ◽  
Author(s):  
Robert W. Powell, III ◽  
M. Pilar Buteler ◽  
Sunidhi Lenka ◽  
Michele Crotti ◽  
Sara Santangelo ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Computational Methods ◽  
X Ray ◽  
X Ray Crystallography ◽  
Sequence Identity

Saccharomyces cerevisiae OYE 3 and OYE 1 share 80% sequence identity, but sometimes differ in stereoselectivities.

Difference Fourier Analysis of Glucose Embedded and Frozen Hydrated Purple Membrane

1982 ◽  
Vol 40 ◽  
pp. 74-75
Author(s):  
Jules S. Jaffe ◽  
Robert M. Glaeser
Keyword(s):  
Purple Membrane ◽  
Data Set ◽  
High Resolution Data ◽  
X Ray ◽  
X Ray Crystallography ◽  
Fourier Techniques ◽  
Versus Protein ◽  
The Difference ◽  
Difference Fourier ◽  
Ideal Method

Although difference Fourier techniques are standard in X-ray crystallography it has only been very recently that electron crystallographers have been able to take advantage of this method. We have combined a high resolution data set for frozen glucose embedded Purple Membrane (PM) with a data set collected from PM prepared in the frozen hydrated state in order to visualize any differences in structure due to the different methods of preparation. The increased contrast between protein-ice versus protein-glucose may prove to be an advantage of the frozen hydrated technique for visualizing those parts of bacteriorhodopsin that are embedded in glucose. In addition, surface groups of the protein may be disordered in glucose and ordered in the frozen state. The sensitivity of the difference Fourier technique to small changes in structure provides an ideal method for testing this hypothesis.

3-D reconstruction of molecular shape from microcrystal thin sections

1983 ◽  
Vol 41 ◽  
pp. 748-749
Author(s):  
S. Cusack ◽  
J.-C. Jésior
Keyword(s):  
Three Dimensional ◽  
Molecular Shape ◽  
Biological Molecules ◽  
Fourier Space ◽  
Single Particles ◽  
Thin Sections ◽  
Standard Methods ◽  
X Ray ◽  
X Ray Crystallography ◽  
Dimensional Reconstruction

Three-dimensional reconstruction techniques using electron microscopy have been principally developed for application to 2-D arrays (i.e. monolayers) of biological molecules and symmetrical single particles (e.g. helical viruses). However many biological molecules that crystallise form multilayered microcrystals which are unsuitable for study by either the standard methods of 3-D reconstruction or, because of their size, by X-ray crystallography. The grid sectioning technique enables a number of different projections of such microcrystals to be obtained in well defined directions (e.g. parallel to crystal axes) and poses the problem of how best these projections can be used to reconstruct the packing and shape of the molecules forming the microcrystal.Given sufficient projections there may be enough information to do a crystallographic reconstruction in Fourier space. We however have considered the situation where only a limited number of projections are available, as for example in the case of catalase platelets where three orthogonal and two diagonal projections have been obtained (Fig. 1).

Electron microscopy of rabbit FC crystals

1983 ◽  
Vol 41 ◽  
pp. 730-731
Author(s):  
Robert A. Grant ◽  
Laura L. Degn ◽  
Wah Chiu ◽  
John Robinson
Keyword(s):  
Electron Microscopy ◽  
High Resolution ◽  
High Resolution Electron Microscopy ◽  
Molecular Replacement ◽  
X Ray ◽  
X Ray Crystallography ◽  
Resolution Electron ◽  
Replacement Technique ◽  
Hydrated Crystal ◽  
Molecular Structure Analysis

Proteolytic digestion of the immunoglobulin IgG with papain cleaves the molecule into an antigen binding fragment, Fab, and a compliment binding fragment, Fc. Structures of intact immunoglobulin, Fab and Fc from various sources have been solved by X-ray crystallography. Rabbit Fc can be crystallized as thin platelets suitable for high resolution electron microscopy. The structure of rabbit Fc can be expected to be similar to the known structure of human Fc, making it an ideal specimen for comparing the X-ray and electron crystallographic techniques and for the application of the molecular replacement technique to electron crystallography. Thin protein crystals embedded in ice diffract to high resolution. A low resolution image of a frozen, hydrated crystal can be expected to have a better contrast than a glucose embedded crystal due to the larger density difference between protein and ice compared to protein and glucose. For these reasons we are using an ice embedding technique to prepare the rabbit Fc crystals for molecular structure analysis by electron microscopy.

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