Vitamin B12: chemistry and biochemistry

2005 ◽  
Vol 33 (4) ◽  
pp. 806-810 ◽  
Author(s):  
B. Kräutler
Keyword(s):  
Vitamin B12 ◽  
Higher Plants ◽  
Enzymatic Reactions ◽  
Natural Sources ◽  
X Ray ◽  
X Ray Crystallography ◽  
Anaerobic Microorganisms ◽  
Animal Metabolism

Vitamin B12, the ‘antipernicious anaemia factor’, is required for human and animal metabolism. It was discovered in the late 1940s and its unique corrin ligand was revealed approx. 10 years later by X-ray crystallography. The B12-coenzymes are cofactors in various important enzymatic reactions and are particularly relevant in the metabolism of anaerobic microorganisms. Microorganisms are the only natural sources of the B12-derivatives, whereas most spheres of life (except for the higher plants) depend on these cobalt corrinoids.

scholarly journals Identification of unknown proteins in X-ray crystallography and cryo-EM

2021 ◽  
Author(s):  
Grzegorz Chojnowski ◽  
Adam J. Simpkin ◽  
Diego A. Leonardo ◽  
Wolfram Seifert-Davila ◽  
Dan E. Vivas-Ruiz ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Protein Structures ◽  
Protein Sequences ◽  
Protein Structure Determination ◽  
Natural Sources ◽  
X Ray ◽  
X Ray Crystallography ◽  
Unknown Protein ◽  
Automated Pipeline ◽  
Unknown Sequence

AbstractAlthough experimental protein structure determination usually targets known proteins, chains of unknown sequence are often encountered. They can be purified from natural sources, appear as an unexpected fragment of a well characterized protein or as a contaminant. Regardless of the source of the problem, the unknown protein always requires tedious characterization. Here we present an automated pipeline for the identification of protein sequences from cryo-EM reconstructions and crystallographic data. We present the method’s application to characterize the crystal structure of an unknown protein purified from a snake venom. We also show that the approach can be successfully applied to the identification of protein sequences and validation of sequence assignments in cryo-EM protein structures.

scholarly journals findMySequence: a neural-network-based approach for identification of unknown proteins in X-ray crystallography and cryo-EM

IUCrJ ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Grzegorz Chojnowski ◽  
Adam J. Simpkin ◽  
Diego A. Leonardo ◽  
Wolfram Seifert-Davila ◽  
Dan E. Vivas-Ruiz ◽  
...  
Keyword(s):  
Neural Network ◽  
Protein Structures ◽  
Protein Sequences ◽  
Protein Structure Determination ◽  
Natural Sources ◽  
X Ray ◽  
X Ray Crystallography ◽  
Unknown Protein ◽  
Automated Pipeline ◽  
Unknown Sequence

Although experimental protein-structure determination usually targets known proteins, chains of unknown sequence are often encountered. They can be purified from natural sources, appear as an unexpected fragment of a well characterized protein or appear as a contaminant. Regardless of the source of the problem, the unknown protein always requires characterization. Here, an automated pipeline is presented for the identification of protein sequences from cryo-EM reconstructions and crystallographic data. The method's application to characterize the crystal structure of an unknown protein purified from a snake venom is presented. It is also shown that the approach can be successfully applied to the identification of protein sequences and validation of sequence assignments in cryo-EM protein structures.

Can Laue catch Maxwell?: observation of short-lived species by Laue X-ray crystallography

1992 ◽  
Vol 340 (1657) ◽  
pp. 273-284 ◽  
Keyword(s):  
Real Time ◽  
Protein Crystal ◽  
Separate Experiment ◽  
Enzymatic Reactions ◽  
X Ray Diffraction ◽  
Single Experiment ◽  
Time Resolved ◽  
X Ray ◽  
X Ray Crystallography ◽  
Novel Strategy

Now that the Laue method has been established as a tool for protein crystallography, the main problem involved in any prospective time-resolved X-ray diffraction study is one of chemistry. The reaction or process in question must be initiated on a timescale that is fast compared with its kinetics. For most biochemical events photochemistry is the most suitable trigger, but not all substrates can be caged for photochemical release. This problem can be solved by the novel strategy of caging the enzyme with a photoreversible covalent inhibitor. The logic of this method will be discussed and its application to a time-resolved study of the reaction of a suicide substrate with the protease gamma chymotrypsin shown. The question of real-time crystallographic ‘movies’ of enzymatic reactions can now be considered. It seems likely that following a reaction in real time in a single experiment will be very difficult if not impossible in most cases, in part because even a synchronized process will rapidly become asynchronous in a protein crystal, and also because it will be very difficult to know exactly what species one is observing at any instant unless one has extremely high resolution. It seems that the best use of the Laue technique will be to study unstable species that can be accumulated in the crystal under defined conditions for short periods of time. An entire reaction sequence can then be obtained as a series of individual steps, each of which is obtained from a separate experiment.

scholarly journals Crystal structure of higher plant heme oxygenase-1 and its mechanism of interaction with ferredoxin

2020 ◽  
pp. jbc.RA120.016271
Author(s):  
Rei Tohda ◽  
Hideaki Tanaka ◽  
Risa Mutoh ◽  
Xuhong Zhang ◽  
Young-Ho Lee ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Heme Oxygenase ◽  
Higher Plants ◽  
Fine Tuning ◽  
Titration Calorimetry ◽  
Heme Oxygenase 1 ◽  
Enzymatic Reactions ◽  
Plant Type ◽  
Higher Plant ◽  
X Ray

Heme oxygenase (HO) converts heme to carbon monoxide, biliverdin, and free iron, products that are essential in cellular redox signaling and iron recycling. In higher plants, HO is also involved in the biosynthesis of photoreceptor pigment precursors. Despite many common enzymatic reactions, the amino acid sequence identity between plant-type and other HOs is exceptionally low (~19.4 %) and amino acids that are catalytically important in mammalian HO are not conserved in plant-type HOs. Structural characterization of plant-type HO is limited to spectroscopic characterization by Electron Spin Resonance, and it remains unclear how the structure of plant-type HO differs from that of other HOs. Here, we have solved the crystal structure of Glycine max (soybean) HO-1 (GmHO-1) at 1.06 Å resolution, and carried out the Isothermal Titration Calorimetry (ITC) measurements and Nuclear Magnetic Resonance (NMR) spectroscopic studies of its interaction with ferredoxin (Fd), the plant-specific electron donor. The high-resolution X-ray structure of GmHO-1 reveals several novel structural components: an additional irregularly structured region, a new water tunnel from the active site to the surface, and a hydrogen-bonding network unique to plant-type HOs. Structurally important features in other HOs, such as His ligation to the bound heme, are conserved in GmHO-1. Based on combined data from X-ray crystallography, ITC, and NMR measurements, we propose the evolutionary fine-tuning of plant-type HOs for Fd dependency in order to allow adaptation to dynamic pH changes on the stroma side of the thylakoid membrane in chloroplast without losing enzymatic activity under conditions of fluctuating light.

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.

Tele-Substitution Reactions in the Synthesis of a Promising Class of Antimalarials

2020 ◽  
Author(s):  
Marat Korsik ◽  
Edwin Tse ◽  
David Smith ◽  
William Lewis ◽  
Peter J. Rutledge ◽  
...  
Keyword(s):  
Heterocyclic Ring ◽  
Ring System ◽  
Substitution Reactions ◽  
Laboratory Notebook ◽  
Polar Solvents ◽  
X Ray ◽  
X Ray Crystallography ◽  
The Core ◽  
Nmr Data

<p></p><p>We have discovered and studied a <i>tele</i>substitution reaction in a biologically important heterocyclic ring system. Conditions that favour the <i>tele</i>-substitution pathway were identified: the use of increased equivalents of the nucleophile or decreased equivalents of base, or the use of softer nucleophiles, less polar solvents and larger halogens on the electrophile. Using results from X-ray crystallography and isotope labelling experiments a mechanism for this unusual transformation is proposed. We focused on this triazolopyrazine as it is the core structure of the <i>in vivo </i>active anti-plasmodium compounds of Series 4 of the Open Source Malaria consortium.</p> <p> </p> <p>Archive of the electronic laboratory notebook with the description of all conducted experiments and raw NMR data could be accessed via following link <a href="https://ses.library.usyd.edu.au/handle/2123/21890">https://ses.library.usyd.edu.au/handle/2123/21890</a> . For navigation between entries of laboratory notebook please use file "Strings for compounds in the article.pdf" that works as a reference between article codes and notebook codes, also this file contain SMILES for these compounds. </p><br><p></p>

Sign in / Sign up

Export Citation Format

Share Document