structure-solution-fluorescent-protein-cerulean-using

Structure Solution of the Fluorescent Protein Cerulean Using MeshAndCollect

X-ray crystallography is the major technique used to obtain high resolution information concerning the 3-dimensional structures of biological ...

fully-autonomous-characterization-data-collection-from-crystals

Fully Autonomous Characterization and Data Collection from Crystals of Biological Macromolecules

High-brilliance X-ray beams coupled with automation have&#160;led to the use of synchrotron-based macromolecular X-ray crystallography (MX) beamlines for ...

Trehalose (alpha-D-glucopyranosyl-1,1-alpha-D-glucopyranose) is a non-reducing diglucoside found in various organisms that serves as a carbohydrate reserve and as an agent that protects against a variety of physical and chemical stresses. Deinococcus radiodurans possesses an alternative biosynthesis pathway for the synthesis of trehalose from maltooligosaccharides. This reaction is mediated by two enzymes: maltooligosyltrehalose synthase (MTSase) and maltooligosyltrehalose trehalohydrolase (MTHase). Here, we present the 1.1A resolution crystal structure of MTHase. It consists of three major domains: two beta-sheet domains and a conserved glycosidase (beta/alpha)8 barrel catalytic domain. Three subdomains consisting of short insertions were identified within the catalytic domain. Subsequently, structures of MTHase in complex with maltose and trehalose were obtained at 1.2 A and 1.5 A resolution, respectively. These structures reveal the importance of the three inserted subdomains in providing the key residues required for substrate recognition. Trehalose is recognised specifically in the +1 and +2 binding subsites by an extensive hydrogen-bonding network and a strong hydrophobic stacking interaction in between two aromatic residues. Moreover, upon binding to maltose, which mimics the substrate sugar chain, a major concerted conformational change traps the sugar chain in the active site. The presence of magnesium in the active site of the MTHase-maltose complex suggests that MTHase activity may be regulated by divalent cations.

Crystal structure of maltooligosyltrehalose trehalohydrolase from Deinococcus radiodurans in complex with disaccharides.

The phasing of macromolecular structures based on the use of the single-wavelength anomalous diffraction method has recently enjoyed a revival. Here, additional evidence is provided that the method may be successfully applied at wavelengths remote from the absorption edge of interest and that it is in principle applicable to a large number of systems. This opens up the possibility of rapid and reliable automatic de novo structure determination using simple experimental configurations with no need for wavelength tunability or absorption-edge scanning. The method should therefore be exploitable at most synchrotron beamlines. The effects of data completeness and multiplicity on the quality of the phases obtained are discussed as are the prospects for the automation of macromolecular structure solution based on the experimental protocols described.

Automatic structure determination based on the single-wavelength anomalous diffraction technique away from an absorption edge.

The production of three-dimensional crystallographic structural information of macromolecules can now be thought of as a pipeline which is being streamlined at every stage from protein cloning, expression and purification, through crystallisation to data collection and structure solution. Synchrotron X-ray beamlines are a key section of this pipeline as it is at these that the X-ray diffraction data that ultimately leads to the elucidation of macromolecular structures are collected. The burgeoning number of macromolecular crystallography (MX) beamlines available worldwide may be enhanced significantly with the automation of both their operation and of the experiments carried out on them. This paper reviews the current situation and provides a glimpse of how a MX beamline may look in the not too distant future.

Automation of macromolecular crystallography beamlines.

Here, an automated procedure is described to identify the positions of many cryocooled crystals mounted on the same sample holder, to rapidly predict and rank their relative diffraction strengths and to collect partial X-ray diffraction data sets from as many of the crystals as desired. Subsequent hierarchical cluster analysis then allows the best combination of partial data sets, optimizing the quality of the final data set obtained. The results of applying the method developed to various systems and scenarios including the compilation of a complete data set from tiny crystals of the membrane protein bacteriorhodopsin and the collection of data sets for successful structure determination using the single-wavelength anomalous dispersion technique are also presented. 

MeshAndCollect: an automated multi-crystal data-collection workflow for synchrotron macromolecular crystallography beamlines.

This article describes , a software providing an intuitive graphical user interface (GUI) and multiple functions to perform hierarchical cluster analysis on multiple crystallographic datasets. The program makes it easier for users to choose, in the case of multi-crystal data collection, those datasets that will be merged together to give good final statistics. It provides a simple GUI to analyse the dendrogram and various options for automated clustering and data merging.

Hierarchical clustering for multiple-crystal macromolecular crystallography experiments: the  program.

Determining macromolecular structures from X-ray data with resolution worse than 3 Å remains a challenge. Even if a related starting model is available, its incompleteness or its bias together with a low observation-to-parameter ratio can render the process unsuccessful or very time-consuming. Yet, many biologically important macromolecules, especially large macromolecular assemblies, membrane proteins and receptors, tend to provide crystals that diffract to low resolution. A new algorithm to tackle this problem is presented that uses a multivariate function to simultaneously exploit information from both an initial partial model and low-resolution single-wavelength anomalous diffraction data. The new approach has been used for six challenging structure determinations, including the crystal structures of membrane proteins and macromolecular complexes that have evaded experts using other methods, and large structures from a 3.0 Å resolution F-ATPase data set and a 4.5 Å resolution SecYEG-SecA complex data set. All of the models were automatically built by the method to  values of between 28.9 and 39.9% and were free from the initial model bias.

A new MR-SAD algorithm for the automatic building of protein models from low-resolution X-ray data and a poor starting model.

ID30B is an undulator-based high-intensity, energy-tuneable (6.0-20 keV) and variable-focus (20-200 µm in diameter) macromolecular crystallography (MX) beamline at the ESRF. It was the last of the ESRF Structural Biology Group's beamlines to be constructed and commissioned as part of the ESRF's Phase I Upgrade Program and has been in user operation since June 2015. Both a modified microdiffractometer (MD2S) incorporating an in situ plate screening capability and a new flexible sample changer (the FlexHCD) were specifically developed for ID30B. Here, the authors provide the current beamline characteristics and detail how different types of MX experiments can be performed on ID30B (http://www.esrf.eu/id30b).

ID30B - a versatile beamline for macromolecular crystallography experiments at the ESRF.

The availability of genomic data from extinct homini such as Neanderthals has caused a revolution in palaeontology allowing the identification of modern human-specific protein substitutions. Currently, little is known as to how these substitutions alter the proteins on a molecular level. Here, we investigate adenylosuccinate lyase, a conserved enzyme involved in purine metabolism for which several substitutions in the modern human protein (hADSL) have been described to affect intelligence and behaviour. During evolution, modern humans acquired a specific substitution (Ala429Val) in ADSL distinguishing it from the ancestral variant present in Neanderthals (nADSL). We show here that despite this conservative substitution being solvent exposed and located distant from the active site, there is a difference in thermal stability, but not enzymology or ligand binding between nADSL and hADSL. Substitutions near residue 429 which do not profoundly affect enzymology were previously reported to cause neurological symptoms in humans. This study also reveals that ADSL undergoes conformational changes during catalysis which, together with the crystal structure of a hitherto undetermined product bound conformation, explains the molecular origin of disease for several modern human ADSL mutants.

ArticleTotal : 2	Year
Publication title Cited by 2	2019
Publication title Cited by 2	2019

Article	Year
Crystal structure of maltooligosyltrehalose trehalohydrolase from Deinococcus radiodurans in complex with disaccharides. Journal of molecular biology\| PubMed ID: 15784255	2005
Automatic structure determination based on the single-wavelength anomalous diffraction technique away from an absorption edge. Acta crystallographica. Section D, Biological crystallography\| PubMed ID: 15805593	2005
Automation of macromolecular crystallography beamlines. Progress in biophysics and molecular biology\| PubMed ID: 15910915	2005
MeshAndCollect: an automated multi-crystal data-collection workflow for synchrotron macromolecular crystallography beamlines. Acta crystallographica. Section D, Biological crystallography\| PubMed ID: 26527148	2015
Hierarchical clustering for multiple-crystal macromolecular crystallography experiments: the program. Journal of applied crystallography\| PubMed ID: 29217993	2017
A new MR-SAD algorithm for the automatic building of protein models from low-resolution X-ray data and a poor starting model. IUCrJ\| PubMed ID: 29765606	2018
ID30B - a versatile beamline for macromolecular crystallography experiments at the ESRF. Journal of synchrotron radiation\| PubMed ID: 29979188	2018
Molecular comparison of Neanderthal and Modern Human adenylosuccinate lyase. Scientific reports\| PubMed ID: 30573755	2018

Gordon Leonard

Biography

JoVE Journal Publications

Other Publications