Laboratory of protein crystallography and structure

Protein crystallography is a technique that utilizes x rays to deduce the three-dimensional structure of proteins.

Protein Crystallography

The proteins examined by this technique must first be crystallized. When x rays are beamed at a crystal, the electrons associated with the atoms of the crystal are able to alter the path of the x rays. If the x rays encounter a film after passing through the crystal, a pattern can be produced following the development of the film. The pattern will consist of a limited series of dots or lines, because a crystal is composed of many repeats of the same molecule.

Through a series of mathematical operations, the pattern of dots and lines on the film can be related to the structure of the molecule that makes up the crystal. Crystallography is a powerful tool that has been used to obtain the structure of many molecules.

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Crystallography data was used, for example, in the determination of the structure of the double helix of deoxyribonucleic acid by American molecular biologist James Watson and British molecular biologist Francis Crick in the s.

Bacteria and virus are also amenable to x-ray crystallography study. For example, the structure of the toxin produced by Vibrio cholerae has been deduced by this technique. Knowledge of the shape of cholera toxin will help in the tailoring of molecules that will bind to the active site of the toxin. In this way, the toxin's activity can be neutralized. Another example is that of the tail region of the virus that specifically infects bacteria bacteriophage.

The tail is the portion of the bacteriophage that binds to the bacteria. Subsequently, the viral nucleic acid is injected into the bacterium via the tail. Details of the three-dimensional structure of the tail are crucial in designing ways to thwart the binding of the virus and the infection of the bacterium.

Proteins are also well suited to crystallography. The determination of the three-dimensional structure of proteins at a molecular level is necessary for the development of drugs that will be able to bind to the particular protein. Not surprisingly, the design of antibiotics relies heavily on protein crystallography. The manufacture of a crystal of a protein species is not easy. Proteins tend to form three-dimensional structures that are quire irregular in shape because of the arrangement of the amino acid building blocks within the molecule.

Some arrangements of the amino acids will produce flat sheets; other arrangements will result in a helix. Irregularly shaped molecules will not readily stack together with their counterparts. Moreover, once a crystal has formed, the structure is extremely fragile and can dissolve easily.

This fragility does have an advantage, however, as it allows other molecules to be incorporated into the crystal during its formation. Thus, for example, an enzyme can become part of a crystal of its protein receptor, allowing the structure of the enzyme-receptor binding site to be studied.

A protein is crystallized by first making a very concentrated solution of the protein and then exposing the solution to chemicals that slowly increase the protein concentration. With the right combination of conditions the protein can spontaneously precipitate. The ideal situation is to have the precipitate begin at one site the nucleation site. This site acts as the seed for more protein to come out of solution resulting in crystal formation.

Once a crystal has formed it must be delicately transferred to the machine where the x-ray diffraction will be performed.Our research focuses on the chemical biology of secondary metabolites produced by Streptomyces soil bacteria.

laboratory of protein crystallography and structure

We are interested in the biosynthesis of aromatic polyketides, an important group of natural products which have been used in medicine and agriculture. Our research combines natural product research, molecular biology, in vitro enzyme chemistry, structural biology, bioinformatics and natural product chemistry. The main goal is to gain insight on the biosynthetic pathways at atomic resolution — to understand the individual biosynthetic reactions and the function and interplay of different enzyme components catalyzing these reactions.

Lysosomal Storage Disorders LSDs result from mutations in genes for lysosomal enzymes or for proteins involved in recognition and transport of lysosomal proteins. Carriers of these severe diseases may be overpopulated in common diseases of the elderly. Treatment or prevention of the disease requires molecular level understanding of the lifecycle and formation of lysosomes. We combine X-ray crystallography, structural and proteomic analysis, and cell biology to increase knowledge on the lysosomal proteins and their targeting.

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The data is collected from structural analysis of known proteins, as well as by studying novel lysosomal proteins and their biology. Research in our group is focused on understanding the structural basis for biological processes, such as the chaperone assisted protein folding and assembly, signal transduction, and program cell death. Molecular chaperones are proteins that assist the non-covalent folding-unfolding and the assembly-disassembly of other macromolecular structures.

To reveal the detail mechanism of this process, we determine structures of chaperones, ushers, and organelle subunits as well as chaperone-subunit and chaperone-subunit-usher complexes, identify the conformational changes in chaperones, ushers, and organelle subunits during the assembly process and measure the associated changes in energy.

We also study the molecular architecture of the assembled organelles and apply this knowledge in designing novel diagnostics and vaccines against gram-negative pathogens. Adenosine deaminase related growth factors ADGFs is a novel family of extracellular signaling proteins, which perform the signaling function both by controlling the level of the signal messenger, adenosine, and by directly binding to the cell surface receptors.

The target of our research is the human adenosine deaminase growth factor, ADA2. Recently we have determined structures of apo-ADA2 and ADA2 complex with transition state analogue and anti-leukemia drug analogue, coformycin.

Among our future goals is to reveal the structural basis for ADA2-glycosoaminoglycan and protein receptor interactions as well as ADA2 structure-based design of immune-modulating drugs. Metacaspases is a family of cystein proteases, which are related to caspases, the executors of program cell death in animals. The study preformed with our collaborators showed that metacaspases play a similar role in plants. We aim at determining the first high-resolution structure of a metacaspase and elucidating the structural basis for its activity.COVID is an emerging, rapidly evolving situation.

Get the latest public health information from CDC: www. Michael W. Krause, Ph. The Developmental Biology Section investigates the transcriptional regulation of cell fate determination during metazoan development. Using the C. Historically, our interest has primarily been directed at understanding muscle cell specification and differentiation as a model for both embryonic and postembryonic development.

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Our goal is to fully describe the transcriptional cascade that orchestrates the formation of this tissue from just after fertilization, throughout embryogenesis, and into adulthood. Kiyoshi Mizuuchi, Ph. The Genetic Mechanisms Section investigates the mechanics of cellular processes that impact the genomic structure and the heritance of the genomic material.

We study mechanisms of reactions that impact the stability of the linear organization of the genome, as well as the 3-dimensional dynamics involved in the heritance of bacterial chromosomes.

Martin Gellert, Ph. This process is essential for the development of lymphoid cells and is unique in sharing some properties with site-specific recombination and with the repair of radiation damage to DNA. Our aim is to understand V D J recombination in detail and to apply this knowledge to the immune system.

This reaction shares many properties with mobile genetic elements transposonsand we are interested in the potential role of transposition in causing chromosomal translocations of the types found in leukemias and lymphomas.

Researchers in this section are also investigating the separate ubiquitin ligase activity of RAG1 and its covalent modification by auto-ubiquitylation. Robert Craigie, Ph. After entering the host cell, a DNA copy of the viral genome is made by reverse transcription.

Integration of this viral DNA into a chromosome of the host cell is an essential step in the retroviral replication cycle. The key player in the retroviral DNA integration process is the virally encoded integrase protein. We study the molecular mechanism of these reactions using biochemical, biophysical, and structural techniques. Our work also investigates cellular proteins that play important accessory roles in the integration process.

Of particular interest is the mechanism that prevents integrase using the viral DNA as a target for integration. Such autointegration would result in destruction of the viral DNA. We have identified a cellular protein, which we called barrier-to-autointegration factor BAF that prevents integration of the viral DNA into itself.

Gary Felsenfeld, Ph.

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The Physical Chemistry Section studies the structure and function of several types of proteins. Specific projects investigate the relationship between chromatin structure and gene expression in eukaryotes.

Researchers focus on the epigenetic mechanisms and the structure of both the individual nucleosomes the fundamental chromatin subunits and the folded polynucleosome fiber. Recent investigations on the role of histone variants in regulation of chromatin structure and gene expression suggest that unstable nucleosome core particles NCPs play a role in making active promoters more accessible for binding by regulatory factors.

Other work examines long-range chromatin organization and the boundaries between independently regulated domains, which play a role in regulation of gene expression. We have focused on the properties of insulator elements that help to establish such boundaries.The intention is to dedicate this chapter to the basics of the major experimental methods used in tertiary protein structure determination.

One of these methods, X-ray crystallography, has made the largest contribution to our understanding of protein structures, although the other methods have complemented our data when crystallography for one or other reason could not be used. Thus, electron microscopy, and particularly Cryo-EM, which provides higher resolution, can be used to study relatively large objects, like cellular organelles or large macromolecular complexes, using the method of single-particle reconstruction.

An advantage of the method of single-particle reconstruction, in comparison to protein crystallography, is that it does not require the protein to be crystallized, since crystallization in many cases may be difficult and may require a lot of effort. However, in electron crystallography, which is primarily used for membrane proteins, we do need crystals, so called two-dimensional crystals of a protein.

Cryo-EM also requires small amounts of material, which is an advantage in comparison to both crystallography and NMR spectroscopy. NMR requires much larger amounts of material and in addition, the protein under study needs to be stable at room temperature under a rather long time of data acquisition.

One of the limitations of Cryo-EM is that the resolution obtained is generally limited in comparison to the resolution obtained from NMR spectroscopy or protein crystallography. Protein crystallography may provide atomic or near atomic resolution, when small details of the protein structure can be resolved with very high accuracy. Although NMR spectroscopy does not provide this level of resolution, the method proved to be valuable when details of the dynamics of the system needed to be studied or when a protein is difficult to crystallize.

Like NMR, measurements are performed in solution, thus having the advantages of controlling the conditions of the experiment directly in solution. Homology modeling may also be used for obtaining three-dimensional structural information of protein structures.

However, for accurate modeling we need high percentage identity between the amino acid sequence of the given protein and its homologue for which the tertiary structure is known the template. Additional methods used in obtaining partial local structural information include mass spectrometry, analytical ultracentrifugation, various fluorescent spectroscopic methods, etc. An outline of X-ray crystallography Crystallography starts from a crystal and to get crystals the protein needs to be crystallized.

People often say: Crystallization is an art and not a science. It is true to a certain extent, there are still some general principles which need to be followed, and most importantly, there are different methods, which have been developed to facilitate protein crystallization.

After obtaining crystals it is time for the X-ray crystallographic experiment, which is placing the crystal in an X-ray beam, rotating it and collecting diffraction data. Once data have been obtained, the rest of the work will be done using specialized computer programs. To start with, I will first give an overview of the method of crystallization and crystallization tools, followed by an overview of crystallography, X-ray data collection, refinement and structure quality: Crystallization Crystallization tools Crystallography overview X-ray data collection Structure quality.

Experimental methods in structural biology: Protein crystallization and X-ray crystallography.The interests of the Laboratory cover a wide range of systems and techniques relevant to macromolecular crystallography and its applications.

laboratory of protein crystallography and structure

Zbigniew Dauter, is involved in developing new macromolecular crystallography methods related to the tunability and high intensity of synchrotron radiation, such as the use of anomalous signals, particularly from comparatively light atoms, and the effects of radiation damage incurred in crystals of proteins. This Section has also been involved in collaborative efforts with a number of groups within and outside MCL in extending the resolution of crystal structures of proteins and nucleic acids to atomic levels and in investigating parameters which would define these structures as "high quality".

The principal interest of Dr. Systems under investigation include RNA-processing proteins, RNA polymerase-associated transcription factors, folate pathway enzymes, and detoxification enzymes. The Protein Engineering Section, headed by Dr. David Waugh, develops and refines methods for high-throughput protein expression and purification, and engages in structure-assisted drug design with particular emphasis on proteins involved in cancer.

Under the direction of Dr. Alexander Wlodawer, the Protein Structure Section is involved in investigating a variety of proteases, with particular emphasis on viral enzymes, retropepsins; lectins with antiviral activity; complexes of antibodies with antigens; and a number of cytokines and cytokine-receptor complexes. Skip to main content.

Macromolecular Crystallography Laboratory Chief. Alexander Wlodawer, Ph. View My Team. Xinhua Ji, Ph. Zbigniew Dauter, Ph. Jacek Tadeusz Lubkowski, Ph. Joseph E. Tropea, Ph.

David S. Waugh, Ph. There are no Open Positions at this time. Check back again later, or take a look at CCR's Careers page. About The interests of the Laboratory cover a wide range of systems and techniques relevant to macromolecular crystallography and its applications. Lori Larson. Veronica Church.This resource is powered by the Protein Data Bank archive-information about the 3D shapes of proteins, nucleic acids, and complex assemblies that helps students and researchers understand all aspects of biomedicine and agriculture, from protein synthesis to health and disease.

The RCSB PDB builds upon the data by creating tools and resources for research and education in molecular biology, structural biology, computational biology, and beyond. Validation reports contain an assessment of the quality of a structure and highlight specific concerns by considering the coordinates of the model, the experimental data and the fit between the two.

laboratory of protein crystallography and structure

Easily interpretable summary information that compares the quality of a model with that of other models in the archive will help users of PDB data to critically assess archived entries and to select the most appropriate structural models for their needs.

Validation reports for manuscript reviewers are created during annotation of deposited structures. Deposit 3D macromolecular structure data to the PDB. From any page on the site, a Basic Search can be run by entering a search term in the top Search Bar.

As you enter a term, you will see suggestions appearing in the dropdown menu that appears below the search bar. The suggestions are grouped by attribute name, indicating in the specific field or fields in which the search term was found. The Advanced Search Query Builder tool allows you to construct complex boolean queries by specifying values for a wide range of structure attributes. Search results can be returned at the structure, entity, or assembly level, and viewed in a variety of formats, for example, as a summary view, an images only gallery view, or in a Tabular Report format.

Any query and its results can be further refined by selecting additional criteria from the 'Refinements' panel. Go to Advanced Search. Search protein and nucleic acid sequences using the mmseqs2 method to find similar protein or nucleic acid chains in the PDB.

The new Advanced Search Query Builder tool can be used to run sequence searches, and to combine the results with the other search criteria that are available. Explore metabolic pathways maps that identify pathway components with PDB structures and homology models. This feature is available in Structure Summary pages and Instance Sequence pages. Illustrates the correspondences between the human genome and 3D structure.

Special features include support for both rigid-body and flexible alignments and detection of circular permutations. The JSmol symmetry display mode select the Symmetry button highlights global, local, and helical symmetry among subunits.

Experimental methods in structural biology: Protein crystallization and X-ray crystallography

The view displays the symmetry axes, a polyhedron that reflects the symmetry, and a color scheme that emphasizes the symmetry.

The slider graphic compares important global quality indicators for a given structure with the PDB archive. Global percentile ranks black vertical boxes are calculated with respect to all X-ray structures available prior to Resolution-specific percentile ranks white vertical boxes are calculated considering entries with similar resolution.

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Mutations in a gene can have profound effects on the function of a protein. This analysis tool highlights the location of a gene location i. The new mapping tool can be used to locate this position on the UniProt sequence and 3D structure. This web server classifies interfaces present in protein crystals to distinguish biological interfaces from crystal contacts. EPPIC Version 3 enumerates all possible symmetric assemblies with a prediction of the most likely assembly based on probabilistic scores from pairwise evolutionary scoring.

Go to the Downloads Page.X-ray crystallography XRC is the experimental science determining the atomic and molecular structure of a crystalin which the crystalline structure causes a beam of incident X-rays to diffract into many specific directions.

By measuring the angles and intensities of these diffracted beams, a crystallographer can produce a three-dimensional picture of the density of electrons within the crystal.

From this electron densitythe mean positions of the atoms in the crystal can be determined, as well as their chemical bondstheir crystallographic disorderand various other information. Since many materials can form crystals—such as saltsmetalsmineralssemiconductorsas well as various inorganic, organic, and biological molecules—X-ray crystallography has been fundamental in the development of many scientific fields.

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In its first decades of use, this method determined the size of atoms, the lengths and types of chemical bonds, and the atomic-scale differences among various materials, especially minerals and alloys. The method also revealed the structure and function of many biological molecules, including vitaminsdrugs, proteins and nucleic acids such as DNA. X-ray crystallography is still the primary method for characterizing the atomic structure of new materials and in discerning materials that appear similar by other experiments.

X-ray crystal structures can also account for unusual electronic or elastic properties of a material, shed light on chemical interactions and processes, or serve as the basis for designing pharmaceuticals against diseases. In a single-crystal X-ray diffraction measurement, a crystal is mounted on a goniometer. The goniometer is used to position the crystal at selected orientations.

The crystal is illuminated with a finely focused monochromatic beam of X-rays, producing a diffraction pattern of regularly spaced spots known as reflections.

X-ray crystallography

The two-dimensional images taken at different orientations are converted into a three-dimensional model of the density of electrons within the crystal using the mathematical method of Fourier transformscombined with chemical data known for the sample. Poor resolution fuzziness or even errors may result if the crystals are too small, or not uniform enough in their internal makeup.

X-ray crystallography is related to several other methods for determining atomic structures. Similar diffraction patterns can be produced by scattering electrons or neutronswhich are likewise interpreted by Fourier transformation. If single crystals of sufficient size cannot be obtained, various other X-ray methods can be applied to obtain less detailed information; such methods include fiber diffractionpowder diffraction and if the sample is not crystallized small-angle X-ray scattering SAXS.

If the material under investigation is only available in the form of nanocrystalline powders or suffers from poor crystallinity, the methods of electron crystallography can be applied for determining the atomic structure. For all above mentioned X-ray diffraction methods, the scattering is elastic ; the scattered X-rays have the same wavelength as the incoming X-ray. By contrast, inelastic X-ray scattering methods are useful in studying excitations of the sample such as plasmonscrystal-field and orbital excitations, magnonsand phononsrather than the distribution of its atoms.

Crystals, though long admired for their regularity and symmetry, were not investigated scientifically until the 17th century.

Johannes Kepler hypothesized in his work Strena seu de Nive Sexangula A New Year's Gift of Hexagonal Snow that the hexagonal symmetry of snowflake crystals was due to a regular packing of spherical water particles.


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