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Wlodawer A.,NCI Inc | Minor W.,University of Virginia | Minor W.,Midwest Center for Structural Genomics | Minor W.,Center for Structural Genomics of Infectious Diseases | And 2 more authors.
FEBS Journal | Year: 2013

The number of macromolecular structures deposited in the Protein Data Bank now approaches 100 000, with the vast majority of them determined by crystallographic methods. Thousands of papers describing such structures have been published in the scientific literature, and 20 Nobel Prizes in chemistry or medicine have been awarded for discoveries based on macromolecular crystallography. New hardware and software tools have made crystallography appear to be an almost routine (but still far from being analytical) technique and many structures are now being determined by scientists with very limited experience in the practical aspects of the field. However, this apparent ease is sometimes illusory and proper procedures need to be followed to maintain high standards of structure quality. In addition, many noncrystallographers may have problems with the critical evaluation and interpretation of structural results published in the scientific literature. The present review provides an outline of the technical aspects of crystallography for less experienced practitioners, as well as information that might be useful for users of macromolecular structures, aiming to show them how to interpret (but not overinterpret) the information present in the coordinate files and in their description. A discussion of the extent of information that can be gleaned from the atomic coordinates of structures solved at different resolution is provided, as well as problems and pitfalls encountered in structure determination and interpretation. This review, addressed to the less experienced macromolecular crystallographers and to users of biological structures, provides an outline of the technical aspects of crystallography, and discusses common problems and pitfalls encountered during structure determination and interpretation. It includes tips on how to interpret, but not overinterpret, the information present in the coordinate files and in their description. © 2013 FEBS. Source

In order to uncover the structure of these proteins, researchers used a technique called protein crystallography. Like a mosquito trapped in amber, compounds that are crystallized are placed in array in identical positions and ordered so that scientists can target them with X-ray beams and work backwards from the scattering patterns produced to recreate their three-dimensional structures atom by atom. In the first study, a group of researchers from the Structural Biology Center, which is funded by DOE's Office of Science, mapped out a protein responsible for breaking down organic compounds in soil bacteria, an important process for recycling carbon in the ecosystem. The bacteria used, called Acinetobacter, is located mostly in soil and water habitats, where it helps to change aromatic compounds (named for their ring shape) into forms that can be used as food. One of the sources of aromatic compounds found in soil is lignin, a tough polymer that is an essential part of all plants and that's hard for many organisms to digest. "But Acinetobacter can utilize these aromatic compounds as their sole source of carbon," said Andrzej Joachimiak, who co-authored both studies and is the director of the Structural Biology Center and the Midwest Center for Structural Genomics at Argonne. In order for Acinetobacter to break down the aromatic compounds, it needs to produce catabolic enzymes, molecular machines built from an organism's DNA that break down molecules into smaller parts that can be digested. Whether or not membrane transporters and catabolic enzymes are produced falls to the HcaR regulator, a sort of molecular policeman that controls when the genes that code for these enzymes can be activated. Joachimiak and his colleagues found that the regulator works in a cycle, activating genes when aromatic compounds are present and shutting genes down when the compounds are used up. "By nature it is very efficient," Joachimiak said. "If you don't have aromatic compounds inside a cell, the operon is shut down." The research team didn't stop at mapping out the regulator itself; to discover how the cycle worked, they crystalized the HcaR regulator during interactions with its two major inputs: the aromatic compounds and DNA. The group found that when aromatic compounds are not present in the cell, two wings found on either side of the HcaR regulator wrap around the DNA. This action is mirrored on both sides of the regulator, covering the DNA regulatory site and preventing genes from being activated. "This is something that has never been seen before," Joachimiak said. When the aromatic compounds are present, however, they attach themselves to the HcaR regulator, making it so stiff that it can no longer grapple with the DNA. Joachimiak said that this knowledge could help outside of the lab, with applications such as a sensor for harmful pesticides and as a template for converting more carbon in soil. "If we can train bacteria to better degrade lignin and other polymers produced by plants during photosynthesis, more natural carbon sources can be utilized for example for production of biofuels and bioproducts," Joachimiak said. The paper was published earlier this year by the Journal of Biological Chemistry under the title "How Aromatic Compounds Block DNA Binding of HcaR Catabolite Regulator." It was supported by the National Institutes of Health and the U.S. Department of Energy (Office of Biological and Environmental Research). A second paper focuses on a family of proteins identified as DUF89, which stands for "domain unknown function." This family is conserved across all three branches of the phylogenetic tree, which means that it is likely essential to many life forms. DUF89 has been identified as a type of enzyme called a phosphatase, which strips molecules of their phosphate groups. The paper's authors hypothesized that DUF89 proteins use this ability to save useful proteins in a cell from rogue molecules which could alter their structure, making them useless or destructive. The study found that DUF89 proteins use a metal ion, probably manganese, to lure in potentially harmful molecules and a water molecule to break off their phosphate group. DUF89 proteins could have an important role in breaking down a specific type of disruptive molecule: sugar. When the concentration of sugar in blood reaches high levels, simple sugars can have unwanted side reactions with proteins and DNA through a process called glycation. "We always have to deal with these side reactions that happen in our cells, and when we get older, we have an accumulation of these errors in our cells," Joachimiak said. Joachimiak said that this research could help scientists develop DUF89 treatments from non-human sources as a way to combat glycation in the bloodstream. The paper was published on the Nature Chemical Biology website on June 20 under the title "A family of metal-dependent phosphatases implicated in metabolite damage-control." Other authors on the paper were from the University of Florida, the University of Toronto, the University of California-Davis and Brookhaven National Laboratory. It was supported by the National Science Foundation, Genome Canada, the Ontario Genomics Institution, the Ontario Research Fund, the Natural Sciences and Engineering Research Council of Canada, the National Institutes of Health, the C.V. Griffin Sr. Foundation and the U.S. Department of Energy (Office of Basic Energy Sciences and Office of Biological and Environmental Research). Both studies used X-rays from the Advanced Photon Source, a DOE Office of Science User Facility, using beamlines 19-ID and 19-BM. Both also stem from the goal of the Midwest Center for Structural Genomics, which is to discover the structure and function of proteins potentially important to biomedicine. Joachimiak said that despite the new findings from these studies, when it comes to understanding what proteins do, we still have a long way to go. "When we sequence genomes, we can predict proteins, but when we predict those sequences we can only say something about function for about half of them," Joachimiak said. Explore further: New crystallization method to ease study of protein structures More information: Youngchang Kim et al. How Aromatic Compounds Block DNA Binding of HcaR Catabolite Regulator, Journal of Biological Chemistry (2016). DOI: 10.1074/jbc.M115.712067 Lili Huang et al. A family of metal-dependent phosphatases implicated in metabolite damage-control, Nature Chemical Biology (2016). DOI: 10.1038/nchembio.2108

Sledz P.,University of Virginia | Sledz P.,University of Warsaw | Sledz P.,Midwest Center for Structural Genomics | Zheng H.,University of Virginia | And 14 more authors.
Protein Science | Year: 2010

Surface lysine methylation (SLM) is a technique for improving the rate of success of protein crystallization by chemically methylating lysine residues. The exact mechanism by which SLM enhances crystallization is still not clear. To study these mechanisms, and to analyze the conditions where SLM will provide the optimal benefits for rescuing failed crystallization experiments, we compared 40 protein structures containing N,N-dimethyl-lysine (dmLys) to a nonredundant set of 18,972 nonmethylated structures from the PDB. By measuring the relative frequency of intermolecular contacts (where contacts are defined as interactions between the residues in proximity with a distance of 3.5 Å or less) of basic residues in the methylated versus nonmethylated sets, dmLys-Glu contacts are seen more frequently than Lys-Glu contacts. Based on observation of the 10 proteins with both native and methylated structures, we propose that the increased rate of contact for dmLys-Glu is due to both a slight increase in the number of aminecarboxyl H-bonds and to the formation of methyl C-H⋯O interactions. By comparing the relative contact frequencies of dmLys with other residues, the mechanism by which methylation of lysines improves the formation of crystal contacts appears to be similar to that of Lys to Arg mutation. Moreover, analysis of methylated structures with the surface entropy reduction (SER) prediction server suggests that in many cases SLM of predicted SER sites may contribute to improved crystallization. Thus, tools that analyze protein sequences and mark residues for SER mutation may identify proteins with good candidate sites for SLM. Published by Wiley-Blackwell. © 2010 The Protein Society. Source

Luo H.-B.,Sun Yat Sen University | Luo H.-B.,University of Virginia | Luo H.-B.,Midwest Center for Structural Genomics | Zheng H.,University of Virginia | And 15 more authors.
Journal of Structural Biology | Year: 2010

A crystal structure of the putative N-carbamoylsarcosine amidase (CSHase) Ta0454 from Thermoplasma acidophilum was solved by single-wavelength anomalous diffraction and refined at a resolution of 2.35 Å. CSHases are involved in the degradation of creatinine. Ta0454 shares a similar fold and a highly conserved C-D-K catalytic triad (Cys123, Asp9, and Lys90) with the structures of three cysteine hydrolases (PDB codes 1NBA, 1IM5, and 2H0R). Molecular dynamics (MD) simulations of Ta0454/N-carbamoylsarcosine and Ta0454/pyrazinamide complexes were performed to determine the structural basis of the substrate binding pattern for each ligand. Based on the MD-simulated trajectories, the MM/PBSA method predicts binding free energies of -24.5 and -17.1 kcal/mol for the two systems, respectively. The predicted binding free energies suggest that Ta0454 is selective for N-carbamoylsarcosine over pyrazinamide, and zinc ions play an important role in the favorable substrate bound states. © 2009 Elsevier Inc. All rights reserved. Source

Chruszcz M.,University of Virginia | Chruszcz M.,Center for Structural Genomics of Infectious Diseases | Chruszcz M.,Midwest Center for Structural Genomics | Domagalski M.,University of Virginia | And 9 more authors.
Current Opinion in Structural Biology | Year: 2010

Structural genomics (SG) programs have developed during the last decade many novel methodologies for faster and more accurate structure determination. These new tools and approaches led to the determination of thousands of protein structures. The generation of enormous amounts of experimental data resulted in significant improvements in the understanding of many biological processes at molecular levels. However, the amount of data collected so far is so large that traditional analysis methods are limiting the rate of extraction of biological and biochemical information from 3D models. This situation has prompted us to review the challenges that remain unmet by SG, as well as the areas in which the potential impact of SG could exceed what has been achieved so far. © 2010 Elsevier Ltd. Source

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