101
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Bastidas AC, Deal MS, Steichen JM, Keshwani MM, Guo Y, Taylor SS. Role of N-terminal myristylation in the structure and regulation of cAMP-dependent protein kinase. J Mol Biol 2012; 422:215-29. [PMID: 22617327 DOI: 10.1016/j.jmb.2012.05.021] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2012] [Revised: 05/03/2012] [Accepted: 05/15/2012] [Indexed: 01/13/2023]
Abstract
The catalytic (C) subunit of cAMP-dependent protein kinase [protein kinase A (PKA)] is a major target of cAMP signaling, and its regulation is of fundamental importance to biological processes. One mode of regulation is N-myristylation, which has eluded structural and functional characterization so far because most crystal structures are of the non-myristylated enzyme, are phosphorylated on Ser10, and generally lack electron density for the first 13 residues. We crystallized myristylated wild-type (WT) PKA and a K7C mutant as binary (bound to a substrate peptide) and ternary [bound to a substrate peptide and adenosine-5'-(β,γ-imido)triphosphate] complexes. There was clear electron density for the entire N-terminus in the binary complexes, both refined to 2.0 Å, and K7C ternary complex, refined to 1.35 Å. The N-termini in these three structures display a novel conformation with a previously unseen helix from residues 1 to 7. The K7C mutant appears to have a more stable N-terminus, and this correlated with a significant decrease in the B-factors for the N-terminus in the myr-K7C complexes compared to the WT binary complex. The N-terminus of the myristylated WT ternary complex, refined to 2.0 Å, was disordered as in previous structures. In addition to a more ordered N-terminus, the myristylated K7C mutant exhibited a 53% increase in k(cat). The effect of nucleotide binding on the structure of the N-terminus in the WT protein and the kinetic changes in the K7C protein suggest that myristylation or occupancy of the myristyl binding pocket may serve as a site for allosteric regulation in the C-subunit.
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Affiliation(s)
- Adam C Bastidas
- Department of Pharmacology, University of California San Diego, San Diego, CA 92093, USA
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102
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Vekilov PG. Phase diagrams and kinetics of phase transitions in protein solutions. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2012; 24:193101. [PMID: 22495288 DOI: 10.1088/0953-8984/24/19/193101] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The phase behavior of proteins is of interest for fundamental and practical reasons. The nucleation of new phases is one of the last major unresolved problems of nature. The formation of protein condensed phases (crystals, polymers, and other solid aggregates, as well as dense liquids and gels) underlies pathological conditions, plays a crucial role in the biological function of the respective protein, or is an essential part of laboratory and industrial processes. In this review, we focus on phase transitions of proteins in their properly folded state. We first summarize the recently acquired understanding of physical processes underlying the phase diagrams of the protein solutions and the thermodynamics of protein phase transitions. Then we review recent findings on the kinetics of nucleation of dense liquid droplets and crystals. We explore the transition from nucleation to spinodal decomposition for liquid-liquid separation and introduce the new concept of solution-to-crystal spinodal. We review the two-step mechanism of protein crystal nucleation, in which mesoscopic metastable protein clusters serve as precursors to the ordered crystal nuclei. The concepts and mechanisms reviewed here provide powerful tools for control of the nucleation process by varying the solution thermodynamic parameters.
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Affiliation(s)
- Peter G Vekilov
- Department of Chemical and Biomolecular Engineering and Department of Chemistry, University of Houston, Houston, TX 77204-4004, USA.
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103
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Liu B, Garnett JA, Lee WC, Lin J, Salgado P, Taylor J, Xu Y, Lambert S, Cota E, Matthews S. Promoting crystallisation of the Salmonella enteritidis fimbriae 14 pilin SefD using deuterium oxide. Biochem Biophys Res Commun 2012; 421:208-13. [PMID: 22497887 PMCID: PMC3522111 DOI: 10.1016/j.bbrc.2012.03.136] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Accepted: 03/26/2012] [Indexed: 10/28/2022]
Abstract
The use of heavy water (D(2)O) as a solvent is commonplace in many spectroscopic techniques for the study of biological macromolecules. A significant deuterium isotope effect exists where hydrogen-bonding is important, such as in protein stability, dynamics and assembly. Here we illustrate the use of D(2)O in additive screening for the production of reproducible diffraction-quality crystals for the Salmonella enteritidis fimbriae 14 (SEF14) putative tip adhesin, SefD.
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Affiliation(s)
- Bing Liu
- Centre for Structural Biology & Division of Molecular Biosciences, Imperial College London, South Kensington, London, SW7 2AZ, UK
| | - James. A. Garnett
- Centre for Structural Biology & Division of Molecular Biosciences, Imperial College London, South Kensington, London, SW7 2AZ, UK
| | - Wei-chao Lee
- Centre for Structural Biology & Division of Molecular Biosciences, Imperial College London, South Kensington, London, SW7 2AZ, UK
| | - Jing Lin
- Centre for Structural Biology & Division of Molecular Biosciences, Imperial College London, South Kensington, London, SW7 2AZ, UK
| | - Paula Salgado
- Centre for Structural Biology & Division of Molecular Biosciences, Imperial College London, South Kensington, London, SW7 2AZ, UK
| | - Jonathan Taylor
- Centre for Structural Biology & Division of Molecular Biosciences, Imperial College London, South Kensington, London, SW7 2AZ, UK
| | - Yingqi Xu
- Centre for Structural Biology & Division of Molecular Biosciences, Imperial College London, South Kensington, London, SW7 2AZ, UK
| | - Sebastian Lambert
- Centre for Structural Biology & Division of Molecular Biosciences, Imperial College London, South Kensington, London, SW7 2AZ, UK
| | - Ernesto Cota
- Centre for Structural Biology & Division of Molecular Biosciences, Imperial College London, South Kensington, London, SW7 2AZ, UK
| | - Steve Matthews
- Centre for Structural Biology & Division of Molecular Biosciences, Imperial College London, South Kensington, London, SW7 2AZ, UK
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104
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McGovern RE, Fernandes H, Khan AR, Power NP, Crowley PB. Protein camouflage in cytochrome c–calixarene complexes. Nat Chem 2012; 4:527-33. [DOI: 10.1038/nchem.1342] [Citation(s) in RCA: 171] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Accepted: 03/22/2012] [Indexed: 01/06/2023]
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105
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Abstract
Protein crystals have catalytic and materials applications and are central to efforts in structural biology and therapeutic development. Designing predetermined crystal structures can be subtle given the complexity of proteins and the noncovalent interactions that govern crystallization. De novo protein design provides an approach to engineer highly complex nanoscale molecular structures, and often the positions of atoms can be programmed with sub-Å precision. Herein, a computational approach is presented for the design of proteins that self-assemble in three dimensions to yield macroscopic crystals. A three-helix coiled-coil protein is designed de novo to form a polar, layered, three-dimensional crystal having the P6 space group, which has a "honeycomb-like" structure and hexameric channels that span the crystal. The approach involves: (i) creating an ensemble of crystalline structures consistent with the targeted symmetry; (ii) characterizing this ensemble to identify "designable" structures from minima in the sequence-structure energy landscape and designing sequences for these structures; (iii) experimentally characterizing candidate proteins. A 2.1 Å resolution X-ray crystal structure of one such designed protein exhibits sub-Å agreement [backbone root mean square deviation (rmsd)] with the computational model of the crystal. This approach to crystal design has potential applications to the de novo design of nanostructured materials and to the modification of natural proteins to facilitate X-ray crystallographic analysis.
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106
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Galline Ex-FABP is an antibacterial siderocalin and a lysophosphatidic acid sensor functioning through dual ligand specificities. Structure 2012; 19:1796-806. [PMID: 22153502 DOI: 10.1016/j.str.2011.09.019] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Revised: 09/23/2011] [Accepted: 09/25/2011] [Indexed: 11/21/2022]
Abstract
Galline Ex-FABP was identified as another candidate antibacterial, catecholate siderophore binding lipocalin (siderocalin) based on structural parallels with the family archetype, mammalian Siderocalin. Binding assays show that Ex-FABP retains iron in a siderophore-dependent manner in both hypertrophic and dedifferentiated chondrocytes, where Ex-FABP expression is induced after treatment with proinflammatory agents, and specifically binds ferric complexes of enterobactin, parabactin, bacillibactin and, unexpectedly, monoglucosylated enterobactin, which does not bind to Siderocalin. Growth arrest assays functionally confirm the bacteriostatic effect of Ex-FABP in vitro under iron-limiting conditions. The 1.8 Å crystal structure of Ex-FABP explains the expanded specificity, but also surprisingly reveals an extended, multi-chambered cavity extending through the protein and encompassing two separate ligand specificities, one for bacterial siderophores (as in Siderocalin) at one end and one specifically binding copurified lysophosphatidic acid, a potent cell signaling molecule, at the other end, suggesting Ex-FABP employs dual functionalities to explain its diverse endogenous activities.
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107
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Entropy-driven binding of opioid peptides induces a large domain motion in human dipeptidyl peptidase III. Proc Natl Acad Sci U S A 2012; 109:6525-30. [PMID: 22493238 DOI: 10.1073/pnas.1118005109] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Opioid peptides are involved in various essential physiological processes, most notably nociception. Dipeptidyl peptidase III (DPP III) is one of the most important enkephalin-degrading enzymes associated with the mammalian pain modulatory system. Here we describe the X-ray structures of human DPP III and its complex with the opioid peptide tynorphin, which rationalize the enzyme's substrate specificity and reveal an exceptionally large domain motion upon ligand binding. Microcalorimetric analyses point at an entropy-dominated process, with the release of water molecules from the binding cleft ("entropy reservoir") as the major thermodynamic driving force. Our results provide the basis for the design of specific inhibitors that enable the elucidation of the exact role of DPP III and the exploration of its potential as a target of pain intervention strategies.
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108
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Ferguson AD. Structure-based drug design on membrane protein targets: human integral membrane protein 5-lipoxygenase-activating protein. Methods Mol Biol 2012; 841:267-290. [PMID: 22222457 DOI: 10.1007/978-1-61779-520-6_12] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Leukotrienes are biologically active lipid metabolites of arachidonic acid that are involved in inflammation and play a significant role in respiratory and cardiovascular disease. The integral nuclear membrane protein 5-lipoxygenase-activating protein (FLAP) is essential for leukotriene biosynthesis in response to cellular activation. The crystal structures of human FLAP with two inhibitors were recently determined. Inhibitors are bound within the lipid-exposed portion of FLAP, and the unexpected location of the inhibitor-binding site suggests a transport mechanism for arachidonic acid and provides functional insights into leukotriene biosynthesis. This chapter describes how this human integral membrane crystal structure was solved by pushing the limits of low-resolution structure determination and refinement, demonstrating how a low-resolution structure can impact biology and chemistry, and discusses future opportunities for structure-based drug design for this therapeutic target.
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109
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Structural basis for basal activity and autoactivation of abscisic acid (ABA) signaling SnRK2 kinases. Proc Natl Acad Sci U S A 2011; 108:21259-64. [PMID: 22160701 DOI: 10.1073/pnas.1118651109] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Abscisic acid (ABA) is an essential hormone that controls plant growth, development, and responses to abiotic stresses. Central for ABA signaling is the ABA-mediated autoactivation of three monomeric Snf1-related kinases (SnRK2.2, -2.3, and -2.6). In the absence of ABA, SnRK2s are kept in an inactive state by forming physical complexes with type 2C protein phosphatases (PP2Cs). Upon relief of this inhibition, SnRK2 kinases can autoactivate through unknown mechanisms. Here, we report the crystal structures of full-length Arabidopsis thaliana SnRK2.3 and SnRK2.6 at 1.9- and 2.3-Å resolution, respectively. The structures, in combination with biochemical studies, reveal a two-step mechanism of intramolecular kinase activation that resembles the intermolecular activation of cyclin-dependent kinases. First, release of inhibition by PP2C allows the SnRK2s to become partially active because of an intramolecular stabilization of the catalytic domain by a conserved helix in the kinase regulatory domain. This stabilization enables SnRK2s to gain full activity by activation loop autophosphorylation. Autophosphorylation is more efficient in SnRK2.6, which has higher stability than SnRK2.3 and has well-structured activation loop phosphate acceptor sites that are positioned next to the catalytic site. Together, these data provide a structural framework that links ABA-mediated release of PP2C inhibition to activation of SnRK2 kinases.
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110
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Soon FF, Ng LM, Zhou XE, West GM, Kovach A, Tan MHE, Suino-Powell KM, He Y, Xu Y, Chalmers MJ, Brunzelle JS, Zhang H, Yang H, Jiang H, Li J, Yong EL, Cutler S, Zhu JK, Griffin PR, Melcher K, Xu HE. Molecular mimicry regulates ABA signaling by SnRK2 kinases and PP2C phosphatases. Science 2011; 335:85-8. [PMID: 22116026 DOI: 10.1126/science.1215106] [Citation(s) in RCA: 356] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Abscisic acid (ABA) is an essential hormone for plants to survive environmental stresses. At the center of the ABA signaling network is a subfamily of type 2C protein phosphatases (PP2Cs), which form exclusive interactions with ABA receptors and subfamily 2 Snfl-related kinase (SnRK2s). Here, we report a SnRK2-PP2C complex structure, which reveals marked similarity in PP2C recognition by SnRK2 and ABA receptors. In the complex, the kinase activation loop docks into the active site of PP2C, while the conserved ABA-sensing tryptophan of PP2C inserts into the kinase catalytic cleft, thus mimicking receptor-PP2C interactions. These structural results provide a simple mechanism that directly couples ABA binding to SnRK2 kinase activation and highlight a new paradigm of kinase-phosphatase regulation through mutual packing of their catalytic sites.
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Affiliation(s)
- Fen-Fen Soon
- Laboratory of Structural Sciences, Van Andel Research Institute, 333 Bostwick Avenue NE, Grand Rapids, MI 49503, USA
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111
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Overton IM, Barton GJ. Computational approaches to selecting and optimising targets for structural biology. Methods 2011; 55:3-11. [PMID: 21906678 PMCID: PMC3202631 DOI: 10.1016/j.ymeth.2011.08.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Revised: 08/18/2011] [Accepted: 08/22/2011] [Indexed: 11/29/2022] Open
Abstract
Selection of protein targets for study is central to structural biology and may be influenced by numerous factors. A key aim is to maximise returns for effort invested by identifying proteins with the balance of biophysical properties that are conducive to success at all stages (e.g. solubility, crystallisation) in the route towards a high resolution structural model. Selected targets can be optimised through construct design (e.g. to minimise protein disorder), switching to a homologous protein, and selection of experimental methodology (e.g. choice of expression system) to prime for efficient progress through the structural proteomics pipeline. Here we discuss computational techniques in target selection and optimisation, with more detailed focus on tools developed within the Scottish Structural Proteomics Facility (SSPF); namely XANNpred, ParCrys, OB-Score (target selection) and TarO (target optimisation). TarO runs a large number of algorithms, searching for homologues and annotating the pool of possible alternative targets. This pool of putative homologues is presented in a ranked, tabulated format and results are also visualised as an automatically generated and annotated multiple sequence alignment. The target selection algorithms each predict the propensity of a selected protein target to progress through the experimental stages leading to diffracting crystals. This single predictor approach has advantages for target selection, when compared with an approach using two or more predictors that each predict for success at a single experimental stage. The tools described here helped SSPF achieve a high (21%) success rate in progressing cloned targets to diffraction-quality crystals.
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Affiliation(s)
- Ian M Overton
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, United Kingdom.
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112
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Cooper DR, Porebski PJ, Chruszcz M, Minor W. X-ray crystallography: Assessment and validation of protein-small molecule complexes for drug discovery. Expert Opin Drug Discov 2011; 6:771-782. [PMID: 21779303 PMCID: PMC3138648 DOI: 10.1517/17460441.2011.585154] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION: Crystallography is the key initial component for structure-based and fragment-based drug design and can often generate leads that can be developed into high potency drugs. Therefore, huge sums of money are committed based on the outcome of crystallography experiments and their interpretation. AREAS COVERED: This review discusses how to evaluate the correctness of an X-ray structure, focusing on the validation of small molecule-protein complexes. Various types of inaccuracies found within the PDB are identified and the ramifications of these errors are discussed. The reader will gain an understanding of the key parameters that need to be inspected before a structure can be used in drug discovery efforts, as well as an appreciation of the difficulties of correctly interpreting electron density for small molecules. The reader will also be introduced to methods for validating small molecules within the context of a macromolecular structure. EXPERT OPINION: One of the reasons that ligand identification and positioning, within a macromolecular crystal structure, is so difficult is that the quality of small molecules widely varies in the PDB. For this reason, the PDB can not always be considered a reliable repository of structural information pertaining to small molecules, and this makes the derivation of general principles that govern small molecule-protein interactions more difficult.
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Affiliation(s)
- David R Cooper
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA
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113
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Ravindran PP, Héroux A, Ye JD. Improvement of the crystallizability and expression of an RNA crystallization chaperone. J Biochem 2011; 150:535-43. [PMID: 21785128 DOI: 10.1093/jb/mvr093] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Crystallizing RNA has been an imperative and challenging task in the world of RNA research. Assistive methods such as chaperone-assisted RNA crystallography (CARC), employing monoclonal antibody fragments (Fabs) as crystallization chaperones have enabled us to obtain RNA crystal structures by forming crystal contacts and providing initial phasing information. Despite the early successes, the crystallization of large RNA-Fab complex remains a challenge in practice. The possible reason for this difficulty is that the Fab scaffold has not been optimized for crystallization in complex with RNA. Here, we have used the surface entropy reduction (SER) technique for the optimization of ΔC209 P4-P6/Fab2 model system. Protruding lysine and glutamate residues were mutated to a set of alanines or serines to construct Fab2SMA or Fab2SMS. Expression with the shake flask approach was optimized to allow large scale production for crystallization. Crystal screening shows that significantly higher crystal-forming ratio was observed for the mutant complexes. As the chosen SER residues are far away from the CDR regions of the Fab, the same set of mutations can now be directly applied to other Fabs binding to a variety of ribozymes and riboswitches to improve the crystallizability of Fab-RNA complex.
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114
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Abstract
While antibody-based therapeutics have become firmly established as front-line drugs, the use of antibodies as research tools in small molecule drug discovery is still in its infancy. In this review we focus on the use of antibody fragments as crystallization chaperones to aid the structural determination of otherwise 'uncrystallizable' or 'undruggable' target proteins. We also highlight a potential application for this technology, in which antibody-mediated structures may be used to inform the design of new chemical entities.
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Affiliation(s)
- L Griffin
- Department of Structural Biology, UCB, Slough, UK
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115
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Lockard MA, Listwan P, Pedelacq JD, Cabantous S, Nguyen HB, Terwilliger TC, Waldo GS. A high-throughput immobilized bead screen for stable proteins and multi-protein complexes. Protein Eng Des Sel 2011; 24:565-78. [PMID: 21642284 PMCID: PMC3118733 DOI: 10.1093/protein/gzr021] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We describe an in vitro colony screen to identify Escherichia coli expressing soluble proteins and stable, assembled multiprotein complexes. Proteins with an N-terminal 6His tag and C-terminal green fluorescent protein (GFP) S11 tag are fluorescently labeled in cells by complementation with a coexpressed GFP 1-10 fragment. After partial colony lysis, the fluorescent soluble proteins or complexes diffuse through a supporting filtration membrane and are captured on Talon(®) resin metal affinity beads immobilized in agarose. Images of the fluorescent colonies convey total expression and the level of fluorescence bound to the beads indicates how much protein is soluble. Both pieces of information can be used together when selecting clones. After the assay, colonies can be picked and propagated, eliminating the need to make replica plates. We used the method to screen a DNA fragment library of the human protein p85 and preferentially obtained clones expressing the full-length 'breakpoint cluster region-homology' and NSH2 domains. The assay also distinguished clones expressing stable multi-protein complexes from those that are unstable due to missing subunits. Clones expressing stable, intact heterotrimeric E.coli YheNML complexes were readily identified in libraries dominated by complexes of YheML missing the N subunit.
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Affiliation(s)
- Meghan A Lockard
- Biosciences Division, MS-M888, Los Alamos National Laboratory, PO Box 1663, Los Alamos, NM 87545, USA
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116
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Zheng M, Cierpicki T, Burdette AJ, Utepbergenov D, Janczyk PŁ, Derewenda U, Stukenberg PT, Caldwell KA, Derewenda ZS. Structural features and chaperone activity of the NudC protein family. J Mol Biol 2011; 409:722-41. [PMID: 21530541 DOI: 10.1016/j.jmb.2011.04.018] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Revised: 04/07/2011] [Accepted: 04/07/2011] [Indexed: 11/19/2022]
Abstract
The NudC family consists of four conserved proteins with representatives in all eukaryotes. The archetypal nudC gene from Aspergillus nidulans is a member of the nud gene family that is involved in the maintenance of nuclear migration. This family also includes nudF, whose human orthologue, Lis1, codes for a protein essential for brain cortex development. Three paralogues of NudC are known in vertebrates: NudC, NudC-like (NudCL), and NudC-like 2 (NudCL2). The fourth distantly related member of the family, CML66, contains a NudC-like domain. The three principal NudC proteins have no catalytic activity but appear to play as yet poorly defined roles in proliferating and dividing cells. We present crystallographic and NMR studies of the human NudC protein and discuss the results in the context of structures recently deposited by structural genomics centers (i.e., NudCL and mouse NudCL2). All proteins share the same core CS domain characteristic of proteins acting either as cochaperones of Hsp90 or as independent small heat shock proteins. However, while NudC and NudCL dimerize via an N-terminally located coiled coil, the smaller NudCL2 lacks this motif and instead dimerizes as a result of unique domain swapping. We show that NudC and NudCL, but not NudCL2, inhibit the aggregation of several target proteins, consistent with an Hsp90-independent heat shock protein function. Importantly, and in contrast to several previous reports, none of the three proteins is able to form binary complexes with Lis1. The availability of structural information will be of help in further studies on the cellular functions of the NudC family.
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Affiliation(s)
- Meiying Zheng
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
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117
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Schalk-Hihi C, Schubert C, Alexander R, Bayoumy S, Clemente JC, Deckman I, DesJarlais RL, Dzordzorme KC, Flores CM, Grasberger B, Kranz JK, Lewandowski F, Liu L, Ma H, Maguire D, Macielag MJ, McDonnell ME, Mezzasalma Haarlander T, Miller R, Milligan C, Reynolds C, Kuo LC. Crystal structure of a soluble form of human monoglyceride lipase in complex with an inhibitor at 1.35 Å resolution. Protein Sci 2011; 20:670-83. [PMID: 21308848 PMCID: PMC3081545 DOI: 10.1002/pro.596] [Citation(s) in RCA: 97] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2010] [Accepted: 01/14/2011] [Indexed: 01/07/2023]
Abstract
A high-resolution structure of a ligand-bound, soluble form of human monoglyceride lipase (MGL) is presented. The structure highlights a novel conformation of the regulatory lid-domain present in the lipase family as well as the binding mode of a pharmaceutically relevant reversible inhibitor. Analysis of the structure lacking the inhibitor indicates that the closed conformation can accommodate the native substrate 2-arachidonoyl glycerol. A model is proposed in which MGL undergoes conformational and electrostatic changes during the catalytic cycle ultimately resulting in its dissociation from the membrane upon completion of the cycle. In addition, the study outlines a successful approach to transform membrane associated proteins, which tend to aggregate upon purification, into a monomeric and soluble form.
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Affiliation(s)
- Céline Schalk-Hihi
- Department of Structural Biology, Johnson & Johnson Pharmaceutical Research and DevelopmentL.L.C., Welsh and McKean Roads, Spring House, Pennsylvania 19477,*Correspondence to: Céline Schalk-Hihi (E-mail: ) or Carsten Schubert (E-mail: )
| | - Carsten Schubert
- Department of Structural Biology, Johnson & Johnson Pharmaceutical Research and DevelopmentL.L.C., Welsh and McKean Roads, Spring House, Pennsylvania 19477,*Correspondence to: Céline Schalk-Hihi (E-mail: ) or Carsten Schubert (E-mail: )
| | - Richard Alexander
- Department of Structural Biology, Johnson & Johnson Pharmaceutical Research and DevelopmentL.L.C., Welsh and McKean Roads, Spring House, Pennsylvania 19477
| | - Shariff Bayoumy
- Department of Structural Biology, Johnson & Johnson Pharmaceutical Research and DevelopmentL.L.C., Welsh and McKean Roads, Spring House, Pennsylvania 19477
| | - Jose C Clemente
- Department of Lead Generation Biology, Johnson & Johnson Pharmaceutical Research and DevelopmentL.L.C., Welsh and McKean Roads, Spring House, Pennsylvania 19477
| | - Ingrid Deckman
- Department of Lead Generation Biology, Johnson & Johnson Pharmaceutical Research and DevelopmentL.L.C., Welsh and McKean Roads, Spring House, Pennsylvania 19477
| | - Renee L DesJarlais
- Department of Structural Biology, Johnson & Johnson Pharmaceutical Research and DevelopmentL.L.C., Welsh and McKean Roads, Spring House, Pennsylvania 19477
| | - Keli C Dzordzorme
- Department of Structural Biology, Johnson & Johnson Pharmaceutical Research and DevelopmentL.L.C., Welsh and McKean Roads, Spring House, Pennsylvania 19477
| | - Christopher M Flores
- Department of Neuroscience, Johnson & Johnson Pharmaceutical Research and DevelopmentL.L.C., Welsh and McKean Roads, Spring House, Pennsylvania 19477
| | - Bruce Grasberger
- Department of Structural Biology, Johnson & Johnson Pharmaceutical Research and DevelopmentL.L.C., Welsh and McKean Roads, Spring House, Pennsylvania 19477
| | - James K Kranz
- Department of Lead Generation Biology, Johnson & Johnson Pharmaceutical Research and DevelopmentL.L.C., Welsh and McKean Roads, Spring House, Pennsylvania 19477
| | - Frank Lewandowski
- Department of Structural Biology, Johnson & Johnson Pharmaceutical Research and DevelopmentL.L.C., Welsh and McKean Roads, Spring House, Pennsylvania 19477
| | - Li Liu
- Department of Medicinal Chemistry, Johnson & Johnson Pharmaceutical Research and DevelopmentL.L.C., Welsh and McKean Roads, Spring House, Pennsylvania 19477
| | - Hongchang Ma
- Department of Structural Biology, Johnson & Johnson Pharmaceutical Research and DevelopmentL.L.C., Welsh and McKean Roads, Spring House, Pennsylvania 19477
| | - Diane Maguire
- Department of Structural Biology, Johnson & Johnson Pharmaceutical Research and DevelopmentL.L.C., Welsh and McKean Roads, Spring House, Pennsylvania 19477
| | - Mark J Macielag
- Department of Medicinal Chemistry, Johnson & Johnson Pharmaceutical Research and DevelopmentL.L.C., Welsh and McKean Roads, Spring House, Pennsylvania 19477
| | - Mark E McDonnell
- Department of Medicinal Chemistry, Johnson & Johnson Pharmaceutical Research and DevelopmentL.L.C., Welsh and McKean Roads, Spring House, Pennsylvania 19477
| | - Tara Mezzasalma Haarlander
- Department of Lead Generation Biology, Johnson & Johnson Pharmaceutical Research and DevelopmentL.L.C., Welsh and McKean Roads, Spring House, Pennsylvania 19477
| | - Robyn Miller
- Department of Structural Biology, Johnson & Johnson Pharmaceutical Research and DevelopmentL.L.C., Welsh and McKean Roads, Spring House, Pennsylvania 19477
| | - Cindy Milligan
- Department of Structural Biology, Johnson & Johnson Pharmaceutical Research and DevelopmentL.L.C., Welsh and McKean Roads, Spring House, Pennsylvania 19477
| | - Charles Reynolds
- Department of Structural Biology, Johnson & Johnson Pharmaceutical Research and DevelopmentL.L.C., Welsh and McKean Roads, Spring House, Pennsylvania 19477
| | - Lawrence C Kuo
- Department of Structural Biology, Johnson & Johnson Pharmaceutical Research and DevelopmentL.L.C., Welsh and McKean Roads, Spring House, Pennsylvania 19477
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118
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Derewenda ZS. It's all in the crystals…. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2011; 67:243-8. [PMID: 21460442 PMCID: PMC3069739 DOI: 10.1107/s0907444911007797] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2010] [Accepted: 03/01/2011] [Indexed: 02/07/2023]
Abstract
Macromolecular crystallography relies on the availability and quality of single crystals; these are typically obtained through extensive screening, which has a very low intrinsic success rate. Crystallization is not a completely stochastic process and many proteins do not succumb to crystallization because of specific microscopic features of their molecular surfaces. It follows that rational surface engineering through site-directed mutagenesis should allow a systematic and significant improvement in crystallization success rates. Here, one such established strategy, surface-entropy reduction (SER), is discussed, including its successes, limitations and possible future developments.
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Affiliation(s)
- Zygmunt S Derewenda
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908-0793, USA.
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119
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Findeisen F, Minor DL. Structural basis for the differential effects of CaBP1 and calmodulin on Ca(V)1.2 calcium-dependent inactivation. Structure 2011; 18:1617-31. [PMID: 21134641 DOI: 10.1016/j.str.2010.09.012] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Revised: 09/08/2010] [Accepted: 09/17/2010] [Indexed: 01/01/2023]
Abstract
Calcium-binding protein 1 (CaBP1), a calmodulin (CaM) homolog, endows certain voltage-gated calcium channels (Ca(V)s) with unusual properties. CaBP1 inhibits Ca(V)1.2 calcium-dependent inactivation (CDI) and introduces calcium-dependent facilitation (CDF). Here, we show that the ability of CaBP1 to inhibit Ca(V)1.2 CDI and induce CDF arises from interaction between the CaBP1 N-lobe and interlobe linker residue Glu94. Unlike CaM, where functional EF hands are essential for channel modulation, CDI inhibition does not require functional CaBP1 EF hands. Furthermore, CaBP1-mediated CDF has different molecular requirements than CaM-mediated CDF. Overall, the data show that CaBP1 comprises two structural modules having separate functions: similar to CaM, the CaBP1 C-lobe serves as a high-affinity anchor that binds the Ca(V)1.2 IQ domain at a site that overlaps with the Ca²+/CaM C-lobe site, whereas the N-lobe/linker module houses the elements required for channel modulation. Discovery of this division provides the framework for understanding how CaBP1 regulates Ca(V)s.
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Affiliation(s)
- Felix Findeisen
- Cardiovascular Research Institute, University of California, San Francisco, CA 94158-2330, USA
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120
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A combinatorial method to enable detailed investigation of protein–protein interactions. Future Med Chem 2011; 3:271-82. [DOI: 10.4155/fmc.10.289] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Background: Successful structural investigations of protein–protein interactions can be facilitated by studying only the core interacting regions of the constituent proteins. However, attempting the discovery of stable core complexes using informed trial-and-error approaches can prove time and resource intensive. Methods: We describe a valuable extension of combinatorial domain hunting (CDH), a technology for the timely elucidation of soluble protein truncations. The new method, CDH2, enables empirical discovery of stable protein–protein core complexes. CDH2 is demonstrated ab initio using a previously well-characterized Hsp90/Cdc37 complex. Results: Without using a priori information, we demonstrate the isolation of stable protein–protein complexes, suitable for further analyses. Discussion: This resource-efficient process can provide protein complexes for screening of compounds designed to modulate protein–protein interactions, thus facilitating novel drug discovery.
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121
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Designed ankyrin repeat protein binders for the crystallization of AcrB: plasticity of the dominant interface. J Struct Biol 2011; 174:269-81. [PMID: 21296164 DOI: 10.1016/j.jsb.2011.01.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2010] [Revised: 01/12/2011] [Accepted: 01/31/2011] [Indexed: 11/23/2022]
Abstract
The formation of well-diffracting crystals is a major bottleneck in structural analysis of membrane proteins by X-ray crystallography. One approach to improve crystal quality is the use of DARPins as crystallization chaperones. Here, we present a detailed analysis of the interaction between DARPins and the integral membrane protein AcrB. We find that binders selected in vitro by ribosome display share a common epitope. The comparative analysis of three crystal structures of AcrB-DARPin complexes allowed us to study the plasticity of the interaction with this dominant binding site. Seemingly redundant AcrB-DARPin crystals show substantially different diffraction quality as a result of subtle differences in the binding geometry. This work exemplifies the importance to screen a number of crystallization chaperones to obtain optimal diffraction data. Crystallographic analysis is complemented by biophysical characterization of nine AcrB binders. We observe that small variations in the interface can lead to differing behavior of the DARPins with regards to affinity, stoichiometry of the complexes and specificity for their target.
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122
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Overton IM, van Niekerk CAJ, Barton GJ. XANNpred: neural nets that predict the propensity of a protein to yield diffraction-quality crystals. Proteins 2011; 79:1027-33. [PMID: 21246630 PMCID: PMC3084997 DOI: 10.1002/prot.22914] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2010] [Revised: 09/22/2010] [Accepted: 10/07/2010] [Indexed: 11/08/2022]
Abstract
Production of diffracting crystals is a critical step in determining the three-dimensional structure of a protein by X-ray crystallography. Computational techniques to rank proteins by their propensity to yield diffraction-quality crystals can improve efficiency in obtaining structural data by guiding both protein selection and construct design. XANNpred comprises a pair of artificial neural networks that each predict the propensity of a selected protein sequence to produce diffraction-quality crystals by current structural biology techniques. Blind tests show XANNpred has accuracy and Matthews correlation values ranging from 75% to 81% and 0.50 to 0.63 respectively; values of area under the receiver operator characteristic (ROC) curve range from 0.81 to 0.88. On blind test data XANNpred outperforms the other available algorithms XtalPred, PXS, OB-Score, and ParCrys. XANNpred also guides construct design by presenting graphs of predicted propensity for diffraction-quality crystals against residue sequence position. The XANNpred-SG algorithm is likely to be most useful to target selection in structural genomics consortia, while the XANNpred-PDB algorithm is more suited to the general structural biology community. XANNpred predictions that include sliding window graphs are freely available from http://www.compbio.dundee.ac.uk/xannpred Proteins 2011. © 2010 Wiley-Liss, Inc.
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Affiliation(s)
- Ian M Overton
- School of Life Sciences Research, College of Life Sciences, University of Dundee, Dundee, UK
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123
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124
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Chayen NE. High-throughput protein crystallization. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2010; 77:1-22. [PMID: 20663479 DOI: 10.1016/s1876-1623(09)77001-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Abstract
Structural genomics projects have led to great progress in the field of structural biology. Considerable advances have been made in the automation of all stages of the pipeline from clone to structure. This chapter focuses on crystallization that is one of the major bottlenecks in this pipeline. It discusses new developments and describes a variety of techniques for high-throughput screening and optimizing of conditions for crystallization.
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Affiliation(s)
- Naomi E Chayen
- Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK
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125
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Sledz P, Zheng H, Murzyn K, Chruszcz M, Zimmerman MD, Chordia MD, Joachimiak A, Minor W. New surface contacts formed upon reductive lysine methylation: improving the probability of protein crystallization. Protein Sci 2010; 19:1395-404. [PMID: 20506323 DOI: 10.1002/pro.420] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
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 A 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 amine-carboxyl 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.
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Affiliation(s)
- Pawel Sledz
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, USA
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126
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Unmet challenges of structural genomics. Curr Opin Struct Biol 2010; 20:587-97. [PMID: 20810277 DOI: 10.1016/j.sbi.2010.08.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2010] [Revised: 07/30/2010] [Accepted: 08/03/2010] [Indexed: 11/22/2022]
Abstract
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.
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127
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Moon AF, Mueller GA, Zhong X, Pedersen LC. A synergistic approach to protein crystallization: combination of a fixed-arm carrier with surface entropy reduction. Protein Sci 2010; 19:901-13. [PMID: 20196072 DOI: 10.1002/pro.368] [Citation(s) in RCA: 122] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Protein crystallographers are often confronted with recalcitrant proteins not readily crystallizable, or which crystallize in problematic forms. A variety of techniques have been used to surmount such obstacles: crystallization using carrier proteins or antibody complexes, chemical modification, surface entropy reduction, proteolytic digestion, and additive screening. Here we present a synergistic approach for successful crystallization of proteins that do not form diffraction quality crystals using conventional methods. This approach combines favorable aspects of carrier-driven crystallization with surface entropy reduction. We have generated a series of maltose binding protein (MBP) fusion constructs containing different surface mutations designed to reduce surface entropy and encourage crystal lattice formation. The MBP advantageously increases protein expression and solubility, and provides a streamlined purification protocol. Using this technique, we have successfully solved the structures of three unrelated proteins that were previously unattainable. This crystallization technique represents a valuable rescue strategy for protein structure solution when conventional methods fail.
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Affiliation(s)
- Andrea F Moon
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA
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128
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To automate or not to automate: this is the question. ACTA ACUST UNITED AC 2010; 11:211-21. [PMID: 20526815 PMCID: PMC2921494 DOI: 10.1007/s10969-010-9092-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2009] [Accepted: 05/14/2010] [Indexed: 11/26/2022]
Abstract
New protocols and instrumentation significantly boost the outcome of structural biology, which has resulted in significant growth in the number of deposited Protein Data Bank structures. However, even an enormous increase of the productivity of a single step of the structure determination process may not significantly shorten the time between clone and deposition or publication. For example, in a medium size laboratory equipped with the LabDB and HKL-3000 systems, we show that automation of some (and integration of all) steps of the X-ray structure determination pathway is critical for laboratory productivity. Moreover, we show that the lag period after which the impact of a technology change is observed is longer than expected.
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129
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Leung DW, Borek D, Farahbakhsh M, Ramanan P, Nix JC, Wang T, Prins KC, Otwinowski Z, Honzatko RB, Helgeson LA, Basler CF, Amarasinghe GK. Crystallization and preliminary X-ray analysis of Ebola VP35 interferon inhibitory domain mutant proteins. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:689-92. [PMID: 20516601 PMCID: PMC2882771 DOI: 10.1107/s1744309110013266] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2009] [Accepted: 04/10/2010] [Indexed: 11/10/2022]
Abstract
VP35 is one of seven structural proteins encoded by the Ebola viral genome and mediates viral replication, nucleocapsid formation and host immune suppression. The C-terminal interferon inhibitory domain (IID) of VP35 is critical for dsRNA binding and interferon inhibition. The wild-type VP35 IID structure revealed several conserved residues that are important for dsRNA binding and interferon antagonism. Here, the expression, purification and crystallization of recombinant Zaire Ebola VP35 IID mutants R312A, K319A/R322A and K339A in space groups P6(1)22, P2(1)2(1)2(1) and P2(1), respectively, are described. Diffraction data were collected using synchrotron sources at the Advanced Light Source and the Advanced Photon Source.
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Affiliation(s)
- Daisy W. Leung
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Dominika Borek
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8816, USA
| | - Mina Farahbakhsh
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
- Biochemistry Undergraduate Program, Iowa State University, Ames, IA 50011, USA
| | - Parameshwaran Ramanan
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
- Biochemistry Graduate Program, Iowa State University, Ames, IA 50011, USA
| | - Jay C. Nix
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Tianjiao Wang
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Kathleen C. Prins
- Department of Microbiology, Mount Sinai School of Medicine, New York, NY 10029, USA
| | - Zbyszek Otwinowski
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8816, USA
| | - Richard B. Honzatko
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Luke A. Helgeson
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
- Biochemistry Undergraduate Program, Iowa State University, Ames, IA 50011, USA
| | | | - Gaya K. Amarasinghe
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
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130
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Park H, Rangarajan ES, Sygusch J, Izard T. Dramatic improvement of crystal quality for low-temperature-grown rabbit muscle aldolase. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:595-600. [PMID: 20445268 PMCID: PMC2864701 DOI: 10.1107/s1744309110011875] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2009] [Accepted: 03/29/2010] [Indexed: 11/10/2022]
Abstract
Rabbit muscle aldolase (RMA) was crystallized in complex with the low-complexity domain (LC4) of sorting nexin 9. Monoclinic crystals were obtained at room temperature that displayed large mosaicity and poor X-ray diffraction. However, orthorhombic RMA-LC4 crystals grown at 277 K under similar conditions exhibited low mosaicity, allowing data collection to 2.2 A Bragg spacing and structure determination. It was concluded that the improvement of crystal quality as indicated by the higher resolution of the new RMA-LC4 complex crystals was a consequence of the introduction of new lattice contacts at lower temperature. The lattice contacts corresponded to an increased number of interactions between high-entropy side chains that mitigate the lattice strain incurred upon cryocooling and accompanying mosaic spread increases. The thermodynamically unfavorable immobilization of high-entropy side chains used in lattice formation was compensated by an entropic increase in the bulk-solvent content owing to the greater solvent content of the crystal lattice.
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Affiliation(s)
- HaJeung Park
- Cell Adhesion Laboratory, Department of Cancer Biology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Erumbi S. Rangarajan
- Cell Adhesion Laboratory, Department of Cancer Biology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Jurgen Sygusch
- Département de Biochimie, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Tina Izard
- Cell Adhesion Laboratory, Department of Cancer Biology, The Scripps Research Institute, Jupiter, FL 33458, USA
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131
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Derewenda ZS. Application of protein engineering to enhance crystallizability and improve crystal properties. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2010; 66:604-15. [PMID: 20445236 PMCID: PMC3089013 DOI: 10.1107/s090744491000644x] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2009] [Accepted: 02/18/2010] [Indexed: 01/05/2023]
Abstract
Until recently, protein crystallization has mostly been regarded as a stochastic event over which the investigator has little or no control. With the dramatic technological advances in synchrotron-radiation sources and detectors and the equally impressive progress in crystallographic software, including automated model building and validation, crystallization has increasingly become the rate-limiting step in X-ray diffraction studies of macromolecules. However, with the advent of recombinant methods it has also become possible to engineer target proteins and their complexes for higher propensity to form crystals with desirable X-ray diffraction qualities. As most proteins that are under investigation today are obtained by heterologous overexpression, these techniques hold the promise of becoming routine tools with the potential to transform classical crystallization screening into a more rational high-success-rate approach. This article presents an overview of protein-engineering methods designed to enhance crystallizability and discusses a number of examples of their successful application.
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Affiliation(s)
- Zygmunt S Derewenda
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA 22908-0736, USA.
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132
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Pan W, Vekilov PG, Lubchenko V. Origin of Anomalous Mesoscopic Phases in Protein Solutions. J Phys Chem B 2010; 114:7620-30. [DOI: 10.1021/jp100617w] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Weichun Pan
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas 77204-4004, and Department of Chemistry, University of Houston, Houston, Texas 77204-5003
| | - Peter G. Vekilov
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas 77204-4004, and Department of Chemistry, University of Houston, Houston, Texas 77204-5003
| | - Vassiliy Lubchenko
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas 77204-4004, and Department of Chemistry, University of Houston, Houston, Texas 77204-5003
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133
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Yasui N, Nogi T, Takagi J. Structural Basis for Specific Recognition of Reelin by Its Receptors. Structure 2010; 18:320-31. [DOI: 10.1016/j.str.2010.01.010] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2009] [Revised: 01/12/2010] [Accepted: 01/20/2010] [Indexed: 11/25/2022]
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134
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Fan Y, Joachimiak A. Enhanced crystal packing due to solvent reorganization through reductive methylation of lysine residues in oxidoreductase from Streptococcus pneumoniae. ACTA ACUST UNITED AC 2010; 11:101-11. [PMID: 20127187 DOI: 10.1007/s10969-010-9079-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2009] [Accepted: 01/12/2010] [Indexed: 10/19/2022]
Abstract
Protein crystallization is in part driven by the changes in the entropy of the system, but opinions differ as to whether the solute (protein) or solvent (water) molecules make more of a contribution to the overall entropic change. Methylation of lysine residues in proteins has been used to enhance protein crystallization. We investigated using molecular dynamics simulations with explicit solvent molecules, the behavior of several native proteins and their methylated counterparts chosen from an earlier large-scale study. Methylated lysines are capable of making a variety of interactions including H-bonds with protein residues and solvent. We demonstrate that methylation on the lysine slightly increases its side chain conformational entropy by about 3.5 J mol(-1) K(-1). Analysis of the radial and spatial distributions of the water molecules around the methylated lysine surface in oxidoreductase from Streptococcus pneumoniae revealed a larger sphere of water molecules with low entropy, as compared with solvent associated with unmethylated lysine. If methylated lysine were to make interactions at the protein-protein interface, the low-entropy water molecules associated with methylated lysines would be released, resulting in a gain of entropy. We show that this gain more than compensates for the loss of protein entropy. Therefore, we propose that lysine methylation favors the formation of crystals through solvent entropic gain.
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Affiliation(s)
- Yao Fan
- Biosciences Division, Midwest Center for Structural Genomics and Structural Biology Center, Argonne National Laboratory, 9700 S Cass Ave., Argonne, IL 60439, USA
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135
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Montange RK, Mondragón E, van Tyne D, Garst AD, Ceres P, Batey RT. Discrimination between closely related cellular metabolites by the SAM-I riboswitch. J Mol Biol 2009; 396:761-72. [PMID: 20006621 DOI: 10.1016/j.jmb.2009.12.007] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2009] [Revised: 11/30/2009] [Accepted: 12/06/2009] [Indexed: 12/17/2022]
Abstract
The SAM-I riboswitch is a cis-acting element of genetic control found in bacterial mRNAs that specifically binds S-adenosylmethionine (SAM). We previously determined the 2.9-A X-ray crystal structure of the effector-binding domain of this RNA element, revealing details of RNA-ligand recognition. To improve this structure, variations were made to the RNA sequence to alter lattice contacts, resulting in a 0.5-A improvement in crystallographic resolution and allowing for a more accurate refinement of the crystallographic model. The basis for SAM specificity was addressed by a structural analysis of the RNA complexed to S-adenosylhomocysteine (SAH) and sinefungin and by measuring the affinity of SAM and SAH for a series of mutants using isothermal titration calorimetry. These data illustrate the importance of two universally conserved base pairs in the RNA that form electrostatic interactions with the positively charged sulfonium group of SAM, thereby providing a basis for discrimination between SAM and SAH.
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Affiliation(s)
- Rebecca K Montange
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Campus Box 215, Boulder, CO 80309-0215, USA
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136
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Abstract
The application of structural genomics methods and approaches to proteins from organisms causing infectious diseases is making available the three dimensional structures of many proteins that are potential drug targets and laying the groundwork for structure aided drug discovery efforts. There are a number of structural genomics projects with a focus on pathogens that have been initiated worldwide. The Center for Structural Genomics of Infectious Diseases (CSGID) was recently established to apply state-of-the-art high throughput structural biology technologies to the characterization of proteins from the National Institute for Allergy and Infectious Diseases (NIAID) category A-C pathogens and organisms causing emerging, or re-emerging infectious diseases. The target selection process emphasizes potential biomedical benefits. Selected proteins include known drug targets and their homologs, essential enzymes, virulence factors and vaccine candidates. The Center also provides a structure determination service for the infectious disease scientific community. The ultimate goal is to generate a library of structures that are available to the scientific community and can serve as a starting point for further research and structure aided drug discovery for infectious diseases. To achieve this goal, the CSGID will determine protein crystal structures of 400 proteins and protein-ligand complexes using proven, rapid, highly integrated, and cost-effective methods for such determination, primarily by X-ray crystallography. High throughput crystallographic structure determination is greatly aided by frequent, convenient access to high-performance beamlines at third-generation synchrotron X-ray sources.
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Affiliation(s)
- W F Anderson
- Department of Molecular Pharmacology and Biological Chemistry, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
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137
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Grabowski M, Chruszcz M, Zimmerman MD, Kirillova O, Minor W. Benefits of structural genomics for drug discovery research. Infect Disord Drug Targets 2009; 9:459-74. [PMID: 19594422 PMCID: PMC2866842 DOI: 10.2174/187152609789105704] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2009] [Accepted: 06/15/2009] [Indexed: 11/22/2022]
Abstract
While three dimensional structures have long been used to search for new drug targets, only a fraction of new drugs coming to the market has been developed with the use of a structure-based drug discovery approach. However, the recent years have brought not only an avalanche of new macromolecular structures, but also significant advances in the protein structure determination methodology only now making their way into structure-based drug discovery. In this paper, we review recent developments resulting from the Structural Genomics (SG) programs, focusing on the methods and results most likely to improve our understanding of the molecular foundation of human diseases. SG programs have been around for almost a decade, and in that time, have contributed a significant part of the structural coverage of both the genomes of pathogens causing infectious diseases and structurally uncharacterized biological processes in general. Perhaps most importantly, SG programs have developed new methodology at all steps of the structure determination process, not only to determine new structures highly efficiently, but also to screen protein/ligand interactions. We describe the methodologies, experience and technologies developed by SG, which range from improvements to cloning protocols to improved procedures for crystallographic structure solution that may be applied in "traditional" structural biology laboratories particularly those performing drug discovery. We also discuss the conditions that must be met to convert the present high-throughput structure determination pipeline into a high-output structure-based drug discovery system.
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Affiliation(s)
- Marek Grabowski
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA
- Midwest Center for Structural Genomics
- Center for Structural Genomics of Infectious Diseases
| | - Maksymilian Chruszcz
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA
- Midwest Center for Structural Genomics
- Center for Structural Genomics of Infectious Diseases
| | - Matthew D. Zimmerman
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA
- Midwest Center for Structural Genomics
- Center for Structural Genomics of Infectious Diseases
| | - Olga Kirillova
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA
- Midwest Center for Structural Genomics
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA
- Midwest Center for Structural Genomics
- Center for Structural Genomics of Infectious Diseases
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138
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Wine Y, Cohen-Hadar N, Lamed R, Freeman A, Frolow F. Modification of protein crystal packing by systematic mutations of surface residues: implications on biotemplating and crystal porosity. Biotechnol Bioeng 2009; 104:444-57. [PMID: 19575413 DOI: 10.1002/bit.22427] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Bioinspired nano-scale biotemplating for the development of novel composite materials has recently culminated in several demonstrations of nano-structured hybrid materials. Protein crystals, routinely prepared for the elucidation of protein 3D structures by X-ray crystallography, present an ordered and highly accurate 3D array of protein molecules. Inherent to the 3D arrangement of the protein "building blocks" in the crystal, a complementary 3D array of interconnected cavities--voids array, exhibiting highly ordered porosity is formed. The porous arrays of protein crystal may serve as a nano-structured, accurate biotemplate by a "filling" process. These cavities arrays are shaped by the mode of protein packing throughout the crystallization process. Here we propose and demonstrate feasibility of targeting site specific mutations to modify protein's surface to affect protein crystal packing, enabling the generation of a series of protein crystal "biotemplates" all originating from same parent protein. The selection of these modification sites was based on in silico analysis of protein-protein interface contact areas in the parent crystal. The model protein selected for this study was the N-terminal type II cohesin from the cellulosomal scaffold in ScaB subunit of Acetivibrio cellulolyticus and mutations were focused on lysine residues involved in protein packing as prime target. The impact of systematically mutating these lysine residues on protein packing and its resulting interconnected cavities array were found to be most significant when surface lysine residues were substituted to tryptophan residues. Our results demonstrate the feasibility of using pre-designed site directed mutations for the generation of a series of protein crystal biotemplates from a "parent" protein.
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Affiliation(s)
- Yariv Wine
- Department of Molecular Microbiology and Biotechnology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
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139
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Bothnia dystrophy is caused by domino-like rearrangements in cellular retinaldehyde-binding protein mutant R234W. Proc Natl Acad Sci U S A 2009; 106:18545-50. [PMID: 19846785 DOI: 10.1073/pnas.0907454106] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cellular retinaldehyde-binding protein (CRALBP) is essential for mammalian vision by routing 11-cis-retinoids for the conversion of photobleached opsin molecules into photosensitive visual pigments. The arginine-to-tryptophan missense mutation in position 234 (R234W) in the human gene RLBP1 encoding CRALBP compromises visual pigment regeneration and is associated with Bothnia dystrophy. Here we report the crystal structures of both wild-type human CRALBP and of its mutant R234W as binary complexes complemented with the endogenous ligand 11-cis-retinal, at 3.0 and 1.7 A resolution, respectively. Our structural model of wild-type CRALBP locates R234 to a positively charged cleft at a distance of 15 A from the hydrophobic core sequestering 11-cis-retinal. The R234W structural model reveals burial of W234 and loss of dianion-binding interactions within the cleft with physiological implications for membrane docking. The burial of W234 is accompanied by a cascade of side-chain flips that effect the intrusion of the side-chain of I238 into the ligand-binding cavity. As consequence of the intrusion, R234W displays 5-fold increased resistance to light-induced photoisomerization relative to wild-type CRALBP, indicating tighter binding to 11-cis-retinal. Overall, our results reveal an unanticipated domino-like structural transition causing Bothnia-type retinal dystrophy by the impaired release of 11-cis-retinal from R234W.
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140
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Derewenda U, Boczek T, Gorres KL, Yu M, Hung LW, Cooper D, Joachimiak A, Raines RT, Derewenda ZS. Structure and function of Bacillus subtilis YphP, a prokaryotic disulfide isomerase with a CXC catalytic motif . Biochemistry 2009; 48:8664-71. [PMID: 19653655 PMCID: PMC2739605 DOI: 10.1021/bi900437z] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2009] [Revised: 08/01/2009] [Indexed: 11/29/2022]
Abstract
The DUF1094 family contains over 100 bacterial proteins, all containing a conserved CXC motif, with unknown function. We solved the crystal structure of the Bacillus subtilis representative, the product of the yphP gene. The protein shows remarkable structural similarity to thioredoxins, with a canonical alphabetaalphabetaalphabetabetaalpha topology, despite low amino acid sequence identity to thioredoxin. The CXC motif is found in the loop immediately downstream of the first beta-strand, in a location equivalent to the CXXC motif of thioredoxins, with the first Cys occupying a position equivalent to the first Cys in canonical thioredoxin. The experimentally determined reduction potential of YphP is E degrees' = -130 mV, significantly higher than that of thioredoxin and consistent with disulfide isomerase activity. Functional assays confirmed that the protein displays a level of isomerase activity that might be biologically significant. We propose a mechanism by which the members of this family catalyze isomerization using the CXC catalytic site.
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Affiliation(s)
- Urszula Derewenda
- Department of Molecular Physiology and Biological Physics and the ISFI PSI2 Center, University of Virginia School of Medicine, Charlottesville, Virginia 22908-0736
| | - Tomasz Boczek
- Department of Molecular Physiology and Biological Physics and the ISFI PSI2 Center, University of Virginia School of Medicine, Charlottesville, Virginia 22908-0736
| | | | - Minmin Yu
- Department of Molecular Physiology and Biological Physics and the ISFI PSI2 Center, University of Virginia School of Medicine, Charlottesville, Virginia 22908-0736
- Departments of Biochemistry
- Chemistry
- University of Wisconsin−Madison, Madison, Wisconsin 53706
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, MS4R0230, Berkeley, California 94720
- Physics Division, MS D454, Los Alamos National Laboratory, Los Alamos, New Mexico 87545
- Biosciences Division, Midwest Center for Structural Genomics and Structural Biology Center, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439
| | - Li-wei Hung
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, MS4R0230, Berkeley, California 94720
- Physics Division, MS D454, Los Alamos National Laboratory, Los Alamos, New Mexico 87545
| | - David Cooper
- Department of Molecular Physiology and Biological Physics and the ISFI PSI2 Center, University of Virginia School of Medicine, Charlottesville, Virginia 22908-0736
| | - Andrzej Joachimiak
- Biosciences Division, Midwest Center for Structural Genomics and Structural Biology Center, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439
| | | | - Zygmunt S. Derewenda
- Department of Molecular Physiology and Biological Physics and the ISFI PSI2 Center, University of Virginia School of Medicine, Charlottesville, Virginia 22908-0736
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141
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Cerutti DS, Le Trong I, Stenkamp RE, Lybrand TP. Dynamics of the streptavidin-biotin complex in solution and in its crystal lattice: distinct behavior revealed by molecular simulations. J Phys Chem B 2009; 113:6971-85. [PMID: 19374419 DOI: 10.1021/jp9010372] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a 250 ns simulation of the wild-type, biotin-liganded streptavidin tetramer in the solution phase and compare the trajectory to two previously published simulations of the protein in its crystal lattice. By performing both types of simulations, we are able to interpret the protein's behavior in solution in the context of its X-ray structure. We find that the rate of conformational sampling is increased in solution over the lattice environment, although the relevant conformational space in solution is also much larger, as indicated by overall fluctuations in the positions of backbone atoms. We also compare the distributions of chi1 angles sampled by side chains exposed to solvent in the lattice and in the solution phase, obtaining overall good agreement between the distributions obtained in our most rigorous lattice simulation and the crystallographic chi1 angles. We observe changes in the chi1 distributions in the solution phase, and note an apparent progression of the distributions as the environment changes from a tightly packed lattice filled with crystallization media to a bath of pure water. Finally, we examine the interaction of biotin and streptavidin in each simulation, uncovering a possible alternate conformation of the biotin carboxylate tail. We also note that a hydrogen bond observed to break transiently in previous solution-phase simulations is predominantly broken in this much longer solution-phase trajectory; in the lattice simulations, the lattice environment appears to help maintain the hydrogen bond, but more sampling will be needed to confirm whether the simulation model truly gives good agreement with the X-ray data in the lattice simulations. We expect that pairing solution-phase biomolecular simulations with crystal lattice simulations will help to validate simulation models and improve the interpretation of experimentally determined structures.
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Affiliation(s)
- David S Cerutti
- Center for Structural Biology and Department of Chemistry, Vanderbilt University, 5142 Medical Research Building III, 465 21st Avenue South, Nashville, Tennessee 37232-8725, USA
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142
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Cieślik M, Derewenda ZS. The role of entropy and polarity in intermolecular contacts in protein crystals. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2009; 65:500-9. [PMID: 19390155 PMCID: PMC2672819 DOI: 10.1107/s0907444909009500] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2008] [Accepted: 03/14/2009] [Indexed: 11/10/2022]
Abstract
The integrity and X-ray diffraction quality of protein crystals depend on the three-dimensional order of relatively weak but reproducible intermolecular contacts. Despite their importance, relatively little attention has been paid to the chemical and physical nature of these contacts, which are often regarded as stochastic and thus not different from randomly selected protein surface patches. Here, logistic regression was used to analyze crystal contacts in a database of 821 unambiguously monomeric proteins with structures determined to 2.5 A resolution or better. It is shown that the propensity of a surface residue for incorporation into a crystal contact is not a linear function of its solvent-accessible surface area and that amino acids with low exposed surfaces, which are typically small and hydrophobic, have been underestimated with respect to their contact-forming potential by earlier area-based calculations. For any given solvent-exposed surface, small and hydrophobic residues are more likely to be involved in crystal contacts than large and charged amino acids. Side-chain entropy is the single physicochemical property that is most negatively correlated with the involvement of amino acids in crystal contacts. It is also shown that crystal contacts with larger buried surfaces containing eight or more amino acids have cores that are depleted of polar amino acids.
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Affiliation(s)
- Marcin Cieślik
- Department of Molecular Physiology and Biological Physics and the PSI2 Integrated Center for Structure–Function Innovation, University of Virginia, Charlottesville, Virginia 22908, USA
| | - Zygmunt S. Derewenda
- Department of Molecular Physiology and Biological Physics and the PSI2 Integrated Center for Structure–Function Innovation, University of Virginia, Charlottesville, Virginia 22908, USA
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143
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Price WN, Chen Y, Handelman SK, Neely H, Manor P, Karlin R, Nair R, Liu J, Baran M, Everett J, Tong SN, Forouhar F, Swaminathan SS, Acton T, Xiao R, Luft JR, Lauricella A, DeTitta GT, Rost B, Montelione GT, Hunt JF. Understanding the physical properties that control protein crystallization by analysis of large-scale experimental data. Nat Biotechnol 2009; 27:51-7. [PMID: 19079241 DOI: 10.1038/nbt.1514] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Crystallization is the most serious bottleneck in high-throughput protein-structure determination by diffraction methods. We have used data mining of the large-scale experimental results of the Northeast Structural Genomics Consortium and experimental folding studies to characterize the biophysical properties that control protein crystallization. This analysis leads to the conclusion that crystallization propensity depends primarily on the prevalence of well-ordered surface epitopes capable of mediating interprotein interactions and is not strongly influenced by overall thermodynamic stability. We identify specific sequence features that correlate with crystallization propensity and that can be used to estimate the crystallization probability of a given construct. Analyses of entire predicted proteomes demonstrate substantial differences in the amino acid-sequence properties of human versus eubacterial proteins, which likely reflect differences in biophysical properties, including crystallization propensity. Our thermodynamic measurements do not generally support previous claims regarding correlations between sequence properties and protein stability.
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Affiliation(s)
- W Nicholson Price
- Northeast Structural Genomics Consortium, Columbia University, New York, New York 10027, USA
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144
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Vetting MW, Hegde SS, Blanchard JS. Crystallization of a pentapeptide-repeat protein by reductive cyclic pentylation of free amines with glutaraldehyde. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2009; 65:462-9. [PMID: 19390151 DOI: 10.1107/s0907444909008324] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2009] [Accepted: 03/06/2009] [Indexed: 11/10/2022]
Abstract
The pentapeptide-repeat protein EfsQnr from Enterococcus faecalis protects DNA gyrase from inhibition by fluoroquinolones. EfsQnr was cloned and purified to homogeneity, but failed to produce diffraction-quality crystals in initial crystallization screens. Treatment of EfsQnr with glutaraldehyde and the strong reducing agent borane-dimethylamine resulted in a derivatized protein which produced crystals that diffracted to 1.6 A resolution; their structure was subsequently determined by single-wavelength anomalous dispersion. Analysis of the derivatized protein using Fourier transform ion cyclotron resonance mass spectrometry indicated a mass increase of 68 Da per free amino group. Electron-density maps about a limited number of structurally ordered lysines indicated that the modification was a cyclic pentylation of free amines, producing piperidine groups.
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Affiliation(s)
- Matthew W Vetting
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA.
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145
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Zheng M, Cooper DR, Grossoehme NE, Yu M, Hung LW, Cieslik M, Derewenda U, Lesley SA, Wilson IA, Giedroc DP, Derewenda ZS. Structure of Thermotoga maritima TM0439: implications for the mechanism of bacterial GntR transcription regulators with Zn2+-binding FCD domains. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2009; 65:356-65. [PMID: 19307717 PMCID: PMC2659884 DOI: 10.1107/s0907444909004727] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2008] [Accepted: 02/09/2009] [Indexed: 11/10/2022]
Abstract
The GntR superfamily of dimeric transcription factors, with more than 6200 members encoded in bacterial genomes, are characterized by N-terminal winged-helix DNA-binding domains and diverse C-terminal regulatory domains which provide a basis for the classification of the constituent families. The largest of these families, FadR, contains nearly 3000 proteins with all-alpha-helical regulatory domains classified into two related Pfam families: FadR_C and FCD. Only two crystal structures of FadR-family members, those of Escherichia coli FadR protein and LldR from Corynebacterium glutamicum, have been described to date in the literature. Here, the crystal structure of TM0439, a GntR regulator with an FCD domain found in the Thermotoga maritima genome, is described. The FCD domain is similar to that of the LldR regulator and contains a buried metal-binding site. Using atomic absorption spectroscopy and Trp fluorescence, it is shown that the recombinant protein contains bound Ni(2+) ions but that it is able to bind Zn(2+) with K(d) < 70 nM. It is concluded that Zn(2+) is the likely physiological metal and that it may perform either structural or regulatory roles or both. Finally, the TM0439 structure is compared with two other FadR-family structures recently deposited by structural genomics consortia. The results call for a revision in the classification of the FadR family of transcription factors.
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Affiliation(s)
- Meiying Zheng
- Integrated Center for Structure–Function Innovation, Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908-0736, USA
| | - David R. Cooper
- Integrated Center for Structure–Function Innovation, Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908-0736, USA
| | | | - Minmin Yu
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, MS4R0230, Berkeley, CA 94720, USA
| | - Li-Wei Hung
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, MS4R0230, Berkeley, CA 94720, USA
- Physics Division, MS D454, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Marcin Cieslik
- Integrated Center for Structure–Function Innovation, Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908-0736, USA
| | - Urszula Derewenda
- Integrated Center for Structure–Function Innovation, Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908-0736, USA
| | - Scott A. Lesley
- The Scripps Research Institute, North Torrey Pines Road, La Jolla, CA 92037, USA
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, CA 92121, USA
| | - Ian A. Wilson
- The Scripps Research Institute, North Torrey Pines Road, La Jolla, CA 92037, USA
| | - David P. Giedroc
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, USA
| | - Zygmunt S. Derewenda
- Integrated Center for Structure–Function Innovation, Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908-0736, USA
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146
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Argiriadi MA, Sousa S, Banach D, Marcotte D, Xiang T, Tomlinson MJ, Demers M, Harris C, Kwak S, Hardman J, Pietras M, Quinn L, DiMauro J, Ni B, Mankovich J, Borhani DW, Talanian RV, Sadhukhan R. Rational mutagenesis to support structure-based drug design: MAPKAP kinase 2 as a case study. BMC STRUCTURAL BIOLOGY 2009; 9:16. [PMID: 19296855 PMCID: PMC2678131 DOI: 10.1186/1472-6807-9-16] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2008] [Accepted: 03/18/2009] [Indexed: 01/07/2023]
Abstract
BACKGROUND Structure-based drug design (SBDD) can provide valuable guidance to drug discovery programs. Robust construct design and expression, protein purification and characterization, protein crystallization, and high-resolution diffraction are all needed for rapid, iterative inhibitor design. We describe here robust methods to support SBDD on an oral anti-cytokine drug target, human MAPKAP kinase 2 (MK2). Our goal was to obtain useful diffraction data with a large number of chemically diverse lead compounds. Although MK2 structures and structural methods have been reported previously, reproducibility was low and improved methods were needed. RESULTS Our construct design strategy had four tactics: N- and C-terminal variations; entropy-reducing surface mutations; activation loop deletions; and pseudoactivation mutations. Generic, high-throughput methods for cloning and expression were coupled with automated liquid dispensing for the rapid testing of crystallization conditions with minimal sample requirements. Initial results led to development of a novel, customized robotic crystallization screen that yielded MK2/inhibitor complex crystals under many conditions in seven crystal forms. In all, 44 MK2 constructs were generated, ~500 crystals were tested for diffraction, and ~30 structures were determined, delivering high-impact structural data to support our MK2 drug design effort. CONCLUSION Key lessons included setting reasonable criteria for construct performance and prioritization, a willingness to design and use customized crystallization screens, and, crucially, initiation of high-throughput construct exploration very early in the drug discovery process.
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Affiliation(s)
- Maria A Argiriadi
- Department of Biochemistry, Abbott Laboratories, Worcester, MA USA,Department of Molecular Pharmacology, Abbott Laboratories, Worcester, MA USA
| | - Silvino Sousa
- Department of Biochemistry, Abbott Laboratories, Worcester, MA USA,Department of Molecular Cell Biology, Abbott Laboratories, Worcester, MA USA
| | - David Banach
- Department of Biochemistry, Abbott Laboratories, Worcester, MA USA,Department of Molecular Pharmacology, Abbott Laboratories, Worcester, MA USA
| | - Douglas Marcotte
- Department of Biochemistry, Abbott Laboratories, Worcester, MA USA,Present address : Department of Physical Biochemistry, Biogen Idec, Cambridge, MA USA
| | - Tao Xiang
- Department of Biochemistry, Abbott Laboratories, Worcester, MA USA,Present address : Department of Process Sciences, Abbott Laboratories, Worcester, MA USA
| | - Medha J Tomlinson
- Department of Biochemistry, Abbott Laboratories, Worcester, MA USA,Department of Molecular Cell Biology, Abbott Laboratories, Worcester, MA USA
| | - Megan Demers
- Department of Biochemistry, Abbott Laboratories, Worcester, MA USA,Present address : 119 North Swain Street, Raleigh, NC 27601, USA
| | - Christopher Harris
- Department of Biochemistry, Abbott Laboratories, Worcester, MA USA,Department of Molecular Pharmacology, Abbott Laboratories, Worcester, MA USA
| | - Silvia Kwak
- Department of Biochemistry, Abbott Laboratories, Worcester, MA USA,Department of Molecular Pharmacology, Abbott Laboratories, Worcester, MA USA
| | - Jennifer Hardman
- Department of Biochemistry, Abbott Laboratories, Worcester, MA USA,Department of Molecular Pharmacology, Abbott Laboratories, Worcester, MA USA
| | - Margaret Pietras
- Department of Biochemistry, Abbott Laboratories, Worcester, MA USA,Department of Molecular Cell Biology, Abbott Laboratories, Worcester, MA USA
| | - Lisa Quinn
- Department of Biochemistry, Abbott Laboratories, Worcester, MA USA,Present address : Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA USA
| | - Jennifer DiMauro
- Department of Biochemistry, Abbott Laboratories, Worcester, MA USA,Present address : Department of Process Sciences, Abbott Laboratories, Worcester, MA USA
| | - Baofu Ni
- Department of Biochemistry, Abbott Laboratories, Worcester, MA USA,Department of Molecular Cell Biology, Abbott Laboratories, Worcester, MA USA
| | - John Mankovich
- Department of Biochemistry, Abbott Laboratories, Worcester, MA USA,Present address : Department of Biologics, Abbott Laboratories, Worcester, MA USA
| | - David W Borhani
- Department of Biochemistry, Abbott Laboratories, Worcester, MA USA,Present address : D. E. Shaw Research, New York, NY USA
| | - Robert V Talanian
- Department of Biochemistry, Abbott Laboratories, Worcester, MA USA,Department of Molecular Pharmacology, Abbott Laboratories, Worcester, MA USA
| | - Ramkrishna Sadhukhan
- Department of Biochemistry, Abbott Laboratories, Worcester, MA USA,Department of Molecular Cell Biology, Abbott Laboratories, Worcester, MA USA
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147
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Kovalevskiy OV, Antson AA, Solonin AS. Truncation of the disordered loop located within the C-terminal domain of the transcriptional regulator HlyIIR remodels its structure. Mol Biol 2009. [DOI: 10.1134/s0026893309010166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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148
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Chruszcz M, Zimmerman MD, Wang S, Koclega KD, Zheng H, Evdokimova E, Kudritska M, Cymborowski M, Savchenko A, Edwards A, Minor W. Function-biased choice of additives for optimization of protein crystallization - the case of the putative thioesterase PA5185 from Pseudomonas aeruginosa PAO1. CRYSTAL GROWTH & DESIGN 2008; 8:4054-4061. [PMID: 19898606 PMCID: PMC2700756 DOI: 10.1021/cg800430f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The crystal structure of PA5185, a putative thioesterase from Pseudomonas aeruginosa strain PAO1, was solved using multi-wavelength anomalous diffraction to 2.4 Å. Analysis of the structure and information about the putative function of the protein were used to optimize crystallization conditions. The crystal growth was optimized by applying additives with chemical similarity to a fragment of a putative PA5185 substrate (CoA or its derivative). Using new crystallization conditions containing this function-biased set of additives, several new crystal forms were produced and structures of three of them (in three different space groups) were determined. One of the new crystal forms had an improved resolution limit of 1.9 Å, and another displayed an alternative conformation of the highly-conserved loop containing Asn26, which could play a physiological role. Surprisingly, none of the additives were ordered in the crystal structures. Application of function-biased additives could be used as a standard optimization protocol for producing improved diffraction, or new crystal forms, which may lead to better understanding of the biological functions of proteins.
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Affiliation(s)
- Maksymilian Chruszcz
- Department of Molecular Biology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, USA
- Midwest Center for Structural Genomics
| | - Matthew D. Zimmerman
- Department of Molecular Biology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, USA
- Midwest Center for Structural Genomics
| | - Shuren Wang
- Department of Molecular Biology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, USA
- Midwest Center for Structural Genomics
| | - Katarzyna D. Koclega
- Department of Molecular Biology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, USA
- Midwest Center for Structural Genomics
| | - Heping Zheng
- Department of Molecular Biology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, USA
- Midwest Center for Structural Genomics
| | - Elena Evdokimova
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario M5G 1L6, Canada
- Midwest Center for Structural Genomics
| | - Marina Kudritska
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario M5G 1L6, Canada
- Midwest Center for Structural Genomics
| | - Marcin Cymborowski
- Department of Molecular Biology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, USA
- Midwest Center for Structural Genomics
| | - Alexei Savchenko
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario M5G 1L6, Canada
- Midwest Center for Structural Genomics
| | - Aled Edwards
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario M5G 1L6, Canada
- Midwest Center for Structural Genomics
| | - Wladek Minor
- Department of Molecular Biology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, USA
- Midwest Center for Structural Genomics
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Sennhauser G, Grütter MG. Chaperone-assisted crystallography with DARPins. Structure 2008; 16:1443-53. [PMID: 18940601 DOI: 10.1016/j.str.2008.08.010] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2008] [Revised: 08/14/2008] [Accepted: 08/18/2008] [Indexed: 11/29/2022]
Abstract
The structure of proteins that are difficult to crystallize can often be solved by forming a noncovalent complex with a helper protein--a crystallization "chaperone." Although several such applications have been described to date, their handling usually is still very laborious. A valuable addition to the present repertoire of binding proteins is the recently developed designed ankyrin repeat protein (DARPin) technology. DARPins are built based on the natural ankyrin repeat protein fold with randomized surface residue positions allowing specific binding to virtually any target protein. The broad potential of these binding proteins for X-ray crystallography is illustrated by five cocrystal structures that have been determined recently comprising target proteins from distinct families, namely a sugar binding protein, two kinases, a caspase, and a membrane protein. This article reviews the opportunities of this technology for structural biology and the structural aspects of the DARPin-protein complexes.
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Affiliation(s)
- Gaby Sennhauser
- Department of Biochemistry, University of Zürich, CH-8057 Zürich, Switzerland
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150
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Senda M, Muto S, Horikoshi M, Senda T. Effect of leucine-to-methionine substitutions on the diffraction quality of histone chaperone SET/TAF-Ibeta/INHAT crystals. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:960-5. [PMID: 18931446 PMCID: PMC2564889 DOI: 10.1107/s1744309108028704] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2008] [Accepted: 09/08/2008] [Indexed: 11/11/2022]
Abstract
One of the most frequent problems in crystallization is poor quality of the crystals. In order to overcome this obstacle several methods have been utilized, including amino-acid substitutions of the target protein. Here, an example is presented of crystal-quality improvement by leucine-to-methionine substitutions. A variant protein with three amino-acid substitutions enabled improvement of the crystal quality of the histone chaperone SET/TAF-Ibeta/INHAT when combined with optimization of the cryoconditions. This procedure improved the resolution of the SET/TAF-Ibeta/INHAT crystals from around 5.5 to 2.3 A without changing the crystallization conditions.
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Affiliation(s)
- Miki Senda
- Structure Guided Drug Development Project, Research and Development Department, Japan Biological Informatics Consortium (JBIC), 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Shinsuke Muto
- Laboratory of Developmental Biology, Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
- Horikoshi Gene Selector Project, Exploratory Research for Advanced Technology (ERATO), Japan Science and Technology Corporation (JST), 5-9-6 Tokodai, Tsukuba, Ibaraki 300-2635, Japan
| | - Masami Horikoshi
- Laboratory of Developmental Biology, Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
- Horikoshi Gene Selector Project, Exploratory Research for Advanced Technology (ERATO), Japan Science and Technology Corporation (JST), 5-9-6 Tokodai, Tsukuba, Ibaraki 300-2635, Japan
| | - Toshiya Senda
- Biomedicinal Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan
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