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1.  Impact of linker strain and flexibility in the design of a fragment-based inhibitor 
Nature chemical biology  2009;5(6):407-413.
The linking together of molecular fragments that bind to adjacent sites on an enzyme can lead to high affinity inhibitors. Ideally, this strategy would employ linkers that do not perturb the optimal binding geometries of the fragments and do not have excessive conformational flexibility that would increase the entropic penalty of binding. In reality, these aims are seldom realized due to limitations in linker chemistry. Here we systematically explore the energetic and structural effects of rigid and flexible linkers on the binding of a fragment-based inhibitor of human uracil DNA glycosylase. Analysis of the free energies of binding in combination with co-crystal structures shows that the flexibility and strain of a given linker can have a significant impact on binding affinity even when the binding fragments are optimally positioned. Such effects are not apparent from inspection of structures and underscore the importance of linker optimization in fragment-based drug discovery efforts.
doi:10.1038/nchembio.163
PMCID: PMC3178264  PMID: 19396178
2.  High regularity of Z-DNA revealed by ultra high-resolution crystal structure at 0.55 ņ 
Nucleic Acids Research  2011;39(14):6238-6248.
The crystal structure of a Z-DNA hexamer duplex d(CGCGCG)2 determined at ultra high resolution of 0.55 Å and refined without restraints, displays a high degree of regularity and rigidity in its stereochemistry, in contrast to the more flexible B-DNA duplexes. The estimations of standard uncertainties of all individually refined parameters, obtained by full-matrix least-squares optimization, are comparable with values that are typical for small-molecule crystallography. The Z-DNA model generated with ultra high-resolution diffraction data can be used to revise the stereochemical restraints applied in lower resolution refinements. Detailed comparisons of the stereochemical library values with the present accurate Z-DNA parameters, shows in general a good agreement, but also reveals significant discrepancies in the description of guanine-sugar valence angles and in the geometry of the phosphate groups.
doi:10.1093/nar/gkr202
PMCID: PMC3152349  PMID: 21459852
3.  The linkage between ribosomal crystallography, metal ions, heteropolytungstates and functional flexibility 
Journal of molecular structure  2008;890(1-3):289-294.
Crystallography of ribosomes, the universal cell nucleoprotein assemblies facilitating the translation of the genetic-code into proteins, met with severe problems owing to their large size, complex structure, inherent flexibility and high conformational variability. For the case of the small ribosomal subunit, which caused extreme difficulties, post crystallization treatment by minute amounts of a heteropolytungstate cluster allowed structure determination at atomic resolution. This cluster played a dual role in ribosomal crystallography: providing anomalous phasing power and dramatically increased the resolution, by stabilization of a selected functional conformation. Thus, four out of the fourteen clusters that bind to each of the crystallized small subunits are attached to a specific ribosomal protein in a fashion that may control a significant component of the subunit internal flexibility, by “gluing” symmetrical related subunits. Here we highlight basic issues in the relationship between metal ions and macromolecules and present common traits controlling in the interactions between polymetalates and various macromolecules, which may be extended towards the exploitation of polymetalates for therapeutical treatment.
doi:10.1016/j.molstruc.2008.03.043
PMCID: PMC2757297  PMID: 19915655
Ribosome; ribosomal functional flexibility; heteropolytungstates; crystal order; protein S2
4.  The structure at 2.4 Å resolution of the protein from gene locus At3g21360, a putative FeII/2-oxo­glutarate-dependent enzyme from Arabidopsis thaliana  
The crystal structure of the 37.2 kDa At3g21360 gene product from A. thaliana was determined at 2.4 Å resolution. The structure establishes that this protein binds a metal ion and is a member of a clavaminate synthase-like superfamily in A. thaliana.
The crystal structure of the gene product of At3g21360 from Arabidopsis thaliana was determined by the single-wavelength anomalous dispersion method and refined to an R factor of 19.3% (R free = 24.1%) at 2.4 Å resolution. The crystal structure includes two monomers in the asymmetric unit that differ in the conformation of a flexible domain that spans residues 178–230. The crystal structure confirmed that At3g21360 encodes a protein belonging to the clavaminate synthase-like superfamily of iron(II) and 2-oxoglutarate-dependent enzymes. The metal-binding site was defined and is similar to the iron(II) binding sites found in other members of the superfamily.
doi:10.1107/S1744309105011565
PMCID: PMC1952295  PMID: 16511070
At3g21360
5.  Direct detection of structurally resolved dynamics in a multi-conformation receptor-ligand complex 
Structure-based drug design relies on static protein structures despite significant evidence for the need to include protein dynamics as a serious consideration. In practice, dynamic motions are neglected because they are not understood well enough to model – a situation resulting from a lack of explicit experimental examples of dynamic receptor-ligand complexes. Here, we report high-resolution details of pronounced ~1 ms timescale motions of a receptor-small molecule complex using a combination of NMR and X-ray crystallography. Large conformational dynamics in Escherichia coli dihydrofolate reductase are driven by internal switching motions of the drug-like, nanomolar-affinity inhibitor. Carr-Purcell-Meiboom-Gill relaxation dispersion experiments and NOEs revealed the crystal structure to contain critical elements of the high energy protein-ligand conformation. The availability of accurate, structurally resolved dynamics in a protein-ligand complex should serve as a valuable benchmark for modeling dynamics in other receptor-ligand complexes and prediction of binding affinities.
doi:10.1021/ja2005253
PMCID: PMC3119194  PMID: 21469679
6.  The structure of Plasmodium vivax phosphatidylethanolamine-binding protein suggests a functional motif containing a left-handed helix 
The crystal structure of a phosphatidylethanolamine-binding protein from P. vivax, a homolog of Raf-kinase inhibitor protein (RKIP), has been solved to a resolution of 1.3 Å. The inferred interaction surface near the anion-binding site is found to include a distinctive left-handed α-helix.
The structure of a putative Raf kinase inhibitor protein (RKIP) homolog from the eukaryotic parasite Plasmodium vivax has been studied to a resolution of 1.3 Å using multiple-wavelength anomalous diffraction at the Se K edge. This protozoan protein is topologically similar to previously studied members of the phosphatidylethanolamine-binding protein (PEBP) sequence family, but exhibits a distinctive left-handed α-helical region at one side of the canonical phospholipid-binding site. Re-examination of previously determined PEBP structures suggests that the P. vivax protein and yeast carboxypeptidase Y inhibitor may represent a structurally distinct subfamily of the diverse PEBP-sequence family.
doi:10.1107/S1744309107007580
PMCID: PMC2330187  PMID: 17329808
phosphatidylethanolamine-binding protein; Plasmodium vivax
7.  Crystal structure of a transcriptional regulator TM1030 from Thermotoga maritima solved by an unusual MAD experiment 
Journal of structural biology  2007;159(3):424-432.
The crystal structure of a putative transcriptional regulator protein TM1030 from Thermotoga maritima, a hyperthermophilic bacterium, was determined by an unusual multi-wavelength anomalous dispersion method at 2.0 Å resolution., in which data from two different crystals and two different beamlines were used. The protein belongs to the tetracycline repressor TetR superfamily. The three-dimensional structure of TM1030 is similar to the structures of proteins that function as multidrug-binding transcriptional repressors, and contains a large solvent-exposed pocket similar to the drug-binding pockets present in those repressors. The asymmetric unit in the crystal structure contains a single protein chain and the two-fold symmetry of the dimer is adopted by the crystal symmetry. The structure described in this paper is an apo-form of TM1030. Although it is known that the protein is significantly overexpressed during heat shock, its detailed function cannot be yet explained.
doi:10.1016/j.jsb.2007.04.012
PMCID: PMC2093942  PMID: 17588774
Transcriptional regulator; TM1030; DNA-binding; MAD
8.  Crystallization and preliminary crystallographic characterization of the origin-binding domain of the bacteriophage λ O replication initiator 
Crystallization and preliminary diffraction data of the N-terminal 19–139 fragment of the origin-binding domain of bacteriophage λ O replication initiator are reported.
The bacteriophage λ O protein binds to the λ replication origin (oriλ) and serves as the primary replication initiator for the viral genome. The binding energy derived from the binding of O to oriλ is thought to help drive DNA opening to facilitate initiation of DNA replication. Detailed understanding of this process is severely limited by the lack of high-resolution structures of O protein or of any lambdoid phage-encoded paralogs either with or without DNA. The production of crystals of the origin-binding domain of λ O that diffract to 2.5 Å is reported. Anomalous dispersion methods will be used to solve this structure.
doi:10.1107/S1744309107022762
PMCID: PMC2335069  PMID: 17554183
bacteriophage λ; O replication initiator; origin-binding domain
9.  Rigidification of a Flexible Protease Inhibitor Variant Upon Binding to Trypsin 
Journal of molecular biology  2006;366(1):230-243.
The Tyr35→Gly replacement in bovine pancreatic trypsin inhibitor (BPTI) has previously been shown to dramatically enhance the flexibility of the trypsin-binding region of the free inhibitor and to destabilize the interaction with the protease by about 3 kcal/mol. The effects of this replacement on the enzyme-inhibitor interaction were further studied here by x-ray crystallography and isothermal titration calorimetry. The co-crystal structure of Y35G BPTI bound to trypsin was determined using 1.65 Å resolution x-ray diffraction data collected from cryopreserved crystals, and a new structure of the complex with wild-type BPTI under the same conditions was determined using 1.62 Å data. These structures reveal that, in contrast to the free protein, Y35G BPTI adopts a conformation nearly identical to that of the wild-type protein, with a water-filled cavity in place of the missing Tyr side chain. The crystallographic temperature factors for the two complexes indicate that the mutant inhibitor is nearly as rigid as the wild-type protein when bound to trypsin. Calorimetric measurements show that the change in enthalpy upon dissociation of the complex is 2.5 kcal/mol less favorable for the complex containing Y35G BPTI than for the complex with the wild-type inhibitor. Thus, the destabilization of the complex resulting from the Y35G replacement is due to a more favorable change in entropy upon dissociation. The heat capacity changes for dissociation of the mutant and wild-type complexes were very similar, suggesting that the entropic effects probably do not arise from solvation effects, but are more likely due to an increase in protein conformational entropy upon dissociation of the mutant inhibitor. These results define the biophysical role of a highly conserved core residue located outside of a protein-binding interface, demonstrating that Tyr35 has little impact on the trypsin-bound BPTI structure and acts primarily to define the structure of the free protein so as to maximize binding affinity.
doi:10.1016/j.jmb.2006.11.003
PMCID: PMC1847787  PMID: 17157870
bovine pancreatic trypsin inhibitor; x-ray crystallography; isothermal titration calorimetry; protein flexibility; binding entropy
10.  Conformational Variability of Benzamidinium Based Inhibitors 
Determining the structure of a small molecule bound to a biological receptor (e.g., a protein implicated in a disease state) is a necessary step in structure-based drug design. The preferred conformation of a small molecule can change when bound to a protein, and a detailed knowledge of the preferred conformation(s) of a bound ligand can help in optimizing the affinity of a molecule for its receptor. However, the quality of a protein/ligand complex determined using X-ray crystallography is dependent on the size of the protein, crystal quality and the realized resolution. The energy restraints used in traditional X-ray refinement procedures typically use “reduced” (i.e., neglect of electrostatics and dispersion interactions) Engh and Huber force field models that, while quite suitable for modeling proteins often are less suitable for small molecule structures due to a lack of validated parameters. Through the use of ab initio QM/MM based X-ray refinement procedures this shortcoming can be overcome especially in the active site or binding site of a small molecule inhibitor. Herein, we demonstrate that ab initio QM/MM refinement of an inhibitor/protein complex provides insights into the binding of small molecules beyond what is available using more traditional refinement protocols. In particular, QM/MM refinement studies of benzamidinium derivatives show variable conformational preferences depending on the refinement protocol used and the nature of the active site region.
doi:10.1021/ja9010833
PMCID: PMC2730048  PMID: 19435349
11.  Benzimidazole inhibitors of the protein kinase CHK2: Clarification of the binding mode by flexible side chain docking and protein–ligand crystallography 
Bioorganic & Medicinal Chemistry  2012;20(22):6630-6639.
Graphical abstract
Unconstrained rigid docking, flexible side chain docking and protein crystal structure determinations reveal a water-mediated hinge binding mode for a series of benzimidazole ligands of the protein kinase CHK2. This binding mode is different from those previously postulated in the literature and may provide a useful approach to selective small molecule inhibitor design.
Two closely related binding modes have previously been proposed for the ATP-competitive benzimidazole class of checkpoint kinase 2 (CHK2) inhibitors; however, neither binding mode is entirely consistent with the reported SAR. Unconstrained rigid docking of benzimidazole ligands into representative CHK2 protein crystal structures reveals an alternative binding mode involving a water-mediated interaction with the hinge region; docking which incorporates protein side chain flexibility for selected residues in the ATP binding site resulted in a refinement of the water-mediated hinge binding mode that is consistent with observed SAR. The flexible docking results are in good agreement with the crystal structures of four exemplar benzimidazole ligands bound to CHK2 which unambiguously confirmed the binding mode of these inhibitors, including the water-mediated interaction with the hinge region, and which is significantly different from binding modes previously postulated in the literature.
doi:10.1016/j.bmc.2012.09.024
PMCID: PMC3778940  PMID: 23058106
ADP, adenosine diphosphate; ATM, ataxia telangiectasia mutated; ATP, adenosine triphosphate; CHK2, checkpoint kinase 2; GOLD, genetic optimisation for ligand docking; GST, glutathione S-transferase; KD, kinase domain; MOE, molecular operating environment; PARP, poly ADP-ribose polymerase; PDB, protein data bank; PLIF, protein ligand interaction fingerprints; SAR, structure activity relationship; SIFt, structural interaction fingerprints; Kinase; CHK2; Flexible docking; Crystallography; Inhibitor
12.  Autotracing of Escherichia coli acetate CoA-transferase α-subunit structure using 3.4 Å MAD and 1.9 Å native data 
The automation of protein structure determination is an essential component for high-throughput structural analysis in protein X-ray crystallography and is a key element in structural genomics. This highly challenging undertaking relies at present on the availability of high-quality native and derivatized protein crystals diffracting to high or moderate resolution, respectively. Obtaining such crystals often requires significant effort. The present study demonstrates that phases obtained at low resolution (>3.0 Å) from crystals of SeMet-labeled protein can be successfully used for automated structure determination. The crystal structure of acetate CoA-transferase α-subunit was solved using 3.4 Å multiwavelength anomalous dispersion data collected from a crystal containing SeMet-substituted protein and 1.9 Å data collected from a native protein crystal.
PMCID: PMC2792021  PMID: 12454473
13.  Structural and dynamic determinants of ligand binding and regulation of Cyclin-dependent Kinase 5 by pathological activator p25 and inhibitory peptide CIP 
Journal of molecular biology  2010;401(3):478-492.
The crystal structure of the cdk5/p25 complex has provided information on possible molecular mechanisms of ligand binding, specificity, and regulation of the kinase. Comparative molecular dynamics simulations are reported here for physiological conditions. This study provides new insight on the mechanisms that modulate such processes, which may be exploited to control the pathological activation by p25. The structural changes observed in the kinase are stabilized by a network of interactions involving highly conserved residues within the cdk family. Collective motions of the proteins (cdk5, p25, and CIP) and their complexes are identified by principal component analysis, revealing two conformational states of the activation loop upon p25 complexation, which are absent in the uncomplexed kinase and not apparent from the crystal. Simulations of the uncomplexed inhibitor CIP show structural rearrangements and increased flexibility of the interfacial loop containing the critical residue E240, which becomes fully hydrated and available for interactions with one of several positively charged residues in the kinase. These changes provide a rationale for the observed high affinity and enhanced inhibitory action of CIP when compared to either p25 or to the physiological activators of cdk5.
doi:10.1016/j.jmb.2010.06.040
PMCID: PMC2919306  PMID: 20599546
14.  Single-molecule FRET analysis of DNA binding and bending by yeast HMGB protein Nhp6A 
Nucleic Acids Research  2012;41(2):1372-1381.
High-mobility group B (HMGB) proteins bind duplex DNA without sequence specificity, facilitating the formation of compact nucleoprotein structures by increasing the apparent flexibility of DNA through the introduction of DNA kinks. It has remained unclear whether HMGB binding and DNA kinking are simultaneous and whether the induced kink is rigid (static) or flexible. The detailed molecular mechanism of HMGB-induced DNA ‘softening’ is explored here by single-molecule fluorescence resonance energy transfer studies of single yeast Nhp6A (yNhp6A) proteins binding to short DNA duplexes. We show that the local effect of yNhp6A protein binding to DNA is consistent with formation of a single static kink that is short lived (lifetimes of a few seconds) under physiological buffer conditions. Within the time resolution of our experiments, this static kink occurs at the instant the protein binds to the DNA, and the DNA straightens at the instant the protein dissociates from the DNA. Our observations support a model in which HMGB proteins soften DNA through random dynamic binding and dissociation, accompanied by DNA kinking and straightening, respectively.
doi:10.1093/nar/gks1208
PMCID: PMC3554232  PMID: 23221634
15.  Internal Water and Microsecond Dynamics in Myoglobin 
The Journal of Physical Chemistry. B  2013;117(47):14676-14687.
Myoglobin (Mb) binds diatomic ligands, like O2, CO, and NO, in a cavity that is only transiently accessible. Crystallography and molecular simulations show that the ligands can migrate through an extensive network of transiently connected cavities but disagree on the locations and occupancy of internal hydration sites. Here, we use water 2H and 17O magnetic relaxation dispersion (MRD) to characterize the internal water molecules in Mb under physiological conditions. We find that equine carbonmonoxy Mb contains 4.5 ± 1.0 ordered internal water molecules with a mean survival time of 5.6 ± 0.5 μs at 25 °C. The likely locations of these water molecules are the four polar hydration sites, including one of the xenon-binding cavities, that are fully occupied in all high-resolution crystal structures of equine Mb. The finding that water escapes from these sites, located 17–31 Å apart in the protein, on the same μs time scale suggests a global exchange mechanism. We propose that this mechanism involves transient penetration of the protein by H-bonded water chains. Such a mechanism could play a functional role by eliminating trapped ligands. In addition, the MRD results indicate that 2 or 3 of the 11 histidine residues of equine Mb undergo intramolecular hydrogen exchange on a μs time scale.
doi:10.1021/jp409234g
PMCID: PMC3966298  PMID: 24195787
16.  Alternaria alternata allergen, Alt a 1 - a unique, β-barrel protein dimer exclusively found in fungi 
Background
Alternaria is one of the most common molds associated with allergic diseases and 80% of Alternaria-sensitive patients produce IgE antibodies to a major protein allergen, Alt a 1. The structure and function of Alt a 1 is unknown.
Objective
To obtain a high resolution structure of Alt a 1 by X-ray crystallography and to investigate structural relationships between Alt a 1 and other allergens and proteins reported in the Protein Data Bank.
Methods
X-ray crystallography was used to determine the structure of Alt a 1 using a custom-designed set of crystallization conditions. An initial Alt a 1 model was determined by the application of a Ta6Br122+ cluster and Single-wavelength Anomalous Diffraction. Bioinformatic analyses were used to compare the Alt a 1 sequence and structure with other proteins.
Results
Alt a 1 is a unique β-barrel comprising 11 β-strands and forms a ‘butterfly-like’ dimer linked by a single disulfide bond, with a large (1345Å2) dimer interface. Intramolecular disulfide bonds are conserved among Alt a 1 homologs. Currently, the Alt a 1 structure has no equivalent in the Protein Data Bank. Bioinformatics analyses suggest that the structure is found exclusively in fungi. Four previously reported putative IgE binding peptides have been located on the Alt a 1 structure.
Conclusions
Alt a 1 has a unique, dimeric β-barrel structure that appears to define a new protein family with unknown function found exclusively in fungi. The location of IgE antibody binding epitopes is in agreement with the structural analysis of Alt a 1.The Alt a 1 structure will allow mechanistic structure/function studies and immunologic studies directed towards new forms of immunotherapy for Alternaria-sensitive allergic patients.
doi:10.1016/j.jaci.2012.03.047
PMCID: PMC3391610  PMID: 22664167
Asthma; Allergens; Molds; Alt a 1; Alternaria; X-ray crystallography; Protein structure; Oligomeric structure
17.  SnugDock: Paratope Structural Optimization during Antibody-Antigen Docking Compensates for Errors in Antibody Homology Models 
PLoS Computational Biology  2010;6(1):e1000644.
High resolution structures of antibody-antigen complexes are useful for analyzing the binding interface and to make rational choices for antibody engineering. When a crystallographic structure of a complex is unavailable, the structure must be predicted using computational tools. In this work, we illustrate a novel approach, named SnugDock, to predict high-resolution antibody-antigen complex structures by simultaneously structurally optimizing the antibody-antigen rigid-body positions, the relative orientation of the antibody light and heavy chains, and the conformations of the six complementarity determining region loops. This approach is especially useful when the crystal structure of the antibody is not available, requiring allowances for inaccuracies in an antibody homology model which would otherwise frustrate rigid-backbone docking predictions. Local docking using SnugDock with the lowest-energy RosettaAntibody homology model produced more accurate predictions than standard rigid-body docking. SnugDock can be combined with ensemble docking to mimic conformer selection and induced fit resulting in increased sampling of diverse antibody conformations. The combined algorithm produced four medium (Critical Assessment of PRediction of Interactions-CAPRI rating) and seven acceptable lowest-interface-energy predictions in a test set of fifteen complexes. Structural analysis shows that diverse paratope conformations are sampled, but docked paratope backbones are not necessarily closer to the crystal structure conformations than the starting homology models. The accuracy of SnugDock predictions suggests a new genre of general docking algorithms with flexible binding interfaces targeted towards making homology models useful for further high-resolution predictions.
Author Summary
Antibodies are proteins that are key elements of the immune system and increasingly used as drugs. Antibodies bind tightly and specifically to antigens to block their activity or to mark them for destruction. Three-dimensional structures of the antibody-antigen complexes are useful for understanding their mechanism and for designing improved antibody drugs. Experimental determination of structures is laborious and not always possible, so we have developed tools to predict structures of antibody-antigen complexes computationally. Computer-predicted models of antibodies, or homology models, typically have errors which can frustrate algorithms for prediction of protein-protein interfaces (docking), and result in incorrect predictions. Here, we have created and tested a new docking algorithm which incorporates flexibility to overcome structural errors in the antibody structural model. The algorithm allows both intramolecular and interfacial flexibility in the antibody during docking, resulting in improved accuracy approaching that when using experimentally determined antibody structures. Structural analysis of the predicted binding region of the complex will enable the protein engineer to make rational choices for better antibody drug designs.
doi:10.1371/journal.pcbi.1000644
PMCID: PMC2800046  PMID: 20098500
18.  Flexible ligand docking to multiple receptor conformations: a practical alternative 
State of the art docking algorithms predict an incorrect binding pose for about 50 to 70% of all ligands when only a single fixed receptor conformation is considered. In many more cases, lack of receptor flexibility results in meaningless ligand binding scores, even when the correct pose is obtained. Incorporating conformational rearrangements of the receptor binding pocket into predictions of both ligand binding pose and binding score is critical for improving structure based drug design and virtual ligand screening methodologies. However, direct modeling of protein binding site flexibility remains challenging due to the large conformational space that must be sampled, and difficulties remain in constructing a suitably accurate energy function. Here we show that using multiple fixed receptor conformations, either experimentally determined by crystallography or NMR, or computationally generated, is a practical shortcut that may improve docking calculations. In several cases, such an approach has led to experimentally validated predictions.
doi:10.1016/j.sbi.2008.01.004
PMCID: PMC2396190  PMID: 18302984
19.  The use of Co2+ for crystallization and structure determination, using a conventional mono­chromatic X-ray source, of flax rust avirulence protein  
It is demonstrated that anomalous diffraction based on the signal from a cobalt ion measured on a conventional monochromatic X-ray source can be used to determine the structure of a protein with a novel fold (M. lini avirulence protein AvrL567-A). The approach could be applicable to many metal-binding proteins, particularly when synchrotron radiation is not readily available.
Metal-binding sites are ubiquitous in proteins and can be readily utilized for phasing. It is shown that a protein crystal structure can be solved using single-wavelength anomalous diffraction based on the anomalous signal of a cobalt ion measured on a conventional monochromatic X-ray source. The unique absorption edge of cobalt (1.61 Å) is compatible with the Cu Kα wavelength (1.54 Å) commonly available in macromolecular crystallography laboratories. This approach was applied to the determination of the structure of Melampsora lini avirulence protein AvrL567-A, a protein with a novel fold from the fungal pathogen flax rust that induces plant disease resistance in flax plants. This approach using cobalt ions may be applicable to all cobalt-binding proteins and may be advantageous when synchrotron radiation is not readily available.
doi:10.1107/S1744309107004599
PMCID: PMC2330185  PMID: 17329816
AvrL567-A; cobalt; plant disease resistance; single-wavelength anomalous diffraction
20.  Purification, crystallization and preliminary crystallographic analysis of a GTP-binding protein from the hyperthermophilic archaeon Sulfolobus solfataricus  
A GTP-binding protein from the hyperthermophilic archaeon Sulfolobus solfataricus has been crystallized. Combined with biochemical analyses, it is expected that the structure of this protein will give insight in the function of a relatively unknown subfamily of the GTPase superfamily.
A predicted GTP-binding protein from the hyperthermophilic archaeon Sulfolobus solfataricus, termed SsGBP, has been cloned and overexpressed in Escherichia coli. The purified protein was crystallized using the hanging-drop vapour-diffusion technique in the presence of 0.05 M cadmium sulfate and 0.8 M sodium acetate pH 7.5. A single-wavelength anomalous dispersion data set was collected to a maximum resolution of 2.0 Å using a single cadmium-incorporated crystal. The crystal form belongs to space group P212121, with approximate unit-cell parameters a = 65.0, b = 72.6, c = 95.9 Å and with a monomer in the asymmetric unit.
doi:10.1107/S1744309107008500
PMCID: PMC2330175  PMID: 17329823
GTP-binding protein; SsGBP; Sulfolobus solfataricus
21.  Expression, crystallization and preliminary crystallographic studies of a novel bifunctional N-­acetylglutamate synthase/kinase from Xanthomonas campestris homologous to vertebrate N-acetylglutamate synthase 
Expression, crystallization and preliminary X-ray diffraction studies of a novel bifunctional N-acetylglutamate synthase/kinase from X. campestris homologous to vertebrate N-acetylglutamate synthase are reported.
A novel N-acetylglutamate synthase/kinase bifunctional enzyme of arginine biosynthesis that was homologous to vertebrate N-acetylglutamate synthases was identified in Xanthomonas campestris. The protein was overexpressed, purified and crystallized. The crystals belong to the hexagonal space group P6222, with unit-cell parameters a = b = 134.60, c = 192.11 Å, and diffract to about 3.0 Å resolution. Selenomethionine-substituted recombinant protein was produced and selenomethionine substitution was verified by mass spectroscopy. Multiple anomalous dispersion (MAD) data were collected at three wavelengths at SER-CAT, Advanced Photon Source, Argonne National Laboratory. Structure determination is under way using the MAD phasing method.
doi:10.1107/S1744309106044101
PMCID: PMC2225375  PMID: 17142901
argA; argB; N-acetylglutamate synthase; N-acetylglutamate kinase; bifunctional enzymes; arginine biosynthesis
22.  Purification, crystallization and preliminary X-ray diffraction analysis of an oomycete-derived Nep1-­like protein 
The first crystallographic study of a member of the NLP (Nep1-like protein) toxin and elicitor protein family is reported.
The elicitor protein Nep1-like protein from the plant pathogen Pythium aphanidermatum was purified and crystallized using the hanging-drop vapour-diffusion method. A native data set was collected to 1.35 Å resolution at 100 K using synchrotron radiation. Since selenomethionine-labelled protein did not crystallize under the original conditions, a second crystal form was identified that yielded crystals that diffracted to 2.1 Å resolution. A multiple-wavelength anomalous dispersion (MAD) experiment was performed at 100 K and all four selenium sites were identified, which allowed solution of the structure.
doi:10.1107/S1744309108037640
PMCID: PMC2593687  PMID: 19052381
elicitor proteins; plant pathogens; MAD; SeMet
23.  Chain Packing in the Inverted Hexagonal Phase of Phospholipids: A Study by X-ray Anomalous Diffraction on Bromine-labeled Chains 
Although lipid phases are routinely studied by X-ray diffraction, their unit cell structures have rarely been constructed from the diffraction data except for the lamellar phases. This is due to the well-known phase problem of X-ray diffraction. Here we successfully applied the multiwavelength anomalous dispersion (MAD) method to solve the phase problem for an inverted hexagonal phase of a phospholipid with brominated chains. Although the principle of the MAD method for all systems is the same, we found that for lipid structures it is necessary to use a procedure of analysis significantly different from that used for protein crystals. The inverted hexagonal phase has been used to study the chain packing in a hydrophobic interstice where three monolayers meet. Hydrophobic interstices are of great interest, because they occur in the intermediate states of membrane fusion. It is generally believed that chain packing in such a region is energy costly. Consequently it has been speculated that the inverted lipid tube is likely to deviate from a circular shape, and the chain density distribution might be non-uniform. The bromine distribution obtained from the MAD analysis provides the information for the chain packing in the hexagonal unit cell. The intensity of the bromine distribution is undulated around the unit cell. The analysis shows that the lipid chains pack the hexagonal unit cell at constant volume per chain, with no detectable effect from a high-energy interstitial region.
doi:10.1021/ja058045t
PMCID: PMC2556076  PMID: 16536555
24.  Structure of O67745_AQUAE, a hypothetical protein from Aquifex aeolicus  
Using single-wavelength anomalous dispersion data obtained from a gold-derivatized crystal, the X-ray crystal structure of the protein 067745_AQUAE from the prokaryotic organism Aquifex aeolicus has been determined to a resolution of 2.0 Å.
Using single-wavelength anomalous dispersion data obtained from a gold-derivatized crystal, the X-ray crystal structure of the protein 067745_AQUAE from the prokaryotic organism Aquifex aeolicus has been determined to a resolution of 2.0 Å. Amino-acid residues 1–371 of the 44 kDa protein were identified by Pfam as an HD domain and a member of the metal-dependent phosphohydrolase superfamily (accession No. PF01966). Although three families from this large and diverse group of enzymatic proteins are represented in the PDB, the structure of 067745_AQUAE reveals a unique fold that is unlike the others and that is likely to represent a new subfamily, further organizing the families and characterizing the proteins. Data are presented that provide the first insights into the structural organization of the proteins within this clan and a distal alternative GDP-binding domain outside the metal-binding active site is proposed.
doi:10.1107/S1744309107018945
PMCID: PMC2335016  PMID: 17565173
067745_AQUAE ; Aquifex aeolicus; HD domains
25.  The structure of Jann_2411 (DUF1470) from Jannaschia sp. at 1.45 Å resolution reveals a new fold (the ABATE domain) and suggests its possible role as a transcription regulator 
The crystal structure of the first representative of the Pfam PF07336 (DUF1470) family reveals a two-domain organization that contains a new fold, termed the ABATE domain, at the N-terminus and a treble-clef zinc finger that is likely to bind DNA at the C-terminus.
The crystal structure of Jann_2411 from Jannaschia sp. strain CCS1, a member of the Pfam PF07336 family classified as a domain of unknown function (DUF1470), was solved to a resolution of 1.45 Å by multiple-wavelength anomalous dispersion (MAD). This protein is the first structural representative of the DUF1470 Pfam family. Structural analysis revealed a two-domain organization, with the N-terminal domain presenting a new fold called the ABATE domain that may bind an as yet unknown ligand. The C-terminal domain forms a treble-clef zinc finger that is likely to be involved in DNA binding. Analysis of the Jann_2411 protein and the broader ABATE-domain family suggests a role as stress-induced transcriptional regulators.
doi:10.1107/S1744309109025196
PMCID: PMC2954205  PMID: 20944211
structural genomics; environmental stress; domains of unknown function; Pfam; bound metal identification

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