Molecular Replacement Techniques Research Articles

Evolution of insect arylalkylamine N -acetyltransferases: Structural evidence from the yellow fever mosquito, Aedes aegypti

Arylalkylamine N-acetyltransferase (aaNAT) catalyzes the transacetylation from acetyl-CoA to arylalkylamines. aaNATs are involved in sclerotization and neurotransmitter inactivation in insects. Phyletic distribution analysis confirms three clusters of aaNAT-like sequences in insects: typical insect aaNAT, polyamine NAT-like aaNAT, and mosquito unique putative aaNAT (paaNAT). Here we studied three proteins: aaNAT2, aaNAT5b, and paaNAT7, each from a different cluster. aaNAT2, a protein from the typical insect aaNAT cluster, uses histamine as a substrate as well as the previously identified arylalkylamines. aaNAT5b, a protein from polyamine NAT -like aaNAT cluster, uses hydrazine and histamine as substrates. The crystal structure of aaNAT2 was determined using single-wavelength anomalous dispersion methods, and that of native aaNAT2, aaNAT5b and paaNAT7 was detected using molecular replacement techniques. All three aaNAT structures have a common fold core of GCN5-related N-acetyltransferase superfamily proteins, along with a unique structural feature: helix/helices between β3 and β4 strands. Our data provide a start toward a more comprehensive understanding of the structure-function relationship and physiology of aaNATs from the mosquito Aedes aegypti and serve as a reference for studying the aaNAT family of proteins from other insect species. The structures of three different types of aaNATs may provide targets for designing insecticides for use in mosquito control.

Crystal structure of a pro-inflammatory lectin from the seeds of Dioclea wilsonii Standl

The crystal structure and pro-inflammatory property of a lectin from the seeds of Dioclea wilsonii (DwL) were analyzed to gain a better understanding of structure/function relationships of Diocleinae lectins. Following crystallization and structural determination by standard molecular replacement techniques, DwL was found to be a tetramer based on PISA analysis, and composed by two metal-binding sites per monomer and loops which are involved in molecular oligomerization. DwL presents 96% and 99% identity with two other previously described lectins of Dioclea rostrata (DRL) and Dioclea grandiflora (DGL). DwL differs structurally from DVL and DRL with regard to the conformation of the carbohydrate recognition domain and related biological activities. The structural analysis of DwL in comparison to other Diocleinae lectins can be related to the differences in the dose-dependent pro-inflammatory effect elicited in Wistar rats, probably via specific interactions with mast cells complex carbohydrate, resulting in significant paw edema. DwL appears to be involved in positive modulation of mast cell degranulation via recognition of surface carbohydrates. Since this recognition is dependent on site volume and CRD configuration, edematogenesis mediated by resident cells varies in potency and efficacy among different Diocleinae lectins.

Genetic analysis of neuronal ionotropic glutamate receptor subunits

In the brain, fast, excitatory synaptic transmission occurs primarily through AMPA- and NMDA-type ionotropic glutamate receptors. These receptors are composed of subunit proteins that determine their biophysical properties and trafficking behaviour. Therefore, determining the function of these subunits and receptor subunit composition is essential for understanding the physiological properties of synaptic transmission. Here, we discuss and evaluate various genetic approaches that have been used to study AMPA and NMDA receptor subunits. These approaches have demonstrated that the GluA1 AMPA receptor subunit is required for activity-dependent trafficking and contributes to basal synaptic transmission, while the GluA2 subunit regulates Ca(2+) permeability, homeostasis and trafficking to the synapse under basal conditions. In contrast, the GluN2A and GluN2B NMDA receptor subunits regulate synaptic AMPA receptor content, both during synaptic development and plasticity. Ongoing research in this field is focusing on the molecular interactions and mechanisms that control these functions. To accomplish this, molecular replacement techniques are being used, where native subunits are replaced with receptors containing targeted mutations. In this review, we discuss a single-cell molecular replacement approach which should arguably advance our physiological understanding of ionotropic glutamate receptor subunits, but is generally applicable to study of any neuronal protein.

Crystallization and preliminary X-ray diffraction studies of the precursor protein of a thermostable variant of papain.

The crystallization of a recombinant thermostable variant of pro-papain has been carried out. The mutant pro-enzyme was expressed in Escherichia coli as inclusion bodies, refolded, purified and crystallized. The crystals belonged to space group P2(1), with unit-cell parameters a = 42.9, b = 74.8, c = 116.5 Å, β = 93.0°, and diffracted to 2.6 Å resolution using synchrotron radiation. Assuming the presence of two molecules in the asymmetric unit, the calculated Matthews coefficient is 2.28 Å(3) Da(-1), corresponding to a solvent content of 46%. Initial attempts to solve the structure using molecular-replacement techniques were successful.

A rational protocol for the successful crystallization of L-amino-acid oxidase from Bothrops atrox.

Despite the valuable contributions of robotics and high-throughput approaches to protein crystallization, the role of an experienced crystallographer in the evaluation and rationalization of a crystallization process is still crucial to obtaining crystals suitable for X-ray diffraction measurements. In this work, the difficult task of crystallizing the flavoenzyme L-amino-acid oxidase purified from Bothrops atrox snake venom was overcome by the development of a protocol that first required the identification of a non-amorphous precipitate as a promising crystallization condition followed by the implementation of a methodology that combined crystallization in the presence of oil and seeding techniques. Crystals were obtained and a complete data set was collected to 2.3 Å resolution. The crystals belonged to space group P2(1), with unit-cell parameters a = 73.64, b = 123.92, c = 105.08 Å, β = 96.03°. There were four protein subunits in the asymmetric unit, which gave a Matthews coefficient V(M) of 2.12 Å(3) Da(-1), corresponding to 42% solvent content. The structure has been solved by molecular-replacement techniques.

Crystallization and preliminary X-ray diffraction analysis of a Lys49-phospholipase A2complexed with caffeic acid, a molecule with inhibitory properties against snake venoms

Phospholipases A(2) (PLA(2)s) are one of the main components of bothropic venoms; in addition to their phospholipid hydrolysis action, they are involved in a wide spectrum of pharmacological activities, including neurotoxicity, myotoxicity and cardiotoxicity. Caffeic acid is an inhibitor that is present in several plants and is employed for the treatment of ophidian envenomations in the folk medicine of many developing countries; as bothropic snake bites are not efficiently neutralized by conventional serum therapy, it may be useful as an antivenom. In this work, the cocrystallization and preliminary X-ray diffraction analysis of the Lys49-PLA(2) piratoxin I from Bothrops pirajai venom in the presence of the inhibitor caffeic acid (CA) are reported. The crystals diffracted X-rays to 1.65 Å resolution and the structure was solved by molecular-replacement techniques. The electron-density map unambiguously indicated the presence of three CA molecules that interact with the C-terminus of the protein. This is the first time a ligand has been observed bound to this region and is in agreement with various experiments previously reported in the literature.

Purification, crystallization and preliminary X-ray diffraction analysis of the thiaminase type II fromStaphylococcus aureus

Thiaminase type II (TenA) catalyzes the deamination of aminopyrimidines, including the cleavage of thiamine to 4-amino-5-hydroxymethyl-2-methylpyrimidine and 5-(2-hydroxyethyl)-4-methylthiazole in the metabolism of thiamine (vitamin B1), in Staphylococcus aureus (Sa). SaTenA was crystallized by the vapour-diffusion method and the resulting crystal diffracted to 2.6 Å resolution usng synchrotron radiation. The crystal is orthorhombic, belonging to space group P2(1)2(1)2(1) with unit-cell parameters a=103.5, b=104.1, c=109.6 Å. With four molecules in the asymmetric unit, the Matthews coefficient is 2.85 Å3 Da(-1). Initial attempts to solve the structure by molecular-replacement techniques were successful.

Structure of the newly found green turtle egg-white ribonuclease.

Marine green turtle (Chelonia mydas) egg-white ribonuclease (GTRNase) was crystallized from 1.1 M ammonium sulfate pH 5.5 and 30% glycerol using the sitting-drop vapour-diffusion method. The structure of GTRNase has been solved at 1.60 A resolution by the molecular-replacement technique using a model based on the structure of RNase 5 (murine angiogenin) from Mus musculus (46% identity). The crystal belonged to the monoclinic space group C2, with unit-cell parameters a = 86.271, b = 34.174, c = 39.738 A, alpha = 90, beta = 102, gamma = 90 degrees . GTRNase consists of three helices and seven beta-strands and displays the alpha+beta folding topology typical of a member of the RNase A superfamily. Superposition of the C(alpha) coordinates of GTRNase and RNase A superfamily members indicates that the overall structure is highly similar to that of angiogenin or RNase 5 from M. musculus (PDB code 2bwl) and RNase A from Bos taurus (PDB code 2blz), with root-mean-square deviations of 3.9 and 2.0 A, respectively. The catalytic residues are conserved with respect to the RNase A superfamily. The three disulfide bridges observed in the reptilian enzymes are conserved in GTRNase, while one further disulfide bond is required for the structural stability of mammalian RNases. GTRNase is expressed in egg white and the fact that its sequence has the highest similarity to that of snapping turtle pancreatic RNase suggests that the GTRNase secreted from oviduct cells to form egg white is probably the product of the same gene as activated in pancreatic cells.

Crystallization and preliminary X-ray crystallographic studies of a Lys49-phospholipase A2homologue fromBothrops pirajaivenom complexed with rosmarinic acid

PrTX-I, a noncatalytic and myotoxic Lys49-phospholipase A(2) from Bothrops pirajai venom, was crystallized in the presence of the inhibitor rosmarinic acid (RA). This is the active compound in the methanolic extract of Cordia verbenacea, a plant that is largely used in Brazilian folk medicine. The crystals diffracted X-rays to 1.8 A resolution and the structure was solved by molecular-replacement techniques, showing electron density that corresponds to RA molecules at the entrance to the hydrophobic channel. The crystals belong to space group P2(1)2(1)2(1), indicating conformational changes in the structure after ligand binding: the crystals of all apo Lys49-phospholipase A(2) structures belong to space group P3(1)21, while the crystals of complexed structures belong to space groups P2(1) or P2(1)2(1)2(1).

Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of the N-terminal carbohydrate-recognition domain of human galectin-4

Galectin-4 is a tandem-repeat-type galectin that is expressed in the epithelium of the alimentary tract from the tongue to the large intestine. Additionally, strong expression of galectin-4 can also be induced in cancers in other tissues, including the breast and liver. In order to explore its potential as a target for anticancer drug design, elucidation of the structural basis of the carbohydrate-binding specificities of galectin-4 has been focused on. As an initial step, the N-terminal carbohydrate-recognition domain of human galectin-4 (hGal4-CRD-1) has been successfully crystallized using the vapour-diffusion technique, a complete data set has been collected to 2.2 A resolution and the structure has been solved by the molecular-replacement technique. The crystals belonged to space group P6(1)22, with unit-cell parameters a = b = 71.25, c = 108.66 A. The asymmetric unit contained one molecule of hGal4-CRD-1, with a V(M) value of 2.34 A(3) Da(-1) and a solvent content of 47.51%.

MUSTANG-MR Structural Sieving Server: Applications in Protein Structural Analysis and Crystallography

BackgroundA central tenet of structural biology is that related proteins of common function share structural similarity. This has key practical consequences for the derivation and analysis of protein structures, and is exploited by the process of “molecular sieving” whereby a common core is progressively distilled from a comparison of two or more protein structures. This paper reports a novel web server for “sieving” of protein structures, based on the multiple structural alignment program MUSTANG.Methodology/Principal Findings“Sieved” models are generated from MUSTANG-generated multiple alignment and superpositions by iteratively filtering out noisy residue-residue correspondences, until the resultant correspondences in the models are optimally “superposable” under a threshold of RMSD. This residue-level sieving is also accompanied by iterative elimination of the poorly fitting structures from the input ensemble. Therefore, by varying the thresholds of RMSD and the cardinality of the ensemble, multiple sieved models are generated for a given multiple alignment and superposition from MUSTANG. To aid the identification of structurally conserved regions of functional importance in an ensemble of protein structures, Lesk-Hubbard graphs are generated, plotting the number of residue correspondences in a superposition as a function of its corresponding RMSD. The conserved “core” (or typically active site) shows a linear trend, which becomes exponential as divergent parts of the structure are included into the superposition.ConclusionsThe application addresses two fundamental problems in structural biology: First, the identification of common substructures among structurally related proteins—an important problem in characterization and prediction of function; second, generation of sieved models with demonstrated uses in protein crystallographic structure determination using the technique of Molecular Replacement.

Protein Structure Determination by Molecular Replacement using High-Accuracy Protein Structure Modeling

Molecular replacement (MR) technique is to solve the phase problem in x-ray crystallography. Currently, many computational methods are available and they can provide MR solutions when a suitable 3D model of the target molecule is available. In practice, the success of the MR method is limited by various factors including unavailability of suitable 3D models and the ambiguity of crystallographic parameters. Accurate 3D modeling of the target molecule can provide a breakthrough in these cases. Recently, we have developed a protein 3D modeling method which can provide accurate protein 3D models both in backbones and side-chains. In addition, the method provides a variety of protein 3D models with structural variation. In recent blind tests, CASP7 and CASP8 experiments, the method produced the very top quality protein 3D models for high-accuracy template-based modeling targets. We combined this modeling method with a MR technique and successfully determined two protein structures, which could not be determined using conventional methods with available protein templates. It appears that high-accuracy protein 3D modeling for backbones as well as side-chains can boost up the success rate of molecular replacement technique allowing us to solve the phase problem in x-ray crystallography without requiring additional experiments with high cost efforts.

Molecular replacement: the probabilistic approach of the programREMO09and its applications

The method of joint probability distribution functions has been applied to molecular replacement techniques. The rotational search is performed by rotating the reciprocal lattice of the protein with respect to the calculated transform of the model structure; the translation search is performed by fast Fourier transform. Several cases of prior information are studied, both for the rotation and for the translation step: e.g. the conditional probability density for the rotation or the translation of a monomer is found both for ab initio and when the rotation and/or the translation values of other monomers are given. The new approach has been implemented in the program REMO09, which is part of the package for global phasing IL MILIONE [Burla, Caliandro, Camalli, Cascarano, De Caro, Giacovazzo, Polidori, Siliqi & Spagna (2007). J. Appl. Cryst. 40, 609-613]. A large set of test structures has been used for checking the efficiency of the new algorithms, which proved to be significantly robust in finding the correct solutions and in discriminating them from noise. An important design concept is the high degree of automatism: REMO09 is often capable of providing a reliable model of the target structure without any user intervention.

Crystallization and preliminary X-ray analysis of betaC-S lyases from two oral Streptococci.

Hydrogen sulfide, which causes oral malodour, is generally produced from L-cysteine by the action of betaC-S lyase from oral bacteria. The betaC-S lyases from two oral bacteria, Streptococcus anginosus and S. gordonii, have been cloned, overproduced, purified and crystallized. X-ray diffraction data were collected from the two types of crystals using synchrotron radiation. The crystal of S. anginosus betaC-S lyase belonged to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 67.0, b = 111.1, c = 216.4 A, and the crystal of S. gordonii betaC-S lyase belonged to the same space group, with unit-cell parameters a = 58.0, b = 73.9. c = 187.6 A. The structures of the betaC-S lyases were solved by molecular-replacement techniques.

Rapid Protein Structure Determination Using Distributed Computing

Structural biology research places significant demands upon high-performance computing. The elucidation of protein structures at atomic resolution is computationally demanding and requires user-friendly interfaces to highperformance computing resources. Fortunately, critical calculations are embarrassingly parallel and thus ideally suited to distributed computing. Here we discuss how we are using grid computing to determine the three dimensional structures of proteins using the technique of Molecular Replacement in a massively parallel fashion, in a timeframe of hours to days orders of magnitude faster than is currently possible.

Salicylate 1,2-Dioxygenase from Pseudaminobacter salicylatoxidans: Crystal Structure of a Peculiar Ring-cleaving Dioxygenase

The crystallographic structure of salicylate 1,2-dioxygenase (SDO), a new ring fission dioxygenase from the naphthalenesulfonate-degrading strain Pseudaminobacter salicylatoxidans BN12, which oxidizes salicylate to 2-oxohepta-3,5-dienedioic acid by a novel ring fission mechanism, has been solved by molecular replacement techniques and refined at 2.9 Å resolution ( R free 26.1%; R-factor 19.3%). SDO is a homo-tetramer member of type III extradiol-type dioxygenases with a subunit topology characteristic of the bicupin β-barrel folds. The catalytic center contains a mononuclear iron(II) ion coordinated to three histidine residues (His119, His121, and His160), located within the N-terminal domain in a solvent-accessible pocket. SDO is markedly different from the known gentisate 1,2-dioxygenases (GDO) or 1-hydroxy-2-naphthoate dioxygenase because of its unique ability to oxidatively cleave numerous salicylates, gentisates and 1-hydroxy-2-naphthoate with high catalytic efficiency. The comparison of the structure and substrate specificity for a series of different substrates with the corresponding data for several GDOs and the docking of salicylates/gentisates in the active site of SDO, allowed the identification of several active site residues responsible for differences of substrate specificity. In particular, a more defined electron density of the N-terminal region allowed the discovery of a novel structure fragment in SDO previously unobserved in GDO. This region contributes several residues to the active site that influence substrate specificity for both of these enzymes. Implications on the catalytic mechanism are discussed.

Crystal structure of the blue multicopper oxidase from the white-rot fungus Trametes trogii complexed with p-toluate

A multicopper oxidase, the fungal laccase glycoenzyme from the white-rot basidiomycete fungus Trametes (Funalia) trogii, was crystallized and its crystal structure was solved at 1.58 Å using molecular replacement techniques. Model refinement resulted in R-factor and R-free values of 17.4% and 19.0%, respectively. The T. trogii laccase structural model reveals the presence of a ligand bound to the T1 active site which resembles a p-toluate molecule, such bound compound is most probably a fungal metabolite. The p-toluate is bound into the T1 active site of the laccase forming, with one of the carboxylate oxygens, a H-bond with His455, one of the T1 copper ion ligands, whereas the methyl group presents hydrophobic interactions within a pocket composed by Phe331, Phe336, Pro390 and Val162. The coordination geometries, the bond distances and the oxidation states of the T1 and T2/T3 copper active sites are analyzed and discussed in terms of the enzymatic mechanism and catalytic functionality.

Crystal structure of the leucine zipper domain of small‐conductance Ca2+‐activated K+ (SKCa) channel from Rattus norvegicus

Crystal structure of the leucine zipper domain of small‐conductance Ca²⁺‐activated K⁺ (SK_Ca) channel from <i>Rattus norvegicus</i>

Expression, purification, crystallization and preliminary crystallographic study of isolated modules of the mouse coactivator-associated arginine methyltransferase 1.

Coactivator-associated arginine methyltransferase 1 (CARM1) plays a crucial role in gene expression as a coactivator of several nuclear hormone receptors and also of non-nuclear receptor systems. Its recruitment by the transcriptional machinery induces protein methylation, leading to chromatin remodelling and gene activation. CARM1(28-507) and two structural states of CARM1(140-480) were expressed, purified and crystallized. Crystals of CARM1(28-507) belong to space group P6(2)22, with unit-cell parameters a = b = 136.0, c = 125.3 A; they diffract to beyond 2.5 A resolution using synchrotron radiation and contain one monomer in the asymmetric unit. The structure of CARM1(28-507) was solved by multiple isomorphous replacement and anomalous scattering methods. Crystals of apo CARM1(140-480) belong to space group I222, with unit-cell parameters a = 74.6, b = 99.0, c = 207.4 A; they diffract to beyond 2.7 A resolution and contain two monomers in the asymmetric unit. Crystals of CARM1(140-480) in complex with S-adenosyl-L-homocysteine belong to space P2(1)2(1)2, with unit-cell parameters a = 74.6, b = 98.65, c = 206.08 A; they diffract to beyond 2.6 A resolution and contain four monomers in the asymmetric unit. The structures of apo and holo CARM1(140-480) were solved by molecular-replacement techniques from the structure of CARM1(28-507).

Atomic Level Insight into the Oxidative Half-reaction of Aromatic Amine Dehydrogenase

The quinoprotein aromatic amine dehydrogenase (AADH) uses a covalently bound tryptophan tryptophylquinone (TTQ) cofactor to oxidatively deaminate primary aromatic amines. Recent crystal structures have provided insight into the reductive half-reaction. In contrast, no atomic details are available for the oxidative half-reaction. The TTQ O7 hydroxyl group is protonated during reduction, but it is unclear how this proton can be removed during the oxidative half-reaction. Furthermore, compared with the electron transfer from the N-quinol form, electron transfer from the non-physiological O-quinol form to azurin is significantly slower. Here we report crystal structures of the O-quinol, N-quinol, and N-semiquinone forms of AADH. A comparison of oxidized and substrate reduced AADH species reveals changes in the TTQ-containing subunit, extending from residues in the immediate vicinity of the N-quinol to the putative azurin docking site, suggesting a mechanism whereby TTQ redox state influences interprotein electron transfer. In contrast, chemical reduction of the TTQ center has no significant effect on protein conformation. Furthermore, structural reorganization upon substrate reduction places a water molecule near TTQ O7 where it can act as proton acceptor. The structure of the N-semiquinone, however, is essentially similar to oxidized AADH. Surprisingly, in the presence of substrate a covalent N-semiquinone substrate adduct is observed. To our knowledge this is the first detailed insight into a complex, branching mechanism of quinone oxidation where significant structural reorganization upon reduction of the quinone center directly influences formation of the electron transfer complex and nature of the electron transfer process.