Crystal structure determination of basic phospholipase A_2 from venom of Agkistrodon halys pallas by molecular replacement method

Basic phospholipase A2 (BPLA2) from the venom of Agkistrodon halys pallas has a strong ability to hemolyze erythrocytes. The asymmetrical unit of P212121 crystal of BPLA2 contains two molecules. Self-rotation function was used to study the orientation relationship of these two molecules. Cross-rotation and translation functions were then used to determine the orientations and positions of the two molecules in the unit cell. The model building and preliminary structure refinement were carried out. The result shows that the two molecules in the asymmetrical unit of orthorhombic crystal are related by a non-crystallographic 2-fold symmetry axis.     

尖吻蝮蛇毒碱性磷脂酶A2的表达及其生化特征

将尖吻蝮蛇毒碱性磷脂酶A₂（A.aBPLA₂）基因克隆至温敏表达载体pBLMVL2,在大肠杆菌RR1中成功诱导表达.表达产物A.aBPLA₂约占细菌蛋白质总量的20％,并以包涵体的形式存在.纯化包涵体后,将产物变性、复性,然后用FPLC Superose^TM12纯化,产物经过SDS-聚丙烯酰胺凝胶电泳检测只有单一条带.对纯化后的表达A.aBPLA₂进行了酶活性、抑制血小板聚集活性和溶血活性的测定.结果显示,表达A.aBPLA₂的酶活性与变性后复性江浙蝮蛇酸性磷脂酶A₂酶活性相近,具有类似变性后复性江浙蝮蛇碱性磷脂酶A₂的溶血活性,没有抑制血小板聚集活性.最后对磷脂酶A₂的结构与这些活性的关系进行了讨论.     

Purification, crystallization and preliminary crystallographic investigations of selenium-containing phycocyanin from selenium-rich algae (Spirulina platensis)

The selenium-containing phycocyanin from the selenium-rich algae (Spirulina platensis) has been crystallized in two crystal forms by the hanging-drop vapor diffusion techniques. A chromatographic procedure of gel filtration and anion exchange was used for purification. Form I crystal with space group P2₁ and cell parameters a =108.0 Å , b = 117.0 Å , c = 184.0 Å , β = 90.2° and 12(αβ ) units in the asymmetric unit was obtained by using (NH₄)₂SO₄ as precipitant. These crystals diffract up to 2.8 Å . Form II crystal obtained by using PEG4000 as precipitant belongs to space group P63 with unit cell constants a = 155.0 Å , c = 40.3 Å , γ =120.0° and one(αβ ) unit in the asymmetric unit. The crystals diffract beyond 2.9 Å . The possible stacking forms of phycocyanin molecules in the first crystal form were discussed.     

Use of molecular replacement in the structure determination of the P21212 and the P21 (Pseudo P21212) crystal forms of oxidized uteroglobin

The structure of the symmetrical dimer of oxidized rabbit Uteroglobin, as determined from the crystal form in space group C222₁, has been used as a model to determine the general parameters of this protein in two other crystal forms; namely, a symmetrical dimer in P2₁2₁2 and an asymmetrical dimer in P2₁ with non-crystallographic symmetry approaching P2₁2₁2. Independently, the structure in P2₁2₁2 was solved by multiple isomorphous replacement.After exchanging data, the analysis was carried out in two different laboratories with different methods of molecular replacement. The result was the same for both approaches, and it could be shown further that the packing of molecules in both crystal forms analysed is so similar that they can be considered pseudoisomorphous, i.e. distinguished only by the fact that two out of three symmetry operators are crystallographically perfect in one case and molecular and approximate only in the other.The principal fold of the polypeptide chain is the same in all crystal forms considered so far, but there is evidence for differences in the detail, which will be worked out later with progressing refinement.     

Purification, crystallization and preliminary crystallographic investigations of selenium-containing phycocyanin from selenium-rich algae ( Spirulina platensis )

The selenium-containing phycocyanin from the selenium-rich algae (Spirulina platensis) has been crystallized in two crystal forms by the hanging-drop vapor diffusion techniques. A chromatographic procedure of gel filtration and anion exchange was used for purification. Form I crystal with space group P2₁ and cell parameters a =108.0 ?, b= 117.0 ?, c = 184.0?, β= 90.2° and 12(αβ) units in the asymmetric unit was obtained by using (NH₄)₂SO₄ as precipitant. These crystals diffract up to 2.8 ?. Form II crystal obtained by using PEG4000 as precipitant belongs to space group P6₃ with unit cell constants a = 155.0 ?, c = 40.3 ?, γ =120.0° and one(αβ) unit in the asymmetric unit. The crystals diffract beyond 2.9 ?. The possible stacking forms of phycocyanin molecules in the first crystal form were discussed.     

Crystallization and Preliminary X-Ray Structure Analysis of 1-Aminocyclopropane-1-carboxylic Acid Deaminase

The enzyme 1-aminocyclopropane-1-carboxylic acid deaminase from the bacterium Pseudomonas sp. has been crystallized using the hanging-drop method. The crystals belong to the orthorhombic space group P 2₁2₁2₁ (a = 70.0 Å, b = 70.0 Å, c = 355.0 Å). An asymmetrical unit contains two trimer molecules of M_r = 110,000. The diffraction data have been collected to 3.5-Å resolution. Analysis of the data using the self-rotation function suggests threefold axes within the trimer molecules and a pseudotetragonal arrangement between the trimer molecules in the cell.     

Molecular structure of L-lysyl-L-alanyl-L-alanine: a tripeptide found in histone H1

The crystal structure of L -lysyl-L -alanyl-L -alanine hydrochloride has been determined by x-ray diffraction. The peptide is in zwitterionic form with the carboxylic group deprotonated, and with positive charges both in the amino terminal and ?-amino groups of lysine. Crystals are monoclinic, space group P2₁ and Z = 4, with two peptide molecules in the asymmetric unit, which show different conformations. While one molecule has torsional angles for the Lys-Ala peptide bond (φ₂, φ₂) in the β-pleated sheet region, the values for the other molecule are close to those for the α-helix. This molecular flexibility is of interest for the study of H1 histone, which contains this sequence repeated several times. The two lysine residues show fully extended side chains. Two methanol molecules and two acetonitrile molecules are also present in the unit cell. An extensive network of hydrogen bonds and ionic interactions stabilize the crystal structure.     

H NMR and X-ray studies on hydrogen bonding in alkyloxy ethanols and their MgCl2 adducts

Adducts of alkyloxy ethanols (2-isobutoxy ethanol, 2-isopropoxy ethanol, 2-ethoxy ethanol, and 2-methoxy ethanol) with MgCl₂ were prepared in the presence of excess alkyloxy ethanol in molar ratios 5:1-15:1. MgCl₂/2-isopropoxy ethanol and MgCl₂/2-isobutoxy ethanol adducts were successfully crystallized and their structures determined by single-crystal X-ray diffraction. Alkyloxy ethanol molecules bind to magnesium in 2:1 mol ratio through oxygens of the alcohol and ether groups forming a chelated structure. In the binuclear complexes [(ipe)₂MgCl₂Mg(ipe)₂][Cl]₂ and [(ibe)₂MgCl₂Mg(ibe)₂][Cl]₂ (structures 1 and 2), where ipe stands for 2-isopropoxy ethanol and ibe for 2-isobutoxy ethanol, the two magnesium centers are connected by two chlorine bridges. The mononuclear structure cis-[Mg(ibe)₂(H₂O)₂][Cl]₂ (structure 3) contains, besides two alkyloxy molecules, two water molecules bound to magnesium. Hydrogen bonding in the adducts, in liquid and solid states, was studied by ¹H NMR spectroscopy and X-ray diffraction, respectively. In liquid state, the sample concentration and temperature used in the measurements were observed to influence hydrogen bonding. All crystal structures show extensive hydrogen bonding from anionic chlorines to the OH hydrogen of alcohols or the water hydrogens.     

Additional criterion for the determination of the handedness of 21 helices in crystals of bile acids: Crystal structure of a tert‐butylphenyl derivative of cholic acid

[3β,5β,7α,12α]‐3‐(4‐t‐Butylbenzoilamine)‐7,12‐dihydroxycholan‐24‐oic acid was synthesized and recrystallized from chlorobenzene and acetone. Orthorhombic P2₁2₁2₁ and monoclinic P2₁ crystals were obtained, respectively, and both crystals include solvent and water molecules with a 1:1:1 stoichiometry. In the second case, there are two nonequivalent molecules of the steroid in the unit cell. In both crystals, a crossing structure results for the molecular packing, stabilized by hydrogen bonds between the steroid molecules. In the second crystal, water links steroid molecules of the same type, which are not directly connected through hydrogen bonds. The steroid molecules define helicoidal assemblies along 2₁ screw axes. The handedness in the crystal in chlorobenzene is unambiguously defined by following the criterion proposed by Miyata et al., as the steroids are in a belly‐to‐belly disposition around the axis. This motif does not appear in the crystal in acetone, and other criterion is required. On the basis of the fact that a staircase and its banister have the same handedness and using the crystal in chlorobenzene as reference, the additional criterion has been established. According to it, in the absence of a belly‐to‐belly orientation, the handedness must be defined by keeping the bile acid with its right side oriented toward the axis. Pitch angles of the helices and tilt angles of the molecules are also determined. Chirality, 2011. © 2011 Wiley‐Liss, Inc.     

Crystal structural characterization reveals novel oligomeric interactions of human voltage‐dependent anion channel 1

Voltage‐dependent anion channel 1 (VDAC1), which is located in the outer mitochondrial membrane, plays important roles in various cellular processes. For example, oligomerization of VDAC1 is involved in the release of cytochrome c to the cytoplasm, leading to apoptosis. However, it is unknown how VDAC1 oligomerization occurs in the membrane. In the present study, we determined high‐resolution crystal structures of oligomeric human VDAC1 (hVDAC1) prepared by using an Escherichia coli cell‐free protein synthesis system, which avoided the need for denaturation and refolding of the protein. Broad‐range screening using a bicelle crystallization method produced crystals in space groups C222 and P22₁2₁, which diffracted to a resolution of 3.10 and 3.15 Å, respectively. Each crystal contained two hVDAC1 protomers in the asymmetric unit. Dimer within the asymmetrical unit of the crystal in space group C222 were oriented parallel, whereas those of the crystal in space group P22₁2₁ were oriented anti‐parallel. From a model of the crystal in space group C222, which we constructed by using crystal symmetry operators, a heptameric structure with eight patterns of interaction between protomers, including hydrophobic interactions with β‐strands, hydrophilic interactions with loop regions, and protein–lipid interactions, was observed. It is possible that by having multiple patterns of interaction, VDAC1 can form homo‐ or hetero‐oligomers not only with other VDAC1 protomers but also with other proteins such as VDAC2, VDAC3 and apoptosis‐regulating proteins in the Bcl‐2 family.     

Multinuclear magnetic resonance studies of the reactions of the antitumor complexes cis-Pt(L)2X2 and cis-Pt(NH3)(L)X2 (L = cyclobutylamine and cyclopentylamine) with guanosine and other bases and crystal structures of Pt(cyclopentylamine)2I2

The crystal structures of two Pt(cyclopentylamine)₂I₂ compounds were determined by X-ray diffraction methods. Both crystals contain disordered cyclopentylamine ligands. Crystal I contains two independent trans-Pt(cyclopentylamine)₂I₂ molecules and all the C atoms are disordered on two positions. The second crystal (II) is most interesting since it contains both cis- and trans-Pt(cyclopentylamine)₂I₂ isomers in the same unit cell. It was prepared from the recrystallization of the cis isomer in acetone. The C atoms of the trans molecule in crystal II are disordered on two positions, while only one position was determined in the cis molecule, although some of the C thermal factors are quite high. The reactions of cis-Pt(amine)₂X₂ and cis-Pt(NH₃)(amine)X₂ (amine = cyclobutylamine and cyclopentylamine) with guanosine in water were studied in different Pt:guanosine proportions by multinuclear (¹H, ¹⁹⁵Pt and ¹⁵N) magnetic resonance spectroscopy. The presence of several species in solution was observed. For the mixed-cyclobutylamine compound, ¹⁵N NMR has shown that some of the NH₃ ligands have been displaced from the coordination sphere in the presence of an excess of guanosine. The reactions of the two mixed-ligand complexes cis-Pt(NH₃)(amine)Cl₂ with 9-methylguanine, inosine and 9-methylhypoxanthine were also studied in water and the results are discussed.     

The crystal structure of a nonalkenic,cyclic trimer of levoglucosenone

A single-crystal, X-ray diffraction study was performed on a nonalkenic, cyclic trimer (C₁₈H₁₈O₉, 4) of levoglucosenone, in order to confirm its chemical structure. Crystals of 4 are orthorhombic, with unit-cell parameters of a = 792.20, b = 1874.35, c = 2383.02 pm, space group P2₁2₁2₁, and z = 8. The structure was solved by direct methods, and refined by least-squares to R = 0.032, based on 2990 unique reflections. Each asymmetrical unit contains two symmetry-independent molecules of 4 and one of acetone. The previously assigned chemical structure and stereochemistry of 4 were found to be correct.     

Non-crystallographic symmetry of crystal of neutral phospholipase A2 from Agkistrodon halys Pallas

Agkistrodotoxin, a neutral phospholipase A₂ with high presynaptic neurotoxicity from the venom of Agkistrodon halys Pallas, has been crystallized by hanging drop vapor diffusion method. The crystal belongs to P2₁ space group with the cell dimensions a = 10.836 nm, b=8.486nm, c = 7.082nm, β=109.87$ showing C2 pseu-do-symmetry. Diffraction data to 0. 26 nm resolution have been collected on a Siemens X-200B area detector. C2 pseu-do-symmetry suggests that there exists a non-crystallographic two-fold axis parallel to crystallographic b axis. Self-rotation function calculation with different integrated radius and resolution ranges using the program POLARRFN yields four stable high peaks corresponding to three more non-crystallographic two-fold axis and one special non-crystal-lographic symmetry. The molecules in the asymmetric unit are suggested to be arranged in a manner of "dimer of dimers" by inference.     

Crystallographic study of plastocyanins

Crystals of plastocyanins from pea and corn leaves have been obtained. Both are suitable for X-ray structure analysis with a resolution up to 1.8 Å. The crystal form of plastocyanin from pea leaves belongs to the space group P2₁2₁2₁ with unit cell dimensions: $\text{a = 49.0}\text{A}\text{?}\text{, b = 53.3}\text{A}\text{?}\text{, c = 82.6}\text{A}\text{?}$. The assumed number of protein molecules per asymmetric unit of the unit cell is two. Crystals of the oxidized (Cu²⁺) and reduced (Cu⁺) forms are isomorphic. No essential differences in spot intensities for the main zone with a resolution of 3 Å were revealed. The crystal form of plastocyanin from corn leaves belongs to the space group P1 with unit cell parameters: $\text{a = 24.8}\text{A}\text{?}\text{, b = 30.0}\text{A}\text{?}\text{, c = 58.5}\text{A}\text{?}$ and α = 96° 10′, β = 87°08′, γ = 78°40′. The assumed number of protein molecules per asymmetric unit is two.     

Crystal and molecular structure of potassium β-d-glucopyranose 6-sulphate

The crystal and molecular structure of potassium β-d-glucopyranose 6-sulphate has been determined by direct methods. The sugar ring has the expected ⁴C₁ conformation although the sulphate group causes flattening of the ring. The potassium ion has octahedral co-ordination involving oxygen atoms of five independent β-d-glucopyranose 6-sulphate molecules. The n.m.r. spectrum of the 6-sulphate in the solid state is consistent with the occurrence of two molecules in the unit cell related by a 2₁ symmetry axis.     

Hydration water molecules of nucleotide-free RNase T1 studied by NMR spectroscopy in solution

The hydration of uncomplexed RNase T₁ was investigated by NMR spectroscopy at pH 5.5 and 313 K. Two-dimensional heteronuclear NOE and ROE difference experiments were employed to determine the spatial proximity and the residence times of water molecules at distinct sites of the protein. Backbone carbonyl oxygens involved in intermolecular hydrogen bonds to water molecules were identified based on¹ J coupling constants. These coupling constants were determined from 2D-H(CA)CO and ¹⁵N-HSQC experiments with selective decoupling of the ^13CC nuclei during the t₁ evolution time. Our results support the existence of a chain of water molecules with increased residence times in the interior of the protein which is observed in several crystal structures with different inhibitor molecules and serves as a space filler between the -helix and the central -sheet. The analysis of¹ J_NC' coupling constants demonstrates that some of the water molecules seen in crystal structures are not involved in hydrogen bonds to backbone carbonyls as suggested by crystal structures. This is especially true for a water molecule, which is probably hydrogen bonded by the protonated carboxylate group of D76 and the hydroxyl group of T93 in solution, and for a water molecule, which was reported to connect four different amino acid residues in the core of the protein by intermolecular hydrogen bonds.     

Structure and phase behavior of O-stearoylethanolamine: A combined calorimetric, spectroscopic and X-ray diffraction study

Recent studies show that O-acylethanolamines (OAEs), structural isomers of the putative stress-fighting lipids, namely N-acylethanolamines (NAEs), can be derived from NAEs and are present in biological membranes under physiological conditions. In view of this, we have synthesized O-stearoylethanolamine (OSEA) as a representative OAE and investigated its phase behavior and crystal structure. The thermotropic phase transitions of OSEA dispersed in water and in 150 mM NaCl were characterized using calorimetric, spectroscopic, turbidimetric and X-ray diffraction studies. These studies have revealed that when dispersed in water OSEA undergoes a cooperative phase transition centered at 53.8 °C from an ordered gel phase to a micellar structure whereas in presence of 150 mM NaCl the transition temperature increases to 55.8 °C and most likely the bilayer structure is retained above the phase transition. O-Stearoylethanolamine crystallized in the orthorhombic space group P2₁2₁2₁ with four symmetry-related molecules in the unit cell. Single-crystal X-ray diffraction studies show that OSEA molecules adopt a linear structure with all-trans conformation in the acyl chain region. The molecules are organized in a tail-to-tail fashion, similar to the arrangement in a bilayer membrane. These studies are relevant to understanding the role of salt on the phase properties of this new class of lipids.     

Crystallization and preliminary X-ray crystallographic analysis of chitinase from barley seeds

Chitinase from barley seeds has been crystallized at room temperature using polyethylene glycol as precipitant. The crystal is monoclinic, belonging to the space group P2₁, with unit cell parameters of a = 69.43 Å, b = 44.55 Å, c = 81.41 Å, and β = 111.95 Å. The asymmetric unit seems to contain two molecules of chitinase with a corresponding crystal volume per protein mass (V_M) of 2.25 ų/Da and a solvent content of 45% by volume. The crystal diffracts to at least 2.0 Å with X-rays from a rotating anode source and is very stable in the X-ray beam. X-ray data have been collected to better than 2.2 Å Bragg spacing from a native crystal. © 1993 Wiley-Liss, Inc.     

Crystallization and preliminary crystallographic studies of the precursor and mature forms of a neutral lipase from the fungus Rhizopus delemar

A neutral lipase from the filamentous fungus Rhizopus delemar has been crystallized in both its proenzyme and mature forms. Although the latter crystallizes readily and produces a variety of crystal forms, only one was found to be suitable for X-ray studies. It is monoclinic (C2, a = 92.8 Å, b = 128.9 Å, c = 78.3 Å, β = 135.8) with two molecules in the asymmetric unit related by a noncrystallographic diad. The prolipase crystals are orthorhombic (P2₁2₁2₁, with a = 79.8 Å, b = 115.2 Å, c = 73.0 Å) and also contain a pair of molecules in the asymmetric unit. Initial results of molecular replacement calculations using the refined coordinates of the related lipase from Rhizomucor miehei identified the correct orientations and positions of the protein molecules in the unit cells of crystals of both proenzyme and the mature form. © 1994 John Wiley & Sons, Inc.     

Helical channels in crystals of gramicidin A and of a cesium--gramicidin A complex: an x-ray diffraction study.

X-ray crystallographic studies of gramicidin A crystallized from methanol (P2₁) and ethanol (P2₁2₁2₁), and of a Cs⁺ gramicidin A complex crystallized from methanol (P222₁, P2₁2₁2 or P2₁2₁2₁) are reported here. The asymmetric unit consists of two molecules of gramicidin A in the native crystals and four molecules in the cesium complex crystal. Patterson analyses show that gramicidin A in these crystals forms a cylindrical helical channel. In the two types of native gramicidin crystals, the diameter of this channel is about 5 å and its length is about 32 å. Cesium ions are bound inside this channel in crystals of the cesium-gramicidin A complex. The channel in this complex is considerably shorter (26 Å) and wider (6·8Å) than in the native forms. The Patterson maps of these three crystal forms are compatible with either the single-stranded β-helix (Urry, 1971) or the double-stranded parallel or anti-parallel, β-helix (Veatch et al., 1974).