Crystal parameters and molecular replacement of an anticholera toxin peptide complex.

TE33 is an Fab fragment of a monoclonal antibody raised against a 15-residue long peptide (CTP3), corresponding in sequence to residues 50-64 of the cholera toxin B subunit. Crystals of the complex between TE33 and CTP3 have been grown from 20% (w/v) polyethylene glycol-8000 at pH 4.0. The crystals are orthorhombic, space group P2(1)2(1)2, with unit cell dimensions a = 104.15, b = 110.61, and c = 40.68 A. X-Ray data have been collected to a resolution of 2.3 A. The asymmetric unit contains one molecule of Fab and one molecule of CTP3. The presence of CTP3 has been demonstrated by fluorescence quenching of the dissolved crystal after X-ray data collection. A molecular replacement solution was found based on the coordinates of DB3, an antiprogesterone Fab fragment.     

Overexpression, crystallization, and preliminary X-ray crystallographic analysis of the alanine racemase from Enterococcus faecalis v583

Alanine racemase, a bacterial enzyme belonging to the fold-type III group of pyridoxal 5'-phosphate (PLP)-dependent enzymes, has been shown to catalyze the interconversion between L- and D-alanine. The alanine racemase from the pathogenic bacterium Enterococcus faecalis v583 has been overexpressed in E. coli and was shown to crystallize an enzyme at 295 K, using polyethylene glycol (PEG) 8000 as a precipitant. X-ray diffraction data to 2.5 A has been collected using synchrotron radiation. The crystal is a member of the orthorhombic space group, C222(1), with unit cell parameter of a=94.634, b=156.516, c=147.878 A, and alpha=beta;=gamma=90 degrees. Two or three monomers are likely to be present in the asymmetric unit, with a corresponding Vm of 3.38 A3 Da(-1) and 2.26 A Da(-1) and a solvent content of 63.7% and 45.5%, respectively.     

Purification, crystallization, and preliminary X-ray crystallographic analysis of thermus thermophilus V(1)-ATPase B subunit.

The gene of V(1)-ATPase B subunit from the thermophilic eubacterium Thermus thermophilus has been cloned and the protein overproduced in Escherichia coli. The purified protein, with a molecular weight of 53.2 kDa, was crystallized from 10% (w/v) polyethylene glycol 1000, 120 mM magnesium chloride, and 100 mM Na-tricine, pH 8.0, by the vapor diffusion method. The crystals diffracted X-rays beyond 3.5 A on a synchrotron radiation source. The crystals belong to the monoclinic space group C2, with unit cell dimensions of a = 153.1 A, b = 129.6 A, c = 92.7 A, and beta = 100.3 degrees. Assuming that three or four molecules are contained in an asymmetric unit, the V(M) value is calculated as 2.8 or 2.1 A (3)/Da, respectively.     

Crystallization of an odorant-binding protein from cow nasal mucosa

The first odorant-binding protein isolated from mammalian nasal mucosa is a dimer of subunits of identical molecular weight (19,000) that specifically binds bell pepper odorants, "green" smelling compounds. The protein can be purified in milligram quantities from tissue extractions by sequential use of a silica based anion exchange column and Mono-P chromatofocussing column. In the presence of the binding compound 2-isobutyl-3-methoxypyrazine and of the organic solvent 2-methyl-2,4-pentanediol (17%, v/v), the protein crystallizes in the monoclinic space group P2(1), with unit cell constants a = 54.3 A, b = 66.7 A, c = 41.5 A, beta = 97.2 degrees. From consideration of the crystal packing densities compatible with its unit cell, it can be concluded that two subunits of 19,000 Mr each are present in the asymmetric unit. The diffraction pattern on still photographs of this crystal form of the protein extends to 2.5 A resolution and allows for a detailed crystallographic investigation.     

Assembly of Acanthamoeba myosin-II minifilaments. Model of anti-parallel dimers based on EM and X-ray diffraction of 2D and 3D crystals

Current models suggest that the first step in the assembly of Acanthamoeba myosin-II is anti-parallel dimerization of the coiled-coil tails with an overlap of 15 nm. Sedimentation equilibrium experiments showed that a construct containing the last 15 heptads and the non-helical tailpiece of the myosin-II tail (15T) forms dimers. To examine the structure of the 15T dimer, we grew 3D and 2D crystals suitable for X-ray diffraction and electron image analysis, respectively. For both conditions, crystals formed in related space and plane groups with similar unit cells (a=87.7 A, b=64.8 A, c=114.9 A, beta=108.0 degrees). Inspection of the X-ray diffraction pattern and molecular replacement analysis revealed the orientation of the coiled-coils in the unit cell. A 3D density map at 15A in-plane resolution derived from a tilt series of electron micrographs established the solvent content of the 3D crystals (75%, v/v), placed the coiled-coil molecules at the approximate translation in the unit cell, and revealed the symmetry relationships between molecules. On the basis of the low-resolution 3D structure, biochemical constraints, and X-ray diffraction data, we propose a model for myosin interactions in the anti-parallel dimer of coiled-coils that guide the first step of myosin-II assembly.     

QSAR studies on acylated histamine derivatives

H(3)-receptor antagonists activity in terms of -log K(i) for a series of acylated histamine derivatives was modeled using topological indices, namely negentropy (N), molecular redundancy (MRI), and valence connectivity index ((m)x(v)) indices. Excellent results were obtained in multiple regression analysis upon the introduction of a dummy parameter (indicator parameter). Consistent increase in R(2)(A) value indicated that inspite of observed collinearity the proposed models are significant.     

Crystallization and preliminary X-ray diffraction study of ferrocytochrome c2 from Rhodopseudomonas viridis

Crystals of ferrocytochrome c2 from a non-sulphur purple photosynthetic bacterium, Rhodopseudomonas viridis, have been grown from ammonium sulphate solution at pH 8.5 by the sitting-drop vapour-diffusion procedure. The crystals belong to the trigonal system, space group P3(1)21 (or its enantiomorph P3(2)21) with unit-cell dimensions of a = b = 75.8 A and c = 40.1 A, and diffract to at least 2.0 A resolution. Assuming that an asymmetric unit contains one protein molecule (approx. 12,300 Mr), the solvent content of the crystal is approximately 54.5% (v/v).     

Brief communication: Molecular characterization of O alleles at the ABO locus in Chilean Aymara and Huilliche Indians

A molecular characterization of alleles O1, O1variant (O1v), and the mutation G542A of the ABO blood group was performed in two Amerindian populations of Chile, the Aymara (n = 84) and the Huilliche (n = 75). In addition, a sample of 82 individuals of Santiago belonging to the mixed Chilean population was typed for comparative purposes. The polymorphisms which allow for molecular differentiation of different alleles of the O blood group were studied in genomic DNA. The mutations G188, G261-, G542A, T646A, and C771T, described for alleles O1, O1v, and G542A, were determined using the PCR-RFLP (polymerase chain reaction-restriction fragment length polymorphism) technique. All individuals studied were group O homozygotes for the deletion G261-, which defines the O1 alleles. Results obtained indicate that allele O1v exhibits frequencies of 0.65, 0.81, and 0.60 in Aymara, Huilliche, and Santiago populations, respectively. The frequencies of allele O1(G542A) were 0.119, 0.113, and 0.079 in the same populations. Frequencies for alleles O1 and O1v obtained in the Chilean populations studied concur with the results obtained by other authors, respecting the greater frequency of allele O1v as well as with its heterogeneous distribution in aboriginal South American populations. In Chilean populations, Allele G542A exhibits lower frequencies than those described for indigenous populations from Brazil and may be used as an Amerind admixture marker.     

The existence of two different forms of apo-electron-transferring flavoprotein

The association process of FAD and apo-electron-transferring flavoprotein (apoETF) from hog kidney was investigated. The reaction schemes which involve the association-dissociation of the protein species could be excluded by the light scattering data, which indicated that the molecular weights of apoETF and holoETF are identical. The binding reaction between FAD and a large excess of apoETF was monophasic and obeyed pseudo-first order kinetics. On the other hand, the reaction between apoETF and a large excess of FAD was biphasic: the fast phase obeyed a pseudo-first order reaction, and the rate of the slow phase was almost independent of FAD concentration. These results suggest the existence of two different forms of apoETF, as represented in the following reaction scheme: [formula: see text] where "F" is FAD, "H" is holoETF, and "A" and "A" are the different forms of apoETF. The kinetic parameters were determined as k-1 = 3.9 x 10(4) M-1.s-1, k-1 approximately 10(-5) s-1, k+2 = 1.0 x 10(-3) s-1, and k-2 = 3.1 x 10(-3) s-1, in 50 mM potassium phosphate buffer, pH 7.6, containing 0.3 mM EDTA, and 5% v/v glycerol, at 7 degrees C. The elution patterns of apoETF on molecular sieve chromatography were very different from that of holoETF although the true molecular weights were identical. This result suggests that the structure of apoETF differs greatly from that of holoETF.     

Molecular organization of cholesterol in polyunsaturated phospholipid membranes: a solid state 2H NMR investigation.

We compared the molecular organization of equimolar [3alpha-2H1]cholesterol in 18:0-18:1PC (1-stearoyl-2-oleoylphosphatidylcholine), 18:0-22:6PC (1-stearoyl-2-docosahexaenoylphosphatidylcholine), 18:0-20:4PC (1-stearoyl-2-arachidonylphosphatidylcholine) and 20:4-20:4PC (1,2-diarachidonylphosphatidylcholine) bilayers by solid state 2H NMR. Essentially identical quadrupolar splittings (delta v(r) = 45 +/- 1 kHz) corresponding to the same molecular orientation characterized by tilt angle alpha0 = 16 +/- 1 degrees were measured in 18:0-18:1PC, 18:0-22:6PC and 18:0-20:4PC. A profound difference in molecular interaction with dipolyunsaturated 20:4-20:4PC, in contrast, is indicated for the sterol. Specifically, the tilt angle alpha0 = 22 +/- 1 degrees (derived from delta v(r) = 37 +/- 1 kHz) is greater and its membrane intercalation is only 15 mol%.     

A 2H-NMR analysis of dihydrosterculoyl-containing lipids in model membranes: structural effects of a cyclopropane ring

The molecular properties of lipid multilayers of 1-palmitoyl-2-[dideutero]dihydrosterculoyl-sn-glycero-3-phosphocholine (PDSPC) were investigated by means of 2H-NMR. The transition from the liquid-crystalline phase to a more highly ordered phase was found to take place between -10 degrees C and -15 degrees C. The temperature variation of the quadrupolar splittings of specifically dideuterated PDSPC molecules was analyzed in terms of 'segmental' and 'geometrical' order parameters: the lower half of the sn-2 chain (from the site of the cyclopropane ring to the terminal methyl group) was more conformationally disordered than the upper half. The apparently abnormal increase of the quadrupolar splitting of the pro-S deuteron at the C-2' position, with increasing temperature, was attributed to a change in the average orientation of that C-2H bond with respect to the axis of motion, resulting in an increase of the 'geometrical' order parameter, S gamma. The molecular order parameter matrix elements, Sij, of the cyclopropane ring were derived from the experimental SC-2H order parameters using similarity transformations. The matrix S was diagonalized and the molecular order parameter of the cyclopropane ring, Smol (or S*33), was determined by assuming axial symmetry for such matrices associated with molecules in a liquid-crystal medium. A value of Smol = 0.59 +/- 0.04 at 25 degrees C was thus calculated. This value represents a discontinuity in the positional dependence of the molecular order parameter for the sn-2 chain of PDSPC, indicating that the cyclopropane ring provides a rigid barrier separating the lipid bilayer into two regions: an ordered region from the bilayer surface to the site of the cyclopropane ring and a much more disordered region thereafter to the center of the bilayer.     

Crystallization and preliminary X-ray study of horse pancreatic lipase

Horse (Equus caballus) pancreatic lipase (EC 3.1.1.3) has been crystallized using the hanging drop method of vapour diffusion at 20 degrees C. The best crystals were grown from an 8 mg/ml solution in 10 to 20% (w/v) polyethylene glycol 8000, 10 mM-MgCl2, 0.1 M-NaCl, 0.1 M-Mes buffer (pH 5.6). They reach dimensions of 0.8 mm x 0.4 mm x 0.6 mm. X-ray examination of the lipase crystals shows that they are orthorombic with a space group P2(1)2(1)2(1). Their cell dimensions are a = 79.8 A, b = 97.2 A c = 145.3 A. Two molecules per asymmetric unit give a Vm value of 2.82 A3/dalton (56% water content). Lipase crystals strongly diffract to at least 1.8 A resolution. Some molecular properties of horse lipase compared to those of the better-known porcine enzyme are also presented.     

Synthesis, in vitro, and in vivo characterization of an integrin alpha(v)beta(3)-targeted molecular probe for optical imaging of tumor

Integrin alpha(v)beta(3) is a widely-recognized target for the development of targeted molecular probes for imaging pathological conditions. alpha(v)beta(3) is a cell-surface receptor protein that is upregulated in various pathological conditions including osteoporosis, rheumatoid arthritis, macular degeneration, and cancer. The synthesis of an alpha(v)beta(3)-targeted optical probe 7 from compound 1, and its in vitro and in vivo characterization is described. A series of aliphatic carbamate derivatives of the potent non-peptide integrin antagonist 1 was synthesized and the binding affinity to alpha(v)beta(3) was determined in both enzyme linked immunosorbent assay (ELISA) and cell adhesion inhibition assays. The hydrophobic carbamate-linked appendages improved the binding affinity of the parent compound for alpha(v)beta(3) by 2-20 times. A Boc-protected neopentyl derivative in the series is shown to have the best binding affinity to alpha(v)beta(3) (IC(50)=0.72 nM) when compared to compound 1 as well as to c-RGDfV. Optical probe 7 utilizes the neopentyl linker and demonstrates increased binding affinity and significant tumor cell uptake in vitro as well as specific tumor accumulation and retention in vivo. These results illustrate the potential of employing integrin-targeted molecular probes based on 1 to image a multitude of diseases associated with alpha(v)beta(3) overexpression.     

Biphasic indentation of articular cartilage--I. Theoretical analysis

A mathematical solution has been obtained for the indentation creep and stress-relaxation behavior of articular cartilage where the tissue is modeled as a layer of linear KLM biphasic material of thickness h bonded to an impervious, rigid bony substrate. The circular (radius = a), plane-ended indenter is assumed to be rigid, porous, free-draining, and frictionless. Double Laplace and Hankel transform techniques were used to solve the partial differential equations. The transformed equations and boundary conditions yielded an integral equation of the Fredholm type which was analyzed asymptotically and solved numerically. Our asymptotic analyses showed that the linear KLM biphasic material behaves like an incompressible (v = 0.5) single-phase elastic solid at t = 0+; the instantaneous response of the material is governed by the shear modulus (mu s) of the solid matrix. The linear KLM biphasic material behaves like a compressible elastic solid with material properties defined by those of the solid matrix, i.e. (lambda s, mu s) or (mu s, v s) as t----infinity. The transient viscoelastic creep and stress-relaxation behavior, 0 less than t less than infinity, of this material is controlled by the frictional drag (which is inversely proportional to the permeability k) associated with the flow of the interstitial fluid through the porous-permeable solid matrix. For given values of the Poisson's ratio of the solid matrix v s and the aspect ratio a/h, where a is the radius of the indenter and h is the thickness of the layer, the creep behavior with respect to the dimensionless time H Akt/a2 is completely controlled by the load parameter P/2 mu sa2 and the stress relaxation behavior is completely controlled by the rate of compression parameter R0 = kH A/V0h where H A = lambda s + 2 mu s and the equilibrium strain u0/h. This mathematical solution may now be used to describe an indentation experiment on articular cartilage to determine the intrinsic material properties of the tissue, i.e. permeability k, and the elastic coefficients of the solid phase (lambda s, mu s) or (mu s, v s).     

Purification and structural determination of nontoxic lipid A obtained from the lipopolysaccharide of Salmonella typhimurium

Endotoxin extracted from the heptose-less mutant of Salmonella typhimurium was hydrolyzed in 0.1 N HCl in methanol/water (1:1, v/v) at 100 degrees C to yield lipid A, which was then fractionated on a Sephadex LH-20 column to yield a major monophosphoryl lipid A fraction. The monophosphoryl lipid A was further fractionated by preparative thin layer chromatography. This process yielded three major bands (TLC-1, -3, and -5) and two minor bands (TLC-7 and -9). The purity of these fractions was established by ion exchange and reverse phase high performance liquid chromatography. The thin layer fractions were analyzed by fast atom bombardment mass spectrometry. TLC-1 and -3 gave molecular ions (M-H)- at m/e 1730 and 1716, respectively. Both of these fractions contained beta-hydroxymyristic, lauric, and 3-myristoxymyristic acids in O-acyl linkages. The molecular formula and Mr of TLC-1 are C95H179O22N2P and 1731.16; those of TLC-3 are C94H177O22N2P and 1717.15. TLC-1 was a methyl homolog of TLC-3. The major component of TLC-5 (C80H151O22N2P and Mr = 1506.99) gave a molecular ion at m/e 1506 and contained two beta-hydroxymyristic acids and a lauric acid in the O-acyl linkages. The major component of TLC-7 (C66H125O19N2P and Mr = 1280.83) and the single component of TLC-9 gave molecular ions at m/e 1280 and 1098, respectively. TLC-7 contained lauric and beta-hydroxymyristic acids in the O-acyl linkages. TLC-9 (C54H103O18N2P and Mr = 1098.69) contained a single O-acylated beta-hydroxymyristate group. TLC-1 and -3 were nontoxic in the chick embryo lethality test and regressed established tumors in the syngeneic guinea pigs.     

ZL-DHP lignin model compound at the air-water interface

In this paper we present our surface chemistry studies of enzymatically polymerized, poly-coniferyl alcohol lignin model compound (dehydrogenate polymer a.k.a. ZL-DHP) at the air-water interface. Using the CHCl(3)/MeOH (5:1 v/v) spreading solvent, we found an average molecular area of ZL-DHP of approximately 1200 A(2). The monolayer expresses a high compressibility with a collapsed area of 500 A(2) and collapsed surface pressure of 28 mN m(-1). In the range of applied surface pressures, ZL-DHP polymer have no phase changes, as shown by the very high linearity (R=0.994) of absorbance vs. surface pressure cure. There was no symmetry transitions observed as shown by absence of shifts of absorption peak maximums.     

Crystallization and preliminary X-ray diffraction analysis of 5,10- methylenetetrahydrofolate dehydrogenase/cyclohydrolase from Thermoplasma acidophilum DSM 1728

The methylenetetrahydrofolate dehydrogenase/ cyclohydrolase (MTHFDC) from the thermoacidophilic archaeon Thermoplasma acidophilum is a 30.6 kDa molecular-mass enzyme that sequentially catalyzes the conversion of formyltetrahydrofolate to methylenetetrahydrofolate, with a preference for NADP as a cofactor, rather than NAD. In order to elucidate the functional and structural features of MTHFDC from archaeons at a molecular level, it was overexpressed in Escherichia coli and crystallized in the presence of its cofactor, NADP, at 295 K using polyethylene glycol (PEG) 4000 as a precipitant. The crystal is a member of the monoclinic space group P21, with the following unit cell parameters: a=66.333 A, b=52.868 A, c=86.099 A, and beta= 97.570o, and diffracts to a resolution of at least 2.40 A at the synchrotron. Assuming a dimer in the crystallographic asymmetric unit, the calculated Matthews parameter (VM) was 2.44 A3/Da and the solvent content was 49.7%.     

Contribution of K(v)2.1 channels to the delayed rectifier current in freshly dispersed smooth muscle cells from rabbit urethra

We have characterized the native voltage-dependent K(+) (K(v)) current in rabbit urethral smooth muscle cells (RUSMC) and compared its pharmacological and biophysical properties with K(v)2.1 and K(v)2.2 channels cloned from the rabbit urethra and stably expressed in human embryonic kidney (HEK)-293 cells (HEK(Kv2.1) and HEK(Kv2.2)). RUSMC were perfused with Hanks' solution at 37°C and studied using the patch-clamp technique with K(+)-rich pipette solutions. Cells were bathed in 100 nM Penitrem A (Pen A) to block large-conductance Ca(2+)-activated K(+) (BK) currents and depolarized to +40 mV for 500 ms to evoke K(v) currents. These were unaffected by margatoxin, κ-dendrotoxin, or α-dendrotoxin (100 nM, n = 3-5) but were blocked by stromatoxin-1 (ScTx, IC(50) ～130 nM), consistent with the idea that the currents were carried through K(v)2 channels. RNA was detected for K(v)2.1, K(v)2.2, and the silent subunit K(v)9.3 in urethral smooth muscle. Immunocytochemistry showed membrane staining for both K(v)2 subtypes and K(v)9.3 in isolated RUSMC. HEK(Kv2.1) and HEK(Kv2.2) currents were blocked in a concentration-dependent manner by ScTx, with estimated IC(50) values of ～150 nM (K(v)2.1, n = 5) and 70 nM (K(v)2.2, n = 6). The mean half-maximal voltage (V(1/2)) of inactivation of the USMC K(v) current was -56 ± 3 mV (n = 9). This was similar to the HEK(Kv2.1) current (-55 ± 3 mV, n = 13) but significantly different from the HEK(Kv2.2) currents (-30 ± 3 mV, n = 11). Action potentials (AP) evoked from RUSMC studied under current-clamp mode were unaffected by ScTx. However, when ScTx was applied in the presence of Pen A, the AP duration was significantly prolonged. Similarly, ScTx increased the amplitude of spontaneous contractions threefold, but only after Pen A application. These data suggest that K(v)2.1 channels contribute significantly to the K(v) current in RUSMC.     

Cell surface-expressed Thomsen-Friedenreich antigen in colon cancer is predominantly carried on high molecular weight splice variants of CD44.

Increased mucosal expression of TF, the Thomsen-Friedenreich oncofetal blood group antigen (galactose beta1-3 N-acetylgalactosamine alpha-) occurs in colon cancer and colitis. This allows binding of TF-specific lectins, such as peanut agglutinin (PNA), which is mitogenic to the colorectal epithelium. To identify the cell surface TF-expressing glycoprotein(s), HT29 and Caco2 colon cancer cells were surface-labeled with Na[(125)I] and subjected to PNA-agarose affinity purification and electrophoresis. Proteins, approximately 110-180 kDa, present in HT29 but not Caco2 were identified by Western blotting as high molecular weight splice variants of CD44 (CD44v). Selective removal of TF antigen by Streptococcus pneumoniae endo-alpha-N-acetylgalactosaminidase substantially reduced PNA binding to CD44v. Immunoprecipitated CD44v from HT29 cell extracts also expressed sialyl-Tn (sialyl 2-6 N-acetylgalactosaminealpha-). Incubation of PNA 15 microg/ml with HT29 cells caused no additional proliferative effect in the presence of anti-CD44v6 mAb. In colon cancer tissue extracts (N = 3) PNA bound to CD44v but not to standard CD44. These data show that CD44v is a major PNA-binding glycoprotein in colon cancer cells. Because CD44 high molecular weight splice variants are present in colon cancer and inflammatory bowel disease tissue but are absent from normal mucosa, these results may also explain the increased PNA reactivity in colon cancer and inflammatory bowel disease. The coexpression of oncofetal carbohydrate antigens TF and sialyl-Tn on CD44 splice variants provides a link between cancer-associated changes in glycosylation and CD44 splicing, both of which correlate with increased metastatic potential.     

Preliminary crystallographic investigations of two phycobiliproteins.

Single crystal x-ray diffraction investigations are in progress on two phycobiliproteins. C-phycocyanin from Anabaena variabilis crystallizes in space group P63 with a = b = 154 A and c = 40 A. The crystallographic asymmetric unit is (alphabeta)2 with a total molecular mass of 7.0-10(4) daltons. B-phycoerythrin from Porphyridium cruentum crystallizes in space group R3 with a = b = 189 A and c = 60 A. This molecule has the unusual molecular stoichiometry (alphabeta)6gamma and the crystallographic asymmetric unit is (alphabeta)2gamma1/3. This requires that the gamma chain undergo a perfect 3-fold disordering about the crystallographic 3 axis, i.e. the gamma chain must occupy three symmetry-equivalent positions, each with an occupancy of one-third.