Structural basis of non-specific lipid binding in maize lipid-transfer protein complexes revealed by high-resolution X-ray crystallography

Non-specific lipid-transfer proteins (nsLTPs) are involved in the movement of phospholipids, glycolipids, fatty acids, and steroids between membranes. Several structures of plant nsLTPs have been determined both by X-ray crystallography and nuclear magnetic resonance. However, the detailed structural basis of the non-specific binding of hydrophobic ligands by nsLTPs is still poorly understood. In order to gain a better understanding of the structural basis of the non-specific binding of hydrophobic ligands by nsLTPs and to investigate the plasticity of the fatty acid binding cavity in nsLTPs, seven high-resolution (between 1.3 A and 1.9 A) crystal structures have been determined. These depict the nsLTP from maize seedlings in complex with an array of fatty acids.A detailed comparison of the structures of maize nsLTP in complex with various ligands reveals a new binding mode in an nsLTP-oleate complex which has not been seen before. Furthermore, in the caprate complex, the ligand binds to the protein cavity in two orientations with equal occupancy. The volume of the hydrophobic cavity in the nsLTP from maize shows some variation depending on the size of the bound ligands. The structural plasticity of the ligand binding cavity and the predominant involvement of non-specific van der Waals interactions with the hydrophobic tail of the ligands provide a structural explanation for the non-specificity of maize nsLTP. The hydrophobic cavity accommodates various ligands from C10 to C18. The C18:1 ricinoleate with its hydroxyl group hydrogen bonding to Ala68 possibly mimics cutin monomer binding which is of biological importance. Some of the myristate binding sites in human serum albumin resemble the maize nsLTP, implying the importance of a helical bundle in accommodating the non-specific binding of fatty acids.

Alleviation of pre-exposure to low-dose 16O8+ ion on mouse testicular histological damage induced by subsequent high-dose irradiation

The testes of the B6C3F1 hybrid strain mice were irradiated with 0.05 Gy of 16O8+ ion as the pre-exposure dose (D1), and were then irradiated with 2 Gy of 16O8+ ion as challenging radiation dose (D2) at 4 h after per-exposure. Testicular morphology was observed by light microscope at 35th day after radiation. The results showed that irradiation of mouse testes with 2 Gy of 16O8+ ion significantly impaired, mainly reduction of tubule diameter and decrease or loss of germ cells in various developing stages, especially spermatogenic elements. Pre-exposure to a low-dose (0.05 Gy) of 16O8+ ion significantly alleviated above mentioned damage on testicular morphology induced by subsequent a high-dose (2 Gy) radiation.

Lactate dehydrogenase from the hyperthermophilic archaeon Methanococcus jannaschii: overexpression, crystallization and preliminary X-ray analysis

L(+)-Lactate dehydrogenase (LDH) is a key enzyme in anaerobic metabolism which converts pyruvate to lactate. LDH from the hyperthermophilic archaebacterium Methanococcus jannaschii has been overexpressed in Escherichia coli and crystallized in two crystal forms at 297 K using 2-methyl-2,4-pentanediol as precipitant. Type I crystals grew rapidly and diffracted to at least 2.8 A Bragg spacing upon exposure to Cu Kalpha X-rays. X-ray diffraction data to 2.9 A have been collected from a native crystal. The type I crystal is tetragonal, belonging to the space group P4(2)2(1)2, with unit-cell parameters a = b = 99.74, c = 170.00 A. The asymmetric unit contains two LDH subunits, with a corresponding crystal volume per protein mass (V(m)) of 3.05 A(3) Da(-1) and a solvent content of 59.7%. Type II crystals, which grew more slowly, diffracted to at least 1.8 A Bragg spacing upon exposure to Cu Kalpha X-rays. X-ray diffraction data to 1.9 A have been collected from a native crystal. The type II crystal is orthorhombic, belonging to the space group P2(1)2(1)2, with unit-cell parameters a = 47.65, b = 125.10, c = 58.08 A. The asymmetric unit contains a single LDH subunit, with a corresponding crystal volume per protein mass (V(m)) of 2.50 A(3) Da(-1) and a solvent content of 50.8%. Therefore, the type II crystal is more suitable for high-resolution structure determination than the type I crystal.

Overexpression of monocyte-derived cytokines in active psoriasis: a relation to coexistent arthropathy

An overexpression of inflammatory cytokines has been found in the lesional skin as well as peripheral blood in patients with psoriasis, although its etiological significance is not yet understood. In order to evaluate the cell type responsible for the elevated cytokines in the peripheral blood, we investigated cytokine profiles of the fractionated peripheral blood mononuclear cells (PBMCs) in 30 patients with psoriasis and 27 healthy controls. Without stimulation, higher levels of interleukin (IL)-1beta, IL-6, and IL-8 were produced by freshly isolated PBMCs from the patients than those from the controls. In the fractionated PBMCs, the monocyte-rich fractions were mainly responsible for the production of these cytokines and mRNA. The elevated levels of monocyte-derived cytokine mRNAs decreased following successful treatment with cyclosporin A. Although no correlation was found between the cytokine levels and the psoriasis area and severity index (PASI) scores, patients with arthropathy showed significantly high production levels of IL-1beta, IL-6, and IL-8. These findings suggest that monocytes are the major cell source producing inflammatory cytokines in the peripheral blood of psoriasis, and the increased cytokine levels are related to the coexistent arthropathy rather than the severity of cutaneous lesions.

Internalization of constitutive desmogleins with the subsequent induction of desmoglein 2 in pemphigus lesions

Acantholytic blisters in pemphigus vulgaris (PV) and pemphigus foliaceus (PF) are caused by a dissociation of desmosomes mediated by autoantibodies against desmoglein (Dsg) 3 and Dsg 1, respectively. The blistering occurs at the suprabasilar level in PV and at the subcorneal level in PF, which corresponds to the distribution of target antigens in the epidermis: there is a more prominent expression of Dsg 1 in the upper layer, whereas Dsg 3 is more prominent in the lower layer. To elucidate the histogenesis of acantholysis, we studied the alterations of the desmosomal components and the expression pattern of Dsg isoforms in the lesional and perilesional epidermis of pemphigus patients. The results demonstrated an internalization of the desmosomes in the lower epidermis of PV, PF and pemphigus vegetans. A similar phenomenon was induced in monolayers of keratinocytes cultured with PV sera. However, little change was observed in E-cadherin expression until acantholysis became manifest. This internalization occurred prior to overt acantholysis, and was frequently associated with the induction of Dsg 2 expression in the basilar or lower layers of the epidermis. These findings indicate an alteration of Dsg isoform expression in subclinical pemphigus lesions, which might be related to the characteristic acantholytic patterns: the suprabasilar layer in PV and the upper epidermis in PF.

Interleukin-15 is not a constitutive cytokine in the epidermis, but is inducible in culture or inflammatory conditions

The regulation in the skin of interleukin-15 (IL-15), a potent modulator of T-cell-mediated immune responses, is not fully understood. We investigated the levels of IL-15 and its mRNA produced by epidermal and cultured keratinocytes and found that normal keratinocytes did not constitutively express IL-15 in the epidermis, but in culture began to produce the cytokine. Some epidermal keratinocytes expressed IL-15 in inflammatory conditions associated with infiltration of neutrophils and eosinophils. IL-15 was detected only in the cell lysates, not in the supernatants of cultured keratinocytes. Dexamethasone (10(-5)-10(-6) M) markedly inhibited IL-15 mRNA expression by normal and transformed keratinocytes in a range of pharmacological concentrations. IFN-gamma (200 and 400 U/ml) slightly increased the IL-15 message level in a squamous cell carcinoma cell line, HSC-5, in a dose-dependent fashion, whereas no significant change was observed in cultured normal human keratinocytes. Our data indicate that IL-15 is not a constitutive cytokine in epidermal keratinocytes but is inducible.

Chromosomal aberrations induced by 12C6+ heavy ion irradiation in spermatogonia and spermatocytes of mice

The testes of Kun-Ming strain mice were radiated with different doses of 12C6+ ion or 60Co gamma-ray. Chromosomal aberrations induced in spermatogonia and spermatocytes were analyzed by the air-drying method. The relative biological effectiveness (RBE) of 12C6+ ion was calculated with respect to 60Co gamma-ray for the induction of chromosomal aberrations. The 12C6+ ion and 60Co gamma-ray dose-response relationships for chromosomal aberrations were plotted by linear quadratic models. The results showed that there was an increase in frequency of chromosomal aberrations in all the treated groups compared to controls. The RBE values were 1.67 for aberrations of spermatogonia and 1.66 for aberrations of spermatocytes for a dose of 2.0 Gy. Moreover, a different distribution of the various types of aberrations has been found for 12C6+ ion and 60Co gamma-ray irradiations. The dose-response relationships for 12C6+ ion and 60Co gamma-ray exhibited negative curvature in both spermatogonia and spermatocytes groups: the frequencies of aberrations increased sharply at low doses and exhibited less sharp increases for higher doses, which may be related to an interaction between the chromosomal damage and a block in cell cycle. Our results may provide useful information for the assessment of genetic risks of humans exposed to heavy ions.

Effects of pre-exposure of mouse testis with low-dose (16)O8+ ions or 60Co gamma-rays on sperm shape abnormalities, lipid peroxidation and superoxide dismutase (SOD) activity induced by subsequent high-dose irradiation

PURPOSE

To investigate the effects of pre-exposure of mouse testis with low-doses of (16)O8+ ions or 60Co gamma-rays on sperm shape abnormalities, lipid peroxidation and superoxide dismutase (SOD) activity induced by subsequent high-dose irradiation.

MATERIALS AND METHODS

Testes of the B6C3F1 hybrid strain mice were pre-irradiated with 0.05 Gy of (16)O8+ ions or 60Co gamma-rays and then after 4 h given a test irradiation with 2 Gy of the same radiation type. SOD activity and thiobarbituric acid reactive substances (TBARS) in the testes were determined by spectrophotometric and TBA methods respectively at 4 h after irradiation. Testis weight, sperm count and sperm morphology were analysed at day 35 after irradiation.

RESULTS

Compared with controls, there was a significant increase in SOD activity and a significant decrease in TBARS level of pretreated testes. Testis weight loss, sperm count reduction and sperm abnormalities were significantly lower in the pretreated testes. The bioeffects of a 2 Gy dose of (16)O8+ ions relative to 60Co gamma-rays were 1.84 +/- 0.28 for testis weight, 1.22 +/- 0.25 for sperm count and 1.29 +/- 0.10 for sperm abnormalities.

CONCLUSIONS

These data suggest that pre-exposure of testes with a low dose of heavy ions or gamma-rays renders the organ more resistant to subsequent high-dose irradiation. The increase of SOD activity and the decrease of lipid peroxidation levels induced by low-dose ionizing irradiation may be involved in this resistance. The effects with heavy ion irradiation were greater than with gamma-rays.

Defining GC-specificity in the minor groove: side-by-side binding of the di-imidazole lexitropsin to C-A-T-G-G-C-C-A-T-G

BACKGROUND

Polyamide drugs, such as netropsin, distamycin and their lexitropsin derivatives, can be inserted into a narrow B-DNA minor groove to form 1:1 complexes that can distinguish AT base pairs from GC, but cannot detect end-for-end base-pair reversals such as TA for AT. In contrast, 2:1 side-by-side polyamide drug complexes potentially are capable of such discrimination. Imidazole (Im) and pyrrole (Py) rings side-by-side read a GC base pair with the Im ring recognizing the guanine side. But the reason for this specific G-Im association is unclear because the guanine NH2 group sits in the center of the groove. A 2:1 drug:DNA complex that presents Im at both ends of a GC base pair should help unscramble the issue of imidazole reading specificity.

RESULTS

We have determined the crystal structure of a 2:1 complex of a di-imidazole lexitropsin (DIM), an analogue of distamycin, and a DNA decamer with the sequence C-A-T-G-G-C-C-A-T-G. The two DIM molecules sit antiparallel to one another in a broad minor groove, with their cationic tails widely separated. Im rings of one drug molecule stack against amide groups of the other. DIM1 rests against nucleotides C7A8T9G10 of strand 1 of the helix, whereas DIM2 rests against G14G15C16C17 on strand 2. All DIM amide nitrogens donate hydrogen bonds to N and O atoms on the floor of the DNA groove and, in addition, the two Im rings on DIM2 accept hydrogen bonds from guanine N2 amines, thereby providing specific reading. The guanine N2 amine can bond to Im on its own side of the groove, but not on the cytosine side, because of limits on close approach of the two Im rings and the geometry of sp2 hybridization about the amide nitrogen.

CONCLUSIONS

Im and Py rings distinguish AT from GC base pairs because of steric factors involving the bulk of the guanine amine, and the ability of Im to form a hydrogen bond with the amine. Side-by-side Im and Py rings differentiate GC from CG base pairs because of tight steric contacts and sp2 hybridization at the amine nitrogen atom, with the favored conformations being G/Im,Py/C and C/Py,Im/G. Discrimination between AT and TA base pairs may be possible using bulkier rings, such as thiazole to select the A end of the base pair.

Structure of a DNA analog of the primer for HIV-1 RT second strand synthesis

The non-self-complementary DNA decamer C-A-A-A-G-A-A-A-A-G/C-T-T-T-T-C-T-T-T-G is a DNA/DNA analogue of a portion of the polypurine tract or PPT, which is a RNA/DNA hybrid that serves as a primer for synthesis of the (+) DNA strand by HIV reverse transcriptase (RT), and which is not digested by the RNase H domain of reverse transcriptase following (-) strand synthesis. The same unusual conformation that eludes RNase H, thought to be a change in width of minor groove, may also be responsible for the inhibition of HIV RT by minor groove binding drugs such as distamycin and their bis-linked derivatives. The present X-ray crystal structure of this DNA decamer exhibits the usual properties of A-tract B-DNA under biologically relevant conditions: large propeller twist of base-pairs, narrowed minor groove, and a straight helix axis. Groove narrowing is fully developed in the A-A-A-A region, but not in the A-A-A region, which previous investigators have proposed as being too short to exhibit typical A-tract properties. The RNA/DNA hybrid produced by HIV reverse transcriptase during (-) strand synthesis presumably forms a "heteromerous" or H-helix with narrower minor groove than an A-helical RNA/RNA duplex. If the narrowing of minor groove in A-tract H-helices is comparable to that seen in A-tract B-helices, then the narrowed minor groove of the polypurine tract could make the second primer site both (1) impervious to RNase H digestion, and (2) susceptible to inhibition by minor groove binding drugs.

Abnormal desmoglein expression by squamous cell carcinoma cells

Abnormal expression of cell adhesion molecules and related proteins has been observed in various carcinoma cells. We compared expression patterns of desmosomal cadherins, E-cadherin, and cytoplasmic plaque proteins of four different human squamous cell carcinoma cell lines and in vivo squamous cell carcinoma cells with those of normal human keratinocytes. Unlike normal human keratinocytes, the squamous cell carcinoma cells, both in culture and in vivo, exhibited diminished or unusual expression of desmoglein 3 and desmoglein 1, which bear pemphigus vulgaris and pemphigus foliaceus antigens, respectively. Abnormal expression of E-cadherin and cytoplasmic plaque proteins such as desmoplakin and plakoglobin was also observed. Western blotting study demonstrated that three squamous cell carcinoma cell lines expressed two desmogleins with a predominant 150 kDa molecule, and a minor 130 kDa one. Although these molecular sizes were similar to those of cultured normal human keratinocytes, the 130 kDa desmoglein, which usually carries pemphigus antigenic epitopes, was weakly or negatively reactive with pemphigus vulgaris serum. One squamous cell carcinoma cell line showed a doublet of 140 and 145 kDa bands in addition to the 130 kDa band. All the carcinoma cell lines constantly expressed desmoglein 2 and desmoglein 3 mRNA, whereas cultured normal human keratinocytes always expressed desmoglein 1 and desmoglein 3 mRNA, with or without desmoglein 2 mRNA. These findings indicate that the squamous cell carcinoma cells revealed abnormal expression of desmoglein isoforms, which may be related to tumor cell kinetics such as cell invasion and metastasis.

Identifying the physiological electron transfer site of cytochrome c peroxidase by structure-based engineering

A technique was developed to evaluate whether electron transfer (ET) complexes formed in solution by the cloned cytochrome c peroxidase [CcP(MI)] and cytochromes c from yeast (yCc) and horse (hCc) are structurally similar to those seen in the respective crystal structures. Site-directed mutagenesis was used to convert the sole Cys of the parent enzyme (Cys 128) to Ala, and a Cys residue was introduced at position 193 of CcP(MI), the point of closest contact between CcP(MI) and yCc in the crystal structure. Cys 193 was then modified with a bulky sulfhydryl reagent, 3-(N-maleimidylpropionyl)-biocytin (MPB), to prevent yCc from binding at the site seen in the crystal. The MPB modification has no effect on overall enzyme structure but causes 20-100-fold decreases in transient and steady-state ET reaction rates with yCc. The MPB modification causes only 2-3-fold decreases in ET reaction rates with hCc, however. This differential effect is predicted by modeling studies based on the crystal structures and indicates that solution phase ET complexes closely resemble the crystalline complexes. The low rate of catalysis of the MPB-enzyme was constant for yCc in buffers of 20-160 mM ionic strength. This indicates that the low affinity complex formed between CcP(MI) and yCc at low ionic strength is not reactive in ET.

Use of the minimal function for partial structure development in direct methods

The shake-and-bake procedure, which is based on the minimal function, has been tested and shown to be extremely effective in molecular-fragment recycling applications. Correctly positioned fragments as small as 5% of the scattering power of the structure typically have a 50% chance of producing a solution in a single recycling trial. While starting models for tangent-formula recycling methods normally require an average r.m.s. displacement error of less than approximately 0.25 A from the refined structure to ensure an adequate chance of success, the shake-and-bake method often tolerates r.m.s. model errors well in excess of 0.5 A. Tests indicate that the new method can outperform traditional tangent-formula procedures in difficult structural applications involving multiple copies of pseudosymmetrically related molecules or low-resolution data.

A cation binding motif stabilizes the compound I radical of cytochrome c peroxidase

Cytochrome c peroxidase reacts with peroxide to form compound I, which contains an oxyferryl heme and an indolyl radical at Trp-191. The indolyl free radical has a half-life of several hours at room temperature, and this remarkable stability is essential for the catalytic function of cytochrome c peroxidase. To probe the protein environment that stabilizes the compound I radical, we used site-directed mutagenesis to replace Trp-191 with Gly or Gln. Crystal structures of these mutants revealed a monovalent cation binding site in the cavity formerly occupied by the side chain of Trp-191. Comparison of this site with those found in other known cation binding enzymes shows that the Trp-191 side chain resides in a consensus K+ binding site. Electrostatic potential calculations indicate that the cation binding site is created by partial negative charges at the backbone carbonyl oxygen atoms of residues 175 and 177, the carboxyl end of a long alpha-helix (residues 165-175), the heme propionates, and the carboxylate side chain of Asp-235. These features create a negative potential that envelops the side chain of Trp-191; the calculated free energy change for cation binding in this site is -27 kcal/mol (1 cal = 4.184J). This is more than sufficient to account for the stability of the Trp-191 radical, which our estimates suggest is stabilized by 7.8 kcal/mol relative to a Trp radical in solution.

Crystal structure of cholesteryl butanoate at 123 K

Cholesteryl butanoate has a complex crystal structure that differs from those of the three main structure type for cholesteryl esters. It contains four molecules (C31H52O2) unrelated by crystal symmetry. The molecules are packed in almost planar sheets and have molecular long axes nearly parallel. However, the molecules have different orientations about their long axes and furthermore, in a given sheet, one of the independent molecules is antiparallel to the other three. Viewed down the molecular long axes, each molecule has six nearest neighbors, but the detailed environment is different for the four independent molecules. Thus the molecular arrangement has features that are characteristic of the short-range order present in the cholesteric mesophase. The monotropic transformation from the crystalline to the cholesteric phase occurs at 98 degrees C. The crystal structure has been accurately determined using 12,146 independent X-ray reflections having sin theta/lambda < 0.63 A-1. All hydrogen atoms were located from a difference Fourier and were included in a refinement that gave R(F2) = 0.064. The C-C bond lengths have sigma = 0.003 A and C-C-C bond angles have sigma = 0.2 degrees. Conformations for the steroid ring system are similar but there are differences in the C17 side chains and the butanoate chains of the four independent molecules. Analysis of atomic m.s. displacement tensors using a segmented-body model indicates that there are internal librations involving both the C17 and butanoate chains in all molecules.

Role of methionine 230 in intramolecular electron transfer between the oxyferryl heme and tryptophan 191 in cytochrome c peroxidase compound II

The kinetics of electron transfer from cytochrome c (CC) to yeast cytochrome c peroxidase (CcP) compound I were studied by flash photolysis and stopped-flow spectroscopy. Flash photolysis studies employed horse CC derivatives labeled at specific lysine amino groups with (dicarboxybipyridine)bis-(bipyridine)ruthenium (Ru-CC). Initial electron transfer from Ru-CC reduced the indole radical on Trp-191 of CcP compound I [CMPI(IV,R.)], producing CMPII(IV,R). This reaction was biphasic for each of several Ru-CC derivatives, with rate constants which varied according to the position of the Ru label. For Ru-27-CC labeled at lysine 27, rate constants of 43,000 and 1600 s-1 were observed at pH 5.0 in 2 mM acetate. After reduction of the indole radical by Ru-CC, intramolecular electron transfer from Trp-191 to the oxyferryl heme in CMPII(IV,R) was observed, producing CMPII(III,R.). The rate constant and extent of this intramolecular electron transfer reaction were independent of both the protein concentration and the Ru-CC derivative employed. The rate constant decreased from 1100 s-1 at pH 5 to 550 s-1 at pH 6, while the extent of conversion of CMPII(IV,R) to CMPII(III,R.) decreased from 56% at pH 5 to 29% at pH 6. The reaction was not detected at pH 7.0 and above. The pH dependence of the rate and extent of this internal electron transfer reaction paralleled the pH dependence of the rate of bimolecular reduction of CMPII(IV,R) by native horse CC measured by stopped-flow spectroscopy at high ionic strength.(ABSTRACT TRUNCATED AT 250 WORDS)

The crystal structure of 1,2-dipalmitoyl-sn-glycerol at 123 K

At 123 K, the crystal structure of 1,2-dipalmitoyl-sn-glycerol (C35H68O5, M(r) = 568.9) is monoclinic with space group P2(1), a = 5.480(1), b = 7.301(1), c = 43.145(7) A, beta = 92.91(1) degrees, V = 1724 A3, Dc = 1.0960 g cm-3 and Z = 2. Integrated X-ray intensities for 3574 independent reflections were measured with Ni-filtered Cu-K alpha radiation (lambda = 1.5418 A, mu = 0.56 mm-1), and these were all used in a full-matrix least-squares refinement which gave R(F2) = 0.142. Bond lengths and angles have e.s.d.s less than 0.01 A and 0.1 degrees for non-hydrogen atoms. Comparison with a previously reported study of the room temperature structure shows a very similar orthorhombic mode of chain packing but significant conformational differences in the polar headgroup. These changes may occur in conjunction with small changes in enthalpy (less than 1 kJ/mol) observed at 202, 193 and 136 K and with a discontinuity in the unit cell volume observed in the range 200-190 K. Analysis of the atomic mean square displacements at 123 K indicates the presence of internal torsional vibrations in the headgroup region that involve the carbonyl and hydroxyl O-atoms.

Crystal structure of cholestanyl caprylate and binary phase behavior with cholesteryl caprylate

The crystal structure of cholestanyl n-octanoate (caprylate) (C35H62O2) is monoclinic with space group A2 and cell dimensions a = 10.103(7), b = 7.646(7), c = 87.63(7) A, beta = 90.51(6) degrees; Z = 8 [two molecules (A, B) in asymmetric unit], V = 6769 A3, Dc = 1.010 g cm-3. Integrated X-ray intensities for 3798 reflections with I greater than 2 sigma (I) were measured with a rotating anode diffractometer at room temperature. The structure was determined using direct methods. Block diagonal least squares refinement gave R = 0.111. Molecules A and B have almost fully extended conformations, but differ significantly in the rotation about the ester bond and in the C17 chains. The molecular packing in the crystal structure of cholestanyl caprylate consists of stacked bilayers each having d002 = 43.8 A in thickness and within each bilayer, cholestanols pack with cholestanols and caprylate chains pack with caprylate chains. The crystal structure is very similar to that of cholesteryl myristate but is quite different from that of cholesteryl caprylate. The phase equilibria of the cholestanyl caprylate/cholesteryl caprylate binary system have been shown to involve limited mutual solubility of the two components and to have a eutectic point at 73% cholestanyl caprylate. The cholesteric mesophase is monotropic at all compositions except for a narrow range near the eutectic point where it is enantiotropic.