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1.
Based on the time-dependent density functional response theory, an approach for the prediction of optical rotations of enantiomers of conformationally flexible molecules was developed. The method was applied successfully for the determination of the absolute configuration of trans-2-fluorocycloalkanol acetates with different ring sizes. The largest deviations between experimental and theoretical [alpha](D) values are 10 deg x [dm x (g/cc)](-1) (about 20% error). These theoretical results suggest that the optical rotation in these molecules is dominated by the local (1R;2R) configuration of the two substituents and that different ring and even axial/equatorial orientations play a less important role. 相似文献
2.
Yersiniabactin (Ybt), the siderophore produced by Yersinia pestis, has been crystallized successfully in the ferric complex form and the crystal structure has been determined. The crystals are orthorhombic with a space group of P2(1)2(1)2(1) and four distinct molecules per unit cell with cell dimensions of a=11.3271(+/-0.0003)A, b=22.3556(+/-0.0006)A, and c=39.8991(+/-0.0011)A. The crystal structure of ferric Ybt shows that the ferric ion is coordinated as a 1:1 complex by three nitrogen electron pairs and three negatively charged oxygen atoms with a distorted octahedral coordination. The molecule displays a Delta absolute configuration with chiral centers at N2, C9, C10, C12, C13, and C19 in R, R, R, R, S, S configurations, respectively. Few of the crystal structures of siderophores have been solved, and those which have been are of simple hydroxamate and catechol types such as ferrioxamine B and agrobactin. To our knowledge this is the first report of the ferric crystal structure of 5-member heterocycle siderophore. 相似文献
4.
The plasmepsins are key enzymes in the life cycle of the Plasmodium parasites responsible for malaria. Since plasmepsin inhibition leads to parasite death, these enzymes have been acknowledged to be important targets for the development of new antimalarial drugs. The development of effective plasmepsin inhibitors, however, is compounded by their genomic diversity which gives rise not to a unique target for drug development but to a family of closely related targets. Successful drugs will have to inhibit not one but several related enzymes with high affinity. Structure-based drug design against heterogeneous targets requires a departure from the classic 'lock-and-key' paradigm that leads to the development of conformationally constrained molecules aimed at a single target. Drug molecules designed along those principles are usually rigid and unable to adapt to target variations arising from naturally occurring genetic polymorphisms or drug-induced resistant mutations. Heterogeneous targets need adaptive drug molecules, characterised by the presence of flexible elements at specific locations that sustain a viable binding affinity against existing or expected polymorphisms. Adaptive ligands have characteristic thermodynamic signatures that distinguish them from their rigid counterparts. This realisation has led to the development of rigorous thermodynamic design guidelines that take advantage of correlations between the structure of lead compounds and the enthalpic and entropic components of the binding affinity. In this paper, we discuss the application of the thermodynamic approach to the development of high affinity (K(i) - pM) plasmepsin inhibitors. In particular, a family of allophenylnorstatine-based compounds is evaluated for their potential to inhibit a wide spectrum of plasmepsins. 相似文献
6.
The aim of the present research is to obtain blending between a polymer and a (polymerized) solvent on the molecular level. Because of its rigid rod structure, poly(gamma-benzyl-L-glutamate) (PBLG) is chosen as the polymer. Benzyl methacrylate (BzMA) has been chosen as the solvent for two reasons. First, the structure of the solvent is very similar to the structure of the side chain of PBLG, favoring interactions between the two materials. Second, the solvent can be polymerized, because of the presence of a C=C bond. In cast films of PBLG and BzMA separate zones of the polymer and solvent are present. Wide-angle X-ray diffraction and Raman results show that upon heating the cast films homogenization occurs and solvent molecules intercalate between the helices of PBLG. At 150 degrees C a hexagonal packing is obtained. The dimensions of the obtained packing depend on the solvent concentration, which confirms that solvent molecules are indeed present within the crystalline lattice. DSC experiments imply that the observed changes upon heating correspond to thermodynamic processes. On cooling the homogeneous samples, disordering of the hexagonal packing occurs. Polymerization of the homogeneous samples results in a disordering of the hexagonal packing and in a contraction of the unit cell. The latter once more confirms that solvent molecules are indeed present within the crystalline lattice. The applied principle of polymerization of a solvent in a molecular homogeneous system can be favorable for many applications, for which morphology control at the molecular level is required. 相似文献
7.
Although the conformation of fibronectin has been widely investigated by various techniques, there has not yet been any determination of its rotational diffusion coefficient. We report here this determination by the transient electric birefringence study of solutions of bovine plasma fibronectin at physiological ionic strength. The solutions showed a positive birefringence. A linear relationship was observed between the intensity of the birefringence at equilibrium and the square of the electric field within the range of fields applied (up to 12.5 kV.cm-1). The field-independent decay of the induced birefringence was described by a single exponential with a relaxation time of 0.76 (+/- 0.08) microsecond at 23 degrees C. This establishes fibronectin in solution as a globally rigid structure with a rotational diffusion coefficient, at 20 degrees C, of 202,000 s-1. This result allows the first rigorous determination of the low-resolution structure of fibronectin. It is important to notice that the analysis combines only results obtained in physiological conditions on native molecules and follows a strict hydrodynamic interpretation. The conclusion of this work is that a hollow sphere of about 20 nm external diameter can be proposed as a model for the three-dimensional structure of the fibronectin molecule in solution. This new model suggests the fibronectin could have the structure of a carrier protein. 相似文献
8.
As a member of the pentraxin family, C-reactive protein plays various roles in the nonspecific immunity of animals. Though soluble, C-reactive protein always functions on membranes. In order to study the structure of the membrane-bound protein and the reaction between protein and membranes, two-dimensional (2D) crystallization of rabbit C-reactive protein on lipid monolayers was performed. The 2D crystals composed of pentameric proteins were obtained on lipid monolayers by specific adsorption for the first time. The projection map at 26-A resolution is presented, which exhibits P2 symmetry with lattice parameters a = 158(+/-3) A, b = 92(+/-1) A, and gamma = 107(+/-1) degrees. The current work may give a basis for the further study on the structure of complexes made up of C-reactive protein with its functional binding molecules on membranes. 相似文献
9.
Synchrotron small-angle X-ray scattering was used to study the nanostructures of the complexes formed by calf thymus DNA interacting with cationic lipids (or surfactants) of didodecyldimethylammonium bromide (DDAB), cetyltrimethylammonium bromide (CTAB), and their mixture with a zwitterionic lipid of 1-palmitoyl-2-hydroxy-sn-glycero-3-phosphocholine (PHGPC). The effects of lipid/DNA ratios, DNA chain flexibility, lipid topology, and neutral lipid mixing on the nanostructures of DNA-lipid complexes were investigated. The complexes between double-stranded DNA (dsDNA) and double-tailed DDAB formed a bilayered lamellar structure, whereas the complexes between dsDNA and single-tailed CTAB preferred a structure of 2D hexagonal close packing of cylinders. With single stranded DNA (ssDNA) interacting with CTAB, the complexes showed a Pm3n cubic structure due to the different chain flexibility between dsDNA and ssDNA. The lipid molecules bound by rigid dsDNA like to form cylindrical micelles, whereas lipids bound to flexible ssDNA could form spherical or short cylindrical micelles. The addition of the neutral single-chained PHGPC lipids to the CTAB lipids could induce a structural transition of dsDNA-lipid complexes from a 2D hexagonal to a multi-bilayered lamellar structure. The parallel DNA strands were intercalated in the water layers of lamellar stacks of the mixed lipid bilayers. The DNA-DNA spacing depended on the ratios of charged lipid to neutral lipid, and charged lipid to DNA, respectively. 相似文献
10.
Dinapsoline ((2); (+/-)-dihydroxy-2,3,7,11b-tetrahydro-1H-naphth[1,2,3-de]isoquinoline) is a full D(1) dopamine agonist that also has significant D(2) receptor affinity. Based on a similar pharmacophore, dinapsoline has pharmacological similarities to dihydrexidine ((1); (+/-)-trans-10,11-dihydroxy-5,6,6a,7,8,12b-hexahydrobenzo[a]phenanthridine), the first high affinity full D(1) agonist. Small alkyl substitutions on the dihydrexidine backbone are known to alter markedly the D(1):D(2) selectivity of dihydrexidine, and it was of interest to determine whether similar SAR exists within the dinapsoline series. This report describes the synthesis and pharmacological evaluation of six analogues of dinapsoline: N-allyl-(3);N-n-propyl- (4); 6-methyl- (5); 4-methyl- (6); 4-methyl-N-allyl- (7); and 4-methyl-N-n-propyl-dinapsoline (8). As expected from earlier studies with the dihydrexidine backbone, N-allyl (3) or N-n-propyl (4) analogues had markedly decreased D(1) affinity. Unexpectedly, and unlike the dihydrexidine series, these same substituents did not markedly increase D(2) affinity. The addition of a methyl group to position 6 (5) increased D(1):D(2) selectivity, but less markedly than did the analogous 2-methyl substituent added to 1. Unlike the analogous 4-methyl substituent of 1, the addition of a 4-methyl-group (6) actually decreased D(1) affinity without affecting D(2) affinity. These data demonstrate that the dinapsoline (2) backbone can be modified to produce dopamine agonists with novel properties. Moreover, as rigid ligands in which small substituents can cause significant changes in selectivity, they are important tools for deriving 'differential' SARs of the dopamine receptor isoforms. 相似文献
11.
Cholesterol molecules were put into a computer-modeled hydrated bilayer of dimyristoyl phosphatidyl choline molecules, and molecular dynamics simulations were run to characterize the effect of this important molecule on membrane structure and dynamics. The effect was judged by observing differences in order parameters, tilt angles, and the fraction of gauche bonds along the hydrocarbon chains between lipids adjacent to cholesterol molecules and comparing them with those further away. It was observed that cholesterol causes an increase in the fraction of trans dihedrals and motional ordering of chains close to the rigid steroid ring system with a decrease in the kink population. The hydrogen-bonding interactions between cholesterol and lipid molecules were determined from radial distribution calculations and showed the cholesterol hydroxyl groups either solvated by water, or forming hydrogen bond contacts with the oxygens of lipid carbonyl and phosphate groups. The dynamics and conformation of the cholesterol molecules were investigated and it was seen that they had a smaller tilt with respect to the bilayer normal than the lipid chains and furthermore that the hydrocarbon tail of the cholesterol was conformationally flexible. 相似文献
12.
E3-19K is a type I membrane glycoprotein expressed by adenoviruses (Ads) to modulate host antiviral immune responses. We have developed an expression system for the endoplasmic reticulum lumenal domain (residues 1 to 100) of Ad type 2 E3-19K tagged with a C-terminal His6 sequence in baculovirus-infected insect cells. In this system, recombinant E3-19K is secreted into the culture medium. A characterization of soluble E3-19K by analytical ultracentrifugation and circular dichroism showed that the protein is monomeric and adopts a stable and correctly folded tertiary structure. Using a gel mobility shift assay and analytical ultracentrifugation, we showed that soluble E3-19K associates with soluble peptide-filled and peptide-deficient HLA-A*1101 molecules. This is the first example of a viral immunomodulatory protein that interacts with conformationally distinct forms of class I major histocompatibility complex molecules. The E3-19K/HLA-A*1101 complexes formed in a 1:1 stoichiometry with equilibrium dissociation constants (Kd) of 50 +/- 10 nM for peptide-filled molecules and of about 10 microM for peptide-deficient molecules. A temperature-dependent proteolysis study revealed that the association of E3-19K with peptide-deficient HLA-A*1101 molecules stabilizes the binding groove. Importantly, our studies showed that peptide-deficient HLA-A*1101 molecules sequestered by E3-19K are capable of binding antigenic peptides and maturing into peptide-filled molecules. This firmly establishes that E3-19K does not block binding of antigenic peptides. Together, our results suggest that Ads have evolved to exploit the late and early stages of the class I antigen presentation pathway. 相似文献
13.
Quantitative structure toxicity relationship (QSTR) equations were obtained to predict and describe the cytotoxicity of 31 phenols using logLD(50) as a concentration to induce 50% cytotoxicity of isolated rat hepatocytes in 2 h and logP as octanol/water partitioning: logLD(50) (microM)=-0.588(+/-0.059)logP+4.652(+/-0.153) (n=27, r(2)=0.801, s=0.261, P<1 x 10(-9)). Hydroquinone, catechol, 4-nitrophenol, and 2,4-dinitrophenol were outliers for this equation. When the ionization constant pK(a) was considered as a contributing factor a two-parameter QSTR equation was derived: logLD(50) (microM)=-0.595(+/-0.051)logP+0.197(+/-0.029)pK(a)+2.665(+/-0.281) (n=28, r(2)=0.859, s=0.218, P<1 x 10(-6)). Using sigma+, the Brown variation of the Hammet electronic constant, as a contributing parameter, the cytotoxicity of phenols towards hepatocytes were defined by logLD(50) (microM)=-0.594(+/-0.052)logP-0.552(+/-0.085)sigma+ +4.540(+/-0.132) (n=28, r(2)=0.853, s=0.223, P<1 x 10(-6)). Replacing sigma+ with the homolytic bond dissociation energy (BDE) for (X-PhOH+PhO.-->X-PhO.+PhOH) led to logLD(50) (microM)=-0.601(+/-0.066)logP-0.040(+/-0.018)BDE+4.611(+/-0.166) (n=23, r(2)=0.827, s=0.223, P<0.05). Hydroquinone, catechol and 2-nitrophenol were outliers for the above equations. Using redox potential and logP led to a new correlation: logLD(50) (microM)=-0.529(+/-0.135)logP+2.077(+/-0.892)E(p/2)+2.806(+/-0.592) (n=15, r(2)=0.561, s=0.383, P<0.05) with 4-nitrophenol as an outlier. Our findings indicate that phenols with higher lipophilicity, BDE, or sigma+ values or with lower pK(a) and redox potential were more toxic towards hepatocytes. We also showed that a collapse of hepatocyte mitochondrial membrane potential preceded the cytotoxicity of most phenols. Our study indicates that one or a combination of mechanisms; i.e. mitochondrial uncoupling, phenoxy radicals, or phenol metabolism to quinone methides and quinones, contribute to phenol cytotoxicity towards hepatocytes depending on the phenol chemical structure. 相似文献
14.
The morphology of F1-ATPases lacking one or more small subunits has been investigated by minimal-beam electron microscopy of close-packed monolayers of molecules. Computer-based rotational analyses of single molecules were performed on reconstituted 3-subunit F1-ATPase (-delta epsilon) from Escherichia coli and both 3-subunit (-delta epsilon) and 4-subunit (-delta) F1-ATPase from chloroplasts. Optical diffraction measurements of close-packed arrays revealed maximal dimensions of 122 +/- 4 A and 129 +/- 9 A for 3-subunit ECF1 and 4-subunit CF1, respectively. Molecules which displayed either hollow or solid hexagonal morphologies were observed in all preparations. Averaged reconstructions were obtained from molecules with hollow morphologies in 3-subunit preparations and demonstrated strong hexagonal symmetry in projection with a central, stain-filled cavity. The average reconstruction obtained from molecules with the solid morphology in 4-subunit CF1 preparations, was also strongly hexagonal with six peripheral units ringed about a central subunit. Differences between hollow and solid morphologies cannot be attributed solely to the presence or absence of the delta and epsilon subunits; therefore, the two image types may represent staining variants of a common structure. Overall, the reconstructions are consistent with an alpha 3 beta 3 gamma stoichiometry for the coupling factors from both E. coli and chloroplasts. 相似文献
15.
This paper reports the study of the three-dimensional structure of the tachykinin-like decapeptide sialokinin I molecule using molecular mechanics and molecular dynamics. Fragment analysis was used to identify the stable spatial structures of sialokinin I, which may be present as a set of conformations that are characterized by the relatively labile N-terminal tripeptide and the conformationally rigid C-terminal heptapeptide. It has been demonstrated that the sialokinin I molecule tends to adopt nearly isoenergetic conformations with different structural types at the N-end of the peptide chain, which change into the alpha-helix turn at its C-end. Molecular dynamics was employed to model the sialokinin I molecule mobility in its stable conformations both in a vacuum and when surrounded by water molecules. 相似文献
17.
1. The metabolism of (+/-)-cis-1-, (+/-)-trans-1-, (+/-)-cis-2- and (+/-)-trans-2-decalone in the rabbit has been investigated. 2. (+/-)-cis-2- and (+/-)-trans-2-Decalone were both reduced to racemic secondary alcohols, conformationally related to the ketones administered, and possessing an equatorial hydroxyl group. These alcohols were excreted in the urine as glucuronides in amounts equal to about half the dose administered. The glucuronides were isolated both as triacetyl methyl esters and as sodium salts. The ester obtained after feeding with (+/-)-cis-2-decalone proved to be methyl (cis-cis-2-decalyl tri-O-acetyl-beta-d-glucosid)uronate, whereas (+/-)-trans-2-decalone yielded methyl (trans-cis-2-decalyl tri-O-acetyl-beta-d-glucosid)uronate. The sodium salts were shown to be sodium (cis-cis-2-decalyl glucosid)uronate and sodium (trans-cis-2-decalyl glucosid)uronate. 3. Enzyme hydrolysis of the sodium salts and acid hydrolysis of the esters derived from (+/-)-cis-2-decalone yielded (+/-)-cis-cis-2-decalol, and of those from (+/-)-trans-2-decalone yielded (+/-)-trans-cis-2-decalol. 4. (+/-)-cis-1-Decalone was reduced mainly to (-)-cis-cis-1-decalol and excreted as [(-)-cis-cis-1-decalyl glucosid]-uronic acid. A small amount of the corresponding (+)-isomer was produced, yielding [(+)-cis-cis-1-decalyl glucosid]uronic acid on isolation. Enzyme hydrolysis of these compounds gave the corresponding aglycones; both alcohols possessed an equatorial hydroxyl group. 5. (+/-)-trans-1-Decalone was reduced to (+)-trans-trans-1-decalol, with an equatorial hydroxyl group, and in smaller amount to (+)-trans-cis-1-decalol possessing an axial group. The former alcohol was excreted as [(+)-trans-cis-1-decalyl glucosid]uronic acid, and the latter as [(+)-trans-cis-1-decalyl glucosid]uronic acid. 6. From a knowledge of the conformations, and in some cases the absolute configurations, of the compounds administered and excreted, and by making the assumption that the coenzyme concerned in the reductions is NADH (or NADPH), an explanation of the above findings in terms of steric hindrance and thermodynamic stability is given. 相似文献
18.
The extracellular surface of the gap junction cell-to-cell channels was imaged in phosphate-buffered saline with an atomic force microscope. The fully hydrated isolated gap junction membranes adsorbed to mica were irregular sheets approximately 1-2 microns across and 13.2 (+/- 1.3) nm thick. The top bilayer of the gap junction was dissected by increasing the force applied to the tip or sometimes by increasing the scan rate at moderate forces. The exposed extracellular surface revealed a hexagonal array with a center-to-center spacing of 9.4 (+/- 0.9) nm between individual channels (connexons). Images of individual connexons with a lateral resolution of < 3.5 nm, and in the best case approximately 2.5 nm, were reliably and reproducibly obtained with high-quality tips. These membrane channels protruded 1.4 (+/- 0.4) nm from the extracellular surface of the lipid membrane, and the atomic force microscope tip reached up to 0.7 nm into the pore, which opened up to a diameter of 3.8 (+/- 0.6) nm on the extracellular side. 相似文献
19.
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. 相似文献
20.
Changes in skeletal troponin C (sTnC) structure during thin filament activation by Ca2+ and strongly bound cross-bridge states were monitored by measuring the linear dichroism of the 5' isomer of iodoacetamidotetramethylrhodamine (5'IATR), attached to Cys98 (sTnC-5'ATR), in sTnC-5'ATR reconstituted single skinned fibers from rabbit psoas muscle. To isolate the effects of Ca2+ and cross-bridge binding on sTnC structure, maximum Ca2+-activated force was inhibited with 0.5 mM AlF4- or with 30 mM 2,3 butanedione-monoxime (BDM) during measurements of the Ca2+ dependence of force and dichroism. Dichroism was 0.08 +/- 0.01 (+/- SEM, n = 9) in relaxing solution (pCa 9.2) and decreased to 0.004 +/- 0.002 (+/- SEM, n = 9) at pCa 4.0. Force and dichroism had similar Ca2+ sensitivities. Force inhibition with BDM caused no change in the amplitude and Ca2+ sensitivity of dichroism. Similarly, inhibition of force at pCa 4.0 with 0.5 mM AlF4- decreased force to 0.04 +/- 0.01 of maximum (+/- SEM, n = 3), and dichroism was 0.04 +/- 0.03 (+/- SEM, n = 3) of the value at pCa 9.2 and unchanged relative to the corresponding normalized value at pCa 4.0 (0.11 +/- 0.05, +/- SEM; n = 3). Inhibition of force with AlF4- also had no effect when sTnC structure was monitored by labeling with either 5-dimethylamino-1-napthalenylsulfonylaziridine (DANZ) or 4-(N-(iodoacetoxy)ethyl-N-methyl)amino-7-nitrobenz-2-oxa-1,3-diazole (NBD). Increasing sarcomere length from 2.5 to 3.6 microm caused force (pCa 4.0) to decrease, but had no effect on dichroism. In contrast, rigor cross-bridge attachment caused dichroism at pCa 9.2 to decrease to 0.56 +/- 0.03 (+/- SEM, n = 5) of the value at pCa 9. 2, and force was 0.51 +/- 0.04 (+/- SEM, n = 6) of pCa 4.0 control. At pCa 4.0 in rigor, dichroism decreased further to 0.19 +/- 0.03 (+/- SEM, n = 6), slightly above the pCa 4.0 control level; force was 0.66 +/- 0.04 of pCa 4.0 control. These results indicate that cross-bridge binding in the rigor state alters sTnC structure, whereas cycling cross-bridges have little influence at either submaximum or maximum activating [Ca2+]. 相似文献
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