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1.
Science ; 191(4233): 1271-2, 1976 Mar 26.
Artigo em Inglês | MEDLINE | ID: mdl-1257747

RESUMO

The crystal and molecular structure of prostaglandin B1( PGB1) has been determined. The conformation is L-shaped, with the alpha and omega side chains roughly perpendicular to one another. This arrangement differs from the "hairpin" or approximately parallel disposition of side chains observed for other prostaglandins. The omega chain, which normally turns at the 15-hydroxyl back toward the alpha chain, is fully extended. The conformation is stabilized by the conjugation of the dienone chromophore. The 15-hydroxyl, which is normally directed away from the centroid of the prostaglandin in the hairpin model, is turned inward in L-shaped PGB1. The low biological activity of PGB1 in many systems and especially its inhibition of the metabolizing enzyme 15-hydroxyprostaglandin dehydrogenase may be attributable directly to the observed L-shape conformation.


Assuntos
Prostaglandinas , Hidroxiprostaglandina Desidrogenases/antagonistas & inibidores , Modelos Estruturais , Conformação Molecular , Prostaglandinas/farmacologia
2.
Science ; 197(4307): 1003-5, 1977 Sep 02.
Artigo em Inglês | MEDLINE | ID: mdl-196333

RESUMO

The conformation of prostaglandin F 2alpha (PGF 2alpha) has been determined by x-ray diffraction techniques. Two independent conformers of PGF 2alpha, studied as the tris(hydroxymethyl)methylamine salt, are observed to adopt the familiar "hairpin" conformation with the alpha and omega chains aligned roughly parallel. The conformers differ in ring conformation and at the C(17)-C(18) bond, one adopting a C(9) envelope ring conformation and a trans geometry at the C(17)-C(18) bond, while the other adopts a C(8) envelope ring conformation and a novel gauche geometry about C(17)-C(18). Comparison of the conformation of PGF 2alpha with that of prostaglandin E2 suggests a recognition mechanism which would permit PGF 2alpha and prostaglandin E receptors to distinguish between the two potent prostaglandins. The recognition model explains much of the binding data for the PGF 2alpha receptor in the corpus luteum and predicts the existence of an interesting PGF 2alpha analog.


Assuntos
Conformação Molecular , Prostaglandinas F/metabolismo , Receptores de Superfície Celular , Receptores de Prostaglandina , Prostaglandinas E/metabolismo
3.
Science ; 259(5100): 1430-3, 1993 Mar 05.
Artigo em Inglês | MEDLINE | ID: mdl-8451639

RESUMO

The Shake-and-Bake method of structure determination is a new direct methods phasing algorithm based on a minimum-variance, phase invariant residual, which is referred to as the minimal principle. Previously, the algorithm had been applied only to known structures. This algorithm has now been applied to two previously unknown structures that contain 105 and 110 non-hydrogen atoms, respectively. This report focuses on (i) algorithmic and parametric optimizations of Shake-and-Bake and (ii) the determination of two previously unknown structures. Traditional tangent formula phasing techniques were unable to unravel these two new structures.


Assuntos
Algoritmos , Modelos Teóricos , Estrutura Molecular , Cristalografia , Matemática , Difração de Raios X
4.
Ann N Y Acad Sci ; 447: 152-68, 1985.
Artigo em Inglês | MEDLINE | ID: mdl-3860171

RESUMO

The structures of a family of biotin and carboxybiotin derivatives have provided information on the mechanism of biotin action. The ureido moiety of the uncarboxylated cofactor is polarized and able to interact with ions and polar molecules; intermolecular interactions in the biotin derivatives suggest biochemical mechanisms resulting in nucleophilic activation to the enol tautomer. N1' carboxylation of biotin is important not only as a chemical reaction to generate the carboxyl-transferring species, carboxybiotin, but also in acting as a switch to depolarize the ureido carbonyl oxygen, and thereby facilitating interactions with non-polar molecules. The structure of an N1' methoxycarbonyl biotin derivative reveals such an interaction between the carbonyl oxygen, O2', and a neighboring methyl group. A computer-generated space-filing model of the van der Waals contacts involved in this interaction reveals that the methyl group is locked with respect to rotation and thus suggests a structural basis for the stereospecificity observed in the carboxyl-transferring half-reaction. The flexibility of the valeryl side chains in this family of structures provides translocation models in line with magnetic resonance data which indicate that the translocation events involve motions of, at most, 7 A. Our models demonstrate that such motions may be accomplished by simple, observed conformational changes in bonds of the valeryl side chain which locally adjoin the bicyclic ring system. High resolution, low temperature diffraction data will allow visualization of the bonding and lone pair electrons in biotin. These studies will serve to extend and fine-tune our description of the electronic structure of biotin which is currently based on accurate measurements of bond distances and angles.


Assuntos
Biotina/análogos & derivados , Cristalografia , Conformação Molecular
5.
Acta Crystallogr A ; 50 ( Pt 2): 203-10, 1994 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-8166951

RESUMO

Eliminating the N atomic position vectors rj, j = 1, 2, ..., N, from the system of equations defining the normalized structure factors EH yields a system of identities that the EH's must satisfy, provided that the set of EH's is sufficiently large. Clearly, for fixed N and specified space group, this system of identities depends only on the set [H], consisting of n reciprocal-lattice vectors H, and is independent of the crystal structure, which is assumed for simplicity to consist of N identical atoms per unit cell. However, for a fixed crystal structure, the magnitudes magnitude of /EH/ are uniquely determined so that a system of identities is obtained among the corresponding phases psi H alone, which depends on the presumed known magnitudes magnitude of /EH/ and which must of necessity be satisfied. The known conditional probability distributions of triplets and quartets, given the values of certain magnitudes magnitude of /E/, lead to a function R(psi) of phases, uniquely determined by magnitudes magnitude of /E/ and having the property that RT < 1/2 < RR, where RT is the value of R(psi) when the phases are equal to their true values, no matter what the choice of origin and enantiomorph, and RR is the value of R(psi) when the phases are chosen at random. The following conjecture is therefore plausible: the global minimum of R(psi), where the phases are constrained to satisfy all identities among them that are known to exist, is attained when the phases are equal to their true values and is thus equal to RT.(ABSTRACT TRUNCATED AT 250 WORDS)


Assuntos
Cristalografia por Raios X , Análise de Fourier , Conformação Molecular
6.
Acta Crystallogr A ; 50 ( Pt 2): 210-20, 1994 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-8166952

RESUMO

The minimal function, R(psi), has been used to provide the basis for a new computer-intensive direct-methods procedure that shows potential for providing fully automatic routine solutions for structures in the 200-400 atom range. This procedure, which has been called shake-and-bake, is an iterative process in which real-space filtering is alternated with phase refinement using a technique that reduces the value of R(psi). It has been successfully tested using experimental data for a dozen known structures ranging in size from 25 to 317 atoms and crystallizing in a variety of space groups. The details of this procedure, the parameters used and the results of these applications are described.


Assuntos
Cristalografia por Raios X , Análise de Fourier , Computadores , Modelos Químicos , Modelos Estatísticos , Conformação Molecular
7.
J Res Natl Inst Stand Technol ; 106(6): 1071-94, 2001.
Artigo em Inglês | MEDLINE | ID: mdl-27500067

RESUMO

An international project was successfully completed which involved two major undertakings: (1) a round-robin to demonstrate the viability of the selected standard and (2) the certification of the lattice parameters of the SRM 1990, a Standard Reference Material(®) for single crystal diffractometer alignment. This SRM is a set of ≈3500 units of Cr-doped Al2O3, or ruby spheres [(0.420.011 mole fraction % Cr (expanded uncertainty)]. The round-robin consisted of determination of lattice parameters of a pair of crystals: the ruby sphere as a standard, and a zeolite reference to serve as an unknown. Fifty pairs of crystals were dispatched from Hauptman-Woodward Medical Research Institute to volunteers in x-ray laboratories world-wide. A total of 45 sets of data was received from 32 laboratories. The mean unit cell parameters of the ruby spheres was found to be a=4.7608 ű0.0062 Å, and c=12.9979 ű0.020 Å (95 % intervals of the laboratory means). The source of errors of outlier data was identified. The SRM project involved the certification of lattice parameters using four well-aligned single crystal diffractometers at (Bell Laboratories) Lucent Technologies and at NRC of Canada (39 ruby spheres), the quantification of the Cr content using a combined microprobe and SEM/EDS technique, and the evaluation of the mosaicity of the ruby spheres using a double-crystal spectrometry method. A confirmation of the lattice parameters was also conducted using a Guinier-Hägg camera. Systematic corrections of thermal expansion and refraction corrections were applied. These rubies- are rhombohedral, with space group [Formula: see text]. The certified mean unit cell parameters are a=4.76080±0.00029 Å, and c=12.99568 ű0.00087 Å (expanded uncertainty). These certified lattice parameters fall well within the results of those obtained from the international round-robin study. The Guinier-Hägg transmission measurements on five samples of powdered rubies (a=4.7610 ű0.0013 Å, and c = 12.9954 ű0.0034 Å) agreed well with the values obtained from the single crystal spheres.

9.
Acta Crystallogr D Biol Crystallogr ; 51(Pt 5): 780-5, 1995 Sep 01.
Artigo em Inglês | MEDLINE | ID: mdl-15299809

RESUMO

The kinetics of water-vapor equilibration in macromolecular crystallization were investigated for sitting droplets of aqueous polyethylene glycol (PEG) 8000 as a function of concentration. Equilibrations, set up with initial concentrations of PEG in the droplet at half those in the reservoir, were very slow for concentrations of relevance to the macromolecular crystal growth problem. At 301 K, 24 micro l droplets at initial concentrations of 2.5, 5.0 and 7.5%(w/v) PEG require 12, 5, and 3 weeks to reach equilibrium, respectively. On the other hand, the addition of modest quantities of sodium chloride to both droplet and reservoir increases the rate of equilibration for aqueous PEG sitting droplets significantly. At 293 K, droplets with initial volumes of 24 micro l and PEG concentrations of 5%(w/v) require 12 weeks to reach equilibrium, while droplets of the same volume and initial concentrations of 5%(w/v) PEG and 200 mM NaCI require less than two weeks to reach equilibrium. The slow vapor-diffusion equilibrations of pure PEG solutions, and the subsequent increase in these rates with colligative agents such as salt, are a consequence of the non-ideality of aqueous PEG solutions. These results are of interest both from a practical and a theoretical viewpoint. They underscore the importance of kinetic factors in macromolecular crystal growth, help to explain apparent inconsistencies of outcome in PEG-mediated crystallizations, and yield another methodology for the optimization of crystal growth conditions, namely the control of the kinetics of equilibration using colligative agents.

10.
Acta Crystallogr D Biol Crystallogr ; 51(Pt 5): 786-91, 1995 Sep 01.
Artigo em Inglês | MEDLINE | ID: mdl-15299810

RESUMO

The kinetics of water equilibration in vapor-diffusion crystallization experiments are sensitive to the residual pressure of air in the vapor chamber. Experiments with sitting droplets of 10%(w/v) PEG, allowed to equilibrate with reservoirs of 20%(w/v) PEG, were conducted at pressures ranging from 80 to 760 mm Hg. Equilibrations were interrupted after one, four, five and seven days to assess their progress. Even down to the lowest pressures examined it was found that a decrease in pressure leads to an increase in the rate of equilibration. The residual pressure of air in the vapor chamber can be varied to tailor the time course of equilibration in macromolecular crystal growth experiments.

11.
Acta Crystallogr D Biol Crystallogr ; 55(Pt 5): 988-93, 1999 May.
Artigo em Inglês | MEDLINE | ID: mdl-10216295

RESUMO

A method is presented for producing a seed-stock mixture for macromolecular crystallization. A PTFE bead and micro-centrifuge tube act as mortar and pestle for pulverizing seed crystals of macromolecules. Energy for the bead's motion is supplied by a vortex mixer or an ultrasonic bath. The crushed crystal is serially diluted to prepare a seed-stock mixture of the desired concentration for crystallization. Crystals produced using both hanging-drop vapor diffusion and a capillary microbatch method show expected dilution behavior. This technique of producing seed stock is compared with traditional means and advantages over the standard protocol are demonstrated.


Assuntos
Bioquímica/métodos , Proteínas/química , Cristalização , Difusão , Vidro , Substâncias Macromoleculares , Biologia Molecular/métodos , Ultrassom
12.
Acta Crystallogr D Biol Crystallogr ; 51(Pt 5): 772-9, 1995 Sep 01.
Artigo em Inglês | MEDLINE | ID: mdl-15299808

RESUMO

Microisopiestic measurements of the concentrations of polyethylene glycol (PEG 8000) paired with the salts sodium chloride, ammonium sulfate and magnesium sulfate heptahydrate have been made in a sitting-drop arrangement with PEG in the droplet and salt in the reservoir. Resulting graphs of the concentrations of PEG and salt that are equivalent with respect to the vapor pressure of water are non-linear, do not intersect their origins, and demonstrate that relatively low (mM) salt concentrations are equivalent to relatively high PEG concentrations. The consequences of each of these observations for macromolecular crystallization by the vapor-diffusion technique when PEG is employed as the crystallizing agent are discussed.

13.
Prostaglandins ; 9(5): 659-65, 1975 May.
Artigo em Inglês | MEDLINE | ID: mdl-1162083

RESUMO

The molecular conformation of the monoclinic crystalline polymorph of prostaglandin A1 has been determined by X-ray diffraction techniques. The space group is P21 with a = 13.637(2), b = 7.567(1), c = 10.576(2) A, beta = 107.37(3) degrees; Dc = 1.073 g.cm-3 for Z = 2. The molecular conformation is characterized by the nearly parallel arrangement of the C1-C7 and C13-C20 side chains, with a general flattening of the overall structure when compared with the orthorhombic polymorph. The cyclopentenone moiety assumes a C8 envelope conformation with C8 and O9 displaced +0.29 A and -0.18 A from the C9-C10=C11-C12 plane respectively. Concerted, small varations of the torsion angles, primarily about the C8-C12, C14-C15 and C16-C17 bonds, bring the monoclinic and orthorhombic conformations into coincidence.


Assuntos
Prostaglandinas A , Modelos Moleculares , Conformação Molecular , Difração de Raios X
14.
Nature ; 281(5728): 237-8, 1979 Sep 20.
Artigo em Inglês | MEDLINE | ID: mdl-481594

RESUMO

The hairpin conformational hypothesis has been proposed to rationalise much of the structure-activity and receptor-binding data which have accumulated for the prostaglandin (PG) hormones. The hairpin conformation, thought to be necessary for PG activity, requires that the alpha- and omega-chains of the molecule be extended and in parallel alignment, separated by a van der Waals contact distance for the full length of the chains, with the ends of the chains approximately 5.5 A apart. The similarity between the structures of the thromboxanes (TXs) and the PGs suggests that the profile of activity of TXs, like that of PGs, centres on subtle conformational variation of the hairpin geometry. Thromboxane B2 (TXB2) is a stable hydrolysis product of a highly reactive, short-lived intermediate, thromboxane A2 (TXA2), which is formed from the prostaglandin endoperoxide (PGH2) as indicated in Fig. 1. An examination of molecular models of TXA2 and TXB2 suggests that the structural differences between the ring moieties may have much less influence in altering the side-chain conformation of TXs than do substitutents on the relatively more flexible cyclopentane ring of a PG molecule. We report here the first diffraction analysis of a thromboxane structure and note that the molecular conformation is not hairpin shaped.


Assuntos
Prostaglandinas , Tromboxanos , Conformação Molecular , Relação Estrutura-Atividade , Tromboxano A2 , Tromboxano B2
15.
Proc Natl Acad Sci U S A ; 77(1): 333-7, 1980 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-6928626

RESUMO

Biotin is a coenzyme that fixes CO2 for transfer in a family of carboxylase, decarboxylase, and transcarboxylase enzymes. Their enzyme reactions involve two basic steps during which a carboxybiotinyl intermediate forms at one site and translocates to a second (distinct) site for CO2 transfer. Our diffraction studies of biotin and its vitamers suggest that translocation involves rotation about one, or at most two, bonds in biotin's valeryl chain. The rotations are energetically economical gauche in equilibrium trans rotations about the two valeryl bonds nearest the biotin bicyclic ring. They move a carbon atom of a CO2 moiety bound at N-1' approximately 7 A, a distance in accord with spectroscopic measurements of one of the biotin enzymes. From our studies we infer that sulfur in biotin imparts to the valeryl chain a conformational variability necessary for bond rotation and, hence, translocation between catalytic sites.


Assuntos
Biotina , Biotina/análogos & derivados , Biotina/metabolismo , Dióxido de Carbono/metabolismo , Cinética , Modelos Moleculares , Conformação Molecular , Movimento (Física) , Relação Estrutura-Atividade , Enxofre , Difração de Raios X
16.
Proc Natl Acad Sci U S A ; 77(3): 1260-4, 1980 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-6929481

RESUMO

The crystal structure of N1'-methoxycarbonylbiotin methyl ester, a model for N1'-carboxybiotin, has been determined. The ureido carbonyl bond has more double bond (keto) character than does the corresponding bound in free biotin, which has single bond (enolate) character. In addition, there is an interesting intermolecular interaction between the ureido carbonyl oxygen and a methyl group. Comparison of the molecular structure and crystal packing with those of free biotin suggests that the coenzyme may have evolved with the incorporation of the ureido moiety because the electronic configuration of this region of the molecule is sensitive to N1' carboxylation. On decarboxylation, the ureido carbonyl bond becomes more polarized (C-O-), thereby facilitating the deprotonation of N1' and increasing its nucleophilicity. As a result, carboxylation can occur readily. On carboxylation, the carbonyl bond is depolarized (C = O), allowing the carboxylated coenzyme to interact with nonpolar groups and carboxylate them. Thus, the carboxylation and decarboxylation of biotin appear to act as a mechanistic switch, turning off and on the polarization of the ureido carbonyl bond as well as modulating the nucleophilicity of N1'.


Assuntos
Biotina/análogos & derivados , Cristalografia , Análise de Fourier , Modelos Químicos , Conformação Molecular , Difração de Raios X
17.
Acta Crystallogr D Biol Crystallogr ; 49(Pt 1): 179-81, 1993 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-15299558

RESUMO

A new direct-methods procedure has been devised which consists of phase refinement via the minimal function, R(phi), alternated with Fourier summation and real space filtering. All phases are initially assigned values by computing structure factors for a randomly positioned set of atoms. These phases are then refined by using a parameter shift method to minimize R(phi). The refined phases are Fourier transformed, and a specified number of the largest peaks in the electron-density function are found and used as a new trial structure. The probability of a trial structure converging to a solution appears to depend on structural complexity and a number of refinement parameters. This procedure shows potential for providing fully automatic routine solutions for structures in the 200-400 atom range.

18.
Acta Crystallogr D Biol Crystallogr ; 52(Pt 6): 1098-106, 1996 Nov 01.
Artigo em Inglês | MEDLINE | ID: mdl-15299569

RESUMO

The rate of water equilibration in hanging-drop vapor-diffusion experiments was studied as a function of the distance separating the hanging drop from the surface of the reservoir solution. Hanging drops of 1.00 M NaCl were allowed to partially equilibrate with reservoirs of 2.00 M NaCl at room temperature. Over the range of droplet-reservoir distances examined, 7.6-119.4 mm, the larger the distance that separated the droplet and reservoir, the slower the droplet equilibrated with the reservoir. The variation of the rate of equilibration with droplet-reservoir distance was non-linear; the rate was most sensitive to variations in the droplet-reservoir separation at short separations. A mathematical model of the equilibration kinetics was developed that fits the experimental data. The model is based on the assumption that the rate-limiting step in vapor-diffusion equilibration is transit of water across the vapor space. A simple device to vary the rate of water equilibration, and thereby optimize macromolecular crystal growth conditions, is described.

19.
Acta Crystallogr D Biol Crystallogr ; 50(Pt 4): 472-8, 1994 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-15299405

RESUMO

Time courses of equilibration for three salts, sodium chloride, ammonium sulfate and magnesium sulfate heptahydrate have been measured in the Z/3 crystallization plate. It is shown that by varying both the diffusant and the reservoir depth the time taken to equilibrate can be as short as 200 or as long as 1400 h. Thus, the present design of the plate should accommodate a wide variety of desired crystallization kinetics.

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