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PubMed1995

[Study of the spatial structure of the product of intracomplex alkylation of the octanucleotide pd(TGTTTGGC) by 4-(N-methyl-N-(2-chloroethyl) amino)benzyl-5'-phosphamide derivative of the heptanucleotide pd(CCAAACA) in an aqueous solution by two-dimensional 1H-NMR spectroscopy and constrained molecular mechanics].

Using one- and two-dimensional 1H NMR spectroscopy (400 MHz), a detailed study of the spatial structure of the covalent adduct, a product of the intracomplex alkylation of octanucleotide pd[TGTTTGGC] by the 4-[N-methyl-N-(2-chloroethyl)amino]benzyl-5'-phosphamide derivative of heptanucleotide pd[CCAAACA] in aqueous solution, was continued. The distances between closely spaced protons of oligonucleotides as well as between protons of the benzylamide fragment and protons of the nearest nucleotide units were determined by measurements of the nuclear Overhauser effect. Analysis of effective correlation times for some pairs of protons of the covalent adduct showed that the values of tau c for the benzylamide fragment and nucleotide units C-1 and C-8, which directly interact with it, coincide and are smaller than those for the internal nucleotide units, suggesting the increased rigidity of the structure in the vicinity of the modification region. Using the method of constrained molecular mechanics, a probable state of the covalent adduct in solution is proposed that is in the best agreement with the experimentally obtained set of interproton distances. Problems connected with calculating the distance between a pair of protons with coincident chemical shifts and any third proton are considered.

Alkylation↗

PubMed1984

Mechanism of action of aspartate aminotransferase proposed on the basis of its spatial structure.

Aspartate aminotransferase is a pyridoxal phosphate-dependent enzyme that catalyses the transamination reaction: L-aspartate + 2-oxoglutarate----oxaloacetate + L-glutamate. The enzyme shuttles between its pyridoxal and pyridoxamine forms in a double-displacement process. This paper proposes a mechanism of action that delineates the dynamic role of the protein moiety of this enzyme. It is based on crystallographically determined spatial structures (at 2.8 A resolution) of the mitochondrial isoenzyme in its unliganded forms and in complexes with substrate analogues, as well as on model building studies. The enzyme is composed of two identical subunits, which consist of two domains. The coenzyme is bound to the larger domain and is situated in a pocket near the subunit interface. The proximal and distal carboxylate group of dicarboxylic substrates are bound to Arg386 and Arg292 , respectively, the latter residue belonging to the adjacent subunit. These interactions largely determine the substrate specificity of the enzyme. They not only position the substrate efficient catalysis but also bring about a bulk movement of the small domain that closes the active site crevice and moves Arg386 about 3 A closer to the coenzyme. The replacement of the epsilon-amino group of Lys258 by the alpha-amino group of the substrate in the aldimine bond to pyridoxal phosphate is accompanied by a tilting of the coenzyme by approximately 30 degrees. The released epsilon-amino group of Lys258 serves as a proton acceptor/donor in the 1,3- prototropic shift producing the ketimine intermediate. At this stage, or after hydrolysis of the ketimine bond, the coenzyme rotates back to an orientation between that in the "external" aldimine intermediate and that in the pyridoxal form. Throughout this process, the protonated pyridine nitrogen atom maintains a hydrogen bond to the beta-carboxylate group of Asp222 . Upon formation of the pyridoxamine form, the small domain moves back to its original position. The proposed mechanism is compatible with the known kinetic and stereochemical features of enzymic transamination.

Aspartate Aminotransferases↗

PubMed1999

Spatial structure of the M2 transmembrane segment of the nicotinic acetylcholine receptor alpha-subunit.

A synthetic peptide corresponding to the transmembrane segment M2 (residues 236-267) of the alpha-subunit of the nicotinic acetylcholine receptor from Torpedo californica has been studied by two dimensional 1H-NMR spectroscopy in a chloroform-methanol (1:1) mixture containing 0.1 M LiClO4. Reconstruction of the spatial structure of M2 from the NMR data resulted in an alpha-helix formed by residues 241-263. Distribution of the molecular hydrophobicity potential on the helix surface is very similar to that in five-helix bundles of proteins with a known three dimensional structure: two hydrophilic bands located on the opposite helix sides separated by strong hydrophobic zones.

Amino Acid Sequence↗

PubMed1997

[Spatial structure of bacterioopsin 87-136 fragment].

The [Nle18]-(87-136)-bacterioopsin, a fragment of bacterioopsin from Halobacterium salinarium synthesized by solid phase technique, was solubilized in a 1:1 chloroform-methanol mixture containing 0.1 M LiClO4 and studied by two-dimensional 1H NMR spectroscopy. The complete assignment of proton resonances was performed in the DQF-COSY, TOCSY, and NOESY spectra of this peptide, and its spatial structure was computed. As a result, two helical regions (92-100 and 108-130) were identified, which correspond to the C-terminal part of segment C and to segment D of bacteriorhodopsin, respectively. The 92-100 region forms a right-handed alpha-helix, and the 108-130 region can adopt right-handed alpha-helical, 3(10)-helical, and combined (from the two) conformations. A comparison of the structure computed with the bacteriorhodopsin model deduced from the electron cryomicroscopy data showed good agreement in the 91-100 region (the root-mean-square deviation of the backbone atoms was less than 0.51 A) and considerable differences in the 108-130 region (1.82 A). A dynamic model of the conformation of the D transmembrane segment was suggested, and the accordance of the model to the functional dynamics of bacteriorhodopsin was discussed.

Amino Acid Sequence↗

PubMed1994

Visual acuity and pupillary responses to spatial structure in infants.

PURPOSE: To determine the age of onset of the pupil grating response (PGR). To compare estimates of resolution acuity obtained by pupillometric and behavioral methods in early infancy. METHODS: Dynamic infrared pupillometry was undertaken on 19 newborn infants while they fixated a uniform background upon which a 0.1 c/deg sine wave grating was briefly presented. Pupillary responses were also recorded to an increment in luminance of a spatially homogeneous target. Longitudinal measurements of PGRs were obtained from a subset of eight infants between 3.5 and 38 weeks of age. In this group, behavioral estimates of visual resolution obtained using the acuity card procedure were compared with the highest spatial frequency grating to elicit a PGR. RESULTS: When presented with the pattern stimulus, newborn infants did not show any pupil reaction indicative of a PGR. This finding could not be attributed to immaturity of pupillomotor function: All infants showed marked pupillary construction to diffuse light stimulation. By 1 month of age, pupillary responses to pattern stimuli were reliably present. For these and older infants, the spatial frequency of the finest grating to elicit a PGR was comparable to the behaviorally determined resolution threshold: mean difference (+/- 95% confidence interval) = 0.28 +/- 0.23 octaves. CONCLUSIONS: A PGR could not be detected in newborn infants. From 1 month of age, responses to spatial structure can provide objective estimates of visual acuity comparable to those determined by established methods.

Age of Onset↗

PubMed2003

Dispersion movements in ants: spatial structuring and density-dependent effects.

This paper examines whether the characteristics of individual dispersion movements in ants are changed when workers are moving solitarily or in a group. We analyzed the trajectories of workers of the species Messor sancta moving solitarily or in groups of different size (5, 10, 15 individuals), tested for density-dependent effects on their trajectory characteristics and investigated through resampling techniques whether ants are able to spatially structure their movements through direct (e.g. contact) or indirect (pheromone deposited on the ground) interactions. In addition to group size, the effects of the nutritional state of the colony and of the state of the area on which ants were dispersing were also examined. Solitary ants moved faster and had more sinuous trajectories than ants moving in a group. We found however no significant differences in trajectory characteristics between groups of different size. Whatever the group size, ants from starved colonies moved more slowly and had more direct trajectories than their counterpart coming from fed colonies. On the other hand, the state of the area on which ants were moving had no direct significant effect on dispersion movement. Ants dispersing in a group moved independently and did not coordinate their movements through direct or indirect interactions. However, the geometry of their path was changed not only through the effect of random encounters with other workers but also through an active modification of their movement when they perceived directly or indirectly the presence of nearby workers.

Journal Article↗

PubMed1985

[Study of the spatial structure of des-Gly9-[Arg8]vasopressin by two-dimensional NMR spectroscopy and theoretical conformation analysis].

2D 1H-NMR spectra of des-Gly9-[Arg8]vasopressin in dimethylsulfoxide have been taken and the 1H resonances have been assigned. The coupling constants and amide proton temperature coefficients (delta delta/delta T) have been measured and the NOE cross-peaks in the NOESY spectrum have been analyzed. The most essential information on the spatial structure of des-Gly9-[Arg8]vasopressin is extracted from the low delta delta/delta T value for Asn5 amide proton and from the NOE between the Cys1 and Cys6 alpha-protons. A diminished accessibility of the Asn5 NH proton for the solvent is ascribed to the presence of a beta-turn in the fragment 2-5. The distance between the Cys1 and Cys6 C alpha H protons seems to be less than 4 A. These constraints were taken into account in the conformational analysis of the title peptide. The derived set of the low-energy backbone conformations was analyzed against the background of the all available NMR data. The most probable conformation of the cyclic moiety in des-Gly9-[Arg8]vasopressin was found to be the type III beta-turn. The corner positions are occupied by the residues 3, 4, while the residues 1-2 and 5-6 are at the extended sites. Some NMR data indicate that this structure is in a dynamic equilibrium with other minor conformers.

Amino Acid Sequence↗

PubMed1996

Formation of polymeric chelate bridges between double-stranded DNA molecules fixed in spatial structure of liquid-crystalline dispersions.

The formation of cholesteric liquid-crystalline dispersions from DNA-daunomycin complexes in water-salt polyethyleneglycol-containing solutions was investigated. In the case of nonclassical complex formation between DNA and daunomycin (DAU), reactive groups of DAU were used for the formation of polymeric chelate complex with divalent copper ions (-DAU-Cu-...-Cu-DAU-), located between neighboring double-stranded DNA molecules, fixed in spatial structure of liquid-crystalline dispersions. The formation of polymeric chelate complex does not depend upon the sense of helicoidal twist of DNA cholesterics. A many-fold increase in the CD band in the DAU absorption region is specific to this process. A reduction of the divalent copper ions as a result of a redox-process is accompanied by destroying of structure of polymeric chelate complex between DNA molecules and by disappearance of the abnormal CD band in daunomycin absorption region.

Ascorbic Acid↗

PubMedDate not supplied

[Effect of forest fires on the population count and spatial structure of the taiga tick (Ixodidae)].

Results of two large-scale surveys of Ixodes persulcatus distribution were compared. Surveys were conducted in a south taiga forest area in the Khabarovsk region two and ten years after a great fire. The direct inhibiting effect of the fire on the population of I. persulcatus was not continuous though apparent. By the moment of pyrogenic small forests formation on slash fires, i.e. during the period not exceeding 2-3 complete developmental cycles of I. persulcatus, the abundance and spatial structure of its population are restored completely.

Animals↗

PubMed1992

[Intracomplex alkylation of octanucleotide pd(TGTTTGGC) by a 5'-(4-N-methyl-N-(2-chloroethyl)-amino)benzylphosphamide derivative of heptanucleotide pd(CCAAACA). Preparation of a covalent adduct and study of its spatial structure in an aqueous solution by two-dimensional (1)H-NMR spectroscopy].

Covalent adduct--the product of intracomplex alkylation at N-3-position of dC-8-nucleoside residue of target octanucleotide pd[TGTTTGGC] was completely synthesized by means of 4-[N-methyl-N-(2-chloroethyl)amino]benzyl-5'-phosphamido derivative of heptanucleotide pd[CCAAACA]. Its melting temperature was shown to be 70 degrees C. Tm did not depend on covalent adduct concentration and was by 40 degrees C higher than that for unmodified duplex pd[TGTTTGGC].pd[CCAAACA] at concentration of 0.5 x 10(-4) M. The spatial structure of the covalent adduct in aqueous solution was investigated by two-dimensional 3H-NMR spectroscopy. The assignment of oligonucleotide protons as well as protons of a modifying group was carried out using COSY, COSY-DQF and NOESY experiments. Conformational analysis of proton-proton coupling constants for H1', H2'a, H2'b and H3' protons showed the sugar residues to be in 2'-endo conformation. Analysis of NOE connectivities observed between the protons of the alkylating group and oligonucleotide protons yielded conclusion, regarding the 4-[N-methyl-N-(2-chloroethyl)amino]benzylamido 5'-residue being localized in the region of the lacked nucleoside residue of the heptanucleotide chain about 5 A apart from the dC-1 residue and from cytosine base of the alkylated dC-8 residue.

Alkylation↗

PubMed1998

Spatial structure of the M3 transmembrane segment of the nicotinic acetylcholine receptor alpha subunit.

The three-dimensional structure of a synthetic peptide corresponding to the putative transmembrane segment M3 (amino acid residues 277-301) of the alpha subunit of the nicotinic acetylcholine receptor from Torpedo californica has been studied by means of two-dimensional 1H-NMR spectroscopy in a chloroform/methanol (1:1) mixture containing 0.1 M LiClO4. Complete resonance assignment has been performed using double-quantum-filtered COSY (DQF-COSY), TOCSY and NOESY spectra. The spatial structure has been calculated using the Diana program on the basis of integrated intensities of NOESY spectra. HN-C(alpha)H and HC(alpha)-C(beta)H spin-spin coupling constants. Residues 279-297 of M3 form a right-handed helix (root mean square deviation is 0.032 nm for backbone atoms and 0.088 nm for all heavy atoms). The conformations of the 17 side chains have been unambiguously determined. The obtained structure is in accord with the photolabeling pattern of the membrane nicotinic acetylcholine receptor (nAChR) which suggests alpha-helical structure of M3 in the labeled portion [Blanton, M. P. & Cohen, J. B. (1994) Biochemistry 33, 2859-2872].

Amino Acid Sequence↗

PubMed1985

[Study of the spatial structure of a cyclic analog of bradykinin in solution by two-dimensional NMR spectroscopy].

H NMR resonances of [cyclo (9----18) Lys1, Gly6]bradykinin (CBK) in (CD3)2SO and H2O solution have been assigned by combined analysis of two-dimensional COSY and NOESY spectra. The presence of two slowly interchangeable conformers of CBK in (CD3)2SO is established, the minor conformer not exceeding 15% in the population. The minor conformer is absent from the aqueous solution, chemical shifts of the CBK and bradykinin NH and C alpha H protons differ insignificantly. The major CBK conformer contains at least two X-Pro trans-peptide groups and three amide protons NH Phe5, NH Arg9 and N zeta H Lys1 protected from solvent. A system of cross-peaks from the NOESY spectra of CBK in (CD3)2SO has been analysed and the maximum distance between backbone protons and neighbouring amino acid residues evaluated. The experimental data agree well with the assumed type II beta-bend in the sequence Pro2-Pro3-Gly4-Phe5. Spatial structure models for the backbone fragment 6-9 of CBK containing two intramolecular hydrogen bonds that involve the NH Arg9 and N zeta H Lys1 protons and the carbonyl groups of Phe5 and Gly4 are proposed.

Amino Acid Sequence↗

PubMed1984

[NMR study of the spatial structure of the Naja naja siamensis toxin 3].

The 300 and 500 MHz 1H NMR spectra of a long-chain neurotoxin, toxin 3 Naja naja siamensis (S-T3), its derivatives and close homolog, toxin 3 Naja naja naja (N-T3), have been analyzed. A combination of double resonance, difference spectroscopy and usage of a series of toxin S-T3 derivatives acetylated or trifluoroacetylated at lysine residues allowed to assign the signals from all aromatic protons and a number of signals in the aliphatic region, and to elucidate the microenvironment of certain functionally important residues. Analysis of chemical shifts pH-dependences in the 1H and 19F NMR spectra of toxin S-T3 and its trifluoroacetylated congeners delineated a considerable region of the neurotoxin molecule affected by the conformational transition, with the midpoint at pH 5,4, between two states. This conformational transition is induced by protonation of His22 and is accompanied by a change in the accessibility of its imidazole ring for the solvent, along with the alteration of the distance between the side chains of functionally important Lys27 and Lys53 residues. According to EPR data (-196 degrees) for the respective S-T3 derivative having spin labels at Lys27 and Lys53 epsilon-amino groups, the inter-label distance increases from 18 A at pH 7,5 to 23 A at pH 3,5. Notwithstanding this conformational change, the totality of the obtained results evidences in favor of considerable similarity of the toxin S-T3 spatial structure in the solution and crystalline state.

Acetylation↗

PubMed1996

Structural characterization of extracellular ribonuclease of Bacillus polymyxa: amino acid sequence determination and spatial structure prediction.

The primary structure of extracellular Bacillus polymyxa ribonuclease (RNase Bpo) was established by mass spectroscopy analysis and automatic Edman degradation of the individual peptides obtained from protein digestion with Glu-specific protease V8. RNase Bpo consists of 111 amino acid residues, with a relative molecular weight of 12 607. RNase Bpo is a close structural homolog of RNases of B. amyloliquefaciens (RNase Ba) and B. intermedius (RNase Bi), the similarity of their primary structures being 68%. Molecular modelling of the structure of the complex of RNase Bpo with substrate analog d(CGAC) was performed and a spatial model based on the known crystal structure of RNase Ba complex with the corresponding nucleotide was constructed using the methods of interactive computer graphics and energy minimization. The differences in the primary and tertiary structures of the enzymes were analyzed in order to understand the substrate specificity of Bacillus RNases.

Amino Acid Sequence↗

PubMed1992

Hierarchical geometric constraint networks as a representation for spatial structural knowledge.

A representation is proposed for capturing generic spatial knowledge about classes of objects in a structural hierarchy of biology. The basic premise is that spatial properties such as shape and relative relationships can be expressed as networks of interacting constraints. The representation is defined, partial implementations that demonstrate practical utility are described for model based organ and protein structure determination, and research issues are presented that must be solved before the representation can be implemented in its entirety. As these issues are resolved the representation will find increasing utility as the foundation for a spatial knowledge base of structural biology.

Computer Simulation↗

PubMedDate not supplied

[The functional organization of the spatial structures of the neuronal receptive fields in field 21 of the cat cerebral cortex].

In result study of structural organization of neural receptive fields (RFs) and their different zones on the prestriate cortex level was shown that neural RFs in this area have hypercomplex structure and consist of some spatial different excitatory zones. Orientation and velocity selectivity and spatial-frequency characteristics of the excitatory zones of the same RF may differ between zones. The number of zones in RFs correlate with RF sizes: the more RF size the more zones number in them (r = 0.05, P < 0.02). About 66% of zones in RFs have approximately identical sizes (12-16 deg) and sizes those zones an dependence as from their number in RFs (r = 0.03, P > 0.05) as from the eccentricity (r = 0.3, P > 0.05). Zones in RF were distributed so that distance their centres was between 56-65 degrees (an average across all 60 degrees). If two or three zones were tested simultaneously the neuron changed own frequency and orientation tuning. Consequently the functional organization of neural RFs of prestriate cortex depend upon number simultaneously tested zones in spatial information processing. Was shown that important properties of prestriate cortex neurons is their ability to integrate and complex processing of spatial information across wide area of the visual field; in the prestriate cortex thus violate of straight retinotopical representation principle of visual field, characteristics of all investigated areas of visual system. The results represented in this review allow suppose that the structural and functional unit of cortex which make integration of spatial information from different compose this information is prestriate cortex neurons and not is no striate cortex modules. Consequently combined of neurons which make images description from different parts of visual field out of dependence of cortical area in turn integrate in neuron networks. Is known that neurons of any level have characteristics different of (from) characteristics of other levels visual system. The interaction of different elements of visual system form ultrastructure of RFs and their different zones in prestriate cortex, and ensure function of networks. So just on prestriate cortex neurons level appear whole system of surrounding world universe system of connections from different cortical areas which is morphological and functional base in process of spatial information integration RFs which have the central and peripheral representation.

Animals↗

PubMedDate not supplied

[From determination of amino acid residue conformation to reconstruction of the spatial structure of proteins (from the data of nuclear Overhauser enhancement spectroscopy].

A new approach to the calculation of the spatial protein structure based on the joint utilization of the theoretical conformational analysis method and nuclear Overhauser enhancement (NOE) spectroscopy data is proposed and verified. The quality in determining various molecule structural parameters is estimated in terms of the expected NOE spectral parameters derived from the X-ray analysis data of the avian pancreatic polypeptide. The proposed approach is shown to correctly determine such structural parameters of protein molecules as local amino acid residue conformations, reciprocal spatial orientation of the C alpha atoms neighbouring along amino acid sequence and reapproached segments of the polypeptide chain. Spatially remote molecule fragments are mainly responsible for the error in determining structural parameters.

Amino Acids↗

PubMed1988

Mathematical modelling of intercellular regulation causing the formation of spatial structures in bacterial colonies.

Bacterial colonies may grow forming stable spatial, particularly circular, structures. For instance, motile bacteria Proteus vulgaris or Escherichia coli grown on agar under certain conditions may form concentric rings with the centre in the inoculation point (Rüss-Münzer, 1935, Bact. Parasit Kde (Abt 1) 7, 214; Budriené, 1985, Dokl. Acad. Nauk SSR, 283, 470). A similar picture can be observed in a different situation, i.e. when a lawn of non-motile Salmonella typhimurium bacteria is cultivated on a solid agar with the locally introduced substrate (Hoppensteadt & Jäger, 1980, Lecture Notes in Biomath. 38, 68). This paper describes a mechanism of bacterial interactions through a hypothetical mediator released by the organisms. A mathematical model has been built. Its analysis has shown that the selected laws of secretion and reception of the mediator can adequately account for the formation of circular structures in the case of both motile and non-motile bacteria.

Animals↗