Intrinsic nature of the three-dimensional structure of proteins as determined by distance geometry with good sampling properties

A protocol for distance geometry calculation is shown to have excellent sampling properties in the determination of three-dimensional structures of proteins from nuclear magnetic resonance (NMR) data. This protocol uses a simulated annealing optimization employing mass-weighted molecular dynamics in four-dimensional space (Havel, T.F. (1991) Prog. Biophys. Mol. Biol., 56, 43-78). It attains an extremely large radius of convergence, allowing a random coil conformation to be used as the initial estimate for the succeeding optimization process. Computations are performed with four systems of simulated distance data as tests of the protocol, using an unconstrained L-alanine 30mer and three different types of proteins, bovine pancreatic trypsin inhibitor, the alpha-amylase inhibitor Tendamistat, and the N-terminal domain of the 434-repressor. The test of the unconstrained polypeptide confirms that the sampled conformational space is that of the statistical random coil. In the larger and more complicated systems of the three proteins, the protocol gives complete convergence of the optimization without any trace of initial structure dependence. As a result of an exhaustive conformational sampling by the protocol, the intrinsic nature of the structures generated with distance restraints derived from NMR data has been revealed. When the sampled structures are compared with the corresponding X-ray structures, we find that the averages of the sampled structures always show a certain pattern of discrepancy from the X-ray structure. This discrepancy is due to the short distance nature of the distance restraints, and correlates with the characteristic shape of the protein molecule.     

Homology modeling by the ICM method

Five models have been built by the ICM method for the Comparative Modeling section of the Meeting on the Critical Assessment of Techniques for Protein Structure Prediction. The targets have homologous proteins with known three-dimensional structure with sequence identity ranging from 25 to 77%. After alignment of the target sequence with the related three-dimensional structure, the modeling procedure consists of two subproblems: side-chain prediction and loop prediction. The ICM method approaches these problems with the following steps: (1) a starting model is created based on the homologous structure with the conserved portion fixed and the nonconserved portion having standard covalent geometry and free torsion angles; (2) the Biased Probability Monte Carlo (BPMC) procedure is applied to search the subspaces of either all the nonconservative side-chain torsion angles or torsion angles in a loop backbone and surrounding side chains. A special algorithm was designed to generate low-energy loop deformations. The BPMC procedure globally optimizes the energy function consisting of ECEPP/3 and solvation energy terms. Comparison of the predictions with the NMR or crystallographic solutions reveals a high proportion of correctly predicted side chains. The loops were not correctly predicted because imprinted distortions of the backbone increased the energy of the near-native conformation and thus made the solution unrecognizable. Interestingly, the energy terms were found to be reliable and the sampling of conformational space sufficient. The implications of this finding for the strategies of future comparative modeling are discussed.     

Structural characterization of the molecular dimer of the peptide antibiotic vancomycin by distance geometry in four spatial dimensions

OBJECTIVE: The objectives of this study were to know the prevalence of hepatitis C virus (HCV) in a population of pregnant women, to evaluate the vertical transmission rates of HCV in a prospective study and to determine the repercussions and consequences in children born to infected mothers. PATIENTS AND METHODS: A total of 6556 pregnant women were tested for HCV antibodies from January 1993 to August 1995. We followed 50 babies born to infected mothers for at least 12 months (mean 15 months). Serological assays employed included a screening ELISA II confirmed with immunoblot. Viral detection was performed by qualitative and quantitative PCR for HCV-RNA. RESULTS: Fifty-nine pregnant women were AcHCV(+). This represents a seroprevalence of 0.9%. Of the 50 babies followed, 6 were PCR(+) and 44 were PCR(-). The risk of transmission is correlated with the titer of HCV-RNA in the mother. All mothers of infected babies were HIV (-). CONCLUSIONS: The rate of prevalence in our pregnant women population is 0.9%. We found a vertical transmission rate of 12%. The high serum HCV-RNA titers in the mothers are a risk factor of transmission of HCV. The viremia in the children does not predict the apparition of the clinical disease, although they can exhibit intermittent increases of transaminases.     

The transmembrane 7-alpha-bundle of rhodopsin: distance geometry calculations with hydrogen bonding constraints

A 3D model of the transmembrane 7-alpha-bundle of rhodopsin-like G-protein-coupled receptors (GPCRs) was calculated using an iterative distance geometry refinement with an evolving system of hydrogen bonds, formed by intramembrane polar side chains in various proteins of the family and collectively applied as distance constraints. The alpha-bundle structure thus obtained provides H bonding of nearly all buried polar side chains simultaneously in the 410 GPCRs considered. Forty evolutionarily conserved GPCR residues form a single continuous domain, with an aliphatic "core" surrounded by six clusters of polar and aromatic side chains. The 7-alpha-bundle of a specific GPCR can be calculated using its own set of H bonds as distance constraints and the common "average" model to restrain positions of the helices. The bovine rhodopsin model thus determined is closely packed, but has a few small polar cavities, presumably filled by water, and has a binding pocket that is complementary to 11-cis (6-s-cis, 12-s-trans, C = N anti)-retinal or to all-trans-retinal, depending on conformations of the Lys296 and Trp265 side chains. A suggested mechanism of rhodopsin photoactivation, triggered by the cis-trans isomerization of retinal, involves rotations of Glu134, Tyr223, Trp265, Lys296, and Tyr306 side chains and rearrangement of their H bonds. The model is in agreement with published electron cryomicroscopy, mutagenesis, chemical modification, cross-linking, Fourier transform infrared spectroscopy, Raman spectroscopy, electron paramagnetic resonance spectroscopy, NMR, and optical spectroscopy data. The rhodopsin model and the published structure of bacteriorhodopsin have very similar retinal-binding pockets.     

Solution structure of a fragment of the dimerization domain of DP-1 determined by 1H-nuclear magnetic resonance and distance geometry

Integrated delivery systems that promote learning and flexibility will be better prepared to face the challenges imposed by a complex and competitive environment. The integration of learning into these systems requires a shared vision, facilitative leadership, and highly functioning communication channels within an organic structure. Strategies that promote positive attitudes toward change are necessary for learning as is the provision of resources, training, incentives, and rewards that support learning, and feedback on how new administrative and clinical practices advance the mission and goals of the system.     

Electrocochleography by mathematical modelling

The aim of this work is to critically review some of the classical electrocochleographic methods in accordance with the systems theory: (a) in describing, by means of mathematical models, the different parts of the auditory system concerned in the generation of stimulus-evoked signals; and: (b) in comparing the outputs of these models with the measurements of the cochlear potentials. It must be stated clearly that we realise that many of the conclusions drawn could be criticised, it is hoped that future research in the field with be stimulated by this work.     

Homology modelling and molecular dynamics aided analysis of ligand complexes demonstrates functional properties of lipid-transfer proteins encoded by the barley low-temperature-inducible gene family, blt4

In the present study an investigation of the structure-activity relationships in 9-ethylpurine derivatives, aimed at preparing A1, A2A, A2B, and A3 selective adenosine receptor antagonists, was undertaken. Our synthetic approach was to introduce various substituents (amino, alkoxy and alkynyl groups) into the 2-, 6-, or 8-positions of the purine ring. The starting compounds for each series of derivatives were respectively: 2-iodo-9-ethyladenine (9), obtained from 2-amino-6-chloropurine (5); 9-ethyl-6-iodo-9H-purine (11), 8-bromo-9-ethyl-adenine (3) and 8-bromo-9-ethyl-6-iodo-9H-purine (13), obtained from 9-ethyl-adenine (2). The synthesized compounds were tested in in vitro radioligand binding assays at A1, A2A, and A3 human adenosine receptor subtypes. Due to the lack of a suitable radioligand the affinity of the 9-ethyladenine derivatives at A2B adenosine receptors was determined in adenylyl cyclase experiments. In general, the series of 9-ethylpurine derivatives exhibited a similar pharmacological profile at A1 and A2A receptors whereas some differences were found for the A3 and the A2B subtypes. 8-Bromo-9-ethyladenine (3) showed higher affinity for all receptors in comparison to the parent compound 2, and the highest affinity in the series for the A2A and A2B subtypes (Ki = 0.052 and 0.84 microM, respectively). Analyzing the different substituents, a phenethoxy group in 2-position (10a) gave the highest A2A versus A2B selectivity (near 400-fold), whereas a phenethylamino group in 2- and 6-position (10b and 12b, respectively) improved the affinity at A2B receptors, compared to the parent compound 2. The presence of a hexynyl substituent in 8-position led to a compound with good affinity at the A3 receptor (4d, Ki = 0.62 microM), whereas (ar)alkynyl groups are detrimental for the potency at the A2B subtype. These differences give raise to the hope that further modifications will result in the development of currently unavailable leads with good affinity and selectivity for A2B adenosine receptors.     

Solution conformation of the Pseudomonas syringae MSU 16H phytotoxic lipodepsipeptide Pseudomycin A determined by computer simulations using distance geometry and molecular dynamics from NMR data

Pseudomycin A is a cyclic lipodepsinonapeptide phytotoxin produced by a strain of the plant pathogenic bacterium Pseudomonas syringae. Like other members of this family of bacterial metabolites, it is characterised by a fatty acylated cyclic peptide with mixed chirality and lactonic closure. Several biological activities of Pseudomycin A are lower than those found for some of its congeners, a difference which might depend on the diverse number and distribution of charged residues in the peptide moiety. Hence, it was of interest to investigate its conformation in solution. After the complete interpretation of the two-dimensional NMR spectra, NOE data were obtained and the structure was determined by computer simulations, applying distance geometry and molecular dynamics procedures. The conformation of the large ring of Pseudomycin A in solution includes three rigid structural regions interrupted by three short flexible regions that act as hinges. The overall three-dimensional structure of the cyclic moiety is similar to that of previously studied bioactive lipodepsinonapeptides produced by other pseudomonads.     

Homology modelling of rat kallikrein rK9, a member of the tissue kallikrein family: implications for substrate specificity and inhibitor binding

The rat kallikrein rK9 is one of the six members of the rat tissue kallikrein family isolated to date. It is 84% identical to rK2 (tonin), and both proteinases are thought to have vasoconstrictive properties. Recently we have shown that rK9 and rK2 have distinct substrate specificities and sensitivities to inhibitors, despite their similar sequences. Unlike all other mammalian kallikrein-related proteinases, rK9 is resistant to inhibition by aprotinin. We have developed a 3-D model of rK9, based on the known X-ray structures of rK2, porcine kallikrein and bovine trypsin, to identify the structural features underlying this functional diversity. The final rK9 model is structurally similar to rK2, but variable regions surrounding the active site differ quite markedly from the reference proteins. The kallikrein loop, which differs from that in porcine kallikrein by a seven-residue insertion, has been generated de novo and subjected to simulated annealing to assess its influence on the restricted substrate specificity of these proteinases. The proposed conformation of the specificity pocket in rK9 differs from that of other serine proteinases, but it can still accommodate both aromatic and basic amino acid side chains at the substrate P1 position, thus explaining the dual chymotrypsin and trypsin-like activity of rK9. The electrostatic potentials of rK9 and aprotinin were calculated using the finite difference Poisson-Boltzmann method. They indicated a large positive region near the active site of rK9 not found in related proteinases because of positively charged residues at positions 61 and 65 in rK9. They generate a positive region, which overlaps a positive region in aprotinin, and may prevent aprotinin binding. A single mutation in aprotinin is suggested that might allow kallikrein rK9 inhibition by aprotinin. This model contributes significantly to our understanding of the structure-function relationships among proteinases of the tissue kallikrein family.     

The NMR solution structure of intestinal fatty acid-binding protein complexed with palmitate: application of a novel distance geometry algorithm

The three-dimensional solution structure of rat intestinal fatty acid-binding protein (I-FABP) complexed with palmitate has been determined using multidimensional triple-resonance NMR methods. The structure is based on 3889 conformational restraints derived mostly from 3-D 13C- and 15N-resolved nuclear Overhauser (NOESY) experiments. The 3-D NOESY data for this 15.4 kDa complex contained an average of nine possible interpretations per cross-peak. To circumvent this ambiguity, an eight-stage iterative procedure was employed to gradually interpret and introduce unambiguous distance restraints during subsequent rounds of structure calculations. The first stage of this procedure relied critically upon an initial structural model based on the consensus 1H/13C chemical shift-derived secondary structure and a set of symmetry-checked restraints derived from the 3-D 13C-resolved NOESY spectrum. The structures were calculated using DISTGEOM, a program that implements a novel distance geometry algorithm with pairwise Gaussian metrization. A central feature of this algorithm is the use of an iteratively optimized Gaussian distribution for the selection of trial distances, which overcomes the tendency of metrization to produce crushed structures. In addition, this algorithm randomly selects pairwise elements of the distance matrix, which results in an improved sampling of conformational space for a given computational effort. The final family of 20 distance geometry/simulated annealing structures exhibited an average pairwise C(alpha) root-mean-square deviation of 0.98 A, and their stereochemical quality, as assessed by PROCHECK, was comparable to that of 2.5 A X-ray crystal structures. The NMR structure was compared with the X-ray crystal structure of the same ligand/protein complex and was found to be essentially identical within the precision of the results. The NMR structure was also compared with that of the palmitate complex with bovine heart FABP, which shares 30% sequence identity with rat I-FABP. The overall folds were the same, but differences were noted with respect to the presence or absence of apparent conformational heterogeneity and the location and conformation of the bound fatty acid.     

Edge geometry of pipe blanks produced by JCOE flexure

For the shaping of welded straight-seam large-diameter pipe in the TESA 1420 production line, methods are proposed for calculating the geometric parameters of the edge of the blank and the profile of the deforming tool. The edge geometry obtained on an edge-bending press is compared when using surface tools of involute and single-radius type. For tools of single-radius type, edge geometry consistent with the required shaping quality may be produced. For the edge-bending presses, a method of calculating the edge geometry in loading and unloading is outlined. The height of the bent edge, the residual radii of curvature, and the coordinates of the loading and unloading points at the external and internal edge contour of the pipe blank are determined. The coordinates of the edge formed by a tool with an involute profile are also calculated. The involute tool profile is universal on passing from one type of tool to another within a standardized group. The calculation permit conversion from an involute edge profile to a multiradial profile, followed by determination of the fixed coordinates of the points of the blank after springback. On the basis of those coordinates, the output edge geometry is estimated. Within the 1220–1420 mm standardized group, the longitudinal edge deformation for the 1220 × 10 mm type is calculated. Standardization is found to be much simpler with a single- radius tool profile. For edge-bending presses, a method of calculating the edge parameters of the pipe blank when using a tool with an involute contact profile is developed and tested in industrial conditions. Single- radius calibration of the profile of the edge-bending tool is proposed, such that fixed time coordinates are ensured. These are analogous to the coordinates with an involute punch profile. The blank’s weighted mean radius of curvature maximizes the agreement of the coordinates of the blank profile at fixed points in both approaches. (The maximum discrepancy is no more than 6–7%.)     

Tie trees generated by distance methods of phylogenetic reconstruction

In examining genetic data in recent publications, Backeljau et al. showed cases in which two or more different trees (tie trees) were constructed from a single data set for the neighbor-joining (NJ) method and the unweighted pair group method with arithmetic mean (UPGMA). However, it is still unclear how often and under what conditions tie trees are generated. Therefore, I examined these problems by computer simulation. Examination of cases in which tie trees occur shows that tie trees can appear when no substitutions occur along some interior branch(es) on a tree. However, even when some substitutions occur along interior branches, tie trees can appear by chance if parallel or backward substitutions occur at some sites. The simulation results showed that tie trees occur relatively frequently for sequences with low divergence levels or with small numbers of sites. For such data, UPGMA sometimes produced tie trees quite frequently, whereas tie trees for the NJ method were generally rare. In the simulation, bootstrap values for clusters (tie clusters) that differed among tie trees were mostly low (< 60%). With a small probability, relatively high bootstrap values (at most 70%-80%) appeared for tie clusters. The bias of the bootstrap values caused by an input order of sequence can be avoided if one of the different paths in the cycles of making an NJ or UPGMA tree is chosen at random in each bootstrap replication.     

Binocular distance perception: Egocentric distance tasks.

Tested an extension of the present author's (1978; see also PA, Vol 64:11699) theory of binocular distance perception, which has been shown to give a good account of performance in relative distance tasks. In 2 experiments, 5 18–36 yr olds indicated perceived egocentric distance of targets (perceived distance from him/herself) by means of a verbal report or manual pointing response. In Exp I, the distance to 2 targets was varied while maintaining a constant disparity between them. In Exp II, 1 target was held fixed while the distance to a 2nd target was varied. In each case, Ss indicated the perceived distance of each target. Manual and verbal responses agreed with each other to within a linear transform. Both sets of data are consistent with the theory and indicate that reference parallax is a weighted average of target parallaxes. The systematic inaccuracy of binocular distance perception is attributed to the misperception of egocentric distance to the configuration. (31 ref) (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Optimal drawplate geometry

A method is proposed for determining optimal drawplate geometry, so as to ensure minimum stress in drawing. The drawplate’s calibration band is taken into account in optimization. For standard draw-plates, a formula has been derived for calculating the optimal extension.     

Homology in natural cryptic plasmids of Bacillus subtilis

Peculiarities of DNA homology in a number of cryptic plasmids isolated from soil bacillary strains and related or identical to Bacillus subtilis were studied. Fragments generated after digestion of one of these plasmids, p1414, were employed as a probe for blot hybridization with identical fragments of other plasmids. The data obtained suggest that nearly all the studied plasmids possess a common homology site that occupies a significant plasmid portion. Regions of detectable and weak homology were located throughout this site. Moreover, plasmid p1414 was shown to carry a large site that lacks homology with plasmids belonging to two groups. Eventually, one of these plasmids demonstrates complete lack of homology with the remaining plasmids.     

Proton nuclear magnetic resonance and distance geometry/simulated annealing studies on the variant-1 neurotoxin from the New World scorpion Centruroides sculpturatus Ewing

The sequence-specific proton resonance assignments for the variant-1 (CsE-v1) neurotoxin from the venom of the New World scorpion Centruroides sculpturatus Ewing (range Southwestern United States) have been performed by 2D 1H NMR spectroscopy at 600 MHz. The stereospecific assignments for the beta-methylene protons of 19 non-proline residues have been determined. A number of short-, medium-, and long-range NOESY contacts as well as the backbone and the side-chain vicinal coupling constants for several residues have been determined. Slowly exchanging amide hydrogens from a number of residues have been identified. On the basis of the NMR data, the solution structure of this protein has been determined by a hybrid procedure consisting of distance geometry and dynamical simulated annealing refinement calculations. Distance constraints from the NOESY data and torsion angle constraints from proton vicinal coupling constant data were used in the simulated annealing calculations. The three-dimensional structure of CsE-v1 is characterized by a three-stranded antiparallel beta-sheet, a short alpha-helix, a cis-proline, and intervening loops. A comparison with the solution NMR data of a homologous protein (CsE-v3) from the Centruroides venom, shows that the structures are essentially similar, except for some minor differences. Some of the NMR spectral perturbations are felt in regions far removed from sites of amino acid substitutions. The hydrophobic surface in CsE-v1 is slightly more extended than in CsE-v3.     

Perception of auditory-visual distance relations by 5-month-old infants.

This study investigated whether, and on what basis, 5-mo-old infants perceive auditory–visual distance relations. A 2-screen visual preference procedure was used in which infants viewed side by side videotaped toy trains (in 4 visual conditions) along with increasing or decreasing amplitude lawnmower engine sounds from a central speaker designed to match one of the videos. Results suggest that 5-mo-olds were sensitive to auditory–visual distance relations and that changing size was an important visual depth cue. Infants did not show evidence of matching in other conditions in which the soundtracks were paired with videos depicting shifts in the train's luminance or showing the train moving vertically with no change in size. The infants' matching performance suggested that 5-mo-olds respond to invariant auditory–visual relations specifying meaningful spatial properties. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Visual perception of egocentric distance as assessed by triangulation.

Two triangulation methods for measuring perceived egocentric distance were examined. In the triangulation-by-pointing procedure, the observer views a target at some distance and, with eyes closed, attempts to point continuously at the target while traversing a path that passes by it. In the triangulation-by-walking procedure, the observer views a target and, with eyes closed, traverses a path that is oblique to the target; on command from the experimenter, the observer turns and walks toward the target. Two experiments using pointing and 3 using walking showed that perceived distance, averaged over observers, was accurate out to 15 m under full cue conditions. For target distances between 15 and 25 m, the evidence indicates slight perceptual underestimation. Results also show that observers, on average, were accurate in imaginally updating the locations of previously viewed targets. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Population substructure and isolation by distance in three continental regions

Isolation by distance and divergence from a shared population history are two sources of population substructure. Isolation by distance erases population history as populations approach migration-drift equilibrium, while diverging populations descended from a single ancestral population will accumulate genetic differences with time. Here I investigate how much of the worldwide genetic diversity from Jorde et al.'s ([1997] Proc. Natl. Acad. Sci. USA 94:3100-3103) 60 tetranucleotide short tandem repeat (STR) data can be explained by isolation by distance. I use Slatkin's measure of population substructure, R(ST), principal components analyses, and Mantel tests to investigate the pattern of genetic diversity at both the intercontinental and intracontinental levels. Geographic distance accounts for almost 60% of world-wide interpopulation genetic relationships. Within continents, the correlations are less, although not significantly so because of wide confidence intervals. These results suggest that populations have not reached migration-drift equilibrium and that there is information in STR data to reconstruct population history. The level of population substructure worldwide is consistent with previous observations, but at the intracontinental level substructure is less. When one examines diversity against distance from the centroid, one sees excess heterozygosity in Africa, a pattern also noted by Stoneking et al. ([1998] Genome Research 7:1061-1071). A larger effective population size in Africa could explain the excess diversity. Greater gene flow in Africa is an unlikely explanation because the African R(ST) value is slightly larger than the Asian and European R(ST)s, pointing to less gene flow and greater substructure among African populations. Furthermore, there are differences in patterns between heterozygosity and allele size variance. Heterozygosity has a higher correlation with distance from the centroid than does allele size variance, and this may reflect demographic history. Kimmel et al. ([1998] Genetics 148:1921-1930) have shown that after a population expansion heterozygosity returns to equilibrium more quickly than does allele size variance. The contrasting patterns between heterozygosity and allele size variance may reflect different times after an expansion. However, simulations and further work need to be done to more thoroughly investigate the possibility that these data reflect population expansions.