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At least 811 records · Page 45Linked to original sources
PubMed1993

An automated method for modeling proteins on known templates using distance geometry.

We present an automated method incorporated into a software package, FOLDER, to fold a protein sequence on a given three-dimensional (3D) template. Starting with the sequence alignment of a family of homologous proteins, tertiary structures are modeled using the known 3D structure of one member of the family as a template. Homologous interatomic distances from the template are used as constraints. For nonhomologous regions in the model protein, the lower and the upper bounds for the interatomic distances are imposed by steric constraints and the globular dimensions of the template, respectively. Distance geometry is used to embed an ensemble of structures consistent with these distance bounds. Structures are selected from this ensemble based on minimal distance error criteria, after a penalty function optimization step. These structures are then refined using energy optimization methods. The method is tested by simulating the alpha-chain of horse hemoglobin using the alpha-chain of human hemoglobin as the template and by comparing the generated models with the crystal structure of the alpha-chain of horse hemoglobin. We also test the packing efficiency of this method by reconstructing the atomic positions of the interior side chains beyond C beta atoms of a protein domain from a known 3D structure. In both test cases, models retain the template constraints and any additionally imposed constraints while the packing of the interior residues is optimized with no short contacts or bond deformations. To demonstrate the use of this method in simulating structures of proteins with nonhomologous disulfides, we construct a model of murine interleukin (IL)-4 using the NMR structure of human IL-4 as the template. The resulting geometry of the nonhomologous disulfide in the model structure for murine IL-4 is consistent with standard disulfide geometry.

Algorithms↗
PubMed1994

Distribution of distances between the tryptophan and the N-terminal residue of melittin in its complex with calmodulin, troponin C, and phospholipids.

We used frequency-domain measurements of fluorescence resonance energy transfer to measure the distribution of distances between Trp-19 of melittin and a 1-dimethylamino-5-sulfonylnaphthalene (dansyl) residue on the N-terminal-alpha-amino group. Distance distributions were obtained for melittin free in solution and when complexed with calmodulin (CaM), troponin C (TnC), or palmitoyloleoyl-L-alpha-phosphatidylcholine (POPC) vesicles. A wide range of donor (Trp-19)-to-acceptor (dansyl) distances was found for free melittin, which is consistent with that expected for the random coil state, characterized by a Gaussian width (full width at half maxima) of 28.2 A. In contrast, narrow distance distributions were found for melittin complexed with CaM, 8.2 A, or with POPC vesicles, 4.9 A. A somewhat wider distribution was found for the melittin complex with TnC, 12.8 A, suggesting the presence of heterogeneity in the mode of binding between melittin and TnC. For all the complexes the mean Trp-19 to dansyl distance was near 20 A. This value is somewhat smaller than expected for the free alpha-helical state of melittin, suggesting that binding with CaM or TnC results in a modest decrease in the length of the melittin molecule.

Calmodulin↗
PubMed2002

Hamming distance geometry of a protein conformational space: application to the clustering of a 4-ns molecular dynamics trajectory of the HIV-1 integrase catalytic core.

Protein structures can be encoded into binary sequences (Gabarro-Arpa et al., Comput Chem 2000;24:693-698) these are used to define a Hamming distance in conformational space: the distance between two different molecular conformations is the number of different bits in their sequences. Each bit in the sequence arises from a partition of conformational space in two halves. Thus, the information encoded in the binary sequences is also used to characterize the regions of conformational space visited by the system. We apply this distance and their associated geometric structures to the clustering and analysis of conformations sampled during a 4-ns molecular dynamics simulation of the HIV-1 integrase catalytic core. The cluster analysis of the simulation shows a division of the trajectory into two segments of 2.6 and 1.4 ns length, which are qualitatively different: the data points to the fact that equilibration is only reached at the end of the first segment. The Hamming distance is compared also to the r.m.s. deviation measure. The analysis of the cases studied so far shows that under the same conditions the two measures behave quite differently, and that the Hamming distance appears to be more robust than the r.m.s. deviation.

Algorithms↗
PubMed2006

Error distribution derived NOE distance restraints.

Errors and imprecisions in distance restraints derived from NOESY peak volumes are usually accounted for by generous lower and upper bounds on the distances. In this paper, we propose a new form of distance restraints, replacing the subjective bounds by a potential function obtained from the error distribution of the distances. We derived the shape of the potential from molecular dynamics calculations and by comparison of NMR data with X-ray crystal structures. We used complete cross-validation to derive the optimal weight for the data in the calculation. In a model system with synthetic restraints, the accuracy of the structures improved significantly compared to calculations with the usual form of restraints. For experimental data sets, the structures systematically approach the X-ray crystal structures of the same protein. Also standard quality indicators improve compared to standard calculations. The results did not depend critically on the exact shape of the potential. The new approach is less subjective and uses fewer assumptions in the interpretation of NOESY peak volumes as distance restraints than the usual approach. Figures of merit for the structures, such as the RMS difference from the average structure or the RMS difference from the data, are therefore less biased and more meaningful measures of structure quality than with the usual form of restraints.

Algorithms↗
PubMed1988

Combined procedure of distance geometry and restrained molecular dynamics techniques for protein structure determination from nuclear magnetic resonance data: application to the DNA binding domain of lac repressor from Escherichia coli.

The technique of two-dimensional nuclear magnetic resonance (2D-NMR) has recently assumed an active role in obtaining information on structures of polypeptides, small proteins, sugars, and DNA fragments in solution. In order to generate spatial structures from the atom-atom distance information obtained by the NMR method, different procedures have been developed. Here we introduce a combined procedure of distance geometry (DG) and molecular dynamics (MD) calculations for generating 3D structures that are consistent with the NMR data set and have reasonable internal energies. We report the application of the combined procedure on the lac repressor DNA binding domain (headpiece) using a set of 169 NOE and 17 "hydrogen bond" distance constraints. Eight of ten structures generated by the distance geometry algorithm were refined within 10 ps MD simulation time to structures with low internal energies that satisfied the distance constraints. Although the combination of DG and MD was designed to combine the good sampling properties of the DG algorithm with an efficient method of lowering the internal energy of the molecule, we found that the MD algorithm contributes significantly to the sampling as well.

Algorithms↗
PubMed1997

Thiol-reactive, luminescent Europium chelates: luminescence probes for resonance energy transfer distance measurements in biomolecules.

Lanthanide chelates have recently been shown to be extremely promising luminescence probes for distance measurements in biomolecules using luminescence resonance energy transfer measurements [P. R. Selvin, T. M. Rana, and J. E. Hearst (1994) J. Am. Chem. Soc. 116, 6029-6030; P. R. Selvin, and J. E. Hearst (1994) Proc. Natl. Acad. Sci. USA 91, 10024-10028]. In this work we describe simple procedures for preparing highly fluorescent thiol-reactive europium chelates. These new compounds contain a uv-absorbing coumarin group which sensitizes europium emission, diethylenetriaminepentaacetic acid or triethylenetetraaminehexaacetic acid groups which provide europium chelating function, and a pyridyl disulfide group which allows specific modification of thiol groups. These reagents can be used to label proteins at Cys residues or synthetic oligonucleotides which contain thiol groups. Modification can be reversed easily by treatment with a reducing agent (dithiothreitol). Luminescence energy transfer between these new chelates and CY5 fluorochrome attached to the opposite ends of 15-bp double-stranded DNA was measured to test their usefulness for distance measurements in macromolecules. The distance measured between the chelate (donor) and CY5 (acceptor) was in the range expected for the length of 15-bp DNA. The stability of europium chelates and their conjugates with a protein, the precision of distance measurements using these chelates, possible errors due to intramolecular energy transfer, and the modulation of the R0 value with deuterium oxide were tested. The results obtained fully confirmed the great potential of these new probes for sensitive, simple, and precise distance measurements in biomolecules using luminescence resonance energy transfer.

Base Sequence↗
PubMed1997

Distance and the presentation of visual stimuli to birds

Artificial visual stimuli in the form of photographs, video sequences and computer-generated images are increasingly being used to explore the visual world of birds but their use is controversial as it is still not clear whether birds see them in the same way that humans do. While differences between bird and human colour vision may be one problem with using such artificial images, another and potentially even more important difficulty is the distance at which stimuli are presented. An experiment is described in which hens, Gallus gallus domesticuswere trained to move towards one of two real objects viewed at two different distances. Even for real objects, discrimination levels were better when the hens were allowed to view the stimuli from 5-25 cm than when they were forced to choose at 120 cm and this correlated with their ability to transfer to photographs of the same objects at different distances. In a colour discrimination at a short distance, five out of seven hens showed 100% correct responses when first shown photographs of real objects that they had previously learnt to discriminate. The results suggest that photographs can be used as substitutes for real stimuli but that care should be taken over the distance at which they are presented. The results are discussed in relation to the visual behaviour of birds and differences in functioning of their frontal and lateral visual fields.Copyright 1997 The Association for the Study of Animal Behaviour1997The Association for the Study of Animal Behaviour

Journal Article↗
PubMed2000

Assessment of auditory distance in a territorial songbird: accurate feat or rule of thumb?

Territorial passerines presumably benefit from their ability to use auditory cues to judge the distance to singing conspecifics, by increasing the efficiency of their territorial defence. Here, we report data on the approach of male territorial chaffinches, Fringilla coelebs, to a loudspeaker broadcasting conspecific song simulating a rival at various distances by different amounts of song degradation. Songs were degraded digitally in a computer-simulated forest emulating distances of 0, 20, 40, 80 and 120 m. The approach distance of chaffinches towards the loudspeaker increased with increasing amounts of degradation indicating a perceptual representation of differences in distance of a sound source. We discuss the interindividual variation of male responses with respect to constraints resulting from random variation of ranging cues provided by the environmental song degradation, the perception accuracy and the decision rules. Copyright 2000 The Association for the Study of Animal Behaviour.

Journal Article↗
PubMed1997

Estimating physical distances from radiation hybrid mapping data.

Radiation hybrid mapping has become an established tool for building physical maps. It represents a powerful way of constructing YAC contigs and high-resolution maps for positional cloning experiments. Ideally, radiation hybrids should not only provide support for the true order of the markers, but also accurate estimates of the physical distances between them. Statistical analysis of radiation hybrids has proved difficult because of the number of parameters (representing the fragment retention probabilities) that must be estimated, and simplifying assumptions are needed to analyze large numbers of markers simultaneously. The ramifications of these assumptions for the calculation of physical distances are investigated. A simple two-locus model is presented to demonstrate that variation in marker retention can lead to distortions in the estimates of distance. Multilocus simulations show that, when marker retention is constant across the chromosome, good estimates of physical distance can be derived using simple models of retention. However, further simulations exploring variable retention schemes demonstrate that significant errors in the estimates of map distances can occur. Ways of minimizing these distortions are discussed.

Chromosome Mapping↗
PubMed1993

Protein structures from distance inequalities.

A computer method for folding protein backbones from distance inequalities is presented. It involves an algorithm that uses a novel approach for handling inequalities through the minimization of a continuous energy function. Tests of the folding algorithm have been carried out on a small protein, the 6PTI (bovine pancreatic trypsin inhibitor) with 56 amino acid residues, and on a medium-size protein, the 1TRM (rat trypsin) with 223 amino acid residues. Reconstructions based on a real-valued distance matrix led to folded three-dimensional structures with root-mean-square values of 0.04 A when compared with the crystallographic data. The obtained root-mean-square measures were of the order of 1 A, when distance inequalities were used for the reconstruction. Subsequently, the folding approach has been applied to distance inequalities predicted by neural network techniques that use the amino acid sequence as the only input. The inaccuracy in the inequalities predicted by the neural network was the reason for the root-mean-square value of 5.2 A. An error analysis of the method for reconstruction was performed and showed that no more than 3% inaccurate distance inequalities could be corrected for. Finally, a simple technique for root-mean-square comparisons of different protein structures is discussed.

Algorithms↗
PubMed1996

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.

Algorithms↗
PubMed1997

Triadic Distance Models: Axiomatization and Least Squares Representation

Distance models for three-way proximity data, which consist of numerical values assigned to triples of objects that indicate their joint (lack of) homogeneity or resemblance, require a generalization of the usual distance concept defined on pairs of objects. An axiomatic framework is given for characterizing triadic dissimilarity, triadic similarity, and triadic distance, where the term triadic implies that each element of the triple is treated on an equal footing. Two kinds of distance models are studied in detail: the Minkowski-p or Mp model, which is based upon dyadic components and includes the perimeter model as an important special case, and several models based on presence-absence variables. They are shown to satisfy the tetrahedral inequality, a condition that is characteristic for the present axiomatization. Two monotonically convergent algorithms are described that find weighted least squares representations of three-way proximity data under the Euclidean M1 model and the Euclidean M2 model. To enable a scalefree evaluation of the quality of the fit, an additive decomposition of the sum of squares of the dissimilarities is derived. As illustrated in one of the examples, distance analysis of three-way, three-mode tables is possible by a suitable manipulation of the least squares weights.

Journal Article↗
PubMed1995

A relaxation-matrix analysis of distance-constraint ranges for NOEs in proteins at long mixing times.

Long-mixing-time data (tau m > 200 ms) from NOE spectra have largely been ignored as a source of protein structural information due to the effects of spin diffusion on calculated interproton distances when using the two-spin approximation. An effective approach for incorporating spin-diffusion effects in an average way into refinements is to choose distance bounds based on distributions of distances observed in NOE back calculations on homologous proteins from a protein structure database. We have determined distributions of interproton distances characteristic of newly observed NOE cross peaks for the proteins crambin, PTI, and echistatin at long mixing times. A relaxation-matrix analysis was used to model the effects of spin diffusion. Constraint ranges were constructed from the interproton distance distributions which can be used in standard protein-refinement programs based on the two-spin approximation. Back calculations are also used to analyze constraint ranges typically used for protein structure determinations based on NOE spectra at shorter mixing times.

Electron Spin Resonance Spectroscopy↗
PubMed1995

Deriving accurate interproton distances from ROESY spectra with limited knowledge of scalar coupling constants via the CARNIVAL algorithm. An iterative complete-relaxation-matrix approach.

A method (termed CARNIVAL) for accurately determining distances from proton homonuclear rotating-frame Overhauser effect spectroscopy (ROESY) is described. The method entails an iterative calculation of the relaxation matrix using methodology introduced with the MARDIGRAS algorithm for analysis of two-dimensional nuclear Overhauser effect spectra (B. A. Borgias and T. L. James, J. Magn. Reson. 87, 475, 1990). The situation is complicated in the case of ROESY as spectral peak intensities are influenced by resonance offset and contributions from homonuclear Hartmann-Hahn (HOHAHA) transfer if the nuclear spins are related by scalar coupling. The effects of spin-locking field strength on distance determinations and the ensuing distance errors incurred when HOHAHA corrections are made with limited knowledge of scalar (J) coupling information have been evaluated using simulated ROESY intensities with a model peptide structure. It has been demonstrated that accurate distances can be obtained with little or no explicit knowledge of the homonuclear coupling constants over a moderate range of spin-locking field strengths. The CARNIVAL algorithm has been utilized to determine distances in a decapeptide using experimental ROESY data without measured coupling constants.

Algorithms↗
PubMed1998

Analysis of error propagation from NMR-derived internuclear distances into molecular structure of cyclo-pro-gly.

Analytical expressions have been derived that translate uncertainties in distance constraints (obtained from NMR investigations) into uncertainties in atom positions in the maximum likelihood (ML) structure consistent with these inputs. As a test of this approach, a comparison was made between test structures reconstructed by the new ML approach, which yields a single structure and a covariance matrix for coordinates, and those reconstructed by metric matrix distance-geometry (MMDG), which yields a family of structures that sample uncertainty space. The test structures used were 560 polyhedra, with edges of arbitrary length containing up to 50 vertices, and one polyhedron, with 100 vertices; randomized distance constraints generated from these structures were used in reconstructing the polyhedra. The uncertainties derived from the two methods showed excellent agreement, and the correlation improved, as expected, with increasingly larger numbers of MMDG structures. This agreement supports the validity of the rapid analytical ML approach, which requires the calculation of only a single structure. As a second test of the ML method, the approach was applied to the determination of uncertainties in the structure of a cyclic dipeptide, cyclo(DL-Pro-Gly) (cPG), derived from NMR cross-relaxation data. The input data were interproton distances calculated from NOEs measured for a solution of the peptide in 2:1 DMSO:H2O at -40 degreesC (so as to yield large negative NOEs). In order to evaluate effects of the quality of the input spectral parameters on the precision of the resulting NMR structure, information from the covalent geometry of cPG was not used in the structure calculations. Results obtained from the analytical ML approach compared favorably with those from the much slower random-walk variant of the Monte Carlo method applied to the same input data. As a third test, the ML approach was used with synthetic structural constraints for a small protein; the results indicate that it will be feasible to use this rapid method to translate uncertainties associated with a given set of distance restraints into uncertainties in atom positions in larger molecules.

Dipeptides↗
PubMed2001

Measurement of interfluorine distances in solids.

(19)F homonuclear dipolar recoupling methods were used to measure internuclear distances ranging from 5 to 12 A in fluorinated organic compounds in the solid state. Magic-angle-spinning-based high-resolution techniques were utilized. Trifluoromethyl and aromatic fluorine groups were separated by rigid aromatic spacers; these compounds were diluted into nonfluorinated host molecule matrices to give isolated homonuclear spin pairs with known internuclear distances. Radiofrequency-driven recoupling (RFDR) was used to elicit magnetization exchange between the spin pairs in 1D and 2D experiments. Simulation of the exchange was accomplished using a Monte Carlo-type algorithm to search the parameter space. These methods allow the determination of distances with an accuracy of 1 A at shorter distances and 2 A at longer distances, with the assumption of no prior knowledge of T(2)(ZQ).

Fluorine↗
PubMed1996

On the nearest neighbour interchange distance between evolutionary trees.

We present some new results on a well-known distance measure between evolutionary trees. The trees we consider are free 3-trees having n leaves labeled 0,...,n - 1 (representing species), and n - 2 internal nodes of degree 3. The distance between two trees is the minimum number of nearest neighbour interchange (NNI) operations required to transform one into the other. First, we improve an upper bound on the nni-distance between two arbitrary n-node trees from 4n log n (Culik & Wood, 1982, Inf. Pro. Letts. 15, 39-42) to n log n. Second, we present a counterexample disproving several theorems in (Waterman & Smith, 1978, J. theor. Biol. 73, 789-800). Roughly speaking, finding an equal partition between two trees does not imply decomposability of the distance finding problem. Third, we present a polynomial-time approximation algorithm that, given two trees, finds a transformation between them of length O(log n) times their distance. We also present some results of computations we performed on small size trees.

Algorithms↗
PubMed1994

Least squares estimation of molecular distance--noise abatement in phylogenetic reconstruction.

Zuckerkandl and Pauling (1962, "Horizons in Biochemistry," pp. 189-225, Academic Press, New York) first noticed that the degree of sequence similarity between the proteins of different species could be used to estimate their phylogenetic relationship. Since then models have been developed to improve the accuracy of phylogenetic inferences based on amino acid or DNA sequences. Most of these models were designed to yield distance measures that are linear with time, on average. The reliability of phylogenetic reconstruction, however, depends on the variance of the distance measure in addition to its expectation. In this paper we show how the method of generalized least squares can be used to combine data types, each most informative at different points in time, into a single distance measure. This measure reconstructs phylogenies more accurately than existing non-likelihood distance measures. We illustrate the approach for a two-rate mutation model and demonstrate that its application provides more accurate phylogenetic reconstruction than do currently available analytical distance measures.

Amino Acid Sequence↗