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At least 19 recordsLinked to original sources
PubMed2005

Covariation analysis of local amino acid sequences in recurrent protein local structures.

Local structural information is supposed to be frequently encoded in local amino acid sequences. Previous research only indicated that some local structure positions have specific residue preferences in some particular local structures. However, correlated pairwise replacements for interacting residues in recurrent local structural motifs from unrelated proteins have not been studied systematically. We introduced a new method fusing statistical covariation analysis and local structure-based alignment. Systematic analysis of structure-based multiple alignments of recurrent local structures from unrelated proteins in representative subset of Protein Databank indicates that covarying residue pairs with statistical significance exist in local structural motifs, in particular beta-turns and helix caps. These residue pairs are mostly linked through polar functional groups with direct or indirect hydrogen bonding. Hydrophobic interaction is also a major factor in constraining pairwise amino acid residue replacement in recurrent local structures. We also found correlated residue pairs that are not clearly linked with through-space interactions. The physical constrains underlying these covariations are less clear. Overall, covarying residue pairs with statistical significance exist in local structures from unrelated proteins. The existence of sequence covariations in local structural motifs from unrelated proteins indicates that many relics of local relations are still retained in the tertiary structures after protein folding. It supports the notion that some local structural information is encoded in local sequences and the local structural codes could play important roles in determining native state protein folding topology.

Algorithms↗
PubMed2001

Local structure of Ge nanocrystals embedded in SiO2 studied by X-ray absorption fine structure.

Local structure of Ge nanocrystals embedded in SiO2 has been studied by X-ray absorption fine structure on the Ge K-edge. The XANES and EXAFS results indicate that Ge atoms in samples with the Ge concentration x=25-40 mol. % are coordinated with oxygen atoms, while they exist as amorphous Ge clusters in samples with x=60 mol. %. Upon annealing, completely relaxed crystalline Ge phase is formed for samples with x=60 mol. %, in contrast to the x=25-40 mol. % sample, which show little or no indication of Ge cluster formation. A possible mechanism of Ge nanocluster formation is discussed.

Journal Article↗
PubMed2003

Local structure prediction with local structure-based sequence profiles.

MOTIVATION: A large body of experimental and theoretical evidence suggests that local structural determinants are frequently encoded in short segments of protein sequence. Although the local structural information, once recognized, is particularly useful in protein structural and functional analyses, it remains a difficult problem to identify embedded local structural codes based solely on sequence information. RESULTS: In this paper, we describe a local structure prediction method aiming at predicting the backbone structures of nine-residue sequence segments. Two elements are the keys for this local structure prediction procedure. The first key element is the LSBSP1 database, which contains a large number of non-redundant local structure-based sequence profiles for nine-residue structure segments. The second key element is the consensus approach, which identifies a consensus structure from a set of hit structures. The local structure prediction procedure starts by matching a query sequence segment of nine consecutive amino acid residues to all the sequence profiles in the local structure-based sequence profile database (LSBSP1). The consensus structure, which is at the center of the largest structural cluster of the hit structures, is predicted to be the native state structure adopted by the query sequence segment. This local structure prediction method is assessed with a large set of random test protein structures that have not been used in constructing the LSBSP1 database. The benchmark results indicate that the prediction capacities of the novel local structure prediction procedure exceed the prediction capacities of the local backbone structure prediction methods based on the I-sites library by a significant margin. AVAILABILITY: All the computational and assessment procedures have been implemented in the integrated computational system PrISM.1 (Protein Informatics System for Modeling). The system and associated databases for LINUX systems can be downloaded from the website: http://www.columbia.edu/~ay1/.

Amino Acid Sequence↗
PubMed2001

Local structure and local compressibilities around Co2+ impurity in ZnSiF6.6H2O crystal determined from electron paramagnetic resonance data.

The perturbation formulas of g-factors gparallel, gperpendicular and hyperfine structure constants Aparallel, Aperpendicular for 3d7 ion in trigonal octahedral crystal field are established on the basis of a cluster approach. These formulas consist of the contributions from configuration interaction and covalency effect and the parameters related to both effects can be estimated from the optical spectra and the structural data of the system under study. According to these formulas, the local trigonal distortion angle beta at pressure P = 0 and the local compressibilities d ln beta/dP in two pressure regions around Co2+ impurity in ZnSiF6.6H2O crystal are estimated by fitting the calculated electron paramagnetic resonance parameters gi, Ai and their pressure coefficients to the observed values. The results show that these local values are different from those of the host crystal because of the influence of impurity.

Cations, Divalent↗
PubMed2001

Local structures of mechanically alloyed Fe100-xCux solid solutions studied by X-ray absorption fine structure.

The local structures of the immiscible Fe(100-x)Cu(x) alloys (x= 0, 10, 20, 40, 60, 80 and 100) produced by mechanical alloying have been investigated by XAFS. For the Fe(100-x)Cu(x) (x > or = 40) solid solutions, the local structures around Fe atoms change from bcc structure to fcc one and the Cu atoms maintain the original coordination geometry after milling for 160 hours. On the contrary, the local structures around Cu atoms in both of Fe80Cu20 and Fe90Cu10 alloys appear a transition from fcc to bcc structure. We found that the Debye-waller factor sigma of fcc Fe-Cu phase is larger than that of bcc Fe-Cu phase, and the sigma (0.099 A) around Fe atoms is larger than that (0.089 A) of Cu in the Fe(100-x)Cu(x) (x > or = 40) solid solutions. This suggests that the mechanically alloyed Fe(100-x)Cu(x) supersaturated solid solution is not a homogeneous alloy, and consists of Fe-rich and Cu-rich regions for various compositions. A possible mechanism for bcc-to-fcc and fcc-to-bcc changes in Fe(100-x)Cu(x) solid solutions is discussed in relation to the interdiffusion and transition induced by the ball milling.

Journal Article↗
PubMed2005

Pre-edge features of Ti K-edge X-ray absorption near-edge structure for the local structure of sol-gel titanium oxides.

Titanium K-edge X-ray absorption near-edge structure (XANES) spectroscopy is used to examine the local Ti environments in the sol, gel, and xerogels of titanium oxide prepared by a sol-gel method. The xerogels were prepared by heat treatment at 200, 300, 400, 500, and 600 degrees C (denoted xero-200, xero-300, xero-400, xero-500, and xero-600), and the xerogels were doped with Fe(II), Ni(II), and Cu(II) ions (xero-Fe, xero-Ni, and xero-Cu). The local structures of the samples are compared using the pre- and post-edge features of the XANES spectra. Further analysis of the pre-edge features using Gaussian functions provides the energy and height of each peak, and the intensity ratios between peaks. Based on the resulting data, the samples can be classified into three groups: a weak Ti-Ti interaction group, an anatase-like structure group, and an anatase group. The sol, gel, xerogel, and xero-Ni are in the weak Ti-Ti interaction group, and the xero-200, xero-Fe, and xero-Cu are in the anatase-like structure group. The remaining samples are in the anatase group.

Journal Article↗
PubMedDate not supplied

Supercontracted spider dragline silk: a solid-state NMR study of the local structure.

The local structure of supercontracted dragline silk from the spider Nephila madagascariensis was investigated by solid-state nuclear magnetic resonance. Two-dimensional (2D) spin-diffusion experiments did not show any significant conformational changes in short-range order (and the secondary structure of the protein) upon supercontraction. Our results are in accordance with the proposal by Vollrath et al. (Proc R Soc London B 1996;263:147-151) that urea-supercontraction does not alter the local structure of spider dragline silk fundamentally. However, significant differences in the dynamics of the polypeptide chain upon supercontraction are detected at room temperature. At low temperature, these dynamics are frozen out. In addition, the role of the solvent (water) in the silk is investigated in Nephila edulis. Mobile water is detected at temperatures significantly below the freezing point of bulk water.

Alanine↗
PubMed1999

Molecular structure, localization and function of biliproteins in the chlorophyll a/d containing oxygenic photosynthetic prokaryote Acaryochloris marina.

We investigated the localization, structure and function of the biliproteins of the oxygenic photosynthetic prokaryote Acaryochloris marina, the sole organism known to date that contains chlorophyll d as the predominant photosynthetic pigment. The biliproteins were isolated by means of sucrose gradient centrifugation, ion exchange and gel filtration chromatography. Up to six biliprotein subunits in a molecular mass range of 15.5-18.4 kDa were found that cross-reacted with antibodies raised against phycocyanin or allophycocyanin from a red alga. N-Terminal sequences of the alpha- and beta-subunits of phycocyanin showed high homogeneity to those of cyanobacteria and red algae, but not to those of cryptomonads. As shown by electron microscopy, the native biliprotein aggregates are organized as rod-shaped structures and located on the cytoplasmic side of the thylakoid membranes predominantly in unstacked thylakoid regions. Biochemical and spectroscopic analysis revealed that they consist of four hexameric units, some of which are composed of phycocyanin alone, others of phycocyanin together with allophycocyanin. Spectroscopic analysis of isolated photosynthetic reaction center complexes demonstrated that the biliproteins are physically attached to the photosystem II complexes, transferring light energy to the photosystem II reaction center chlorophyll d with high efficiency.

Amino Acid Sequence↗
PubMed2005

Computation of conformational entropy from protein sequences using the machine-learning method--application to the study of the relationship between structural conservation and local structural stability.

A complete protein sequence can usually determine a unique conformation; however, the situation is different for shorter subsequences--some of them are able to adopt unique conformations, independent of context; while others assume diverse conformations in different contexts. The conformations of subsequences are determined by the interplay between local and nonlocal interactions. A quantitative measure of such structural conservation or variability will be useful in the understanding of the sequence-structure relationship. In this report, we developed an approach using the support vector machine method to compute the conformational variability directly from sequences, which is referred to as the sequence structural entropy. As a practical application, we studied the relationship between sequence structural entropy and the hydrogen exchange for a set of well-studied proteins. We found that the slowest exchange cores usually comprise amino acids of the lowest sequence structural entropy. Our results indicate that structural conservation is closely related to the local structural stability. This relationship may have interesting implications in the protein folding processes, and may be useful in the study of the sequence-structure relationship.

Amino Acid Sequence↗
PubMed1996

Global properties of the mapping between local amino acid sequence and local structure in proteins.

Local protein structure prediction efforts have consistently failed to exceed approximately 70% accuracy. We characterize the degeneracy of the mapping from local sequence to local structure responsible for this failure by investigating the extent to which similar sequence segments found in different proteins adopt similar three-dimensional structures. Sequence segments 3-15 residues in length from 154 different protein families are partitioned into neighborhoods containing segments with similar sequences using cluster analysis. The consistency of the sequence-to-structure mapping is assessed by comparing the local structures adopted by sequence segments in the same neighborhood in proteins of known structure. In the 154 families, 45% and 28% of the positions occur in neighborhoods in which one and two local structures predominate, respectively. The sequence patterns that characterize the neighborhoods in the first class probably include virtually all of the short sequence motifs in proteins that consistently occur in a particular local structure. These patterns, many of which occur in transitions between secondary structural elements, are an interesting combination of previously studied and novel motifs. The identification of sequence patterns that consistently occur in one or a small number of local structures in proteins should contribute to the prediction of protein structure from sequence.

Amino Acid Sequence↗
PubMedDate not supplied

[Analysis of structural motifs of proteins using sets of codes, describing local structures].

An amino acid sequence pattern conserved among a family of proteins is called motif. It is usually related to the specific function of the family. On the other hand, functions of proteins are achieved by their 3D structures. Specific local structures, called structural motifs, are considered related to their functions. However, searching for common structural motifs in different proteins is much more difficult than for common sequence motifs. We are attempting in this study to convert the information about the structural motifs into a set of one-dimensional digital strings, i.e., a set of codes, to compare them more easily by computer and to investigate their relationship to functions more quantitatively. By applying the Delaunay tessellation to a 3D structure of a protein, we can assign each local structure to a unique code that is defined so as to reflect its structural feature. Since a structural motif is defined as a set of the local structures in this paper, the structural motif is represented by a set of the codes. In order to examine the ability of the set of the codes to distinguish differences among the sets of local structures with a given PROSITE pattern that contain both true and false positives, we clustered them by introducing a similarity measure among the set of the codes. The obtained clustering shows a good agreement with other results by direct structural comparison methods such as a superposition method. The structural motifs in homologous proteins are also properly clustered according to their sources. These results suggest that the structural motifs can be well characterized by these sets of the codes, and that the method can be utilized in comparing structural motifs and relating them with function.

Amino Acid Motifs↗
PubMed2002

Composites of local structure propensities: evidence for local encoding of long-range structure.

To estimate how extensively the ensemble of denatured-state conformations is constrained by local side-chain-backbone interactions, propensities of each of the 20 amino acids to occur in mono- and dipeptides mapped to discrete regions of the Ramachandran map are computed from proteins of known structure. In addition, propensities are computed for the trans, gauche-, and gauche+ rotamers, with or without consideration of the values of phi and psi. These propensities are used in scoring functions for fragment threading, which estimates the energetic favorability of fragments of protein sequence to adopt the native conformation as opposed to hundreds of thousands of incorrect conformations. As finer subdivisions of the Ramachandran plot, neighboring residue phi/psi angles, and rotamers are incorporated, scoring functions become better at ranking the native conformation as the most favorable. With the best composite propensity function, the native structure can be distinguished from 300,000 incorrect structures for 71% of the 2130 arbitrary protein segments of length 40, 48% of 2247 segments of length 30, and 20% of 2368 segments of length 20. A majority of fragments of length 30-40 are estimated to be folded into the native conformation a substantial fraction of the time. These data suggest that the variations observed in amino acid frequencies in different phi/psi/chi1 environments in folded proteins reflect energetically important local side-chain-backbone interactions, interactions that may severely restrict the ensemble of conformations populated in the denatured state to a relatively small subset with nativelike structure.

Amino Acids↗
PubMed2003

Stochastic resonance in the presence of spatially localized structures.

Stable spatially localized structures exist in a wide variety of spatially extended nonlinear systems, including nonlinear optical devices. We study stochastic resonance (SR) in models of optical parametric oscillators in the presence of a spatially uniform time-periodic driving and in a regime where two equivalent states with equal intensity but opposite phase exist. Diffraction and nonlinearity enable the existence of localized states, formed by the locking of kinks and antikinks and displaying spatially damped oscillatory tails (in one dimension) or the stabilization of dark ring cavity solitons (in two dimensions). We show that SR is inhibited at low driving amplitudes by the presence of localized states which obstruct the front motion. For larger driving amplitudes, in the regime where localized states cease to be stable, we observe instead an enhancement of SR.

Journal Article↗
PubMed1998

Novel method to detect a motif of local structures in different protein conformations.

In order to detect a motif of local structures in different protein conformations, the Delaunay tessellation is applied to protein structures represented by C(alpha) atoms only. By the Delaunay tessellation the interior space of the protein is uniquely divided up into Delaunay tetrahedra whose vertices are the C(alpha) atom positions. Some edges of the tetrahedra are virtual bonds connecting adjacent residues' C(alpha) atoms along the polypeptide chain and others indicate interactions between residues nearest neighbouring in space. The rules are proposed to assign a code, i.e., a string of digits, to each tetrahedron to characterize the local structure constructed by the vertex residues of one relevant tetrahedron and four surrounding it. Many sets comprised of the local structures with the same code are obtained from 293 proteins, each of which has relatively low sequence similarity with the others. The local structures in each set are similar enough to each other to represent a motif. Some of them are parts of secondary or supersecondary structures, and others are irregular, but definite structures. The method proposed here can find motifs of local structures in the Protein Data Bank much more easily and rapidly than other conventional methods, because they are represented by codes. The motifs detected in this method can provide more detailed information about specific interactions between residues in the local structures, because the edges of the Delaunay tetrahedra are regarded to express interactions between residues nearest neighbouring in space.

Models, Molecular↗
PubMed1998

Local structure study of dilute Er in III-V semiconductors by fluorescence EXAFS.

For understanding the luminescence of Er atoms in III-V semiconductors, OMVPE-grown InP doped with Er has been investigated by fluorescence EXAFS (extended X-ray absorption fine structure) in order to study the local structure around Er atoms. The local structures around the Er atoms doped in InP, with doping as dilute as 3 x 10(12) Er atoms in a 1.5 mm x 1.0 mm spot, were successfully measured by fluorescence EXAFS. The EXAFS analysis revealed that the Er atoms doped in InP above 853 K (which showed low luminescence) formed the rock-salt-structure ErP, while the Er atoms doped in InP below 823 K (which showed high luminescence) substituted on the In site of InP. The dependence of the local structure on growth temperature was observed for the samples doped with 3 x 10(12) atoms and 1.2 x 10(13) atoms of Er.

Journal Article↗
PubMed2004

Theoretical studies of the local structure for the trigonal Ti(3+) center in LiF crystal.

The local structure of the trigonal Ti(3+) center in LiF crystal is theoretically investigated by using the perturbation formulas of the anisotropic g factors and g(//) and g(/_) for a 3d(1) ion in trigonally distorted octahedra based on the cluster approach. From the studies on the basis of various possible structure models, the local structure of the trigonal Ti(3+) center may be characterized as [TiF(3)O(3)](6-) cluster (or model I). In this model, the impurity Ti(3+) is expected to substitute for the host Li(+) ion and shift away from its regular lattice site along the [111] (or C(3)) axis by about 0.19 A due to the strong electrostatic attraction of the O(2-) triangle replacing the original F(-) triangle. The magnitude of the above displacement obtained in this work is comparable with that ( approximately 0.2-0.3A) given by ENDOR experiment. Moreover, the cubic field parameter Dq (approximately 1497 cm(-1)) based on the above structure model is also in agreement with that (approximately 1500 cm(-1)) obtained from the experimental optical spectra of the studied system. The theoretical investigations of the local structure in this work may be useful to understand optical properties of Ti-doped LiF.

Electron Spin Resonance Spectroscopy↗
PubMed2005

Molecular modeling of phosphorylation sites in proteins using a database of local structure segments.

A new bioinformatics tool for molecular modeling of the local structure around phosphorylation sites in proteins has been developed. Our method is based on a library of short sequence and structure motifs. The basic structural elements to be predicted are local structure segments (LSSs). This enables us to avoid the problem of non-exact local description of structures, caused by either diversity in the structural context, or uncertainties in prediction methods. We have developed a library of LSSs and a profile--profile-matching algorithm that predicts local structures of proteins from their sequence information. Our fragment library prediction method is publicly available on a server (FRAGlib), at http://ffas.ljcrf.edu/Servers/frag.html . The algorithm has been applied successfully to the characterization of local structure around phosphorylation sites in proteins. Our computational predictions of sequence and structure preferences around phosphorylated residues have been confirmed by phosphorylation experiments for PKA and PKC kinases. The quality of predictions has been evaluated with several independent statistical tests. We have observed a significant improvement in the accuracy of predictions by incorporating structural information into the description of the neighborhood of the phosphorylated site. Our results strongly suggest that sequence information ought to be supplemented with additional structural context information (predicted with our segment similarity method) for more successful predictions of phosphorylation sites in proteins.

Amino Acid Sequence↗