Prediction of protein secondary structure based on continuous wavelet transform

In this paper, continuous wavelet transform (CWT) is used to extract the number and the relevant positions of the α-helices and short peptides connecting α-helices and β-strands (connecting peptides) from the amino acid sequences of proteins. The amino acid sequence is first mapped into hydrophobicity sequence, and then transformed into CWT value of sequence domain in appropriate scale via CWT. The number and the relevant positions of the α-helices and connecting peptides can be extracted easily and accurately according to the minima of wavelet coefficient in corresponding CWT plot of hydrophobic value sequences with appropriate scale. The analytical results demonstrate that α-helices and connecting peptides can be predicted conveniently and rapidly when this method is used in the processing of 100 non-homologous sequences. However, this method is not suitable for predicting the length of α-helices and connecting peptides.     

Algorithm for rapid reconstruction of protein backbone from alpha carbon coordinates

A method for generating a full backbone protein structure from the coordinates of α-carbons, is presented. The method extracts information from known protein structures to generate statistical positions for the reconstructed atoms. Tests on a set of proteins structures show the algorithm to be of comparable accuracy to existing procedures. However, the basic advantage of the presented method is its simplicity and speed. In a test run, the present program is shown to be much faster than existing database searching algorithms, and reconstructs about 8000 residues per second. Thus, it may be included as an independent procedure in protein folding algorithms to rapidly generate approximate coordinates of backbone atoms. © 1997 by John Wiley & Sons, Inc.     

Peptide C(alpha)D(alpha) stretch frequencies in a hydrated conformation are perturbed mainly by C(alpha)-D(alpha)...O hydrogen bonding

We have shown (J. Phys. Chem. A 2004, 108, 10923; 2007, 111, 5300) that the C(alpha)D(alpha) stretch frequency, nu(CD), can discriminate between uniform alpha(R), beta, and polyproline II conformations of isolated peptides. Similar results for such peptides to which explicit waters are hydrogen bonded exhibit shifts in nu(CD) from those of the isolated structures. We demonstrate that the main source of these frequency shifts is the formation of C(alpha)-D(alpha)...O hydrogen bonds to water. Taking into account C-H...O(water) hydrogen bonding, together with the traditional bonding of peptide groups to water, can be expected to increase our understanding of the interaction of proteins with their aqueous environment.     

Prospects for tertiary structure prediction of RNA based on secondary structure information

We developed a method, called RNA Assembler using Secondary Structure Information Effectively (RASSIE), for predicting RNA tertiary structures using known secondary structure information. We attempted a fragment assembly-based method that uses a secondary structure-based fragment library. For several typical target structures such as stem-loops, bulge-loops, and 2-way junctions, our method provided numerous good quality candidate structures in less computational time than previously proposed methods. By using a high-resolution potential energy function, we were able to select good predicted structures from candidate structures. This method of efficient conformational search and detailed structure evaluation using high-resolution potential is potentially useful for the tertiary structure prediction of RNA.     

A dipolar coupling based strategy for simultaneous resonance assignment and structure determination of protein backbones.

A new approach for simultaneous protein backbone resonance assignment and structure determination by NMR is introduced. This approach relies on recent advances in high-resolution NMR spectroscopy that allow observation of anisotropic interactions, such as dipolar couplings, from proteins partially aligned in field ordered media. Residual dipolar couplings are used for both geometric information and a filter in the assembly of residues in a sequential manner. Experimental data were collected in less than one week on a small redox protein, rubredoxin, that was 15N enriched but not enriched above 1% natural abundance in 13C. Given the acceleration possible with partial 13C enrichment, the protocol described should provide a very rapid route to protein structure determination. This is critical for the structural genomics initiative where protein expression and structural determination in a high-throughput manner will be needed.     

First-principles investigation on the geometry and electronic structure of the three-dimensional cuboidal C(60) polymer

The structural stability and electronic properties of the recently characterized three-dimensional (3D) cuboid-shaped C(60) polymer are studied using periodic ab initio density functional methods. It is shown that the experimentally observed structure is metastable and not fully relaxed from the high pressure state. A second polymorph, which is more stable than the experimental structure, is identified from the calculations. This new structure differs from the observed structure in the number of fourfold-coordinated atoms per C(60) molecule. Both structures are found to be metallic with bulk moduli only about one-third that of diamond. The cuboidal C(60) is not the long sought after superhard 3D carbon polymer; however, the two polymorphs studied here reveal unusual electronic band structures that might suggest interesting electronic properties.     

Filamentous phage studied by magic-angle spinning NMR: resonance assignment and secondary structure of the coat protein in Pf1

Assignments are presented for resonances in the magic-angle spinning solid-state NMR spectra of the major coat protein subunit of the filamentous bacteriophage Pf1. NMR spectra were collected on uniformly 13C and 15N isotopically enriched, polyethylene glycol precipitated samples of fully infectious and hydrated phage. Site-specific assignments were achieved for 231 of the 251 labeled atoms (92%) of the 46-residue-long coat protein, including 136 of the 138 backbone atoms, by means of two- and three-dimensional 15N and 13C correlation experiments. A single chemical shift was observed for the vast majority of atoms, suggesting a single conformation for the 7300 subunits in the 36 MDa virion in its high-temperature form. On the other hand, multiple chemical shifts were observed for the Calpha, Cbeta, and Cgamma atoms of T5 in the helix terminus and the Calpha and Cbeta atoms of M42 in the DNA interaction domain. The chemical shifts of the backbone atoms indicate that the coat protein conformation involves a 40-residue continuous alpha-helix extending from residue 6 to the C-terminus.     

New one-, two-, and three-dimensional metal-organic frameworks based on magnesium(II): synthesis and structure

Russian Chemical Bulletin - Six new metal-organic frameworks based on magnesium(II) ions of various dimensionality were synthesized: chain-like [Mg(Hazdc)2(nmp)2] (1, H2azdc is...     

StructSorter: a method for continuously updating a comprehensive protein structure alignment database

Advances in protein crystallography and homology modeling techniques are producing vast amounts of high resolution protein structure data at ever increasing rates. As such, the ability to quickly and easily extract structural similarities is a key tool in discovering important functional relationships. We report on an approach for creating and maintaining a database of pairwise structure alignments for a comprehensive database comprising the PDB and homology models for the human and select pathogen genomes. Our approach consists of a novel, multistage method for determining pairwise structural similarity coupled with an efficient clustering protocol that approximates a full NxN assessment in a fraction of the time. Since biologists are commonly interested in recently released structures, and the homology models built from them, an automatically updating database of structural alignments has great value. Our approach yields a querying system that allows scientists to retrieve databank-wide protein structure similarities as easily as retrieving protein sequence similarities via BLAST or PSI-BLAST. Basic, noncommercial access to the database can be requested at https://tip.eidogen-sertanty.com/.     

Self-assembly and crystal structure of a three-dimensional copper(II) complex

A copper(II) complex of a sulfonate derivative of chrysin, 5,7-bihydroxyflavone-6-sulfonate, Cu(C₁₅H₈O₇S)(3H₂O), has been prepared. The complex was characterized by elemental analysis, spectroscopic measurements and single-crystal X-ray diffraction studies. It crystallizes in the monoclinic space group C2/c, with a?=?16.036(18), b?=?6.944(8), c?=?28.03(3)?Å, β?=?94.463(17)°, V?=?3112(6)?ų, Z?=?8. In the complex, Cu(II) is five-coordinate and all donors are oxygen atoms. Hydrogen bonds and π–π stacking interactions in the crystal lead to the formation of a three-dimensional supramolecular motif.     

UF3(H2O)(C2O4)0.5: a fluorooxalate of tetravalent uranium with a three-dimensional framework structure

A new uranium(IV) fluorooxalate, UF3(H2O)(C2O4)0.5, has been synthesized by a hydrothermal method and structurally characterized by single-crystal X-ray diffraction, infrared spectroscopy, and thermogravimetric analysis. The structure consists of two-dimensional layers of corner- and edge-sharing tricapped trigonal prisms with the composition UF(4/2)F(2/2)O3 linked by bisbidentate oxalate ligands to form a three-dimensional framework. Magnetic susceptibilities were measured to confirm the tetravalent state of uranium. Crystal data: monoclinic, space group C2/c, a = 17.246(3) Angstroms, b = 6.088(1) Angstroms, c = 8.589(2) Angstroms, beta = 95.43(3) degrees, and Z = 8.     

CSSP2: an improved method for predicting contact-dependent secondary structure propensity

The calculation of contact-dependent secondary structure propensity (CSSP) has been reported to sensitively detect non-native β-strand propensities in the core sequences of amyloidogenic proteins. Here we describe a noble energy-based CSSP method implemented on dual artificial neural networks that rapidly and accurately estimate the potential for the non-native secondary structure formation in local regions of protein sequences. In this method, we attempted to quantify long-range interaction patterns in diverse secondary structures by potential energy calculations and decomposition on a pairwise per-residue basis. The calculated energy parameters and seven-residue sequence information were used as inputs for artificial neural networks (ANNs) to predict sequence potential for secondary structure conversion. The trained single ANN using the >(i, i ± 4) interaction energy parameter exhibited 74% accuracy in predicting the secondary structure of test sequences in their native energy state, while the dual ANN-based predictor using (i, i ± 4) and >(i, i ± 4) interaction energies showed 83% prediction accuracy. The present method provides a simple and accurate tool for predicting sequence potential for secondary structure conversions without using 3D structural information.     

Nomenclature of polymers (based on structure)

In the complete absence of a systematic polymer nomenclature, a scheme of nomenclature based on structure is proposed. The problem of naming a “mer” has been solved for an addition polymer by adding “ne” to the monomer name, the justification being on withdrawal of a π bond a monomer becomes a mer. To furnish completeness to the nomenclature, condensation polymers were included in the system. The present nomenclature system of polymers is very arbitrary. Some polymers are not chemically named, some named incorrectly, and there are some fantastic names. After pointing these out, the possible solutions were shown, encompassing a systematic discussion on nearly every type of polymer–linear, branched, or crosslinked–and copolymer (including block or graft), and plastic, fiber, or rubber, and stereospecific polymer. One or more names were proposed for different cases.     

Hydrothermal synthesis and structure of a three-dimensional cobalt(II) triazolate magnet

The reaction of CoCl2.6H2O, 1,2,4-triazole, and H(2)O at 200 degrees C for 96 h yields purple rods of [Co2(trz)3Cl] (1; trz = 1,2,4-triazolate) in 90% yield. The structure of 1 consists of {Co(trz)3}n(n-) chains of Co(II) sites linked through tetrahedral sites of {CoN(3)Cl} geometry into a three-dimensional framework. The competing antiferromagnetic interactions of the octahedral and tetrahedral Co(II) centers result in weak ferromagnetic behavior below Tc = 9 K.     

Prediction of extended aromaticity for a novel C(48)N(12) azafullerene structure

We report the existence of a novel C48N12 molecular structure to the recently reported thin-film formation of nano-onions of carbon and nitrogen with similar composition [Phys. Rev. Lett. 2001, 87, 225503]. An extended local aromaticity of eight all-carbon hexagonal rings is the driving force toward the maximum stability of this molecule, which is found to be 13.1 kcal/mol energetically more stable at the B3LYP/6-31G* level of theory than the recently reported structure [Chem. Phys. Lett. 2001, 340, 227]. The extended region of electron delocalization enhances the stability of this molecule via resonance energy contribution. On the basis of HUMO-LUMO gap of 2.74 eV, the new material is predicted to be an insulator.     

Measurement of (13)C(alpha)-(13)C(beta) dipolar couplings in (15)N,(13)C,(2)H-labeled proteins: application to domain orientation in maltose binding protein.

TROSY-based HN(CO)CA 2D and 3D pulse schemes are presented for measurement of (13)C(alpha)-(13)C(beta) dipolar couplings in high molecular weight (15)N,(13)C,(2)H-labeled proteins. In one approach, (13)C(alpha)-(13)C(beta) dipolar couplings are obtained directly from the time modulation of cross-peak intensities in a set of 2D (15)N-(1)HN correlated spectra recorded in both the presence and absence of aligning media. In a second approach 3D data sets are recorded with (13)C(alpha)-(13)C(beta) couplings encoded in a frequency dimension. The utility of the experiments is demonstrated with an application to an (15)N,(13)C,(2)H-labeled sample of the ligand free form of maltose binding protein. A comparison of experimental dipolar couplings with those predicted from the X-ray structure of the apo form of this two-domain protein establishes that the relative orientation of the domains in solution and in the crystal state are very similar. This is in contrast to the situation for maltose binding protein in complex with beta-cyclodextrin where the solution structure can be generated from the crystal state via a 11 degrees domain closure.     

Stereoselective cycloaddition of 1,3-cyclohexadiene on Si(100): a simple algorithm for product identification based on secondary orbital interactions

We consider the reaction of 1,3-cyclohexadiene (1,3-CHD) on Si(100) and show that the observed reactivity and stereoselectivity cannot be explained on the basis of thermodynamics. We postulate the existence of secondary orbital interactions (SOIs) and introduce a simple algorithm that examines all possible secondary interactions between the frontier orbitals of the molecule and the surface. We demonstrate using an orbital symmetry-based algorithm supported by DFT calculations that SOIs favor a particular molecular configuration, consistent with the experimental observations. The potential role of SOIs in controlling surface chemical reactions is discussed.     

Aza-amino acid scan for rapid identification of secondary structure based on the application of N-Boc-aza(1)-dipeptides in peptide synthesis

Azapeptides, peptide analogues in which the alpha-carbon of one or more of the amino acid residues is replaced with a nitrogen atom, exhibit propensity for adopting beta-turn conformations. A general protocol for the synthesis of azapeptides without racemization on solid phase has now been developed by introducing the aza-amino acid residue as an N-Boc-aza(1)-dipeptide. This approach has been validated by the synthesis of six N-Boc-aza(1)-dipeptides and their subsequent introduction into analogues of the C-terminal peptide fragment of the human calcitonin gene-related peptide (hCGRP). By performing an aza-amino acid scan of such antagonist peptides, a set of aza-hCGRP analogues was synthesized to examine the relationship between turn secondary structure and biological activity.     

Synthesis and crystal structure of a three-dimensional network coordination polymer: [Pb(C5H4NCOO)2(H2O)] n

A new coordination polymer [Pb(C₅H₄NCOO)₂(H₂O)] _n has been prepared by reaction of Pb(NO₃)₂ with isonicotinic acid in the presence of equimolar NaOH. Single-crystal X-ray diffraction analysis reveals that the coordination geometry of each lead(II) centre in [Pb(C₅H₄NCOO)₂(H₂O)] _n is a distorted square antiprism comprised of five O atoms and one N atom from three distinct isonicotinate ligands, and two water molecules. The complex displays a three-dimensional network structure, in which isonicotinate ligands adopt two different bridging coordination modes.