Network properties of protein-decoy structures

Convergence of the vast sequence space of proteins into a highly restricted fold/conformational space suggests a simple yet unique underlying mechanism of protein folding that has been the subject of much debate in the last several decades. One of the major challenges related to the understanding of protein folding or in silico protein structure prediction is the discrimination of non-native structures/decoys from the native structure. Applications of knowledge-based potentials to attain this goal have been extensively reported in the literature. Also, scoring functions based on accessible surface area and amino acid neighbourhood considerations were used in discriminating the decoys from native structures. In this article, we have explored the potential of protein structure network (PSN) parameters to validate the native proteins against a large number of decoy structures generated by diverse methods. We are guided by two principles: (a) the PSNs capture the local properties from a global perspective and (b) inclusion of non-covalent interactions, at all-atom level, including the side-chain atoms, in the network construction accommodates the sequence dependent features. Several network parameters such as the size of the largest cluster, community size, clustering coefficient are evaluated and scored on the basis of the rank of the native structures and the Z-scores. The network analysis of decoy structures highlights the importance of the global properties contributing to the uniqueness of native structures. The analysis also exhibits that the network parameters can be used as metrics to identify the native structures and filter out non-native structures/decoys in a large number of data-sets; thus also has a potential to be used in the protein ‘structure prediction’ problem.     

Network structures and thermal properties of polyurethane films prepared from liquefied wood

Polyurethane (PU) films were prepared by solution-casting after co-polymerization of liquefied woods (LWs) and polymeric methylene diphenylene diisocyanate (PMDI). The resulting PU films had various [NCO]/[OH] ratios ranging from 0.6 to 1.4 and contained 5.0-16.8% dissolved woody components at the [NCO]/[OH] ratio of 1.0. The crosslink densities of the films with [NCO]/[OH] ratios of 0.6-1.4 increased remarkably with increasing [NCO]/[OH] ratio. Similarly, there were large increases in glass transition temperatures (Tg). These characteristics could be attributed to effective incorporation of PMDI into the LW. The crosslink densities and Tg of the PU films prepared at the [NCO]/[OH] ratio of 1.0 increased because the amounts of dissolved woody components in the films increased. It is concluded that the dissolved woody components acted as crosslinking points in PU network formations. The thermal degradation of the PU films at an [NCO]/[OH] ratio of more than 0.8 or with more than 10.6% dissolved wood started above 262 degrees C under an N2 atmosphere. The thermostability was lost at low crosslink density or with large amount of co-polymerized glycerol structures in the PU networks.     

Frictional properties of multisubunit structures

The translational drag, rotational drag, and intrinsic viscosity of spherical multisubunit structures have been calculated analytically using the Felderhof–Deutch theory of polymer frictional properties. The structures considered were hollow shells, spheres with uniform subunit density, and spheres covered with a subunit layer of different density. Changes in the transport coefficients resulting from the random removal of subunits and from the variation of subunit size are calculated. For the case of the shell, the results agree with the numerical computations of Bloomfield, Dalton, and Van Holde [Biopolymers 5 , 135, 149 (1967)].     

167 Network properties of decoy and CASP predicted models: a comparison with native protein structures

Principles that govern protein folding still remain elusive. Given the huge sequence space, it is reasonable to assume that sequences follow a particular pattern to attain one of the folds already defined in the relatively small structural space. In this study, we have used protein structure networks at different interaction strengths of non-covalent interactions (I_min) (Brinda & Vishveshwara, 2005; Kannan & Vishveshwara, 1999), to identify patterns that can distinguish a native protein from decoy/modelled structures. This is a rigorous extension of an earlier study performed at I_min???0% (Chatterjee, Bhattacharyya et al., 2012). Network properties such as the size of the largest cluster (SLClu), largest k-2 communities (ComSk2) and clustering coefficients (CCoe) are analysed for 5422 native structures and 29543 decoy/modelled structures. Steeper transition profile of the native structures as a function of I_min is consistently observed (see Figure) . The network properties generated at different I_min and main-chain hydrogen bonds (MHB) are integrated into support vector machine to build a classifier, giving an accuracy of 94.11%. The uniqueness of the protein structures through side-chain interactions are captured by the network parameters, while MHB represents the backbone packing. Quality predictions for the recently concluded CASP 10 predicted models are also performed using the model with the selected ones showing RMSD values?<?2.5?Å with respect to the native structures. Amongst the network properties, ComSk2 is maximally able to capture the transition properties of the structures. Importance of ComSk2 has earlier been implicated to capture the percolating behaviour of a protein structure (Deb & Vishveshwara, 2009). Overall, a robust classifier is obtained, and patterns specific to native structures have been analysed and discussed. The study highlights the importance of side-chain interactions at different I_mins, along with backbone level interactions.     

Network structures and algorithms in Bioconductor

In this paper, we review the central concepts and implementations of tools for working with network structures in Bioconductor. Interfaces to open source resources for visualization (AT&T Graphviz) and network algorithms (Boost) have been developed to support analysis of graphical structures in genomics and computational biology. AVAILABILITY: Packages graph, Rgraphviz, RBGL of Bioconductor (www.bioconductor.org).     

Thermodynamic properties of bulk knitted structures

The mechanism of interaction of an external magnetic field with liquid was proposed. The statistical integral and configurational contributions for a free energy, entropy and specific heat for the soliton model of bulk knitted structures in a magnetic field were calculated. It was shown that the concentration of solitons depends on the effect of external fields. In the specific case of bulk knitted structures (liquid water without magnetic field), the theoretical data are consistent with experimental. The memory effects in systems with hydrogen bonds in magnetic field was explained in the framework of the continuum soliton concept.     

Transport properties of oligomeric subunit structures

The translational friction coefficients, rotational friction coefficient, and intrinsic viscosity of rigid regular structures composed of up to eight identical spherical subunits have been accurately calculated. The aim of this calculation is to interpret the hydrodynamic properties of oligomeric subunit proteins. To avoid the well-known failure of the theory in the evaluation of rotational coefficients and intrinsic viscosities, each subunit is hydrodynamically modeled as a polyhedral array of smaller spheres. The analysis of several alternatives suggests that a cubic array is the best choice. The reliability of this strategy is checked by comparison of the calculated values for all the transport properties of a sphere and the translational friction coefficients of a dimer with their exact values. Finally, the hydrodynamic properties of a number of subunit structures with varying number of subunits and different geometries are tabulated.     

pH-dependent structures and properties of casein micelles

The association behavior of casein over a broad pH range has first been investigated by fluorescent technique together with DLS and turbidity measurements. Casein molecules can self-assemble into casein micelles in the pH ranges 2.0 to 3.0, and 5.5 to 12.0. The hydrophobic interaction, hydrogen bond and electrostatic action are the main interactions in the formation of casein micelles. The results show that the structure of casein micelles is more compact at low pH and looser at high pH. The casein micelle has the most compact structure at pH 5.5, when it has almost no electrostatic repulsion between casein molecules.     

Combinatorial properties of RNA secondary structures.

The secondary structure of an RNA molecule is of great importance and possesses influence, e.g., on the interaction of tRNA molecules with proteins or on the stabilization of mRNA molecules. The classification of secondary structures by means of their order proved useful with respect to numerous applications. In 1978, Waterman, who gave the first precise formal framework for the topic, suggested to determine the number a(n,p) of secondary structures of size n and given order p. Since then, no satisfactory result has been found. Based on an observation due to Viennot et al., we will derive generating functions for the secondary structures of order p from generating functions for binary tree structures with Horton-Strahler number p. These generating functions enable us to compute a precise asymptotic equivalent for a(n,p). Furthermore, we will determine the related number of structures when the number of unpaired bases shows up as an additional parameter. Our approach proves to be general enough to compute the average order of a secondary structure together with all the r-th moments and to enumerate substructures such as hairpins or bulges in dependence on the order of the secondary structures considered.     

Comparative structures and properties of elastic proteins

Elastic proteins are characterized by being able to undergo significant deformation, without rupture, before returning to their original state when the stress is removed. The sequences of elastic proteins contain elastomeric domains, which comprise repeated sequences, which in many cases appear to form beta-turns. In addition, the majority also contain domains that form intermolecular cross-links, which may be covalent or non-covalent. The mechanism of elasticity varies between the different proteins and appears to be related to the biological role of the protein.     

Compressed representations of macromolecular structures and properties

We introduce a new and unified, compressed volumetric representation for macromolecular structures at varying feature resolutions, as well as for many computed associated properties. Important caveats of this compressed representation are fast random data access and decompression operations. Many computational tasks for manipulating large structures, including those requiring interactivity such as real-time visualization, are greatly enhanced by utilizing this compact representation. The compression scheme is obtained by using a custom designed hierarchical wavelet basis construction. Due to the continuity offered by these wavelets, we retain very good accuracy of molecular surfaces, at very high compression ratios, for macromolecular structures at multiple resolutions.     

Ferrocenylboronates: Crystal structures and electrochemical properties

The electrochemical behavior of a series of eight previously reported monoferrocenyl- and diferrocenyl-boronates derived from tridentate ligands has been studied. Even if most mononuclear and all the dinuclear complexes examined showed to undergo slow decomposition in nonaqueous solution (releasing free ferrocenyl boronic acid), their redox activity has been investigated. It has been proved that the oxidation of the two ferrocenyl subunits in the dimeric species proceeds simultaneously, indicating that no mutual electronic interaction exists between them. Additionally, the solid-state molecular structures of two diferrocenyl complexes (2a and 2b) were studied by X-ray diffraction. The analysis confirms the formation of a [5.4.0] heterobicycle with the presence of two different boron atoms, one in a tetrahedral geometry and the other one in a trigonal geometry.     

Rheological properties and wall structures of large veins

The static and dynamic viscoelastic properties were studied of longitudinal and circumferential strips excised from various large veins of dogs. The mechanical behavior in longitudinal direction could be regarded as elastic, while that in circumferential direction was highly viscoelastic. No distinct regionality was observed in either of the longitudinal and the circumferential groups. Noradrenaline and papaverine did not alter the elastic behavior of the longitudinal strips. In circumferential strips, however, noradrenaline caused a considerable decrease in stress relaxation and some steepening in the slope of the upper limb of hysteresis loop. Papaverine did not affect the circumferential characteristics. These findings suggest the dominant contribution of smooth muscle tone to the circumferential characteristics of venous walls. Pretreatment with formic acid abolished the occurrence of stress relaxation in circumferential direction but produced no change in the longitudinal behavior. This indicates that elastin fibers may be a principal determinant of the elastic behavior in longitudinal direction and that a residual tension observed in stress-relaxation tests of circumferential strips may be due to stretched elastin fibers. The elastic moduli of elastase pretreated venous walls were in the order of 10(8) dynes/cm2, about 1000 times higher than those of the control. Accordingly, collagen fibers seemed not to play any appreciable role in the rheological behavior of venous walls under physiological conditions. This inference was supported by histological observations of venous walls under unstretched and stretched states. Models were proposed in regard to the architecture of the fibrous elements in the venous walls.     

Network analysis of the protein chain tertiary structures of heterocomplexes

In this paper, the tertiary structures of protein chains of heterocomplexes were mapped to 2D networks; based on the mapping approach, statistical properties of these networks were systematically studied. Firstly, our experimental results confirmed that the networks derived from protein structures possess small-world properties. Secondly, an interesting relationship between network average degree and the network size was discovered, which was quantified as an empirical function enabling us to estimate the number of residue contacts of the protein chains accurately. Thirdly, by analyzing the average clustering coefficient for nodes having the same degree in the network, it was found that the architectures of the networks and protein structures analyzed are hierarchically organized. Finally, network motifs were detected in the networks which are believed to determine the family or superfamily the networks belong to. The study of protein structures with the new perspective might shed some light on understanding the underlying laws of evolution, function and structures of proteins, and therefore would be complementary to other currently existing methods.     

Syntheses, structures and properties of three metal pyridinecarboxylates

Three new metal pyridinecarboxylates, namely [Co₂(pydc)₂(H₂O)₅] (1), [Mn(pydc)(H₂O)₂] (2) and [Cd₂(OH)₂(2,4-pydc)] (3), were hydrothermally synthesized. X-ray single crystal structural analysis revealed: 1 and 2 have polymeric one-dimensional chain-like structure constructed by dinuclear cobalt units and Mn-O chains, respectively; 3 has a three-dimensional layer pillared structure constructed from inorganic Cd-O layer and pydc pillars. 1 shows antiferromagnetic interaction but 2 shows alternative antiferromagnetic and ferromagnetic interactions.     

Viscoelastic properties and nanoscale structures of composite oligopeptide-polysaccharide hydrogels

Biocompatible and biodegradable peptide hydrogels are drawing increasing attention as prospective materials for human soft tissue repair and replacement. To improve the rather unfavorable mechanical properties of our pure peptide hydrogels, in this work we examined the possibility of creating a double hydrogel network. This network was created by means of the coassembly of mutually attractive, but self-repulsive oligopeptides within an already-existing fibrous network formed by the charged, biocompatible polysaccharides chitosan, alginate, and chondroitin. Using dynamic oscillatory rheology experiments, it was found that the coassembly of the peptides within the existing polysaccharide network resulted in a less stiff material as compared to the pure peptide networks (the elastic modulus G' decreased from 90 to 10 kPa). However, these composite oligopeptide-polysaccharide hydrogels were characterized by a greater resistance to deformation (the yield strain γ grew from 4 to 100%). Small-angle neutron scattering (SANS) was used to study the 2D cross-sectional shapes of the fibers, their dimensional characteristics, and the mesh sizes of the fibrous networks. Differences in material structures found with SANS experiments confirmed rheology data, showing that incorporation of the peptides dramatically changed the morphology of the polysaccharide network. The resulting fibers were structurally very similar to those forming the pure peptide networks, but formed less stiff gels because of their markedly greater mesh sizes. Together, these findings suggest an approach for the development of highly deformation-resistant biomaterials.     

The structures and properties of poly-5-methylcytidylic acid

The optical rotatory dispersion properties of poly 5MeC, poly diMeC, and 5MeCMP-(5′) in 0.1M Na+ have been studied at various pH values and temperatures. Poly 5MeC and poly diMeC have optical properties which are similar to those for poly C; however, poly 5MeC has a biphasic melting profile in the pH range from 3.8 to 5.4 similar to that observed for poly 51C. Using titration, ionic strength, and pH dependence measuements, the data for poly 5MeC are interpreted in terms of the following scheme at pH 4.0 and 0.1 ionic strength: triple-strand helix ^37°C double-strand helix ^79°C single-strand coil. Support for this scheme is discussed. The effect of the methyl group is discussed in terms of similar structural possibilities for other polymers of cytidylic acid.     

Supramolecular structures and fluorescence properties of three transition-metal complexes

Three mononuclear transition-metal(II) compounds [Co(imidazole)₆]CO₃ · 5H₂O (1), [Co(nicotinate)₂(H₂O)₄] (2) and [Mn(isonicotinate)₂(H₂O)₄] (3) ware obtained under the hydrothermal conditions. It deserves to note that they all exhibit interesting supramolecular topologies: in a crystal host of 1 three crystallographically unique free H₂O molecules form a two-dimensional (2-D) water network based on the cyclic dodecamers with the occluded anions; both 2 and 3 possess 3-D network structures formed through the π-π stacking interactions of the pyridine rings and multi-types of O?Ow hydrogen-bonded interactions. All of these compounds show the strong fluorescence emissions with the peaks at 389, 650 and 390-420 nm (broad band) when excited at 220, 360 and 254 nm, respectively, which can be assigned to the charge transfer between the metal and the ligand.     

The structures and properties of lakes of some azo dyes

The azo group by itself is a weak ligand, but when it is part of a chelate ring it often forms quite stable complexes in which the azo group occupies a single coordination position. The other coordinating member (or members) of the chelate ring (or rings) may be parts of neutral groups (e.g. NH₂ or OCH₃) or potentially negative groups (e.g. −OH, −SH or −COOH). Thus, a variety of structures can be constructed, depending upon the nature of the metal and the functionality of the azo dyes. This article describes some lakes of azo dyes in which the dye contains three coordinating atoms, one of which is acidic.