Main Chain Backbone Research Articles

Tonal interface to MacroMolecules (TIMMol)

We developed the three-dimensional visualization software, Tonal Interface to MacroMolecules or TIMMol, for studying atomic coordinates of protein structures. Key features include audio tones indicating x, y, z location, identification of the cursor location in one-dimensional and three-dimensional space, textual output that can be easily linked to speech or Braille output, and the ability to scroll along the main chain backbone of a protein structure. This program was initially designed for visually impaired users, and it already has shown its effectiveness in helping a blind researcher study X-ray crystal structure data. Subsequently, TIMMol has been enhanced with a graphical display to act as a bridge to ease communication between sighted and visually impaired users as well as to serve users with spatial visualization difficulties. We performed a pilot study to assess the efficacy of the program in conveying three-dimensional information about proteins with and without graphical output to a general scientific audience. Attitudes regarding using TIMMol were assessed using Rasmol, a common visualization package, for comparison. With the use of text and tones exclusively, a majority of users were able to identify specific secondary structure elements, three-dimensional relationships among atoms, and atoms coordinating a ligand. In addition, a majority of users saw benefits in using TIMMol and would recommend it to those having difficulty with standard tools.

Structural and functional consequences of the replacement of proximal residues Cys172 and Cys192 in the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase from Chlamydomonas reinhardtii

Proximal Cys(172) and Cys(192) in the large subunit of the photosynthetic enzyme Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase; EC 4.1.1.39) are evolutionarily conserved among cyanobacteria, algae and higher plants. Mutation of Cys(172) has been shown to affect the redox properties of Rubisco in vitro and to delay the degradation of the enzyme in vivo under stress conditions. Here, we report the effect of the replacement of Cys(172) and Cys(192) by serine on the catalytic properties, thermostability and three-dimensional structure of Chlamydomonas reinhardtii Rubisco. The most striking effect of the C172S substitution was an 11% increase in the specificity factor when compared with the wild-type enzyme. The specificity factor of C192S Rubisco was not altered. The V(c) (V(max) for carboxylation) was similar to that of wild-type Rubisco in the case of the C172S enzyme, but approx. 30% lower for the C192S Rubisco. In contrast, the K(m) for CO(2) and O(2) was similar for C192S and wild-type enzymes, but distinctly higher (approximately double) for the C172S enzyme. C172S Rubisco showed a critical denaturation temperature approx. 2 degrees C lower than wild-type Rubisco and a distinctly higher denaturation rate at 55 degrees C, whereas C192S Rubisco was only slightly more sensitive to temperature denaturation than the wild-type enzyme. X-ray crystal structures reveal that the C172S mutation causes a shift of the main-chain backbone atoms of beta-strand 1 of the alpha/beta-barrel affecting a number of amino acid side chains. This may cause the exceptional catalytic features of C172S. In contrast, the C192S mutation does not produce similar structural perturbations.

Templated synthesis of silver nanoparticles in amphiphilic poly(vinylidene fluoride‐co‐chlorotrifluoroethylene) comb copolymer

AbstractIn this study, poly(vinylidene fluoride‐co‐chlorotrifluoroethylene)‐graft‐poly(oxyethylene methacrylate), P(VDF‐co‐CTFE)‐g‐POEM, an amphiphilic comb copolymer with hydrophobic P(VDF‐co‐CTFE) backbone and hydrophilic POEM side chains at 73:27 wt % was synthesized. The POEM side chains were grafted from the P(VDF‐co‐CTFE) mainchain backbone via atom transfer radical polymerization (ATRP) using direct initiation of the chlorine atoms in CTFE units. Synthesis of microphase‐separated P(VDF‐co‐CTFE)‐g‐POEM comb copolymer was successful, as confirmed by nuclear magnetic resonance (1H NMR), FTIR spectroscopy, and transmission electron microscopy (TEM). Nanocomposite films were prepared using the comb copolymer as a template film and the in situ reduction of AgCF3SO3 precursor to silver nanoparticles under UV irradiation. Silver nanoparticles with 4–8 nm in average size were in situ created in the solid state template film, as revealed by TEM, UV–visible spectroscopy, and wide angle X‐ray scattering (WAXS). Differential scanning calorimetry (DSC) and thermogravimetric analysis (TGA) presented the selective incorporation and the in situ growth of silver nanoparticles within the hydrophilic POEM domains of microphase‐separated comb copolymer film. © 2008 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 46: 702–709, 2008

Influence of N-Glycosylation on Saccharomyces cerevisiae Morphology: A Golgi Glycosylation Mutant Shows Cell Division Defects

The N-glycosylation mutants (mnn1 and mnn1 och1) show different morphological characteristics at the restrictive and nonpermissive temperature. We deleted the MNN1 to eliminate the terminal alpha1, 3-linked mannose of hypermannosylation and deleted the OCH1 to block the elongation of the main backbone chain. The mnn1 cells exhibited no observable change with respect to the wild-type strain at 28 degrees C and 37 degrees C, but the mnn1 och1 double mutant exhibited defects in cell cytokinesis, showed a slower growth rate, and became temperature-sensitive. Meanwhile, the mnn1 och1 mutant tended to aggregate, which was probably due to the glycolsylation defect. Loss of mannosyl-phosphate-accepting sites in this mutant migth result in reduced charge repulsion between cell surfaces. Pyridylaminated glycans were profiled and purified through an NH(2) column by size-fractionation high-performance liquid chromatography. Matrix assisted laser desoption/ionization time of flight mass spectrometry (MALDI TOF/MS) analysis of the N-glycan structure of the mnn1 och1 mutant revealed that the main component is Man(8)GlcNAc(2).

Synthesis and Asymmetric Enantioselective Addition of Chiral Polybinaphthyl and Polybinaphthol Ligands

AbstractFour chiral polymers P‐1, P‐2, P‐3 and P‐4 were synthesized by the polymerization of (S)‐2,2′‐dioctoxy‐1,1′‐ binaphthyl‐6,6′‐boronic acid (S‐M‐3) with (S)‐6,6′‐dibromo‐1,1′‐binaphthol (S‐M‐1), (R)‐6,6′‐dibromo‐1,1′‐ binaphthol (R‐M‐1), (S)‐3,3′‐diiodo‐1,1′‐binaphthol (S‐M‐2) and (R)‐3,3′‐diiodo‐1,1′‐binaphthol (R‐M‐2) under Pd‐catalyzed Suzuki reaction, respectively. All four polymers can show good solubility in some common solvents due to the nonplanarity of the polymers in the main chain backbone and flexible alkyl groups in the side chain. The analysis results indicate that specific rotation and circular dichroism (CD) spectral signals of the alternative S‐S chiral polymers P‐1 and P‐3 are larger than those of S‐R chiral polymers P‐2 and P‐4, but their UV‐Vis and fluorescence spectra are almost similar. The results of asymmetric enantioselectivity of four polymers for diethylzinc addition to benzaldehyde indicate that catalytically active center is (R) or (S)‐1,1′‐binaphthol moieties.

Photoinduced chirality in azobenzene-containing polymer systems

In this article, we will review the phenomena on circularly-polarized-light (CPL)-induced chirality in polymeric systems with photochromophores in their side-chain or main-chain. In the side-chain polymeric systems, the photoinduced chirality arises from superstructural chirality, i.e., helix structure, via aggregating of achiral azobenzene molecules in side chains. On the other hand, in the main-chain polymeric system, the macroscopically induced chirality can originate from individual chirality of chromophores in their main-chain backbone. The CPL irradiation on polymeric films with photochromophores to produce macroscopic chirality has been realized as potentially useful in the development of optical-switching, optical-storage, and light-driven devices.

The Effects of Crowding in Dendronized Polymers

We present a comprehensive numerical study of the effect of degree of polymerization, generation of dendron growth, length of dendron tether, and dendron grafting density on the conformational statistics of dendronized polymers. This class of supramolecular assembly promises to find application in a number of nanotechnological devices in which their dimensions and conformations are key. We find that the radius of gyration estimates obtained from Brownian dynamics simulations yield to a "Flory" scaling argument in the high degree of polymerization regime and that these data from a range of topologically distinct molecules collapse onto a single curve in this limit. The size of the tethered dendrons serve as the key parameter in the scaling theory. Close examination of the dendrons also reveals some curious trends. In particular, we observe that as the grafting density is increased, spatial packing constraints around the main chain backbone force the dendrons further away from the backbone and compress them, significantly affecting the spatial distribution and accessibility of terminal groups; in contrast to dendrimers, the terminal groups of these molecules display a tendency to partition near the surface at high dendron grafting densities.

Molecular dynamics and interactions of aqueous and dichloromethane solutions of polyvinylpyrrolidone

We have investigated the dynamics of polyvinylpyrrolidone solutions (PVP, M(w)=10 000) on time scales from 20 fs to 42 ps using femtosecond optically heterodyne-detected Raman-induced Kerr effect spectroscopy. To compare the dynamics of polymer solutions with those of the analogous monomer, we also characterized solutions of 1-ethyl-2-pyrrolidone (EP). Dynamics of both PVP and EP solutions have been characterized for sample concentrations of 6.4, 12.7, 24.5, 33.3, and 40.7 wt %. The longest time scale relaxations observed in the Kerr transients for these solutions occur on the picosecond time scale and are best fit to triexponential functions. The intermediate and slow relaxation time constants for PVP and EP solutions are concentration dependent. The time constants for the PVP solutions are not consistent with the predictions of hydrodynamic models, while the analogous time constants for the EP solutions do display hydrodynamic scaling. The predominant relaxation of the polymer is assigned to reorientations of the pyrrolidone side group or torsional motions of the constitutional repeat unit, with additional relaxation pathways including hydrogen bond reorganization in aqueous solution and segmental motion of multiple repeat units. The vibrational dynamics of PVP and EP solutions occur on the femtosecond time scale. These dynamics are analyzed with a focus on the additional degrees of freedom experienced by EP relative to PVP that result from the absence of the tether from the pyrrolidone group on the main chain backbone. The intermolecular Kerr spectra of PVP in H(2)O and CH(2)Cl(2) differ because H(2)O can donate a hydrogen bond to the carbonyl acceptor group on the pyrrolidone ring, while CH(2)Cl(2) cannot.

Photophysical properties and morphology of fluorene‐alt‐benzene based conjugated polymers

AbstractA series of fluorene‐alt‐benzene based conjugated main chain polymers attached chemically with different lengths of alkyl side chains on phenylene rings were designed and synthesized by a palladium catalyzed Suzuki coupling reaction. The UV‐vis absorption and fluorescence spectra, thermal stability of spectral property, phase transition behavior and morphology of the synthesized polymers were investigated. With increasing the length of the alkyl side chain, the UV and fluorescence spectra exhibit obvious blue shift compared with those of the unsubstituted polymer. The alkyl substitution improves the thermal stability of the spectra due to the steric hindrance of the alkyl side chains and thus the effective separation of the main chain backbones. The phase transition behavior is closely related to the length of alkyl side chains attached on the phenylene rings. The annealed polymer films display characteristic nematic liquid crystalline texture. Transmission electron microscopy (TEM) observations indicate that solvent‐cast thin deposits of all the polymers show typical fibrillar morphology. Copyright © 2006 John Wiley & Sons, Ltd.

The photophysical properties and morphology of fluorene-alt-benzene based conjugated polymer

A series of fluorene-alt-benzene based conjugated main chain polymers chemically attached with alkyl side chains of different lengths on phenylene rings were designed and synthesized by a palladium catalyzed Suzuki coupling reaction. The UV-vis absorption and fluorescence spectra, thermal stability of spectral property, phase transition behavior and morphology of the synthesized polymers were investigated. With increasing the length of the alkyl side chain, the UV and fluorescence spectra exhibit an obvious blue shift compared with those of the unsubstituted polymer. The alkyl substitution improves the thermal spectral stability of the polymers due to the steric hindrance of the alkyl side chains, thus leading to efficient separation of the main chain backbones. The phase transition behavior is closely related to the length of the alkyl side chains attached on the phenylene rings. The annealed films of the polymers display characteristic nematic liquid crystalline texture. TEM observations indicate that solvent-cast thin deposits of all the polymers show typical fibrillar morphology.

Light-Induced Macroscopic Chirality in Thin Films of Achiral Main-Chain Amorphous Polyazourea System

We have demonstrated circularly polarized light-induced chirality in polymer thin films containing azobenzene linkages in their main-chain backbone. The material used in this study was an amorphous main-chain polyazourea with a high glass transition temperature, which was used to form the fine surface relief gratings. The induction of chirality was confirmed by measuring circular dichroism spectra of achiral polyazourea thin films irradiated with right or left circularly polarized light and was discussed in view of the massive displacement of the material. The repeatability and thermostability of the induced chirality were evaluated and compared with those of the polymers with azobenzene moieties in their side chains.

Dispersion Characteristics and Rheology of Organoclay Nanocomposites Based on a Segmented Main-Chain Liquid-Crystalline Polymer Having Pendent Pyridyl Group

The dispersion characteristics and rheology of organoclay nanocomposites based on a thermotropic liquid-crystalline polymer (TLCP) having pendent functional group were investigated using X-ray diffraction (XRD), transmission electron microscopy (TEM), and oscillatory shear rheometry. For the study, a segmented main-chain TLCP having pendent pyridyl group (PyHQ12) was synthesized and, for comparison, another segmented main-chain TLCP having pendent phenylsulfonyl group (PSHQ12) was synthesized, both TLCPs having the identical chemical structure for the main-chain backbone. The differences in phase transition temperature and rheological behavior observed between PyHQ12 and PSHQ12 are explained in terms of the self-associating characteristics of the pendent pyridyl group in PyHQ12. PyHQ12 and PSHQ12 were used to prepare nanocomposites with two commercial organoclays: one (Cloisite 30B) was natural clay (montmorillonite) treated with a surfactant (MT2EtOH) having hydroxyl groups, and the other (Cloisite 20A)...

Rheology of a Combined Main-Chain/Side-Chain Liquid-Crystalline Polymer in the Thermotropic and Lyotropic States

The rheological behavior of a combined main-chain/side-chain liquid-crystalline polymer, PSHQ4−7CNCOOH, has been investigated in both the thermotropic and lyotropic states. The synthesis procedures for PSHQ4−7CNCOOH are described in a previous paper. In this study transient shear flow, steady-state shear flow, oscillatory shear flow, and time evolution of dynamic moduli upon cessation of shear flow of PSHQ4−7CNCOOH in the thermotropic state have been investigated. Only positive values of first normal stress difference (N1) in steady-state shear flow were observed over the entire range of shear rates and temperatures investigated. One of the objectives of this study was to investigate the role of the side-chain mesogenic groups (7CNCOOH), which were grafted onto the flexible methylene units of the main-chain backbone (PSHQ4), in influencing the rheological behavior of PSHQ4−7CNCOOH in the thermotropic state. Thus, for comparison, the rheological behavior of PSHQ4 was also investigated. Another objective of...

Synthesis and Characterization of a Combined Main-Chain/Side-Chain Liquid-Crystalline Polymer Exhibiting Both Thermotropic and Lyotropic Characteristics and Its Lyotropic Phase Behavior

A combined main-chain/side-chain liquid-crystalline polymer (PSHQ4−7CNCOOH), which is composed of poly[(phenylsulfonyl-p-phenylenene 1,4-tetramethylene bis(oxybenzoate)] (PSHQ4) as the main-chain backbone and 8-[(4-cyano-4‘-phenyl)oxy]octanoic acid (7CNCOOH) as the side-chain mesogenic groups, has been synthesized. It has been found that 7CNCOOH has a clearing temperature of 150 °C and exhibits nematic mesophase, and PSHQ4−7CNCOOH exhibits both thermotropic and lyotropic characteristics. The thermotropic characteristics of PSHQ4−7CNCOOH have been investigated using differential scanning calorimetry (DSC), fiber and powder patterns of wide-angle X-ray diffraction (WAXD), and polarized optical microscopy (POM). It has been found that in the thermotropic state PSHQ4−7CNCOOH has a glass transition temperature (Tg) of 85 °C and a nematic-to-isotropic (N−I) transition temperature (TNI) of 172 °C, and it is a glassy polymer. Interestingly, PSHQ4−7CNCOOH is found to exhibit lyotropic characteristics, undergoing isotropic-to-nematic biphasic separation over a wide range of concentrations in m-dibromobenzene, o-dichlorobenzene, and tetrachloroethane, enabling us to construct a phase diagram. The thermal transitions and phase structures of the main-chain backbone of PSHQ4−7CNCOOH, PSHQ4, were compared with those of PSHQ4−7CNCOOH. It has been found that PSHQ4 has a Tg of ca. 130 °C and a TNI of ca. 260 °C, and it undergoes, during isothermal annealing, crystallization at about 240 °C as determined from DSC. Both the fiber and powder patterns of WAXD indicate that PSHQ4 is a semicrystalline polymer, which is consistent with the findings from DSC. It has been found that, in contrast to PSHQ4−7CNCOOH, PSHQ4 does not exhibit lyotropic characteristics. Both the very large decrease (about 90 °C) in TNI after the attachment of side-chain mesogenic groups (7CNCOOH) onto the main-chain backbone (PSHQ4) and the lyotropic characteristics of PSHQ4−7CNCOOH are attributable to the significant increase in the bulkiness of PSHQ4−7CNCOOH, which apparently cannot pack well, giving rise to a glassy state.

On the functional role of Arg172 in substrate binding and allosteric transition in Escherichia coli glucosamine-6-phosphate deaminase

Glucosamine-6-phosphate deaminase from Escherichia coli (EC 3.5.99.6) is an allosteric enzyme, activated by N-acetylglucosamine 6-phosphate, which converts glucosamine-6-phosphate into fructose 6-phosphate and ammonia. X-ray crystallographic structural models have showed that Arg172 and Lys208, together with the segment 41–44 of the main chain backbone, are involved in binding the substrate phospho group when the enzyme is in the R activated state. A set of mutants of the enzyme involving the targeted residues were constructed to analyze the role of Arg172 and Lys208 in deaminase allosteric function. The mutant enzymes were characterized by kinetic, chemical, and spectrometric methods, revealing conspicuous changes in their allosteric properties. The study of these mutants indicated that Arg172 which is located in the highly flexible motif 158–187 forming the active site lid has a specific role in binding the substrate to the enzyme in the T state. The possible role of this interaction in the conformational coupling of the active and the allosteric sites is discussed.

Fragment Finder: a web-based software to identify similar three-dimensional structural motif

FF (Fragment Finder) is a web-based interactive search engine developed to retrieve the user-desired similar 3D structural fragments from the selected subset of 25 or 90% non-homologous protein chains. The search is based on the comparison of the main chain backbone conformational angles (φ and ϕ). Additionally, the queried motifs can be superimposed to find out how similar the structural fragments are, so that the information can be effectively used in molecular modeling. The engine has facilities to view the resultant superposed or individual 3D structure(s) on the client machine. The proposed web server is made freely accessible at the following URL: or .

Effects of UV irradiation on calf thymus DNA in aqueous solution. A Raman spectroscopic study

The Raman spectra of calf thymus DNA in aqueous solution before and after irradiation in two UV regions (UVA, 320–340 nm; UVA–UVB, 280–400 nm) were investigated. Damage to the molecular structure in part was found in the DNA solution after UVA–UVB irradiation. The bands near 811 (±7) and 832 (±7) cm−1 appeared in all Raman spectra after UV irradiation. This result indicates that DNA in solution has a mixture of A- and B-form conformations under UV irradiation. In this experiment, all the main characteristic Raman peaks appeared at almost the original position after UVA irradiation, except for some bands corresponding to deoxyribose phosphate. This indicated that serious changes to the molecular structure did not occur in the DNA solution after UVA irradiation. The spatial structures of the DNA main chain backbone and phosphoric acid backbone were almost unchanged, and the bands corresponding to adenine also appeared at almost the original sites after UVA–UVB irradiation. The bands at 949 and 1445 cm−1 corresponding to deoxyribose shifted and were obviously hypochromic, and the bands assigned to thymine showed a large shift and decline after 5 h of UVA–UVB irradiation. Hence the pyrimidine bases and deoxyribose were likely first damaged when the calf thymus DNA in aqueous solution was irradiated by UVA–UVB. Copyright © 2004 John Wiley & Sons, Ltd.

Design of Mechanically Robust High-Tg Polymers: Synthesis and Dynamic Mechanical Relaxation Behavior of Glassy Poly(ester carbonate)s with Cyclohexylene Rings in the Backbone

High-Tg yet mechanically robust polymers are desirable but difficult to realize. To explore whether the insertion of a motionally active molecular entity in the backbone could produce polymers with both high Tg and yet are not brittle, three series of high-Tg glassy polycarbonates/polyesters/poly(ester carbonate)s were designed and synthesized. The secondary relaxation behavior of these polymers was studied by dynamical mechanical analysis (DMA). Incorporation of cyclohexylene groups (C-rings) in the main chain of polymers made from two rigid and bulky monomers, spirobiindane bisphenol (SBI) and trimethylcyclohexylbisphenol (Tmc), respectively, changes the γ relaxation process dramatically in peak shape and position in these polymers. No such change is observed in polycarbonate polymers made from cyclohexylbisphenol (BPAZ), or ZPC for short. Through monitoring the γ relaxation with gradual structural change, C-rings in the main chain backbone are proposed to undergo active ring inversion. The γ relaxation of ZPC is proposed to be mainly due to side-chain C-ring inversion. The narrowing on the high-temperature side of the γ relaxation peak of the polycarbonate of Tmc is proposed to be due to the restricted motion of its axial phenyl rings. A linear correlation between relaxation strength and total C-ring concentration was found for all the polymers.

Structural models of osteogenesis imperfecta-associated variants in the COL1A1 gene.

Osteogenesis imperfecta (OI) is a genetic disease in which the most common mutations result in substitutions for glycine residues in the triple helical domain of the chains of type I collagen. Currently there is no way to use sequence information to predict the clinical OI phenotype. However, structural models coupled with biophysical and machine learning methods may be able to predict sequences that, when mutated, would be associated with more severe forms of OI. To build appropriate structural models, we have applied a high throughput molecular dynamic approach. Homotrimeric peptides covering 57 positions in which mutations are associated with OI were simulated both with and without mutations. Our models revealed structural differences that occur with different substituting amino acids. When mutations were introduced, we observed a decrease in helix stability, as caused by fewer main chain backbone hydrogen bonds, and an increase in main chain root mean square deviation and specifically bound water molecules.

Surface Modification of Sylgard-184 Poly(dimethyl siloxane) Networks by Ultraviolet and Ultraviolet/Ozone Treatment

We report on the surface modification of Sylgard-184 poly(dimethyl siloxane) (PDMS) networks by ultraviolet (UV) radiation and ultraviolet/ozone (UVO) treatment. The effects of the UV light wavelength and ambient conditions on the surface properties of Sylgard-184 are probed using a battery of experimental probes, including static contact angle measurements, Fourier transform infrared spectroscopy, near-edge X-ray absorption fine structure, and X-ray reflectivity. Our results reveal that when exposed to UV, the PDMS macromolecules in the surface region of Sylgard-184 undergo chain scission, involving both the main chain backbone and the side groups. The radicals formed during this process recombine and form a network whose wetting properties are similar to those of a UV-modified model PDMS. In contrast to the UV radiation, the UVO treatment causes very significant changes in the surface and near-surface structure of Sylgard-184. Specifically, the molecular oxygen and ozone created during the UVO process interact with the UV-modified specimen. As a result of these interactions, the surface of the sample contains a large number of hydrophilic (mainly –OH) groups. In addition, the material density within the first ≈5 nm reaches about 50% of that of pure silica. A major conclusion that can be drawn from the results and analysis described in this work is that the presence of the silica fillers in Sylgard-184 does not alter the surface properties of the UVO- and UV-modified Sylgard-184.