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PubMedDate not supplied

Evaluation of radius of gyration and intrinsic viscosity molar mass dependence and stiffness of hyaluronan.

Nine hyaluronan (HA) samples were fractionated by size-exclusion chromatography, and molar mass (M), radius of gyration (Rg), and intrinsic viscosity ([eta]) were measured in 0.15 M NaCl at 37 degrees C by on-line multiangle light scattering and viscometer detectors. Using such method, we investigated the Rg and [eta] molar mass dependence for HA over a very wide range of molar masses: M ranging from 4 x 10(4) to 5.5 x 10(6) g/mol. The Rg and the [eta] molar mass dependence found for HA showed a meaningful difference. The Rg = f(M) power law was substantially linear in the whole range of molar masses explored with a constant slope of 0.6. In contrast, the [eta] = f(M) power law (Mark-Houwink-Sakurada plot) showed a marked curve shape, and a linear regression over the whole range of molar masses does not make sense. Also the persistence length (stiffness) for HA was estimated. The persistence length derived by using both the Odijk's model (7.5 nm from Rg vs M data) and the Bohdanecky's plot (6.8 nm from [eta] vs M data) were quite similar. These persistence length values are congruent with a semistiff conformation of HA macromolecules.

Chromatography, Gel↗
PubMed2006

A study of the chain stiffness and extension of alginates, in vitro epimerized alginates, and periodate-oxidized alginates using size-exclusion chromatography combined with light scattering and viscosity detectors.

A series of alginates isolated from the stem and leaf of a brown algae (Laminaria hyperborea), bacterial mannuronan, in vitro epimerized mannuronans, and periodate oxidized alginates were analyzed by size-exclusion chromatography (SEC) combined with online multiangle laser light scattering (MALS) and viscometry (collectively abbreviated SMV). Selected samples were also analyzed off-line using low-angle laser light scattering and capillary viscometry. Excellent agreement between the two methods was obtained for properly purified samples. In contrast, abnormal results were obtained for some industrial samples due to the presence of particulate material. Naturally occurring alginates and in vitro epimerized mannuronans were found to obey essentially the same RG-M and [eta]-M relations, and hence, the same Mark-Houwink-Sakurada (MHS) equations (valid for I = 0.10 M): 20 000 g/mol < M < 100 000 g/mol, [eta] = 0.0054 .M(1.00); 100 000 g/mol < M < 1 000 000 g/mol, [eta] = 0.071 .M(0.89). Application of the wormlike chain model to the [eta]-M data obtained by SMV yielded persistence lengths (q) of 15 nm for all alginates at an ionic strength of 0.17 M. Intrinsic viscosities corresponding to infinite ionic strength were estimated on the basis of Smidsrød's B-parameter, and the wormlike chain model then yielded q = 12 nm. Periodate oxidized alginates showed, in contrast, a pronounced decrease in persistence length with increasing degree of oxidation, reaching values below 4 nm at 44% oxidation. Periodate oxidation also resulted in some depolymerization, even in the presence of a free-radical scavenger.

Alginates↗
PubMedDate not supplied

Neurite development in PC12 cells on flexible micro-textured substrates under cyclic stretch.

We investigated the combined effect of micro-texture and mechanical strain on neuronal cell development such as neurite length and neurite density in a rat pheochromocytoma cell line (PC12 cells). Cells were seeded on flexible silicone substrates with micro-texture or no texture (smooth) and cultured under static and dynamic conditions. In the static condition substrates were not stretched and in the dynamic conditions substrates were subjected to cyclic uniaxial stretching at three different strain levels of 4%, 8%, and 16% with each at three different strain rates at 0.1, 0.5, and 1.0 Hz. Results showed that of all cell cultures there was no significant difference in neurite development between cells on smooth and textured substrates, except in the static and 4% at 0.1 Hz conditions, where micro-texture induced significantly longer neurites. With both types of substrates, a lower mechanical condition (4% at 1.0 Hz or 16% at 0.1 Hz) resulted in more and longer neurites and lower cell density, and a higher mechanical condition (16% at 1.0 Hz) resulted in fewer and shorter neurites and lower cell density as compared to the static condition. These findings suggest that the effect of the micro-texture on neurite development is more prominent in low mechanical conditions than in high mechanical conditions and that the strain level and strain rate have an interrelated effect on neurite development: a higher strain level at a lower strain rate has a similar effect as a lower strain level at a higher strain rate in terms of promoting neurite development.

Animals↗
PubMedDate not supplied

Structure, dynamics and solvation of HIV-1 protease/saquinavir complex in aqueous solution and their contributions to drug resistance: molecular dynamic simulations.

As it is known that the understanding of the basic properties of the enzyme/inhibitor complex leads directly to enhancing the capability in drug designing and drug discovery. Molecular dynamics simulations have been performed to examine detailed information on the structure and dynamical properties of the HIV-1 PR complexed with saquinavir in the three protonated states, monoprotonates at Asp25 (Mono-25) and Asp25'(Mono-25') and diprotonate (Di-Pro) at both Asp25 and Asp25'. The obtained results support clinical data which reveal that Ile84 and Gly48 are two of the most frequent residues where mutation toward a protease inhibitor takes place. In contrast to the Ile84 mutation due to high displacement of Ile84 in the presence of saquinavir, source of the Gly48 mutation was observed to be due to the limited space in the HIV-1 PR pocket. The Gly48 was, on one side, found to form strong hydrogen bonds with saquinavir, while on the other side this residue was repelled by the hydrophobic Phe53 residue. In terms of inhibitor/enzyme binding, interactions between saquinavir and a catalytic triad of the HIV-1 PR were calculated using the ab initio method. The results show an order of the binding energy of Mono25<Di-pro<<Mono-25', suggesting that the active site in the HIV-1 PR complexed with saquinavir is monoprotonated states on Asp25. In contrast to the binding energy, 3, 6 and 12 hydrogen bonds between saquinavir and HIV-1 PR were found for the Mono-25, Mono-25' and Di-pro states, respectively. Discrepancy between the two trends suggests us to conclude that interaction between inhibitor and catalytic residues should be used as a criteria to enhance capability in drug designing and drug screening instead of using the total inhibitor/enzyme interaction which is normally reported in the literature. In addition, the distribution and binding of water molecules, in terms of hydrogen bonding, to the donor atoms of saquinavir were investigated and discussed, referring to that which was reported experimentally.

Catalysis↗
PubMedDate not supplied

Impact of conformational flexibility on three-dimensional similarity searching using correlation vectors.

Many three-dimensional (3D) virtual screening concepts, like automated docking or pharmacophore searching, rely on the calculation of a "bioactive" or "receptor-relevant" conformation of a molecule to assess its biological activity. We investigated the dependence of the presence of conformations near the "bioactive" conformation on three-dimensional similarity searching with pharmacophore-based correlation vectors (CATS3D approach). Cocrystal structures of 11 target classes served as queries for virtual screening of a database of annotated ligands. Different numbers of conformations were calculated. Single 3D structures were obtained using the 3D structure generator CORINA and conformational ensembles by the conformation generation program ROTATE. This approach was able to reproduce conformations for high resolution cocrystal structures. For virtual screening we found that using only the CORINA-generated single conformation already resulted in a significant enrichment of isofunctional molecules having the same biological property profile. This observation was also made for ligand classes with many rotatable bonds. Although more similar conformations were considered to be more similar in the CATS3D description, the impact of using multiple conformations on the enrichment of actives was not as high as expected. CATS3D provides an alignment-free three-dimensional virtual screening approach that is less dependent on the presence of conformations which are close to the "bioactive" conformation of a molecule compared to methods that rely on an explicit three-dimensional alignment of molecules.

Algorithms↗
PubMedDate not supplied

Screening drug-like compounds by docking to homology models: a systematic study.

In the absence of an experimentally solved structure, a homology model of a protein target can be used instead for virtual screening of drug candidates by docking and scoring. This approach poses a number of questions regarding the choice of the template to use in constructing the model, the accuracy of the screening results, and the importance of allowing for protein flexibility. The present study addresses such questions with compound screening calculations for multiple homology models of five drug targets. A central result is that docking to homology models frequently yields enrichments of known ligands as good as that obtained by docking to a crystal structure of the actual target protein. Interestingly, however, standard measures of the similarity of the template used to build the homology model to the targeted protein show little correlation with the effectiveness of the screening calculations, and docking to the template itself often is as successful as docking to the corresponding homology model. Treating key side chains as mobile produces a modest improvement in the results. The reasons for these sometimes unexpected results, and their implications for future methodologic development, are discussed.

Computer Simulation↗
PubMed2004

Acetylcholinesterase: enhanced fluctuations and alternative routes to the active site in the complex with fasciculin-2.

A 15 ns molecular dynamics simulation is reported for the complex of mouse acetylcholinesterase (mAChE) and the protein neurotoxin fasciculin-2. As compared to a 15 ns simulation of apo-mAChE, the structural fluctuations of the enzyme are substantially increased in magnitude for the enzyme in the complex. Fluctuations of part of the long omega loop (residues 69-96) are particularly enhanced. This loop forms one wall of the active site, and the enhanced fluctuations lead to additional routes of access to the active site.

Acetylcholinesterase↗
PubMed2000

Combined effect of sourdough lactic acid bacteria and additives on bread firmness and staling.

The effect of various sourdoughs and additives on bread firmness and staling was studied. Compared to the bread produced with Saccharomyces cerevisiae 141, the chemical acidification of dough fermented by S. cerevisiae 141 or the use of sourdoughs increased the volume of the breads. Only sourdough fermentation was effective in delaying starch retrogradation. The effect depended on the level of acidification and on the lactic acid bacteria strain. The effect of sourdough made of S. cerevisiae 141-Lactobacillus sanfranciscensis 57-Lactobacillus plantarum 13 was improved when fungal alpha-amylase or amylolytic strains such as L. amylovorus CNBL1008 or engineered L. sanfranciscensis CB1 Amy were added. When pentosans or pentosans, endoxylanase enzyme, and L. hilgardii S32 were added to the same sourdough, a greater delay of the bread firmness and staling was found. When pentosans were in part hydrolyzed by the endoxylanase enzyme, the bread also had the highest titratable acidity, due to the fermentation of pentoses by L. hilgardii S32. The addition of the bacterial protease to the sourdough increased the bread firmness and staling.

Bread↗
PubMed2000

Study of the temperature effect on the formation of wheat gluten network: influence on mechanical properties and protein solubility.

Modifications of mechanical properties of wheat dough during thermal treatments depend mainly on the capacity of wheat gluten proteins to establish intra- and intermolecular interactions when subjected to high-temperature processing. The present study investigates the effect of thermal treatments on the mechanical properties and protein solubility of wheat gluten-based network. The increase in treatment temperatures (from 80 to 135 C) induces an increase in mechanical resistance of the gluten network (tensile strength increases from 0.26 to 2.04 MPa) and a decrease in deformability (elongation decreases from 468 to 236%). The increase in temperature (from 80 to 135 C) also induces a very strong reduction of protein solubility in 2% SDS (from 68 to 0%) that could be correlated to the mechanical changes observed. It was concluded that the modifications of the wheat gluten network properties seem to depend mainly on the temperature level, as temperatures >108-116 C allow activation of thermosetting reactions.

Elasticity↗
PubMed2004

Determinants of retinoid X receptor transcriptional antagonism.

The synthesis and bioactivity of the retinoid X receptor (RXR) antagonist 4-[(3'-n-butyl-5',6',7',8'-tetrahydro-5',5',8',8'-tetramethyl-2'-naphthalenyl)(cyclopropylidene)methyl]benzoic acid and several heteroatom-substituted analogues are described. Ligand design was based on the scaffold of the 3'-methyl RXR-selective agonist analogue and reports that 3'-n-propyl and longer n-alkyl groups conferred RXR antagonism. The transcriptional antagonism of the 3'-n-butyl analogue was demonstrated by its blockade of retinoic acid receptor (RAR) beta expression induced by the RXRalpha/peroxisome proliferator-activated receptor (PPAR) gamma heterodimer complexed with an RXRalpha agonist plus the PPARgamma agonist ciglitazone and the inhibition of 9-cis-RA-induced coactivator SRC-1a recruitment to RXRalpha. Receptor-ligand docking studies using full-atom flexible ligand and flexible receptor suggested that binding of the antagonist to the RXRalpha antagonist conformation was favored because the salt bridge that formed between the retinoid carboxylate and the RXRalpha helix H5 arginine-321 was far stronger than that formed on its binding to the agonist conformation. The antagonist also blocked activation of RAR subtypes alpha and beta by 9-cis-RA but not that of RARgamma.

Benzoates↗
PubMed2004

Functionality maps of the ATP binding site of DNA gyrase B: generation of a consensus model of ligand binding.

The Multiple Copy Simultaneous Search method (MCSS) was used to construct consensus functionality maps for functional group binding in the ATP binding site of DNA gyrase B. To account for the conformational flexibility of the protein active site, which involves small side chain fluctuations as well as large-scale loop motions, the calculations were done for three different conformations of the 24 kDa subdomain of DNA gyrase B. A postprocessing procedure that employs a continuum dielectric model to include solvent effects was used to calculate the binding free energy for every functional group. These results were ranked according to their affinity for DNA gyrase B and clustered using a new procedure based on van der Waals contacts that is better adapted for cases where multiple conformations are being considered. A total of 23 different functional groups were tested. The results gave consensus maps that indicate those functional group binding sites that are insensitive to the specific protein conformation. The maps also demonstrate that functional groups other than those found in the known ligands may bind competitively in the binding sites of known ligands. This suggests numerous scaffolds that can be used in the development of new ligands for the ATP and coumarinic binding sites in DNA gyrase B. Finally, the calculations show the existence of alternative binding sites near the known binding sites that could be targeted in the rational design for new inhibitors.

Adenosine Triphosphate↗
PubMed2005

A systematic analysis of the effect of small-molecule binding on protein flexibility of the ligand-binding sites.

Using atomic B-factors from high-resolution crystal structures of proteins and protein-ligand complexes, we have studied the effect of small-molecule ligand binding on protein flexibility. For the majority of proteins studied, ligand binding to a protein results in an increase in atomic mobility for some protein atoms at the ligand-binding site, and it leads to an increase in protein flexibility of the entire ligand-binding site in several cases.

Binding Sites↗
PubMed2005

Flexibility of "polyunsaturated fatty acid chains" and peptide backbones: A comparative ab initio study.

The conformational properties of omega-3 type of polyunsaturated fatty acid (PUFA) chains and their fragments were studied using Hartree-Fock (RHF/3-21G) and DFT (B3LYP/6-31G(d)) methods. Comparisons between a unit (U) fragment of the PUFA chain and a mono N-Ac-glycine-NHMe residue show that both structures have the same sequence of sp2-sp3-sp2 atoms. The flexibility of PUFA originates in the internal rotation about the above pairs of sigma bonds. Therefore, potential energy surfaces (PESs) were generated by a scan around the terminal dihedral angles (phi t1 and phi t2) as well as the phi 1 and psi 1 dihedrals of both 1U congeners (Me-CHCH-CH2-CHCHMe and MeCONH-CH2-CONHMe) at the RHF/3-21G level of theory. An interesting similarity was found in the flexibility between the cis allylic structure and the trans peptide models. A flat landscape can be seen in the cis 1U (hepta-2,5-diene) surface, implying that several conformations are expected to be found in this (PES). An exhaustive search carried out on the 1U and 2U models revealed that straight chain structures such as trans and cis beta (phi 1 approximately psi 1 approximately 120 degrees; phi 2 approximately psi 2 approximately -120 degrees) or trans and cis extended (phi 1 approximately psi 1 approximately phi 2 approximately psi 2 approximately 120 degrees) can be formed at the lowest energy of both isomers. However, forming helical structures, such as trans helix (phi 1 approximately -120 degrees, psi 1 approximately 12 degrees; phi 2 approximately -120 degrees, psi 2 approximately 12 degrees) or cis helix (phi 1 approximately -130 degrees, psi 1 approximately 90 degrees; phi 2 approximately -145 degrees, psi 2 approximately 90 degrees) will require more energy. These six conformations, found in 2U, were selected to construct longer chains such as 3U, 4U, 5U, and 6U to obtain the thermochemistry of secondary structures. The variation in the extension or compression of the chain length turned out to be a factor of 2 between the helical and nonhelical structures. The inside diameter of the "tube" of cis helix turned out to be 3.5 A after discounting the internal H atoms. Thermodynamic functions were computed at the B3LYP/6-311+G(2d,p)//B3LYP/6-31G(d). The cis-trans isomerization energy of 1.7 +/- 0.2 kcal mol(-1) unit(-1) for all structure pairs indicates that the conformer selection was consistent. A folding energy of 0.5 +/- 0.1 kcal mol(-1) unit(-1) has been extracted from the energy comparison of the helices and most extended nonhelical structures. The entropy change associated with the folding (Delta S(folding)) is decreases faster with the degree of polymerization (n) for the cis than for the trans isomer. As a consequence, the linear relationships between (Delta G(folding)) and n for the cis and trans isomer crossed at about n = 3. This suggested that the naturally occurring cis isomer less ready to fold than the trans isomer since a greater degree of organization is exhibited by the cis isomer during the folding process. The result of this work leads to the question within the group additivity rule: could the method applied in our study of the folding of polyallylic hydrocarbons be useful in investigating the thermochemistry of protein folding?

Carbon↗
PubMed2006

Effects of chain flexibility on polymer conformation in dilute solution studied by lattice monte carlo simulation.

Effects of chain flexibility on the conformation of homopolymers in good solvents have been investigated by Monte Carlo simulation. Bond angle constraint coupled with persistence length of polymer chains has been introduced in the modified eight-site bond fluctuation simulation model. The study about the effects of chain flexibility on polymer sizes reveals that the orientation of polymer chains under confinement is driven by the loss of conformation entropy. The conformation of polymer chains undergoing a gradual change from spherical iso-diametric ellipsoid to rodlike iso-diametric ellipsoid with the decrease of polymer chain flexibility in a wide region has been clearly illustrated from several aspects. Furthermore, a comparison of the freely jointed chain (FJC) model and the wormlike chain (WLC) model has also been made to describe the polymer sizes in terms of chain flexibility and quasi-quantitative boundary toward the suitability of the models.

Adsorption↗
PubMed2006

Measuring the flexibility of immunoglobulin by gold nanoparticles.

We measured the flexibility of Fab and Fc arms of immunoglobulin using gold nanoparticles (GNPs). Enzyme-linked immunosorbent assay was performed to measure the affinity of anti-5 nm GNP antiserum against various sizes of GNPs. The flexibility of Fc was also measured by electron microscopy. The restricted binding affinity indicated that only a very limited amount of freedom was allowed for the Fab-Fab hinge, while Fab-Fc showed a much larger degree of freedom.

Enzyme-Linked Immunosorbent Assay↗
PubMed2005

Effect of guest molecule flexibility in access to dendritic interiors.

[structure: see text] Dendrimers are attractive scaffolds for catalysis, since catalytic sites can be isolated and the catalysts are recoverable and reusable. Herein, we show that conformationally constrained molecules have better access to dendritic cores compared to the more flexible counterparts. The results reported here should have implications in utilizing dendrimers as scaffolds for artificial selectivity in catalysis.

Catalysis↗
PubMed1999

Hybrid-hybrid matrix structural refinement of a DNA three-way junction from 3D NOESY-NOESY.

Homonuclear 3D NOESY-NOESY has shown great promise for the structural refinement of large biomolecules. A computationally efficient hybrid-hybrid relaxation matrix refinement methodology, using 3D NOESY-NOESY data, was used to refine the structure of a DNA three-way junction having two unpaired bases at the branch point of the junction. The NMR data and the relaxation matrix refinement confirm that the DNA three-way junction exists in a folded conformation with two of the helical stems stacked upon each other. The third unstacked stem extends away from the junction, forming an acute angle (approximately 60 degrees) with the stacked stems. The two unpaired bases are stacked upon each other and are exposed to the solvent. Helical parameters for the bases in all three strands show slight deviations from typical values expected for right-handed B-form DNA. Inter-nucleotide imino-imino NOEs between the bases at the branch point of the junction show that the junction region is well defined. The helical stems show mobility (+/- 20 degrees) indicating dynamic processes around the junction region. The unstacked helical stem adjacent to the unpaired bases shows greater mobility compared to the other two stems. The results from this study indicate that the 3D hybrid-hybrid matrix MORASS refinement methodology, by combining the spectral dispersion of 3D NOESY-NOESY and the computational efficiency of 2D refinement programs, provides an accurate and robust means for structure determination of large biomolecules. Our results also indicate that the 3D MORASS method gives higher quality structures compared to the 2D complete relaxation matrix refinement method.

Base Pairing↗
PubMed1999

Conformational flexibility in calcitonin: the dynamic properties of human and salmon calcitonin in solution.

We have studied the dynamic properties of human (h) and salmon (s) calcitonin (CT) in solution. For both hormones, distance geometry in torsion-angle space has been used to generate three-dimensional structures consistent with NMR data obtained in sodium dodecyl sulfate micelles. For sCT and hCT we used, respectively, 356 and 275 interproton distances together with hydrogen-bonds as restraints. To better characterize their flexibility and dynamic properties two fully unrestrained 1100-ps molecular dynamics (MD) simulations in methanol were performed on the lowest-energy structures of both hormones. Statistical analyses of average geometric parameters and of their fluctuations performed in the last 1000 ps of the MD run show typical helical values for residues 9-19 of sCT during the whole trajectory. For hCT a shorter helix was observed involving residues 13-21, with a constant helical region in the range 13-19. Angular order parameters S(phi) and S(psi) indicate that hCT exhibits a higher flexibility, distributed along the whole chain, including the helix, while the only flexible amino acid residues in sCT connect three well-defined domains. Finally, our study shows that simulated annealing in torsion-angle space can efficiently be extended to NMR-based three-dimensional structure calculations of helical polypeptides. Furthermore, provided that a sufficient number of NMR restraints describes the system, the method allows the detection of equilibria in solution. This identification occurs through the generation of 'spurious' high-energy structures, which, for right-handed alpha-helices, are likely to be represented by left-handed alpha-helices.

Amino Acid Sequence↗