• Molecules and Cells
• /
• v.27 no.6
• /
• pp.681-687
• /
• 2009

We examined the effects of synthetic signal peptides, wild-type (WT) and export-defective mutant (MT) of ribose-binding protein, on the conformational changes of signal recognition particle 54 homologue (Ffh) in Escherichia coli. Upon interaction of Ffh with WT peptide, the intrinsic Tyr fluorescence, the transition temperature of thermal unfolding, and the GTPase activity of Ffh decreased in a peptide concentration-dependent manner, while the emission intensity of 8-anilinonaphthalene-1-sulfonic acid increased. In contrast, the secondary structure of the protein was not affected. Additionally, polarization of fluorescein-labeled WT increased upon association with Ffh. These results suggest that WT peptide induces the unfolded states of Ffh. The WT-mediated conformational change of Ffh was also revealed to be important in the interaction between SecA and Ffh. However, MT had marginal effect on these conformational changes suggesting that the in vivo functionality of signal peptide is important in the interaction with Ffh and concomitant structural change of the protein.

• Journal of Sensor Science and Technology
• /
• v.19 no.3
• /
• pp.214-220
• /
• 2010

Three-dimensional(3D) structure of specific DNA can be changed between two conformations under an external environmental transition such as pH and salt concentration variations. We have experimentally observed the conformational transitions of i-motif DNA using AFM cantilever bioassay. It is shown that pH change of a solvent induces the bending defleciton change of a cantilever functionalized by i-motif DNA. This indicates that cantilever bioassay enables the label-free detection of DNA structural changes upon pH change. It is implied that cantilever bioassay can be a de novo route to quantitatively understand the conformational transitions of biological molecules under environmental changes.

• Bulletin of the Korean Chemical Society
• /
• v.33 no.3
• /
• pp.770-774
• /
• 2012

Protein loops are often involved in diverse biological functions, and some functional loops show conformational changes upon ligand binding. Since this conformational change is directly related to ligand binding pose and protein function, there have been numerous attempts to predict this change accurately. In this study, we show that it is plausible to obtain meaningful ensembles of loop conformations for flexible, ligand-binding protein loops efficiently by applying a loop modeling method. The loop modeling method employs triaxial loop closure algorithm for trial conformation generation and conformational space annealing for global energy optimization. When loop modeling was performed on the framework of ligand-free structure, loop structures within $3\AA$ RMSD from the crystal loop structure for the ligand-bound state were sampled in 4 out of 6 cases. This result is encouraging considering that no information on the ligand-bound state was used during the loop modeling process. We therefore expect that the present loop modeling method will be useful for future developments of flexible protein-ligand docking methods.

• Korea-Australia Rheology Journal
• /
• v.16 no.2
• /
• pp.91-99
• /
• 2004

For the Rouse chain composed of infinite number of beads (continuous limit), conformational changes during the creep and creep recovery processes was recently analyzed to reveal the interplay among all Rouse eigenmodes under the constant stress condition (Watanabe and Inoue, Rheol. Acta, 2004). For completeness of the analysis of the Rouse model, this paper analyzes the conformational changes of the discrete Rouse chain having a finite number of beads (N = 3 and 4). The analysis demonstrates that the chain of finite N exhibits the affine deformation on imposition/removal of the stress and this deformation gives the instantaneous component of the recoverable compliance, $J_{R}$(0) = 1/(N-l)v $k_{B}$T with v and $k_{B}$ being the chain number density and Boltzmann constant, respectively. (This component vanishes for N\longrightarrow$\infty$.) For N = 2, it is known that the chain has only one internal eigenmode so that the affinely deformed conformation at the onset of the creep process does not change with time t and $J_{R}$(t) coincides with $J_{R}$(0) at any t (no transient increase of $J_{R}$(t)). However, for N$\geq$3, the chain has N-l eigenmodes (N-l$\geq$2), and this coincidence vanishes. For this case, the chain conformation changes with t to the non-affine conformation under steady flow, and this change is governed by the interplay of the Rouse eigenmodes (under the constant stress condition). This conformational change gives the non-instantaneous increase of $J_{R}$(t) with t, as also noted in the continuous limit (N\longrightarrow$\infty$).X>).TEX>).X>).

• Archives of Pharmacal Research
• /
• v.10 no.2
• /
• pp.110-114
• /
• 1987

To correlate the conformational changes of DNA (Calf Thymus) with entrapment of DNA into liposomes, the effect of ions ($Na^+$, $Mg^{++}$on the entrapment of calf thymus DNA into liposomes was investigated. The effect of divalent ion ($Mg^{++}$ on the structural changes of DNA indicated by decrease of observed ellipticity at 274 nm and nonspecific binding of DNA to lipid bilayers was greater than monovalent ion ($\Na^+$). But the efficiency of DNA encapsulated was not altered. These results show that entrapment of DNA into liposomes is not due to nonspecific binding and structural changes because of electrostatic forces but to mechanical capture of DNA by the internal aqueous space of liposomes although divalent ion contributes large structural changes and more nonspecific association of DNA with liposomes due to strong charges.

• BMB Reports
• /
• v.38 no.5
• /
• pp.533-538
• /
• 2005

The kinetics of thermal dissociation of superoxide dismutase (SOD) was studied in 0.05 M Tris-HCl buffer at pH 7.4 containing $10^{-4}\;M$ EDTA. The number of conformational locks and contact areas and amino acid residues of dimers of SOD were obtained by kinetic analysis and biochemical calculation. The cleavage bonds between dimers of SOD during thermal dissociation and type of interactions between specific amino acid residues were also simulated. Two identical contact areas between two subunits were identified. Cleavage of these contact areas resulted in dissociation of the subunits, with destruction of the active centers, and thus, lost of activity. It is suggested that the contact areas interact with active centers by conformational changes involving secondary structural elements.

• Bulletin of the Korean Chemical Society
• /
• v.16 no.12
• /
• pp.1153-1162
• /
• 1995

The conformational details of β-lactose are investigated through molecular dynamics simulations in conjunction with the adiabatic potential energy map. The adiabatic energy map generated in vacuo contains five local minima. The lowest energy structure on the map does not correspond to the structure determined experimentally by NMR and the X-ray crystallography. When aqueous solvent effect is incorporated into the energy map calculation by increasing the dielectric constant, one of the local minima in the vacuum energy map becomes the global minimum in the resultant energy map. The lowest energy structure of the energy map generated in aquo is consistent with the one experimentally determined. Molecular dynamics simulations starting from those fivelocal minima on the vacuum energy map reveal that conformational transitions can take place among various conformations. Molecular dynamics simulations of the lactose and ricin B chain complex system in a stochastic boundary indicate that the most stable conformation in solution phase is bound to the binding site and that there are conformational changes in the exocyclic region of the lactose molecule upon binding.

• Bulletin of the Korean Chemical Society
• /
• v.30 no.11
• /
• pp.2723-2728
• /
• 2009

The conformational properties of oligosaccharides are important to understand carbohydrate-protein interactions. A trimannoside, methyl 3,6-di-O-($\alpha$-D-Man)-$\alpha$-D-Man (TRIMAN) is a basic unit of N-linked oligosaccharides. This TRIMAN moiety was further modified by GlcNAc (BISECT), which is important to biological activity of N-glycan. To characterize the trimannoside and its bisecting one we performed a molecular dynamics simulation in water. The resulting models show the conformational transition with two major and minor conformations. The major conformational transition results from the $\omega$ angle transition; another minor transition is due to the $\psi$ angle transition of $\alpha$ (1 $\rightarrow$ 6) linkage. The introduction of bisecting GlcNAc on TRIMAN made the different population of the major and minor conformations of the TRIMAN moiety. Omega ($\omega$) angle distribution is largely changed and the population of gt conformation is increased in BISECT oligosaccharide. The inter-residue hydrogen bonds and water bridges via bisecting GlcNAc residue make alterations on the local and overall conformation of TRIMAN moiety. These changes of conformational distribution for TRIMAN moiety can affect the overall conformation of N-glycan and the biological activity of glycoprotein.

• Journal of Life Science
• /
• v.17 no.6 s.86
• /
• pp.783-790
• /
• 2007

G protein coupled receptors (GPCRs) transmit various extracellular signals into the cells. Upon binding of the ligands, conformational changes in the extracellular and/or transmembrane (TM) domains of CPCRs were propagated into the cytoplasmic (CP) domain of the molecule leading to the activation of their cognate heterotrimeric C proteins and kinases. Constitutively active GPCR mutants causing the activation of C Protein signaling even in the absence of ligand binding are of interest for the study of activation mechanism of GPCRs. Two classes of constitutively active mutations, categorized by their effects on the salt bridge between Ell3 and K296, were found in the TM domain of rhodopsin. Opsin mutants containing combinations of the mutations were constructed to study the conformational changes required for the activation of rhodopsin. Rhodopsin chromophore regenerated with 11-cis-retinal showed a thermal stability inversely correlated with its constitutive activity. In contrast, rhodopsin mutants exhibited a binding affinity to an agonist, all-trans-retinal, in a constitutive activity-dependent manner. In order to test whether the conformational changes responsible for the activation of trans-ducin (Gt) are the same as the conformation required for the recognition of rhodopsin kinase, analysis of the mutants were carried out with phosphorylation by rhodopsin kinase. Rhodopsin mutants containing combinations of different classes of the mutations showed a strong synergistic effect on the phosphorylation of the mutants in the dark as similar to that of Gt activation. The results suggest that at least two or three kinds of segmental and independent conformational changes are required for the activation of rhodopsin and the conformational changes responsible for activating rhodopsin kinase and Gt are similar to each other.

• Applied Microscopy
• /
• v.19 no.2
• /
• pp.59-73
• /
• 1989

To investigate the effect of cadmium and cadmium binding protein on the electron transport system and conformational changes of rat kidney mitochondria, various cadmium concentration were treated in vitro and respiration rate, NADH-CoQ reductase activity were measured. Ultrastructural changes at state IV respiration were also observed. CdBP was isolated from the rat liver by Sephadex G-75 column fractionation and treated in vitro with cadmium. Also mitochondrial state IV respiration rate was measured. When cadmium was treated in vitro, state IV respiration and enzyme activity were decreased and ultrastructural transformation of mitochondria from a condensed to an orthodox conformation was inhibited under state IV respiration. In case cadmium and CdBP were treated together, oxygen consumption was more increased than cadmium only. Conformational changes of mitochondria from a condensed to orthodox conformation were also observed. This indicates that CdBP have a protective effect against cadmium toxicity.