Real-time observation of integrin bending/unbending conformational changes on living cells

Introduction Integrins are a large family of adhesion molecules broadly expressed on the surface of a wide variety of cells as heterodimers. Binding of integrins to ligands provides not only mechanical anchorage for the cell to another cell or

The Local Environmental and Conformational Changes of BSA Varied with pH

The structure and function of protein are strongly pH-dependence. However, the inonization state of the protein varied with the pH value also depends on the local structure

Anionic surfactant sulfate dodecyl sodium (SDS)-induced thermodynamics and conformational changes of collagen by ultrasensitive microcalorimetry

In this communication,sulfate dodecyl sodium(SDS)-induced thermodynamics and conformational changes of collagen were studied.We used ultrasensitive differential scanning calorimetry(US-DSC)to directly monitor the thermal transition of collagen in the presence of SDS.The results show that SDS affects the conformation and thermal stability of collagen very differently depending on its concentrations.At C SDS≤0.05mM,the enhanced thermal stability of collagen indicates the stabilizing effect by SDS.However,a further increase of SDS leads to the denaturation of collagen,verifying the well-known ability of SDS to unfold proteins.This striking difference in thermodynamics and conformational changes of collagen caused by SDS concentrations can be explained in terms of their interactions.With increasing SDS,the binding of SDS to collagen can be dominated by electrostatic interaction shifting to hydrophobic interaction,and the latter plays a key role in loosening and unfolding the triple-helix structure of collagen.The important finding in the present study is the stabilizing effect of SDS on collagen molecules at extreme low concentration.

Conformational Changes in HL60 Cells during Differentiation and Apoptosis Induced by Genistein

Genistein can induce not only differentiation but also apoptosis in HL60 human leukemia cells. During the differentiation and apoptosis, the HL60 cells undergo some conformational changes. Fourier transform infrared (FT IR) was employed to detect those changes. The results showed that the contents of DNA/protein and glycoprotein/protein increased. The α helix of the membrane protein also increased. In addition, the CO (H) stretching mode of serine, threonine and tyrosine residues of the cell proteins also changed. Those conformational changes suggest some mechanisms for how genistein affects the HL60 cells.

Selecting small molecule DNA aptamers with significant conformational changes for constructing transcriptional switches and biosensors

Small molecule aptamers discovered by traditional selection methods usually lack conformational changes upon target binding.This limits the use of aptamers as molecular probes for small molecule detection and regulatory elements of genetic circuits.Here,we report a new method called capture and in vitro transcription-systematic evolution of ligands by exponential enrichment(CIVT-SELEX)to select DNA aptamers that can not only bind to small molecule ligands but also undergo significant conformational changes.Through this method,we select a structure-switching aptamer of uridine-5′-diphosphate(UDP).Taking advantage of its conformational changes,we first construct a UDP-responsive transcriptional switch by inserting the aptamer in a genetic circuit and demonstrate that it can respond to the addition of UDP and regulate the transcription of downstream genes.We also build a UDP aptamer-based biosensor that can be used for active glycosyltransferase screening.We believe this method can provide a universal platform for selecting small molecule aptamers with conformational changes and expand the use of aptamers in small molecule detection and genetic regulation.

Probing conformational change of T7 RNA polymerase and DNA complex by solid-state nanopores

Proteins are crucial to most biological processes, such as enzymes, and in various catalytic processes a dynamic motion is required. The dynamics of protein are embodied as a conformational change, which is closely related to the flexibility of protein. Recently, nanopore sensors have become accepted as a low cost and high throughput method to study the features of proteins. In this article, we used a SiN nanopore device to study the flexibility of T7 RNA polymerase（RNAP） and its complex with DNA promoter. By calculating full-width at half-maximum（FWHM） of Gaussian fits to the blockade histograms, we found that T7 RNAP becomes more flexible after binding DNA promoter. Moreover, the distribution of fractional current blockade suggests that flexibility alters due to a breath-like change of the volume.

Molecular Mechanisms of Cyclic Nucleotide-Gated Ion Channel Gating

Cyclic nucleotide-gated ion channels （CNGs） are distributed most widely in the neuronal cell. Great progress has been made in molecular mechanisms of CNG channel gating in the recent years. Results of many experiments have indicated that the stoichiometry and assembly of CNG channels affect their property and gating. Experiments of CNG mutants and analyses of cys- teine accessibilities show that cyclic nucleotide-binding domains （CNBD） bind cyclic nucleotides and subsequently conformational changes occurred followed by the concerted or cooperative conformational change of all four subunits during CNG gating. In order to provide theoretical assistances for further investigation on CNG channels, especially regarding the disease pathogenesis of ion channels, this paper reviews the latest progress on mechanisms of CNG channels, functions of subunits, processes of subunit assembly, and conformational changes of subunit regions during gating.

Investigation of the binding behavior of human serum albumin and phosphorothioate oligodeoxynucleotide

Aim To study the binding behavior between human serum albumin （HSA） and phosphorothioate oligodeoxynucleotide （PS- ODN） and the effects of bivalent cations on the interaction. Methods Surface plasma resonance, circular dichroism and fluorescence experiments were conducted. Results （ 1 ） the binding ability was decreased along with the increase of pH; （2） Zn^2＋and Ni^2＋ enhanced the interaction between PS-ODN and HSA; （3） Upon PS-ODN binding, the conformation of HSA was changed with an increase of β - sheet. Conclusion The results provide experimental evidences to the hypothesis that PS-ODN binds with HSA in the positive potential region, and histidine residues located in the region play a crucial rule in the interaction.

SOLVENT QUALITY AND SOLUTION BEHAVIOR OF NYLON 12

The refractive index increment, dynamic and static laser light scattering, intrinsic viscosity [η] and Huggins constant （KH） of nylon 12 have been measured in m-cresol and sulphuric acid/water system at 10-60℃. The intrinsic viscosity, Rn, Rg, A2, and （〈 S 〉2）^1/2 （calculated from viscosity data） and ＂a＂ values of nylon 12 are found to be higher in m-cresol than in sulphuric acid. All these parameters decrease with the increase in water contents in sulphuric acid. The refractive index increment, KH and activation energy show an opposite trend to that of [η]. The intrinsic viscosity, RH, Rg, A2, and （〈 S 〉2）^1/2 have maximum values around 30-40℃ in sulphuric acid/water system, whereas in m-cresol they fall at about 20℃. It has been concluded that the variation in size, interaction parameter （second virial coefficient）, [η] and KH of the polymer solutions with the alteration in solvent composition and temperature are the out come of change in thermodynamic quality of solvents, selective adsorption, hydrogen bonding and conformational transitions. It has also been concluded that the increase in temperature first enhances the quality of the solvent, encourages hydrogen bonding and specific adsorption, and then deteriorates, bringing conformational transitions in the polymer molecules. However, the addition of water to sulphuric acid continuously deteriorates the solvent quality. This characteristic of the solvent system brings conformational changes in the polymer especially at low temperatures.

Destabilization of Basic Fibroblast Growth Factor by Oligodeoxynucleotides

The effects of oligodeoxynucleotide （ODN） on the conformation of basic fibroblast growth factor （bFGF） were studied by spectral method. The results showed that ODN destabilized the protein.

Biphasic modulation of chemerin peptide-induced calcium flux and ERK phosphorylation by amyloid beta peptide

OBJECTIVE The chemokine-like receptor 1(CMKLR1,Chem R23) is a functional receptor for chemerin,the chemerin-derived nonapeptide(C9),and the amyloid β peptide 1-42(Aβ_(42)).Because these peptides share little sequence homology,studies were conducted to investigate their pharmacological properties and regulation at CMKLR1.METHODS Cells expressing CMKLR1 were incubated with Aβ_(42) before stimulation with a strong agonist,the C9 peptide.Calcium mobilization,c AMP inhibition and MAP kinase activation were measured.Intramolecular FRET were determined using CMKLR1 constructs with an ECFP attached to the C-terminus and a Fl As H binding motif embedded in the first intracellular loop(IL1).RESULTS Binding of both Aβ_(42) and the C9 peptide induced CMKLR1 internalization,but only the Aβ_(42)-induced receptor internalization involved clathrin-coated pits.Likewise,Aβ_(42) but not C9 stimulated β-arrestin 2 translocation to plasma membranes.A robust Ca^(2+)flux was observed following C9 stimulation,whereas Aβ_(42) was ineffective even at micromolar concentrations.Despite its low potency in calcium mobilization assay,Aβ_(42) was able to alter C9-induced Ca^(2+) flux in dose-dependent manner:a potentiation effect at 100 pmol·L^(-1) of Aβ_(42) was followed by a suppression at 10 nmol·L^(-1) and further potentiation at 1 μmol·L^(-1).This unusual and biphasic modulatory effect was also seen in the C9-induced ERK phosphorylation but the dose curve was opposite to that of Ca^(2+) flux and c AMP inhibition,suggesting a reciprocal regulatory mechanism.Intramolecular FRET assay confirmed that Aβ_(42) modulates CMKLR1 rather than its downstream signaling pathways.CONCLUSION These findings suggest Aβ_(42) as an allosteric modulator that can both positively and negatively regulate the activation state of CMKLR1 in a manner that differs from existing allosteric modulatory mechanisms.

Functionally diverse ligands modulate different activation states of the formyl peptide receptor 2,a G protein-coupled receptor

OBJECTIVE To identify the mechanisms by which the formyl peptide receptor 2(FPR2)mediates both inflammatory and anti-inflammatory signaling in an agonist-dependent manner.METHODS Cells expressing FPR2 were incubated with weak agonists,Aβ42 and Ac2-26,before stimulation with a strong agonist,WKYMVm.Calcium mobilization,c AMP inhibition and MAP kinase activation were measured.Intramolecular FRET were determined using FPR2 constructs with an ECFP attached to the C-terminus and a Fl As H binding motif embedded in the first or third intracellular loop(IL1 or IL3,respectively).RESULTS Aβ42 did not induce significant Ca^(2+) mobilization,but positively modulated WKYMVm-induced Ca^(2+) mobilization and c AMP reduction in a dose-variable manner within a narrow range of ligand concentrations.Treating FPR2-expressing cells with Ac2-26,a peptide with anti-inflammatory activity,negatively modulated WKYMVm-induced Ca^(2+) mobilization and c AMP reduction.Intramolecular FRET assay showed that stimulation of the receptor constructs with Aβ42 brought the C-terminal domain closer to IL1 but away from IL3.An opposite conformational change was induced by Ac2-26.The FPR2 conformation induced by Aβ42 corresponded to enhanced ERK phosphorylation and attenuated p38 MAPK phosphorylation,whereas Ac2-26 induced FPR2 conformational change corresponding to elevated p38 MAPK phosphorylation and reduced ERK phosphorylation.CONCLUSION Aβ42 and Ac2-26 induce different conformational changes in FPR2.These findings provide a structural basis for FPR2 mediation of inflammatory vs anti-inflammatory functions and identify a type of receptor modulation that differs from the classic positive and negative allosteric modulation.

Effect of solution conditions on depression of chlorite using CMC as depressant

The effect of solution conditions on the depression of chlorite using CMC (carboxymethyl cellulose) as depressant was studied through flotation tests and adsorption measurements. Flotation and adsorption tests were first studied as a function of initial solution conditions. The results show that electrostatic repulsion between CMC molecules and chlorite surface hinders the approach of the CMC molecules to the chlorite surface and CMC adsorbs to a great extent at high ionic concentration (10-4 mol/L ions as opposed to 0 mol/L ions) or low pH (3 as opposed to 9). The enhanced adsorption density is attributed to the decreased electrostatic repulsion between CMC and mineral surface. The solution condition that yielded the lowest initial adsorbed amount (0 mol/L ions, pH 9) was used as a reference to investigate the response of the adsorbed CMC layer to a switch in solution conditions after adsorption. The two kinds of solution switches (reducing the solution pH or increasing ionic concentration) result in an increased depression effect of CMC on chlorite flotation, as a result of conformational change of CMC pre-adsorbed layer. The change in the flotation recovery of the CMC-coated chlorite following the solution switches is reversible.

Network models for molecular kinetics and their initial applications to human health

Molecular kinetics underlies all biological phenomena and, like many other biological processes, may best be understood in terms of networks. These networks, called Markov state models （MSMs）, are typically built from physical simulations. Thus, they are capable of quantitative prediction of experiments and can also provide an intuition for complex couformational changes. Their primary application has been to protein folding; however, these technologies and the insights they yield are transferable. For example, MSMs have already proved useful in understanding human diseases, such as protein misfolding and aggregation in Alzheimer＇s disease.

Denatured Thermodynamics of Proteins in Weak Cation-exchange Chromatography

The thermostability of some proteins in weak cation-exchange chromatography was investigated at 20-80 ℃. The results show that there is a fixed thermal denaturation transition temperature for each protein. The appearance of the thermal transition temperature indicates that the conformations of the proteins are destroyed seriously. The thermal behavior of the proteins in weak cation-exchange and hydrophobic interaction chromatographies were compared in a wide temperature range. It was found that the proteins have a higher thermostability in a weak cation-exchange chromatography system. The thermodynamic parameters(Δ H 0, Δ S 0) of those proteins were determined by means of Vant Hoff relationship(ln k -1/ T ). According to standard entropy change(Δ S 0), the conformational change of the proteins was judged in the chromatographic process. The linear relationships between Δ H 0 and Δ S 0 can be used to evaluate 'compensation temperature'( β ) at the protein denaturation and identify the identity of the protein retention mechanism in weak cation-exchange chromatography.

Urea-induced Inactivation and Unfolding of Recombinant Phospholipid Hydroperoxide Glutathione Peroxidase from Oryza sativa

Phospholipid hydroperoxide glutathione peroxidase is an antioxidant enzyme that has the highest capability of reducing membrane-bound hydroperoxy lipids as compared to free organic and inorganic hydroperoxides amongst the glutathione peroxidases.In this study,urea-induced effects on the inactivation and unfolding of a recombinant phospholipid hydroperoxide glutathione peroxidase（PHGPx）from Oryza sativa were investigated by means of circular dichroism and fluorescence spectroscopy.With the increase of urea concentration,the residual activity of OsPHGPx decreases correspondingly.When the urea concentration is above 5.0 mol/L,there was no residual activity.In addition,the observed changes in intrinsic tryptophan fluorescence,the binding of the hydrophobic fluorescence probe ANS,and the far UV CD describe a common dependence on the concentration of urea suggesting that the conformational features of the native OsPHGPx are lost in a highly cooperative single transition.The unfolding process comprises of three zones：the native base-line zone between 0 and 2.5 mol/L urea,the transition zone between 2.5 and 5.5 mol/L urea,and the denatured base-line zone above 5.5 mol/L urea.The transition zone has a midpoint at about 4.0 mol/L urea.

Comparison of Conformational Changes and Inactivation of Penaeus Penicillatus Acid Phosphatase during Unfolding by Urea

It has been reported that inactivation occurs before noticeable conformational changes can be detected during denaturation of creatine kinase and other enzymes. Therefore, Tsou suggested that enzyme active sites may display more conformational flexibility than the enzyme molecules as a whole. In the present investigation, the conformational changes of Penaeus penicillatus acid phosphatase during denaturation in urea solutions were studied by following changes in the intrinsic fluorescence, ultraviolet difference absorption, and circular dichroism spectra. Inactivation of the enzyme in urea solutions was compared with unfolding of the enzyme molecule. The results show that the extent of unfolding in guanidine solutions measured by several different methods closely coincides with each other and that slightly lower concentrations of guanidine are required to bring about inactivation than are required to produce significant conformational changes of the enzyme molecule. At the same concentrations, the inactivation rate constants are markedly faster than the rate constants for unfolding of the enzyme. The above results suggest that the active sites of this enzyme display more conformational flexibility than the enzyme molecule as a whole.

Dynamic mechanism for encapsulating two HIV replication inhibitor peptides with carbon nanotubes

Encapsulation of biomolecules inside a carbon nanotube （CNT） has attracted great interest because it could enable the delivery of nanoscale pharmaceutical drugs with CNT-based devices. Using a molecular dynamics simulation, we investigate the dynamic process by which human immunodeficiency virus （HIV） replication inhibitor peptides （HRIPs） are encapsulated in a water solution contained inside a CNT. The van der Waals attraction between the HRIPs and the CNT and the root-mean-square deviation are used to analyse the evolution of the encapsulation. It is found that the interaction between the HRIPs and the CNT is the main driving force for the encapsulation process, which does not cause an obvious conformational change to the HRIPs.

Effect of Calcium Cation on Thermophilic Acylamino Acid-releasing Enzyme Ape1547 from Aeropyrum pernix K1

The gene of enzyme（Ape1547） was cloned from hyperthermophilic archaeon Aeropyrum pernix K1 and expressed in Escherichia coil.The effect of calcium cation on the properties of Ape1547 was studied.Ape1547 exhibits both peptidase activity and esterase activity.The fluorescence spectrum shows that calcium cation quenches the fluorescence of the enzyme through static quenching mechanism,indicating that calcium cation was bound to the enzyme.Based on the study of calcium cation on CD ellipticity of Ape1547 by circular dichroism,we concluded that the change of enzyme structure induced by calcium cation may be responsible for the change of enzyme activity.Calcium cation has dual effects on Ape1547：it could activate the enzyme activity when its concentration was 0.1 mol/L,and the enzyme had the highest activity;however,when its concentration was higher than 0.2 mol/L,the enzyme activity was inhibited.The results indicate that the activity center of peptidase activity might involve more amino acid residues than that of esterase activity.

Molecular modeling study of the effect of base methylation on internal interactions and motions in DNA and implication to B-Z conformation change

Methylation in the bases of DNA is known to induce B-Z conformation change. In this work, molecular mechanics and normal mode analysis are used to probe how certain methylation affects the internal interactions and thermodynamic motions in the DNA double helixes in both B and Z conformations, and its implication to B-Z conformation change. By molecular modeling with Insight II, two cases involving cytosine C5 and guanine C8 methylation on both B and Z-form DNA duplex d(CGCGCG)2 are studied in comparison with the corresponding unmethylated duplexes. The internal interaction energies computed based on a molecular mechanics force field and the entropies due to internal motions computed according to a normal mode analysis are in fare agreement with respective observed thermodynamic quantities. The analysis on the computed individual energy terms suggests that the observed B-Z conformation change induced by methylation is primarily driven by enthalpic factors. A combination of changes in Van der Waals interaction, electrostatic interaction and hydrogen bonding likely contributes to the change of enthalpy that favors Z-conformation in the methylated states.