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.

Identification of Three Interactions to Determine the Conformation Change and to Maintain the Function of Kir2.1 Channel Protein

We find that a conserved mutation residue Glu to residue Asp （E303D）, which both have the same polar and charged properties, makes Kit2.1 protein lose its function. To understand the mechanism, we identify three interactions which control the conformation change and maintain the function of the Kit2.1 protein by combining homology modeling and molecular dynamics with targeted molecular dynamics. We find that the E303D mutation weakens these interactions and results in the loss of the related function. Our data indicate that not only the amino residues but also the interactions determine the function of proteins.

In cell measurement of fluorescence lifetime imaging microscopy revealed C-terminal conformation changes of Ferroportin upon addition of Mn^2＋

Fluorescence microscopy, as a sensitive method to detect microenvironment of molecules, is widely used in protein conformation and dynamic studies in live cells. Fluorescence lifetime imaging microscopy（FLIM）, which is independent of fluorophore concentrations, scattering and bleaching, is a suitable tool to analyze membrane proteins in a single cell. Ferroportin（FPN）, a multi-ion exporter in vertebrates, was modulated by metal ions with unknown mechanism. Herein, we fused green fluorescence protein on Cterminal of FPN（FPN-eGFP） and applied fluorescence lifetime to monitor conformation changes of FPN in a live cell. The fluorescence lifetime distribution showed a shift to shorter lifetime upon Mn^（2＋） treatment,suggesting a preference conformation of FPN in Mn^（2＋） exposure. It is also observed that the lifetime（rather than intensity） measurement was not strongly influenced by laser power. The observed fluorescence lifetime changes of FPN-eGFP upon Mn^（2＋） treatments indicated that extracellular metal ions can modulate FPN through conformation exchanges between several different states.

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.

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

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.

Conformation Disturbance of CopC by α-Naphthylamine

It is known that urea and guanidine hydrochloride（GuHC1） induce conformational change of proteins in a certain range of molar ratios. In our research, a-naphthylamine（NA） above 10^-4 mol/L at pH 7.0 was discovered to perturb the conformation of CopC, a copper resistant protein with a Greek fl-barrel motif; this was reflected by the greater fluorescence quenching and red-shifted emission peak of CopC. The conformation change of CopC was also verified in acrylamide collision experiment by comparing quenching levels of CopC in the presence or the abscence of NA. Comparison of emission change of CopC-Cu^2＋ with that of apo-CopC showed a consistent result with their denaturation in GuHCl. And decreasing fluorescence polarization of CopC with increasing NA concentration is consistent with a more extend conformation of CopC. Interaction mechanism was also explored.

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.

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.

Conformational change of E.coli sulfurtransferase YgaP upon SCN- in intact native membrane revealed by fluorescence lifetime and anisotropy

Fluorescence lifetime and anisotropy has become a prevalent tool to detect the structure change and motility property of proteins. YgaP is the only membrane-integrated rhodanese in E. coli. The sulfur transfer process has been characterized by various studies. However, the mechanism of the outward transportation of SCN-remains unclear. In this work, we examined the fluorescence lifetime and anisotropy of site-specific incorporated unnatural amino acid 7-HC to study the conformational change of YgaP upon SCN-binding. We also compared the fluorescence changes between detergent-wrapped environment in DPC and intact native membrane environment in SMA. Our results suggested the presence of at least two different conformations in YgaP protein. Both the residues in the middle of TMH2 and the residues near extracellular side play important roles in the binding and/or output of SCN-. SMA is a good material to reflect the in situ conformation changes of protein than micelles.

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.

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.

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.

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.

Influence of conformational change of chain unit on the intrinsic negative thermal expansion of polymers

Negative thermal expansion(NTE) behavior has roused wide interest for the control of thermomechanical properties of functional materials.Although NTE behaviors have been found in kinds of compounds,it remains challenging for polymers to achieve intrinsic NTE property.In this work,we systematically studied the conformational change of dibenzocyclooctadiene(DBCOD) derivatives between chair(C) and twist-boat(TB) forms based on density-functional theo ry(DFT) calculations,and found clear evidence of the relationship between the structure of DBCOD units and the thermal contraction behavior of the related polymers.In order to obtain the polymer with NTE property,two conditions should be met for the thermal contracting DBCOD related units as follows:(i) the TB conformation can turn into C conformation as the temperature increases,and(ii) the volume of C conformation is smaller than that of TB conformation.This rule should offer a guidance to exploration of the new intrinsic NTE polymers in the future.

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.

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.

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.