Reproducibility in the unfolding process of protein induced by an external electric field

The dynamics of proteins are crucial for their function. However, commonly used techniques for studying protein structures are limited in monitoring time-resolved dynamics at high resolution. Combining electric fields with existing techniques to study gas-phase proteins, such as single particle imaging using free-electron lasers and gas-phase small angle X-ray scattering, has the potential to open up a new era in time-resolved studies of gas-phase protein dynamics. Using molecular dynamics simulations, we identify well-defined unfolding pathways of a protein, induced by experimentally achievable external electric fields. Our simulations show that strong electric fields in conjunction with short-pulsed X-ray sources such as free-electron lasers can be a new path for imaging dynamics of gas-phase proteins at high spatial and temporal resolution.

Controlled unfolding of proteins can reveal structural properties and give insights of the proteins'' dynamics. We show the feasibility of unfolding proteins in the gas phase using electric fields, with a well-defined path at high field strengths.     

Catalytic unfolding and proteolysis of cytochrome C induced by synthetic binding agents

A class of polyanionic copper porphyrin dimers is shown to selectively increase the susceptibility of cytochrome c to proteolysis through binding-induced disruption of tertiary and secondary structure. The free energy of the protein conformation leading to proteolytic attack is stabilized by about 2.4 kcal/mol in the bound state. The proteolytic acceleration is catalytic in nature, requiring only a fraction of an equivalent of metalloporphyrin to effect complete, rapid digestion in the presence of a protease.     

Reorganization of immobilized horse and yeast cytochrome c induced by pH changes or nitric oxide binding

The redox properties of horse and yeast cytochrome c electrostatically immobilized on carboxylic acid-terminated self-assembled monolayers (SAMs) have been determined over a broad pH range (pH 3.5-8) in the absence and presence of nitric oxide. Below pH 6, both proteins exhibit comparable midpoint potentials, coverages, and electron-transfer rate constants, which suggests that they are adsorbed on the SAM in a similar fashion. Above pH 6, a sharp decrease in electron-transfer rate constants is observed for immobilized yeast cytochrome c, which is indicative of a change in the electron tunneling pathway between the heme and the electrode and hence suggests that the protein reorients on the surface. Such a decrease is not observed for horse cytochrome c and therefore must be related to the specific charge distribution on yeast cytochrome c. Apart from the charge distribution on the protein, the reorientation also seems to be related to the charge on the SAM surface. The presence of nitric oxide causes a decrease in electron-transfer rate constants of both yeast and horse cytochrome c at low pH. This is probably due to the fact that nitric oxide induces a conformational change of the protein and also changes the reorganization energy for electron transfer.     

国产硅藻土结构的研究

系统地研究了硅藻土结构, 发现除浙江白土表面具有双生的硅羟基外, 其它只有连生的与孤立的硅羟基; 经IR谱证明, 其内部尚有Si-O与Al-O振动, 酸洗或焙烧都能使硅藻体的孔径、孔径分布和结构发生改变; 经焙烧后, 结构均发生改变, 其自由水消失, 束缚水逐渐减少; 焙烧达1150℃时, 原组成无定形二氧化硅则晶化为α-方石英, 除吉林土具有一级孔洞, 云南土具有三级孔洞外, 本文中其它硅藻土均有二级孔洞。     

Characterisation of cytochrome c unfolding by nano-electrospray ionization time-of-fight and Fourier transform ion cyclotron resonance mass spectrometry

Protein charge-state distributions (CSDs) in electrospray-ionization mass spectrometry (ESI-MS) represent a sensitive tool to probe different conformational states. We describe here the effect of trifluoroethanol (TFE) on cytochrome c equilibrium unfolding at different pH by nano-ESI-MS. While even low concentrations of TFE destabilize the protein native structure at low pH, a TFE content of 2.5%-5% is found to favor cyt c folding at pH approximately 7. Furthermore, we perform comparison of CSDs obtained by time-of-flight (ToF) and Fourier-transform-ion- cyclotron-resonance (FT-ICR) mass analyzers. To this purpose, we analyze spectra of cyt c in the presence of different kind of denaturants. In particular, experiments with 1-propanol suggest that also by FT-ICR-MS, as previously observed on an ESI-ToF instrument, CSDs do not appear to be controlled by the solvent surface tension as predicted by the Rayleigh-charge model. Moreover, there is general good agreement in conformational effects revealed by the different instruments under several buffer conditions. Nevertheless, the ToF instrument appears to discriminate better between unfolded and partially unfolded forms.     

Effect of electrode surface microstructure on electron transfer induced conformation changes in cytochrome c monitored by in situ UV and CD spectroelectrochemistry

Electrochemical redox processes of bovine heart cytochrome c were investigated by in situ UV-vis and CD spectroelectrochemistry at bare glassy carbon electrode (GCE) and single-wall carbon nanotubes (SWNTs) modified glassy carbon electrode (SWNTs/GCE) using a long optical path thin layer cell. The spectra obtained at GCE and SWNTs/GCE reflect electrode surface microstructure-dependent changes in protein conformation during redox transition. Potential-dependent conformational distribution curves of cytochrome c obtained by analysis of in situ circular dichroism (CD) spectra using singular value decomposition least square (SVDLS) method show that SWNTs can retain conformation of cytochrome c. Some parameters of the electrochemical reduction process, i.e. the product of electron transfer coefficient and number of electrons (alpha n = 0.3), apparent formal potential (E0' = 0.04 V), were obtained by double logarithmic analysis and standard heterogeneous electron transfer rate constant k0 was obtained by electrochemistry and double logarithmic analysis, respectively.     

尿素诱导牛血红蛋白变性的微量热和平衡渗析研究

应用恒温微量热技术和平衡渗析技术,对尿素与牛血红蛋白在30℃水溶液中的结合作用及造成牛血红蛋白变性的过程进行了研究,得到了尿素在牛血红蛋白上的平均结合数、二者之间的结合焓及每摩尔尿素与牛血红蛋白结合的焓效应,并根据简单结合模型,计算了它们之间的结合常数、结合自由能.对实验结果的热力学分析表明,尿素是通过直接和间接的两种作用造成牛血红蛋白变性的,它们之间的相互作用分为三个阶段:尿素浓度达到4molL-1之前为第一阶段,主要产生的是尿素与牛血红蛋白的直接结合作用,在弱酸性条件下这种作用较强;尿素浓度为4molL-1到6molL-1之间为第二阶段,主要通过尿素与溶剂水的作用造成牛血红蛋白周围水结构的变化,在尿素浓度达到6molL-1时两种作用的叠加造成牛血红蛋白结构的破坏,暴露出原来处于结构内部的基团;尿素浓度超过6molL-1之后为第三阶段,尿素分子继续与暴露出来的基团进行结合.牛血红蛋白次级结构的维系具有协作性,其结构的破坏不是渐进的,而是一次性全部打开,结构破坏产生的热效应并不太大.     

A study of the local structure of aluminas obtained by different methods

The local structure of aluminas obtained from hydroxides (pseudo-boehmites) synthesized by different methods is studied using the radial density distribution function,. The occupancy of the cation sites of different types (tetrahedral and octahedral, spinel and non-spinel) in the structure of the studied oxides is analyzed.     

荧光光谱法研究牛血清蛋白在尿素体系中的变性

应用荧光光谱技术,对尿素与牛血清蛋白在30℃水溶液中的结合作用及造成牛血清蛋白变性的过程进行了研究,获取了尿素诱导牛血清蛋白变性时相对荧光强度和峰位的变化规律.用Pace等提出的公式分析了相对荧光强度数据,得到了牛血清蛋白变性时的伸展分数fu随溶液pH值和尿素浓度的变化规律.求出了变性平衡常数Ku,伸展吉布斯自由能△G...     

A molecular dynamics study of associations in solution. an NPT simulation of the urea dimer in water

A molecular dynamics simulation of a urea dimer dissolved in a cluster of water molecules has been performed using the NPT ensemble. The results indicate that dimers are unstable against the breaking of NH-CO urea H-bonds induced by the solvent. From a methodological point of view the present study shows that equilibration times longer than those currently used become mandatory when large rearrangements are involved. Furthermore NVT simulations (contrary to NPT ones) can constrain the rearrangement if the system undergoes a significant expansion in its transition between the starting and the final structure.     

Dynamic spectroelectrochemical measurement for the conformational transition of cytochrome c induced by bromopyrogal red

The conformational transition of horse heart cytochrome c induced by bromopyrogal red (BPR) in very low concentration has been firstly investigated by dynamic spectroelectrochemical technique, both at the BPR adsorbed platinum gauze electrode and at a bare platinum gauze electrode in a solution containing BPR. The effect of BPR on the structure of cytochrome c was studied by UV-visible and Fourier transform IR spectroscopy. The unfolded cytochrome c behaves simply as an electron transfer protein with a formal potential of −142 mV vs. a normal hydrogen electrode. The difference between the formal potentials of the native and unfolded cytochrome c is coupled to a difference in conformational energy of the two states of about 40 kJ mol⁻¹, which agrees well with the result reported. The stability and slow refolding of the unfolded cytochrome c are discussed.     

Directed denaturation: room temperature and stoichiometric unfolding of cytochrome C by a metalloporphyrin dimer

Using circular dichroism, UV-vis, and trypsin proteolysis, we have shown how a metalloporphyrin dimer induces the unfolding of a protein, cytochrome c, under physiologically relevant conditions and accelerates its rate of proteolytic degradation.     

The effect of global compaction on the local secondary structure of folded dendrimers

The effect of nonlocal interactions on the local structural propensities of folded dendrimers was evaluated in this work by comparing, under identical conditions, the conformational properties of isomeric dendrimers differing in their global packing efficiency. Accordingly, a modular synthesis of two series of dendrimers up to the third generation was developed to provide efficient access to isomeric dendrimers displaying different levels of overall compaction. Dendrimer compaction levels were adjusted by connecting the folded dendrons to 1,3,5-benzenetricarbonyl chloride, as the central core, via either a 2- or a 4-aminobenzamide linkage to induce relatively "compacted" or "expanded" conformations, respectively. The hydrodynamic volumes of the dendrimers were measured by time-resolved fluorescence anisotropy (TRFA) measurements as a function of the dendrimer series, generation level, and solvent. Packing efficiencies (compaction levels) were estimated by the ratio (V(h)/V(vw)) of the experimental hydrodynamic volume (V(h)) to the calculated van der Waals volume (V(vw)). The extent and stability of local helical bias was measured using circular dichroism and correlated with the packing efficiency (V(h)/V(vw)). These studies suggested that compaction plays an extremely important role in determining the secondary structural preferences of the dendrimers; however, the nature of compaction was more important than the extent of compaction.     

A conductive crosslinked graphene/cytochrome c networks for the electrochemical and biosensing study

The direct electrochemistry of catalytically active cytochrome C (Cyt c) adsorbed together with a 3-dimensional network of chemically synthesized graphene on glassy carbon electrode has been readily obtained in aqueous phosphate buffer. Direct electrical communication between the redox center of Cyt c and the modified graphene-based electrode was established. The modified electrode was employed as a high-performance hydrogen peroxide (H₂O₂) biosensor. The Cyt c present in modified electrode exhibited a pair of quasi-reversible redox peaks with a midpoint potential of ?0.380 and ?0.2 V, cathodic and anodic, respectively. Investigations into the electrocatalytic activity of the modified electrode upon hydrogen peroxide exposure revealed a rapid amperometric response (5 s). Under optimized conditions, the linear range of response to H₂O₂ concentration ranged from 5 × 10^?7 to 2 × 10^?4 M with a detection limit of 2 × 10^?7 M at a signal-to-noise ratio of 3. The stability, reproducibility, and selectivity of the proposed biosensor are discussed in relation to the morphology and composition of the modified electrode.     

Intramolecular cross-linking experiments on cytochrome c and ribonuclease A using an isotope multiplet method.

Mass spectral analysis of tryptic digests of cross-linked proteins offers considerable promise as a simple technique to probe protein structure and study protein-protein interactions. We describe the use of a 1:1 mixture of isotopically labeled and unlabeled cross-linkers, disuccinimidyladipate (DSA) and dimethyladipimidate (DMA), to enhance visualization of cross-linked peptides in a tryptic digest. Optimized intramolecular reactions of cytochrome c and ribonuclease A (RNase A) with DSA yielded an average of two cross-links per protein molecule. After digestion of the cross-linked cytochrome c with trypsin and analysis by liquid chromatography/mass spectrometry (LC/MS) and matrix-assisted laser desorption/ionization (MALDI), eight modified peptides, five cross-linked and two end-capped, were detected by virtue of their doublet character. An eighth modified peptide's identity remained ambiguous because of its inability to fragment. The lysine-lysine distance constraints obtained are discussed in the context of the known NMR and X-ray structures of cytochrome c. Analysis of cross-linked RNase A by LC/MS and MALDI yielded nine modified peptides, four of which were modified twice, as indicated by the isotopic triplets. Although seven of these peptides contained cross-links, few distance constraints were gained due to the fact that the cross-linked products were variations of modification of the same three lysine residues.     

Calculations on the structure and spectral properties of cytochrome c551 using DFT and ONIOM methods

The active site geometry of cytochrome (Cyt) c(551) and its mutated form containing Fe(II) and Fe(III) ions have been calculated using density functional theory (DFT)-based Becke's three-parameter hybrid exchange and Lee-Yang-Parr correlation (B3LYP) method. In addition, calculations have also been carried out using hybrid meta DFT-based M06 functional. The effect of the protein milieu on the active site geometry has also been probed using two-layer via our own N-layered integrated molecular orbital + molecular mechanics (ONIOM) method. Evidence from the calculations reveal that the active site geometry is not significantly affected by the oxidation state of metal ion. The difference in the geometry of the active site and that of the same with the entire protein environment is only minimal, which shows that the protein milieu does not influence the structure of the active site. The calculated electronic transition energies from the time-dependent DFT (TDDFT) calculations are in close agreement with the experimental values. Although there are no significant variations in the active site geometry upon oxidation, the changes in the electronic transition energies have been attributed to the reduction in the overlap of metal ion with the ligand orbitals. In addition, it is found that mutation does not influence the active site geometry and the electronic transition energies. Nevertheless, mutation leads to the formation of more compact structure than the native Cyt c(551).     

Structural transitions in polyriboadenylic acid induced by the changes in pH and temperature: vibrational circular dichroism study in solution and film states

A correlation of the changes in vibrational absorption and vibrational circular dichroism (VCD) spectral features with the structural changes of polyriboadenylic acid (polyA) as a function of pH is reported. Analysis of the solution spectral data as a function of pH led us to establishing the importance of a previously unrecognized absorption band at approximately 1665 cm(-1). The present studies indicate that this absorption band and associated VCD originate from the double-helical structure of polyA. The observed changes in solution-state VCD features are indicative of the pH-dependent transitions among the three acidic forms of polyA (A, B, and "frozen" form). In addition to the solution-state spectral data, pH-dependent absorption and VCD spectra for films of polyA, derived from dilute H2O solutions, are also presented. The pH-dependent changes in the absorption and VCD spectra of films are also correlated to the polyA structural changes.     

Canonical orbital contributions to the magnetic fields induced by global and local diatropic and paratropic ring currents

The induced magnetic field (IMF) of naphthalene, biphenyl, biphenylene, benzocyclobutadiene, and pentalene is dissected to contributions from the total π system, canonical π‐molecular orbitals (CMO), and HOMO→π* excitations, to evaluate and interpret relative global and local diatropicity and paratropicity. Maps of the IMF of the total π system reveal its relative strength and topology that corresponds to global and local diatropic and paratropic ring currents. The total π magnetic response is determined by this of canonical HOMOs and particularly by paratropic contributions of rotational excitations from HOMOs to unoccupied π * orbitals. Low energy excitations and similar nodal structure of HOMO and π * induce strong paratropic fields that dominate on antiaromatic rings. High energy excitations and different nodal structures lead to weak paratropic contributions of canonical HOMOs, which are overwhelmed by diatropic response of lower energy canonical orbitals in aromatic rings. CMO‐IMF analysis is found in agreement with ring current analysis. © 2017 Wiley Periodicals, Inc.     

Utilization of the significant structure concepts in the study of the adsorption process from a solution

Summary The significant structures theory of the liquid state is used to find a model of the adsorption process from a solution. This model leads to an expression of the adsorption rate. From this an adsorption isotherm and an interfacial equation of state are deduced. The boundary cases are studied.