Millisecond analysis of double stranded DNA with fluorescent intercalator by micro-thermocontrol-device

Study of interaction between DNA and intercalator at molecular level is important to understand the mechanisms of DNA replication and repair. A micro-fabricated local heating thermodevice was adapted to perform denaturation experiments of DNA with fluorescent intercalator on millisecond time scale. Response time of complete unzipping of double stranded DNA, 16 μm in length, was measured to be around 5 min by commercial thermocycler. Response time of quenching of double stranded DNA with fluorescent intercalator SYBR Green was measured to be 10 ms. Thus, quenching properties owing to strand unzipping and denaturation at base pair level were distinguished. This method has provided easy access to measure this parameter and may be a powerful methodology in analyzing biomolecules on millisecond time scale.     

利用尺寸排阻色谱法研究蛋白质的变性

通过比较蛋白质变性时的色谱行为和生物物理特性，提出利用尺寸排阻色谱法研究蛋白质变性时的构象变化，根据色谱参数中保留时间，比较蛋白质变性时体积的相对变化，利用色谱峰数，确定形成变体的数目，根据峰形和峰数的变化，描述蛋白质的伸展程度，利用不同波长下峰高的变化，推断蛋白质变性芳香族基酸残基的暴露情况，利用建立的尺寸排阻色谱观察了液体和固液α－淀粉酶在低温下放置时的变性情况，讨论了变性时间和变性温度对蛋白     

Temperature-cycle single-molecule FRET microscopy on polyprolines

Accessing the microsecond dynamics of a single fluorescent molecule in real time is difficult because molecular fluorescence rates usually limit the time resolution to milliseconds. We propose to apply single-molecule temperature-cycle microscopy to probe molecular dynamics at microsecond timescales. Here, we follow donor and acceptor signals of single FRET-labeled polyprolines in glycerol to investigate their conformational dynamics. We observe a steady-state FRET efficiency distribution which differs from theoretical distributions for isotropically orientated fluorescent labels. This may indicate that the orientation of fluorescent labels in glycerol is not isotropic and may reflect the influence of the dye linkers. With proper temperature-cycle parameters, we observed large FRET changes in long series of cycles of the same molecule. We attribute the main conformational changes to reorientations of the fluorescent labels with respect to the oligopeptide chain, which take place in less than a few microseconds at the highest temperature of the cycle (250 K). We were able to follow the FRET efficiency of a particular construct for more than 2000 cycles. This trajectory displays switching between two conformations, which give rise to maxima in the FRET efficiency histogram. Our experiments open the possibility to study biomolecular dynamics at a time scale of a few microseconds at the single-molecule level.     

Quantum dots for single bio-molecule imaging.

The emerging nanomaterial, quantum dots or QDs, offers numerous potential applications in the biological area. As cell labeling probes, QDs become now an alternative of existing organic fluorescent dyes and fluorescent proteins. In this short review, we cover typical and successful applications of QDs as fluorescent probes in cell labeling and genomic diagnosis. As a future important application, biomolecular detection at a single molecule level utilizing QDs is also discussed.     

Semibiological molecular machine with an implemented "AND" logic gate for regulation of protein folding

A semibiological molecular machine with an implemented "AND" logic gate was developed, which was capable of controlling the folding process of proteins in response to ATP and light as input stimuli. The molecular design made use of a genetically engineered chaperonin GroEL bearing, at both entrance parts of its cylindrical cavity, cysteine residues, which were functionalized by an azobenzene derivative to construct photoresponsive mechanical gates (azo-GroEL). This engineered chaperonin trapped denatured green fluorescent protein (GFP(denat)) and prohibited its refolding. However, when hosting azo-GroEL detected ATP (input stimulus 1) and UV light (input stimulus 2) at the same time, it quickly released GFP(denat) to allow its refolding. In contrast, reception of either input stimulus 1 or 2 resulted in only very slow or no substantial refolding of GFP(denat). Implementation of such "AND" logic gate mechanisms in mechanically driven biomolecular systems is an important step toward the design of secured drug delivery systems.     

Phase transitions of polycrystalline [Fe(H2O)6](ClO4)3 and [Cr(H2O)6](ClO4)3 studied by DSC

The effects of heat treatment on soymilk protein denaturation were studied by differential scanning calorimetry (DSC) and electrophoresis. Transition behavior of soymilk was studied by DSC. Three endotherms were found in DSC heating curves; the transition observed at around 70°C is attributed to the denaturation of 7S (b-conglycinin) and the transition at around 90°C is to 11S (glycinin). The denaturation temperature increased with the increasing soymilk protein content. The change of electrophoretic patterns after heat treatments indicated that soy proteins were dissociated into subunits, some of which coalesced. When the heating temperature is below their denaturation temperature, the protein fractions cannot completely be denatured even after heat exposure for extended periods of time. This revised version was published online in August 2006 with corrections to the Cover Date.     

Multifunctional stable fluorescent magnetic nanoparticles

Because of their multifunctionality and unique magnetic properties, superparamagnetic iron oxide nanoparticles (SPIONs) have been recognized as very promising materials for various biomedical applications. The main difficulty with the use of SPIONs as multimodal bioimaging agents is their lack of fluorescence. Since cells can act as extremely efficient filters for the elution of surface-bound fluorescent tags with nanoparticles, the surface loaded fluorescence dyes significantly decay after a short period of time. Here, for the first time, we introduce novel, engineered multimodal SPIONs with a permanent fluorescence capability, the study of which can lead to a deeper understanding of biological processes at the biomolecular level, greatly influencing molecular diagnostics, imaging and therapeutic applications.     

Pressure—A Gateway to Fundamental Insights into Protein Solvation,Dynamics, and Function

Now that the centennial anniversary of the first report on pressure denaturation of proteins by Nobel Laureate P. W. Bridgman can be celebrated, this Review on the application of high pressure as a key variable for studying the energetics and interactions of proteins appears. We demonstrate that combined temperature–pressure‐dependent studies help delineate the free‐energy landscape of proteins and elucidate which features are essential in determining their stability. Pressure perturbation also serves as an important tool to explore fluctuations in proteins and reveal their conformational substates. From shaping the free‐energy landscape of proteins themselves to that of their interactions, conformational fluctuations not only dictate a plethora of biological processes, but are also implicated in a number of debilitating diseases. Finally, the advantages of using pressure to explore biomolecular assemblies and modulate enzymatic reactions are discussed.     

Towards the analysis of high molecular weight proteins and protein complexes using TIMS-MS

In the present work, we demonstrate the potential and versatility of TIMS for the analysis of proteins, DNA-protein complexes and protein-protein complexes in their native and denatured states. In addition, we show that accurate CCS measurement are possible using internal and external mobility calibration and in good agreement with previously reported CCS values using other IMS analyzers (<5 % difference). The main challenges for the TIMS-MS analysis of high mass proteins and protein complexes in the mobility and m/z domain are described. That is, the analysis of high molecular weight systems in their native state may require the use of higher electric fields or a small compromise in the TIMS mobility resolution by reducing the bath gas velocity in order to effectively trap at lower electric fields. This is the first report of CCS measurements of high molecular weight biomolecules and biomolecular complexes (~150 kDa) using TIMS-MS.     

Cold Denaturation of α‐Synuclein Amyloid Fibrils

Although amyloid fibrils are associated with numerous pathologies, their conformational stability remains largely unclear. Herein, we probe the thermal stability of various amyloid fibrils. α‐Synuclein fibrils cold‐denatured to monomers at 0–20 °C and heat‐denatured at 60–110 °C. Meanwhile, the fibrils of β2‐microglobulin, Alzheimer’s Aβ1‐40/Aβ1‐42 peptides, and insulin exhibited only heat denaturation, although they showed a decrease in stability at low temperature. A comparison of structural parameters with positive enthalpy and heat capacity changes which showed opposite signs to protein folding suggested that the burial of charged residues in fibril cores contributed to the cold denaturation of α‐synuclein fibrils. We propose that although cold‐denaturation is common to both native proteins and misfolded fibrillar states, the main‐chain dominated amyloid structures may explain amyloid‐specific cold denaturation arising from the unfavorable burial of charged side‐chains in fibril cores.     

Effect of sodium dodecyl sulfate on protein separation by hollow fiber flow field-flow fractionation

Effects of protein denaturation and formation of protein-sodium dodecyl sulfate (SDS) complexes on protein separation and identification were investigated using hollow fiber flow field-flow fractionation (HF5) and nanoflow liquid chromatography-electrospray ionization-tandem mass spectrometry (nLC-ESI-MS-MS). Denaturation and formation of protein-SDS complexes prior to HF5 separation resulted an increase in the retention of few protein standards due to unfolding of the protein structures and complexation, yielding ~30% increase in hydrodynamic diameter. In addition, low molecular weight proteins which could be lost from the HF membrane due to the pore size limitation showed an increase of peak recovery about 2-6 folds for cytochrome C and carbonic anhydrase. In the case of proteins composed of a number of subunits, denaturation resulted in a decrease in retention due to dissociation of protein subunits. A serum proteome sample, denatured with dithiothreitol and SDS, was fractionated by HF5, and the eluting protein fractions after tryptic digestion were analyzed for protein identification using nLC-ESI-MS-MS. The resulting pools of identified proteins were found to depend on whether the serum sample was treated with or without denaturation prior to the HF5 run due to differences in the aqueous solubility of the proteins. The enhancement of protein solubility by SDS also increased the number of identified membrane proteins (54 vs. 31).     

Noncovalent labeling of myoglobin for capillary electrophoresis with laser-induced fluorescence detection by reconstitution with a fluorescent porphyrin

Traditional protein labeling reactions for capillary electrophoresis (CE) with laser-induced fluorescence (LIF) detection suffer from a variety of disadvantages. The reactions can be nonquantitative on a reasonable time scale, require relatively high concentrations of protein and fluorophore, and can give multiple reaction products that can not be separated. Herein, we describe a new noncovalent labeling technique that is rapid, selective for myoglobin, and gives a simple reaction product. Myoglobin is denatured with either 5.4 M urea or low pH (2.0). The denatured myoglobin releases its nonfluorescent heme group. A fluorescent porphyrin (protoporphyrin IX (PPIX) or its zinc (II) complex, Zn-PPIX), is added to the mixture and the solution conditions are altered (dilute to 0.54 M urea or adjust pH to 7.0) to allow myoglobin refolding. Upon refolding, the protein incorporates PPIX from solution, thus making the reaction product fluorescent. The experimental conditions have been optimized for both urea and low-pH denaturation of myoglobin. The latter procedure produces a detection limit of 50 nM. Alternatively, the reaction can be performed without denaturation by a simple exchange of the porphyrins. The use of Zn-PPIX yields the most efficient reaction. The low-pH reaction is unaffected by a 2000-fold excess of bovine serum albumin.     

Studies of irreversible heat denaturation of green fluorescent protein by differential scanning microcalorimetry

Heat denaturation of green fluorescent protein (the GFP-cycle3 mutant) was studied by the method of differential scanning microcalorimetry. Activation energy values for two stages of GFP unfolding were calculated from the calorimetric data using the model of irreversible denaturation. Dependences of activation energy and denaturation enthalpy on the temperature of the maxima of corresponding stages of denaturation were obtained, which allow estimating the corresponding increments of heat capacity. Based on the known correlations of the structure and energy parameters, it was concluded that the first transition state is close to the native state, whereas the second transition state is close to the denatured state, judging by the exposure of hydrophobic groups to the solvent.     

Covalent photochemical functionalization of amorphous carbon thin films for integrated real-time biosensing

Recent studies have demonstrated that carbon, in the form of diamond, can be functionalized with molecular and/or biomolecular species to yield interfaces exhibiting extremely high stability and selectivity in binding to target biomolecules in solution. However, diamond and most other crystalline forms of carbon involve high-temperature deposition or processing steps that restrict their ability to be integrated with other materials. Here, we demonstrate that photochemical functionalization of amorphous carbon films followed by covalent immobilization of DNA yields highly stable surfaces with excellent biomolecular recognition properties that can be used for real-time biological detection. Carbon films deposited onto substrates at 300 K were functionalized with organic alkenes bearing protected amine groups and characterized using X-ray photoelectron spectroscopy and Fourier transform infrared spectroscopy. The functionalized carbon surfaces were covalently linked to DNA oligonucleotides. Measurements show very high selectivity for binding to the complementary sequence, and a high density of hybridizing DNA molecules. Samples repeatedly hybridized and denatured 25 times showed no significant degradation. The ability to use amorphous carbon films as a basis for real-time biosensing is demonstrated by coating quartz crystal microbalance (QCM) crystals with a thin carbon film and using this for covalent modification with DNA. Measurements of the resonance frequency show the ability to detect DNA hybridization in real time with a detection limit of <3% of a monolayer, with a high degree of reversibility. These results demonstrate that functionalized films of amorphous carbon can be used as a chemically stable platform for integrated biosensing using only room-temperature processing steps.     

Single-photon atomic force microscopy

In the last few years, an array of novel technologies, especially the big family of scanning probe microscopy, now often integrated with other powerful imaging tools such as laser confocal microscopy and total internal reflection fluorescence microscopy, have been widely applied in the investigation of biomolecular interactions and dynamics. But it is still a great challenge to directly monitor the dynamics of biomolecular interactions with high spatial and temporal resolution in living cells. An innovative method termed “single-photon atomic force microscopy” (SP-AFM), superior to existing techniques in tracing biomolecular interactions and dynamics in vivo, was proposed on the basis of the combination of atomic force microscopy with the technologies of carbon nanotubes and single-photon detection. As a unique tool, SP-AFM, capable of simultaneous topography imaging and molecular identification at the subnanometer level by synchronous acquisitions and analyses of the surface topography and fluorescent optical signals while scanning the sample, could play a very important role in exploring biomolecular interactions and dynamics in living cells or in a complicated biomolecular background.     

Studies on gelation of soybean globulin solutions

Thermal denaturation of soybean globulin fraction (SBGF) in diluted solution (protein concentration 0.15–0.63%) has been studied by the method of differential adiabatic scanning calorimetry. SBGF thermograms have two maxima. The low temperature maximum is consistent with denaturation of 7S component, while the high temperature maximum with denaturation of 11S components of this fraction. In the investigated range of protein concentrations the thermodynamic parameters (temperature and enthalpy) of denaturation of SBGF and its main components are constant. This fact suggests that differential adiabatic scanning calorimetry gives information purporting a change in the protein state at molecular level. The temperatures and enthalpies of denaturation of the main SBGF components linearly rise with increase of NaCl concentration. The slope of dependences of denaturation temperature on salt concentration,K _s, is extremely large (nearly 20 K · l/mole). The elementary thermodynamic theory of lyotropic effects in thermal denaturation of proteins has been developed based on the two-state model and linear approximation of protein-salt interactions by means of the corresponding second virial coefficient. It shows that the dependences of thermodynamic parameters of thermal denaturation on salt concentration should be linear in the initial section. This conclusion is consistent with the experiment. The differences of enthalpies and entropies of transferring denatured and native forms of the main SBGF components from water into NaCl solution have been determined. They are positive and their quantity increases linearly with salt concentration. This fact is consistent with the concept to the effect that the main factor of salt influence on thermal denaturation of SBGF is confined to a decrease of protein hydration. The effect of protein nature on the quantity of lyotropic effect in thermal denaturation has been considered. Using simple considerations as a basis, the dependence of the ratio betweenK _s and the denaturation temperature in water has been obtained, which characterizes the lyotropic effect, on the molar fraction of hydrophobic residues in the protein molecule. This dependence is linear and the lyotropic effect rises with increase in the content of hydrophobic residues. It is satisfactorily consistent with the experimental data on NaCl effect on thermal denaturation temperature for ichthyocol gelatin, ribonuclease, lysozyme, 7S and 11S SBGF components. An extraordinary strong influence of NaCl on thermal denaturation temperatures for the main SBGF components can be accounted for by a relatively high content of hydrophobic residues.     

Slow Unfolded-State Structuring in Acyl-CoA Binding Protein Folding Revealed by Simulation and Experiment

Protein folding is a fundamental process in biology, key to understanding many human diseases. Experimentally, proteins often appear to fold via simple two- or three-state mechanisms involving mainly native-state interactions, yet recent network models built from atomistic simulations of small proteins suggest the existence of many possible metastable states and folding pathways. We reconcile these two pictures in a combined experimental and simulation study of acyl-coenzyme A binding protein (ACBP), a two-state folder (folding time ～10 ms) exhibiting residual unfolded-state structure, and a putative early folding intermediate. Using single-molecule FRET in conjunction with side-chain mutagenesis, we first demonstrate that the denatured state of ACBP at near-zero denaturant is unusually compact and enriched in long-range structure that can be perturbed by discrete hydrophobic core mutations. We then employ ultrafast laminar-flow mixing experiments to study the folding kinetics of ACBP on the microsecond time scale. These studies, along with Trp-Cys quenching measurements of unfolded-state dynamics, suggest that unfolded-state structure forms on a surprisingly slow (～100 μs) time scale, and that sequence mutations strikingly perturb both time-resolved and equilibrium smFRET measurements in a similar way. A Markov state model (MSM) of the ACBP folding reaction, constructed from over 30 ms of molecular dynamics trajectory data, predicts a complex network of metastable stables, residual unfolded-state structure, and kinetics consistent with experiment but no well-defined intermediate preceding the main folding barrier. Taken together, these experimental and simulation results suggest that the previously characterized fast kinetic phase is not due to formation of a barrier-limited intermediate but rather to a more heterogeneous and slow acquisition of unfolded-state structure.     

Slow exchange in the chromophore of a green fluorescent protein variant

Green fluorescent protein and its mutants have become valuable tools in molecular biology. They also provide systems rich in photophysical and photochemical phenomena of which an understanding is important for the development of new and optimized variants of GFP. Surprisingly, not a single NMR study has been reported on GFPs until now, possibly because of their high tendency to aggregate. Here, we report the (19)F nuclear magnetic resonance (NMR) studies on mutants of the green fluorescent protein (GFP) and cyan fluorescent protein (CFP) labeled with fluorinated tryptophans that enabled the detection of slow molecular motions in these proteins. The concerted use of dynamic NMR and (19)F relaxation measurements, supported by temperature, concentration- and folding-dependent experiments provides direct evidence for the existence of a slow exchange process between two different conformational states of CFP. (19)F NMR relaxation and line shape analysis indicate that the time scale of exchange between these states is in the range of 1.2-1.4 ms. Thermodynamic analysis revealed a difference in enthalpy (Delta)H(0) = (18.2 +/- 3.8) kJ/mol and entropy T(Delta)S(0) = (19.6 +/- 1.2) kJ/mol at T = 303 K for the two states involved in the exchange process, indicating an entropy-enthalpy compensation. The free energy of activation was estimated to be approximately 60 kJ/mol. Exchange between two conformations, either of the chromophore itself or more likely of the closely related histidine 148, is suggested to be the structural process underlying the conformational mobility of GFPs. The possibility to generate a series of single-atom exchanges ("atomic mutations") like H --> F in this study offers a useful approach for characterizing and quantifying dynamic processes in proteins by NMR.