SDS-induced multi-stage unfolding of a small globular protein through different denatured states revealed by single-molecule fluorescence

Ionic surfactants such as sodium dodecyl sulfate (SDS) unfold proteins in a much more diverse yet effective way than chemical denaturants such as guanidium chloride (GdmCl). But how these unfolding processes compare on a molecular level is poorly understood. Here, we address this question by scrutinising the unfolding pathway of the globular protein S6 in SDS and GdmCl with single-molecule Förster resonance energy transfer (smFRET) spectroscopy. We show that the unfolding mechanism in SDS is strikingly different and convoluted in comparison to denaturation in GdmCl. In contrast to the reversible two-state unfolding behaviour in GdmCl characterised by kinetics on the timescale of seconds, SDS demonstrated not one, but four distinct regimes of interactions with S6, dependent on the surfactant concentration. At ≤1 mM SDS, S6 and surfactant molecules form quasi-micelles on a minute timescale; at millimolar [SDS], the protein denatures through an unfolded/denatured ensemble of highly heterogeneous states on a multi-second timescale; at tens of millimolar of SDS, the protein unfolds into a micelle-packed conformation on the second timescale; and >50 mM SDS, the protein unfolds with millisecond timescale dynamics. We propose a detailed model for multi-stage unfolding of S6 in SDS, which involves at least three different types of denatured states with different level of compactness and dynamics and a continually changing landscape of interactions between protein and surfactant. Our results highlight the great potential of single-molecule fluorescence as a direct probe of nanoscale protein structure and dynamics in chemically complex surfactant environments.

Multi-stage unfolding of S6 in SDS involving various types of denatured states with different levels of compactness and dynamics.     

Value-true walks in finite,connected, valuated graphs

Starting from Problem 4 on p. 36 ofK. Wagner's book “Graphentheorie” the following question is investigated: Suppose an (undirected) graphG having its edges valuated with nonnegative integers; does there exist a closed walk inG such that each 0-valuated edge is passed the same number of times in both directions, while ak-valuated edge fork>0, is passed exactlyk times in one direction and not at all in the other direction (without having the direction prescribed)? A general criterion and a sufficient condition for the existence of such “value-true walks” are proved. For the analogous question for directed graphs an algorithm for the construction of such walks is established.     

Direct Electrochemical Oxidation of Cellulose: A Cellulose‐Based Fuel Cell System

Direct electricity generation from cellulose without saccharification and fermentation processes was achieved on gold electrode under the alkaline conditions. We (i) overcame problems with the insolubility of cellulose, and captured its electrochemical potential, and (ii) showed that cellulose was converted to cellulose derivatives due to electrochemical oxidation. In addition, we (iii) constructed a cellulose‐based fuel cell, demonstrating that cellulose can be direct electrical based fuel source. The presented fuel cell system overcomes the enormous distribution challenges encountered with other alternative bioenergy sources such as hydrogen.     

Heat of adsorption of naphthalene on Pt(111) measured by adsorption calorimetry

The heat of adsorption of naphthalene on Pt(111) at 300 K was measured with single-crystal adsorption calorimetry. The heat of adsorption on the ideal, defect-free surface is estimated to be (300 - 34 - 199(2)) kJ/mol. From this, a C-Pt bond energy for aromatic hydrocarbons on Pt(111) of approximately 30 kJ/mol is estimated, consistent with earlier results for benzene on Pt(111). There is higher heat of adsorption at very low coverage, attributed to step sites where the adsorption heat is >/=330 kJ/mol. Saturation coverage, = 1 ML, corresponds to 1.55 x 10(14) molecules/cm(2). Sticking probability measurements of naphthalene on Pt(111) give a high initial value of 1.0 and a Kisliuk-type coverage dependence that implies precursor-mediated sticking. The ratio of the hopping rate to the desorption rate of this precursor is approximately 51. Naphthalene adsorbs transiently on top of chemisorbed naphthalene molecules with a heat of adsorption of 83-87 kJ/mol.     

Propagation of a reaction front accompanied by island formation: CO/Au/Ni(1 1 1)

Recent high-pressure scanning tunneling microscopy studies, performed at room temperature, have explicitly demonstrated the specifics of the CO-mediated removal of Ni atoms from the topmost layer of an Au/Ni(1 1 1) surface alloy. After an incubation period, the reaction is found to start at step edges. On each edge, a large fraction of Ni atoms is removed from the terrace in certain areas, whereas other areas are nearly intact after a given time. With increasing time, the former areas begin to overlap and the reaction front becomes somewhat more homogeneous. The Au atoms remaining behind the front form nm-sized islands. Here, we present Monte Carlo simulations reproducing all these observations.     

A rapid gel electrophoretic chip for serum cholesterol determination

We present a rapid gel electrophoretic chip, composed of 2.5% (w/v) acrylamide and 1% (w/v) agarose gel, for serum cholesterol determination using a photo lithography technique. After optimizations, we determined the lipoprotein concentration of standard serum using a conventional enzyme method. The serum was diluted, stained and loaded for 15 min onto the chip. After loading, the intensities of low density lipoprotein cholesterol (LDL-C) and high density lipoprotein cholesterol (HDL-C) bands separated at the chip were estimated using an image analyzer. The intensities of these bands corresponded to concentrations obtained from a standard enzyme-based method. The detected LDL-C and HDL-C concentrations were linear up to 146 mg dL(-1) and 53 mg dL(-1) respectively. Finally, we carried out the cholesterol analysis using real biological samples obtained from nine volunteers using our electrophoretic chip. The LDL-C and HDL-C levels detected using our chip correlated well with the results obtained using the conventional enzyme-based method r(2) = 0.98 and r(2) = 0.86 for LDL-C and HDL-C, respectively. Although our sample size is small and confined only to health volunteers, we have demonstrated that this proof-of-concept gel electrophoretic chip can determine lipoproteins, simultaneously.     

Well covered simplicial,chordal, and circular arc graphs

A graph G is called well covered if every two maximal independent sets of G have the same number of vertices. In this paper, we characterize well covered simplicial, chordal and circular arc graphs. © 1996 John Wiley & Sons, Inc.