Switching the aptamer attachment geometry can dramatically alter the signalling and performance of electrochemical aptamer-based sensors

Electrochemical aptamer-based (EAB) sensors, composed of an electrode-bound DNA aptamer with a redox reporter on the distal end, offer the promise of high-frequency, real-time molecular measurements in complex sample matrices and even in vivo. Here we assess the extent to which switching the aptamer terminus that is electrode-bound and the one that is redox-reporter-modified affects the performance of these sensors. Using sensors against doxorubicin, cocaine, and vancomycin as our test beds, we find that both signal gain (the relative signal change seen in the presence of a saturating target) and the frequency dependence of gain depend strongly on the attachment orientation, suggesting that this easily investigated variable is a worthwhile parameter to optimize in the design of new EAB sensors

Origins of Chevron Rollovers in Non-Two-State Protein Folding Kinetics

Chevron rollovers of some proteins imply that their logarithmic folding rates are nonlinear in native stability. This is predicted by lattice and continuum G\=o models to arise from diminished accessibilities of the ground state from transiently populated compact conformations under strongly native conditions. Despite these models' native-centric interactions, the slowdown is due partly to kinetic trapping caused by some of the folding intermediates' nonnative topologies. Notably, simple two-state folding kinetics of small single-domain proteins are not reproduced by common G\=o-like schemes.Comment: 10 pages, 4 Postscript figures (will appear on PRL

High-precision gigahertz-to-terahertz spectroscopy of aqueous salt solutions as a probe of the femtosecond-to-picosecond dynamics of liquid water

Because it is sensitive to fluctuations occurring over femtoseconds to picoseconds, gigahertz-to-terahertz dielectric relaxation spectroscopy can provide a valuable window into water's most rapid intermolecular motions. In response, we have built a vector network analyzer dielectric spectrometer capable of measuring absorbance and index of refraction in this frequency regime with unprecedented precision. Using this to determine the complex dielectric response of water and aqueous salt solutions from 5.9 GHz to 1.12 THz (which we provide in the SI), we have obtained strong new constraints on theories of water's collective dynamics. For example, while the salt-dependencies we observe for water's two slower relaxations (8 and 1 ps) are easily reconciled with suggestions that they arise due to rotations of fully and partially hydrogen bonded molecules, respectively, the salt-dependence of the fastest relaxation (180 fs) appears difficult to reconcile with its prior assignment to liberations of single hydrogen bonds.Comment: 14 pages, 3 figures, Published in Journal of Chemical Physic

Nucleation phenomena in protein folding: The modulating role of protein sequence

For the vast majority of naturally occurring, small, single domain proteins folding is often described as a two-state process that lacks detectable intermediates. This observation has often been rationalized on the basis of a nucleation mechanism for protein folding whose basic premise is the idea that after completion of a specific set of contacts forming the so-called folding nucleus the native state is achieved promptly. Here we propose a methodology to identify folding nuclei in small lattice polymers and apply it to the study of protein molecules with chain length N=48. To investigate the extent to which protein topology is a robust determinant of the nucleation mechanism we compare the nucleation scenario of a native-centric model with that of a sequence specific model sharing the same native fold. To evaluate the impact of the sequence's finner details in the nucleation mechanism we consider the folding of two non- homologous sequences. We conclude that in a sequence-specific model the folding nucleus is, to some extent, formed by the most stable contacts in the protein and that the less stable linkages in the folding nucleus are solely determined by the fold's topology. We have also found that independently of protein sequence the folding nucleus performs the same `topological' function. This unifying feature of the nucleation mechanism results from the residues forming the folding nucleus being distributed along the protein chain in a similar and well-defined manner that is determined by the fold's topological features.Comment: 10 Figures. J. Physics: Condensed Matter (to appear

Thermodynamically Important Contacts in Folding of Model Proteins

We introduce a quantity, the entropic susceptibility, that measures the thermodynamic importance-for the folding transition-of the contacts between amino acids in model proteins. Using this quantity, we find that only one equilibrium run of a computer simulation of a model protein is sufficient to select a subset of contacts that give rise to the peak in the specific heat observed at the folding transition. To illustrate the method, we identify thermodynamically important contacts in a model 46-mer. We show that only about 50% of all contacts present in the protein native state are responsible for the sharp peak in the specific heat at the folding transition temperature, while the remaining 50% of contacts do not affect the specific heat.Comment: 5 pages, 5 figures; to be published in PR

Microsecond folding dynamics of the F13W G29A mutant of the B domain of staphylococcal protein A by laser-induced temperature jump

The small size (58 residues) and simple structure of the B domain of staphylococcal protein A (BdpA) have led to this domain being a paradigm for theoretical studies of folding. Experimental studies of the folding of BdpA have been limited by the rapidity of its folding kinetics. We report the folding kinetics of a fluorescent mutant of BdpA (G29A F13W), named F13W*, using nanosecond laser-induced temperature jump experiments. Automation of the apparatus has permitted large data sets to be acquired that provide excellent signal-to-noise ratio over a wide range of experimental conditions. By measuring the temperature and denaturant dependence of equilibrium and kinetic data for F13W*, we show that thermodynamic modeling of multidimensional equilibrium and kinetic surfaces is a robust method that allows reliable extrapolation of rate constants to regions of the folding landscape not directly accessible experimentally. The results reveal that F13W* is the fastest-folding protein of its size studied to date, with a maximum folding rate constant at 0 M guanidinium chloride and 45°C of 249,000 (s-1). Assuming the single-exponential kinetics represent barrier-limited folding, these data limit the value for the preexponential factor for folding of this protein to at least ≈2 x 10(6) s(-1)

Role of Secondary Motifs in Fast Folding Polymers: A Dynamical Variational Principle

A fascinating and open question challenging biochemistry, physics and even geometry is the presence of highly regular motifs such as alpha-helices in the folded state of biopolymers and proteins. Stimulating explanations ranging from chemical propensity to simple geometrical reasoning have been invoked to rationalize the existence of such secondary structures. We formulate a dynamical variational principle for selection in conformation space based on the requirement that the backbone of the native state of biologically viable polymers be rapidly accessible from the denatured state. The variational principle is shown to result in the emergence of helical order in compact structures.Comment: 4 pages, RevTex, 4 eps figure

Protein structures and optimal folding emerging from a geometrical variational principle

Novel numerical techniques, validated by an analysis of barnase and chymotrypsin inhibitor, are used to elucidate the paramount role played by the geometry of the protein backbone in steering the folding to the correct native state. It is found that, irrespective of the sequence, the native state of a protein has exceedingly large number of conformations with a given amount of structural overlap compared to other compact artificial backbones; moreover the conformational entropies of unrelated proteins of the same length are nearly equal at any given stage of folding. These results are suggestive of an extremality principle underlying protein evolution, which, in turn, is shown to be associated with the emergence of secondary structures.Comment: Revtex, 5 pages, 5 postscript figure

Modeling study on the validity of a possibly simplified representation of proteins

The folding characteristics of sequences reduced with a possibly simplified representation of five types of residues are shown to be similar to their original ones with the natural set of residues (20 types or 20 letters). The reduced sequences have a good foldability and fold to the same native structure of their optimized original ones. A large ground state gap for the native structure shows the thermodynamic stability of the reduced sequences. The general validity of such a five-letter reduction is further studied via the correlation between the reduced sequences and the original ones. As a comparison, a reduction with two letters is found not to reproduce the native structure of the original sequences due to its homopolymeric features.Comment: 6 pages with 4 figure