Single chain force spectroscopy - Reading the sequence of HP protein models

We study the elastic properties of single A/B random copolymer chains, with a specific sequence and use them as theoretical model for so called HP proteins. HP proteins carry hydrophilic (P) and hydrophobic (H) monomers. We predict a rich structure in the force-extension relations which can be attributed to the information in the sequence. The variational method is used to probe local minima on the path of stretching and releasing for the chain molecules. At a given force, we find multiple configurations which are separated by energy barriers. A collapsed globular configuration consists of several domains which unravel cooperatively. Upon stretching, the unfolding path shows a stepwise pattern corresponding to the unfolding of each domain. While releasing, several cores can be created simultaneously in the middle of the chain, resulting in a different path of collapse. The long-range interactions and stiffness of the chain simplify the potential landscape given by the disorder in sequence. Received 5 March 2002 / Received in final form 16 May 2002 Published online 13 August 2002     

Structural transition of the human lymphocyte plasma membrane: an ESR approach

Summary The electron spin resonance spectroscopy and the spin label technique have been used to study the thermotropic structural transition of the plasma membrane ofin toto human peripheral blood lymphocytes in the temperature range (25÷41)°C. A discontinuity in the plot probe order parametervs. temperature, at a temperature of about 31°C, is observed. This discontinuity is upward shifted to a temperature of 35°C in the presence of staphylococcal enterotoxinB and is no longer observed when using isolated plasma membrane. These results are interpreted as being due to a change in the structural properties of the lipid phase of plasma membrane during the activation of the lymphocyte cells.     

Stochastic resonance in perspective

Summary We outline the historical development of stochastic resonance (SR), a phenomenon in which the signal and/or the signal-to-noise ratio in a nonlinear system increase with increasing intensity of noise. We discuss basic theoretical ideas explaining and describing SR, and we review some revealing experimental data that place SR within the wider context of statistical physics. We emphasize the close relationship of SR to some effects that are well known in condensed-matter physics. Paper presented at the International Workshop ?Fluctuations in Physics and Biology: Stochastic Resonance, Signal Processing and Related Phenomena?, Elba, 5–10 June 1994.     

Statistical mechanics of warm and cold unfolding in proteins

We present a statistical mechanics treatment of the stability of globular proteins which takes explicitly into account the coupling between the protein and water degrees of freedom. This allows us to describe both the cold and the warm unfolding, thus qualitatively reproducing the known thermodynamics of proteins. Received: 19 March 1998 / Revised and Accepted: 25 May 1998     

Phase equilibria in polymer/solvent systems. Part V: Thermodynamic theory of the swelling pressure equilibrium of a crosslinked substance with a solvent in various phases

A thermodynamic theory has been developed to define the swelling pressure equilibrium between a homogeneous gel and a pure solvent, where phase transitions of the solvent, such as evaporation and crystallization can occur. It is shown that the equilibrium curve, which describes the temperature dependence of the composition in the gel phase under the condition of a constant swelling pressure, has distinct bends at the transition temperatures. These bends are related to the enthalpies of transition of the pure solvent at the transition temperatures. As a consequence of the phase transition of the solvent the swelling pressure-temperature curve at constant composition of the gel shows a discontinuous behavior at the transition point. Numerical calculations with a modified Flory-Huggins expression, based on results of swelling and deswelling measurements of the system crosslinked PEG/water, are presented.The discussion includes natural systems, which are in the gel state, where water may crystallize in the extracellular space.     

Stochastic detection of motor protein-RNA complexes by single-channel current recording.

A label- and immobilization-free approach to detecting the reversible formation of complexes between nucleic acids and proteins at the single-molecule level is described. The voltage-driven translocation of individual oligoribonucleotides through a nanoscale protein pore is observed by single-channel current recordings. The oligoribonucleotide 5'-C25A(25)-3' gives rise to current blockades with an average duration of approximately 0.5 ms. In the presence of the RNA-binding ATPase P4, a viral packaging motor from bacteriophage phi8, longer events of tens to hundreds of milliseconds are observed. Upon addition of ATP the long events disappear, indicating the dissociation of the P4RNA complex. The frequency of events also depends on the concentration of P4 and the length of the oligoribonucleotide, thereby confirming the specificity of the P4RNA events. This study shows that single-channel current recordings can be used to monitor RNA-protein complex formation, thus opening up a new means to examine the motor activity of RNA- or DNA-processing enzymes.     

Pulsed EPR Dipolar Spectroscopy under the Breakdown of the High-Field Approximation: The High-Spin Iron(III) Case

Pulsed EPR dipolar spectroscopy (PDS) offers several methods for measuring dipolar coupling and thus the distance between electron-spin centers. To date, PDS measurements to metal centers were limited to ions that adhere to the high-field approximation. Here, the PDS methodology is extended to cases where the high-field approximation breaks down on the example of the high-spin Fe³⁺/nitroxide spin-pair. First, the theory developed by Maryasov et al. (Appl. Magn. Reson. 2006 , 30, 683–702) was adapted to derive equations for the dipolar coupling constant, which revealed that the dipolar spectrum does not only depend on the length and orientation of the interspin distance vector with respect to the applied magnetic field but also on its orientation to the effective g-tensor of the Fe³⁺ ion. Then, it is shown on a model system and a heme protein that a PDS method called relaxation-induced dipolar modulation enhancement (RIDME) is well-suited to measuring such spectra and that the experimentally obtained dipolar spectra are in full agreement with the derived equations. Finally, a RIDME data analysis procedure was developed, which facilitates the determination of distance and angular distributions from the RIDME data. Thus, this study enables the application of PDS to for example, the highly relevant class of high-spin Fe³⁺ heme proteins.     

Extending the Sensitivity of CEST NMR Spectroscopy to Micro-to-Millisecond Dynamics in Nucleic Acids Using High-Power Radio-Frequency Fields

Biomolecules undergo motions on the micro-to-millisecond timescale to adopt low-populated transient states that play important roles in folding, recognition, and catalysis. NMR techniques, such as Carr–Purcell–Meiboom–Gill (CPMG), chemical exchange saturation transfer (CEST), and R_1ρ are the most commonly used methods for characterizing such transitions at atomic resolution under solution conditions. CPMG and CEST are most effective at characterizing motions on the millisecond timescale. While some implementations of the R_1ρ experiment are more broadly sensitive to motions on the micro-to-millisecond timescale, they entail the use of selective irradiation schemes and inefficient 1D data acquisition methods. Herein, we show that high-power radio-frequency fields can be used in CEST experiments to extend the sensitivity to faster motions on the micro-to-millisecond timescale. Given the ease of implementing high-power fields in CEST, this should make it easier to characterize micro-to-millisecond dynamics in biomolecules.