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We present a unified framework for extracting kinetic information from single-molecule pulling experiments at constant force or constant pulling speed. Our procedure provides estimates of not only (i) the intrinsic rate coefficient and (ii) the location of the transition state but also (iii) the free energy of activation. By analyzing simulated data, we(More)
Laser tweezers and atomic force microscopes are increasingly used to probe the interactions and mechanical properties of individual molecules. Unfortunately, using such time-dependent perturbations to force rare molecular events also drives the system away from equilibrium. Nevertheless, we show how equilibrium free energy profiles can be extracted(More)
Dynamic force spectroscopy probes the kinetic and thermodynamic properties of single molecules and molecular assemblies. Here, we propose a simple procedure to extract kinetic information from such experiments. The cornerstone of our method is a transformation of the rupture-force histograms obtained at different force-loading rates into the force-dependent(More)
A method is presented for the determination of values of the spectral density function, J(omega), describing the dynamics of amide bond vectors from 15N relaxation parameters alone. Assuming that the spectral density is given by the sum of Lorentzian functions, the approach allows values of J(omega) to be obtained at omega = 0, omega N and 0.870 omega H,(More)
Regular physical activity plays a crucial role in health maintenance and disease prevention. However, excessive exercise has the potential to have adverse effects on both physical and mental health. The scholastic and empirical discussion of excessive physical activity focuses on obsessive and compulsive exercising, and uses several labels. However, in this(More)
Innate immunity and urinary tract response play a central role in the development of urinary tract infection (UTI). Heat shock protein (HSP) 72 and Toll-like receptor (TLR) 4 are among the key elements of innate defence mechanisms. This study assesses the role of HSPA1B A(1267)G and TLR4 A(896)G polymorphisms using allele-specific polymerase chain reaction(More)
Mechanical forces exerted by laser tweezers or atomic force microscopes can be used to drive rare transitions in single molecules, such as unfolding of a protein or dissociation of a ligand. The phenomenological description of pulling experiments based on Bell's expression for the force-induced rupture rate is found to be inadequate when tested against(More)
Enzymes are dynamic entities: both their conformation and catalytic activity fluctuate over time. When such fluctuations are relatively fast, it is not surprising that the classical Michaelis-Menten (MM) relationship between the steady-state enzymatic velocity and the substrate concentration still holds. However, recent single-molecule experiments have(More)
How fast can a protein fold? The rate of polypeptide collapse to a compact state sets an upper limit to the rate of folding. Collapse may in turn be limited by the rate of intrachain diffusion. To address this question, we have determined the rate at which two regions of an unfolded protein are brought into contact by diffusion. Our nanosecond-resolved(More)