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To determine whether Forster resonance energy transfer (FRET) measurements can provide quantitative distance information in single-molecule fluorescence experiments on polypeptides, we measured FRET efficiency distributions for donor and acceptor dyes attached to the ends of freely diffusing polyproline molecules of various lengths. The observed mean FRET(More)
A hybrid analysis that combines the maximum entropy method (MEM) with nonlinear least squares (NLS) fitting has been developed to interpret a general time-dependent signal. Data that include processes of opposite sign and a slow baseline drift can be inverted to obtain both a continuous distribution of lifetimes and a sum of discrete exponentials. Fits by(More)
In cell lines from advanced lung cancer, breast cancer, and melanoma, endogenous tensin-3 contributes to cell migration, anchorage-independent growth, and tumorigenesis. Although SH2 domains have not been reported previously to be phosphorylated, the tensin-3 SH2 domain is a physiologic substrate for Src. Tyrosines in the SH2 domain contribute to the(More)
Rate processes in proteins are often not adequately described by simple exponential kinetics. Instead of modeling the kinetics in the time domain, it can be advantageous to perform a numerical inversion leading to a rate distribution function f(lambda). The features observed in f(lambda) (number, positions, and shapes of peaks) can then be interpreted. We(More)
We describe solid state NMR measurements on frozen solutions of the complex of the 24-residue HIV-1 gp120 V3 loop peptide RP135 with the Fab fragment of the anti-gp120 antibody 0.5beta, using rotational echo double resonance (REDOR). In order to probe possible hydrogen bonding between arginine side chains and glycine backbone carbonyls in the region of the(More)
Ribonucleases H have mostly been implicated in eliminating short RNA primers used for initiation of lagging strand DNA synthesis. Escherichia coli RNase HI cleaves these RNA-DNA hybrids in a distributive manner. We report here that eukaryotic RNases H1 have evolved to be processive enzymes by attaching a duplex RNA-binding domain to the RNase H region.(More)
A bootstrapped model is used to improve the lifetime distribution recovered using the maximum entropy method from kinetics that involves overlapping exponential and distributed phases. The model defaulted to in the limit of low signal-to-noise is iteratively derived from the data to counter the tendency of regularization methods to over-smooth sharp(More)
The maximum entropy method (MEM) has been used in many studies to reliably recover effective lifetimes from kinetics, whether measured experimentally or simulated computationally. Here, recent claims made by Mulligan et al. regarding MEM analyses of kinetics (Anal. Biochem. 421 (2012) 181-190) are shown to be unfounded. Their assertion that their software(More)
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