Rate constants measured for hydrated electron reactions with peptides and proteins

Effects of ionizing radiation on the amino acids of proteins and the reactivity of the protonated amino group depends upon the pK subscript a of the group. Estimates of the rate constants for reactions involving the amino acid side chains are presented. These rate constants gave an approximate rate constant for three different protein molecules

ATPase mechanism of the 5'-3' DNA helicase, RecD2: evidence for a pre-hydrolysis conformation change

The superfamily 1 helicase, RecD2, is a monomeric, bacterial enzyme with a role in DNA repair, but with 5'-3' activity unlike most enzymes from this superfamily. Rate constants were determined for steps within the ATPase cycle of RecD2 in the presence of ssDNA. The fluorescent ATP analog, mantATP (2'(3')-O-(N-methylanthraniloyl)ATP), was used throughout to provide a complete set of rate constants and determine the mechanism of the cycle for a single nucleotide species. Fluorescence stopped-flow measurements were used to determine rate constants for adenosine nucleotide binding and release, quenched-flow measurements were used for the hydrolytic cleavage step, and the fluorescent phosphate biosensor was used for phosphate release kinetics. Some rate constants could also be measured using the natural substrate, ATP, and these suggested a similar mechanism to that obtained with mantATP. The data show that a rearrangement linked to Mg(2+) coordination, which occurs before the hydrolysis step, is rate-limiting in the cycle and that this step is greatly accelerated by bound DNA. This is also shown here for the PcrA 3'-5' helicase and so may be a general mechanism governing superfamily 1 helicases. The mechanism accounts for the tight coupling between translocation and ATPase activity

Rate constants for diffusive processes by partial path sampling

We introduce a path sampling method for the computation of rate constants for systems with a highly diffusive character. Based on the recently developed algorithm of transition interface sampling (TIS) this procedure increases the efficiency by sampling only parts of complete transition trajectories confined within a certain region. The algorithm assumes the loss of memory for highly diffusive progression along the reaction coordinate. We compare the new technique to the TIS method for a simple diatomic system and show that the computation time of the new method scales linearly, instead of quadraticaly, with the length of the diffusive barrier. The validity of the memory loss assumption is also discussed.Comment: 12 pages, including 8 figures, RevTeX

Mechanistic studies on DNA damage by minor groove binding copper–phenanthroline conjugates

Copper–phenanthroline complexes oxidatively damage and cleave nucleic acids. Copper bis-phenanthroline and copper complexes of mono- and bis-phenanthroline conjugates are used as research tools for studying nucleic acid structure and binding interactions. The mechanism of DNA oxidation and cleavage by these complexes was examined using two copper–phenanthroline conjugates of the sequence-specific binding molecule, distamycin. The complexes contained either one or two phenanthroline units that were bonded to the DNA-binding domain through a linker via the 3-position of the copper ligand. A duplex containing independently generated 2-deoxyribonolactone facilitated kinetic analysis of DNA cleavage. Oxidation rate constants were highly dependent upon the ligand environment but rate constants describing elimination of the alkali-labile 2-deoxyribonolactone intermediate were not. Rate constants describing DNA cleavage induced by each molecule were 11–54 times larger than the respective oxidation rate constants. The experiments indicate that DNA cleavage resulting from β-elimination of 2-deoxyribonolactone by copper–phenanthroline complexes is a general mechanism utilized by this family of molecules. In addition, the experiments confirm that DNA damage mediated by mono- and bis-phenanthroline copper complexes proceeds through distinct species, albeit with similar outcomes

Universal rate constants for reactive collisions of ultracold molecules

A simple quantum defect model gives analytic expressions for the complex scattering length and threshold collision rates of ultracold molecules. If the probability of reaction in the short-range part of the collision is high, the model gives universal rate constants for s- and p-wave collisions that are independent of short-range dynamics. This model explains the magnitudes of the recently measured rate constants for collisions of two ultracold 40K87Rb molecules, or an ultracold 40K atom with the 40K87Rb molecule [Ospelkaus et al., Science 327, 853 (2010)].Comment: 4 pages, 2 figures; v2: final version, accepted for publication in Physical Review Letter

Invariant Manifolds and Rate Constants in Driven Chemical Reactions

Reaction rates of chemical reactions under nonequilibrium conditions can be determined through the construction of the normally hyperbolic invariant manifold (NHIM) [and moving dividing surface (DS)] associated with the transition state trajectory. Here, we extend our recent methods by constructing points on the NHIM accurately even for multidimensional cases. We also advance the implementation of machine learning approaches to construct smooth versions of the NHIM from a known high-accuracy set of its points. That is, we expand on our earlier use of neural nets, and introduce the use of Gaussian process regression for the determination of the NHIM. Finally, we compare and contrast all of these methods for a challenging two-dimensional model barrier case so as to illustrate their accuracy and general applicability.Comment: 28 pages, 13 figures, table of contents figur