Enzyme-mediated reactions may proceed through multiple intermediate conformational states before creating a final product molecule, and one often wishes to identify such intermediate structures from observations of the product creation. In this paper, we address this problem by solving the chemical master equations for various enzymatic reactions. We devise a perturbation theory analogous to that used in quantum mechanics that allows us to determine the first (<n>) and the second (variance) cumulants of the distribution of created product molecules as a function of the substrate concentration and the kinetic rates of the intermediate processes. The mean product flux V=d<n>/dt (or 'dose-response' curve) and the Fano factor F=variance/<n> are both realistically measurable quantities, and while the mean flux can often appear the same for different reaction types, the Fano factor can be quite different. This suggests both qualitative and quantitative ways to discriminate between different reaction schemes, and we explore this possibility in the context of four sample multistep enzymatic reactions. We argue that measuring both the mean flux and the Fano factor can not only discriminate between reaction types, but can also provide some detailed information about the internal, unobserved kinetic rates, and this can be done without measuring single-molecule transition events.
Date: January 1, 2008
Creator: Nemenman, Ilya; Sinitsyn, Nikolai A; De Ronde, Wiet H; Daniels, Bryan C & Mugler, Andrew
XPG is a structure-specific endonuclease required for nucleotide excision repair (NER). XPG incision defects result in the cancer-prone syndrome xeroderma pigmentosum, whereas truncating mutations of XPG cause the severe postnatal progeroid developmental disorder Cockayne syndrome. We show that XPG interacts directly with WRN protein, which is defective in the premature aging disorder Werner syndrome, and that the two proteins undergo similar sub-nuclear redistribution in S-phase and co-localize in nuclear foci. The co-localization was observed in mid- to late-S-phase, when WRN moves from nucleoli to nuclear foci that have been shown to contain protein markers of both stalled replication forks and telomeric proteins. We mapped the interaction between XPG and WRN to the C-terminal domains of each and show that interaction with the C-terminal domain of XPG strongly stimulates WRN helicase activity. WRN also possesses a competing DNA single-strand annealing activity that, combined with unwinding, has been shown to coordinate regression of model replication forks to form Holliday junction/chicken foot intermediate structures. We tested whether XPG stimulated WRN annealing activity and found that XPG itself has intrinsic strand annealing activity that requires the unstructured R- and C-terminal domains, but not the conserved catalytic core or endonuclease activity. Annealing by XPG is cooperative, rather than additive, with WRN annealing. Taken together, our results suggest a novel function for XPG in S-phase that is at least in part carried out coordinately with WRN, and which may contribute to the severity of the phenotypes that occur upon loss of XPG.
Date: April 20, 2011
Creator: Trego, Kelly S.; Chernikova, Sophia B.; Davalos, Albert R.; Perry, J. Jefferson P.; Finger, L. David; Ng, Cliff et al.
Because of its excellent energy resolution, ORELA is particularly well suited for measurements in the resolved resonance region that impact nuclear reaction model calculations. These measurements allow the determination of average level widths, level densities, and cross sections for potential scattering and radiative capture. These quantities can be used to determine parameters in reaction models (such as the optical model and Hauser-Feshbach calculations) and to understand the limitations imposed on these models. Particular attention is given to the importance of improved experimental data to characterize intermediate structure (or doorway states).
Some years ago, Perez and de Saussure reported evidence for intermediate structure in the radiative capture cross sections of /sup 238/U. More recently, these and additional data, obtained by a different experimental technique but which showed the same non-statistical behavior, were analyzed by Perez et al. Under the assumption that the structure could be attributed to doorway states in the p/sup 3/2/ neutron channel. The results of an experimental determination of the parity of the structure, using neutron capture-gamma ray spectroscopy are reported. Much of the structure below 50 keV appears to be due to s-wave interactions. The magnitude of the fluctuations is much larger than can be calculated with the usual unresolved - resonance treatment unless the average neutron and radiative-capture widths are correlated. It is shown that such an apparent correlation can arise as a result of multiple-scattering enhancement of radiative capture in the samples used, and it is concluded that the evidence for intermediate structure in the capture of neutrons by /sup 238/U is not yet firmly established.
Date: January 1, 1981
Creator: Moore, M. S.; Corvi, F.; Mewissen, L. & Poortmans, F.
Recent experimental and theoretical investigations have led to the characterization of a new reaction mechanism called quasi-fission. This process is characterized by the emergence of fission-like fragments, which do not originate from the fission decay of a compound nucleus formed by heavy-ion fusion, but rather from the break up of a short-lived intermediate complex. The occurrence of quasi-fission processes appear to be limited to heavy reaction systems and/or large angular momenta, although the present work demonstrates that such reactions occur for somewhat lighter projectiles than previously believed. It is thus shown that measurements of fragment angular distributions provide a signature for quasifission by being sensitive to whether or not a compound nucleus was formed during the reaction. From an analysis of such data it is concluded that the possibilities for synthesizing super-heavy elements in the range Z=112-116 are reduced considerably over previous estimates.
It appears that the system we have studied here, /sup 24/Mg(/sup 16/O,/sup 12/C)/sup 28/Si representing /sup 40/Ca as the composite nucleus, is perhaps the heaviest one that exhibits strong enough resonances that quantitative measurements may be contemplated. But we have uncovered only a small corner of what is there and even within this system a huge amount of work remains. The nature of these resonances is not yet clear. The sequence may perhaps have an explanation that is schematically outlined, namely that there are several families of quasistationary states in /sup 40/Ca, but that the slopes of these families do not necessarily coincide with the slope of the grazing partial waves that provide us with a narrow transparent strip of a window on the underlying structure of the nucleus. We must concentrate a lot of effort and ingenuity in order to maximize the information we gather through this window and only then may we hope to sensibly attempt forming hypotheses about the underlying simple pattern.
Evidence is presented for the formation of a long-lived rotating dinuclear complex in the early stages of the collision between light heavy nuclei. A study of the variation of the total kinetic energy of the outgoing fragments with bombarding energy allows a determination of the average dinuclear separation prior to scission. At higher bombarding energies the study reveals that the system of the two colliding nuclei has reached a critical value of angular momentum beyond which it can not be trapped into an orbiting configuration.
Date: January 1, 1983
Creator: Shapira, D.; Erb, K.A.; Ford, J.L.C. Jr.; Gomez del Campo, J.; Shivakumar, B.; Novotny, R. et al.
Evidence for the existence of intermediate structure in the unresolved resonance fission and capture cross sections of /sup 235/U and in the capture cross section of /sup 238/U is reviewed. Certain of the statistical tests that have been used are known to be compromised by finite resolution when applied to unresolved resonance data, but it is concluded that over most of the energy range the test results are valid. Parity assignments for the structure in /sup 238/U(n, ..gamma..) suggest that s-wave neutron absorption is responsible for much of the structure. If this is the case, the cross section fluctuations are most likely due to fluctuations in the radiative capture width, rather than in the neutron width. Finally, the practical effect of the possible presence of width correlations in fertile and fissile nuclides is addressed. 1 figure, 1 table.
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