| X-Ray Structure Determination of Three Mutants of the Bacterial Photosynthetic Reaction Centers from Rb. sphaeroides Structure, Volume 12, Issue 4, 1 April 2004, Pages 703-715 Qiang Xu, Herbert L. Axelrod, Edward C. Abresch, Mark L. Paddock, Melvin Y. Okamura and George Feher Summary In the photosynthetic reaction center (RC) from , the reduction of a bound quinone molecule Q is coupled with proton uptake. When Asp-L213 is replaced by Asn, proton transfer is inhibited. Proton transfer was restored by two second-site revertant mutations, Arg-M233→Cys and Arg-H177→His. Kinetic effects of Cd on proton transfer showed that the entry point in revertant RCs to be the same as in the native RC. The structures of the parental and two revertant RCs were determined at resolutions of 2.10, 1.80, and 2.75 Å. From the structures, we were able to delineate alternate proton transfer pathways in the revertants. The main changes occur near Glu-H173, which allow it to substitute for the missing Asp-L213. The electrostatic changes near Glu-H173 cause it to be a good proton donor and acceptor, and the structural changes create a cavity which accommodates water molecules that connect Glu-H173 to other proton transfer components. Summary | Full Text | PDF (386 kb) |
| Spectroscopic and Molecular Dynamics Evidence for a Sequential Mechanism for the A-to-B Transition in DNA Biophysical Journal, Volume 95, Issue 1, 1 July 2008, Pages 257-272 Kelly M. Knee, Surjit B. Dixit, Colin Echeverría Aitken, Sergei Ponomarev, D.L. Beveridge and Ishita Mukerji Abstract The A-to-B form transition has been examined in three DNA duplexes, d(CGCGAATTCGCG), d(CGCGAATTGCGC), and d(CGCAAATTTCGC), using circular dichroism spectroscopy, ultraviolet resonance Raman (UVRR) spectroscopy, and molecular dynamics (MD) simulation. Circular dichroism spectra confirm that these molecules adopt the A form under conditions of reduced water activity. UVRR results, obtained under similar conditions, suggest that the transition involves a series of intermediate forms between A and B. Cooperative and distinct transitions were observed for the bases and the sugars. Independent MD simulations on d(CGCGAATTCGCG) show a spontaneous change from the A to B form in aqueous solution and describe a kinetic model that agrees well with UVRR results. Based on these observations, we predict that the mechanism of the transition involves a series of A/B hybrid forms and is sequential in nature, similar to previous crystallographic studies of derivatized duplexes. A simulation in which waters were restrained in the major groove of B DNA shows a rapid, spontaneous change from B to A at reduced water activity. These results indicate that a quasiergodic sampling of the solvent distribution may be a problem in going from B to A at reduced water activity in the course of an MD simulation. Abstract | Full Text | PDF (2029 kb) |
| Loss of tumorigenicity correlates with a reduction in pp60 kinase activity in a revertant subclone of avian sarcoma virus-infected field vole cells Cell, Volume 23, Issue 3, 1 March 1981, Pages 815-823 Alan F. Lau, Richard A. Krzyzek and Anthony J. Faras Summary We have recently isolated an interesting revertant subclone (revertant 866-4) of ESV-infected field vole cells that is indistinguishable from uninfected vole cells with respect to its lack of transformed cell properties. These revertants are not only normal morphologically, but they do not grow in soft agar and are nontumorigenic in athymic nude mice. Despite this lack of transformed cell properties, we have found that this cell line still contains pp60 at concentrations (0.30 μg/mg cell protein) similar to those (0.13–0.42 μg/mg cell protein) found in transformed and morphologically reverted, but tumorigenic vole cells (partial revertants). However, the most interesting aspect of this newly isolated subclone is the marked reduction in its pp60 kinase activity (2–3%) when compared with the specific activity of pp60 immunoprecipitated from transformed and partially revertant vole cell lines. Since the reduction in pp60 kinase activity strongly correlates with the loss of tumorigenicity in this particular revertant cell line, these data support the contention that this enzymatic activity is a crucial factor in the tumorigenic conversion of cells by avian sarcoma virus. Proteolytic peptide analysis of the structure of pp60 from revertant 866–4 indicates that it is similar to pp60 obtained from avian sarcoma virus-transformed chick embryo fibroblasts. Moreover, the reduction in kinase activity does not appear to be due to a lack of phosphorylation of the tyrosine residue in pp60. Thus neither an obvious structural alteration nor a reduction in phosphorylation of pp60 appears responsible for the reduced kinase activity observed, suggesting that some as of yet undetermined feature of pp60 can influence the pp60 phosphorylating event. Summary | PDF (2320 kb) |
Copyright © 1995 The Biophysical Society. All rights reserved.
Biophysical Journal, Volume 69, Issue 6, 2703-2709, 1 December 1995
doi:10.1016/S0006-3495(95)80141-4
Research Article
S.W. Chi, G.S. Yi, J.Y. Suh, B.S. Choi and H. Kim
Recently we reported (Yi et al., 1994) that the alpha-helical content of the signal peptide of Escherichia coli ribose binding protein, when determined by circular dichroism (CD) and two-dimensional NMR in trifluoroethanol/water solvent, is higher than that of its nonfunctional mutant signal peptide. In the present investigation, the structures of the signal peptides of two revertant ribose binding proteins in the same solvent were also determined with CD and two-dimensional 1H NMR spectroscopy. According to the CD results, both of these revertant signal peptides showed an intermediate helicity between those of wild-type and mutant signal peptides, the helical content of the revertant peptide with higher recovery of the translocation capability being higher. On the other hand, the alpha-helix regions of the wild-type and the revertant peptides as determined by NMR were shown to be the same. This discrepancy may be due to the difference in stability between identical alpha-helical stretches in wild-type and revertant peptides. A good correlation was observed between the helical content of these four ribose binding protein signal peptides in TFE/water as studied by CD and their in vivo translocation activities. It appears, therefore, that both the proper length of the helix and the stability are of functional significance.