A Proton Magnetic Resonance Study of the Association of Lysozyme with Monosaccharide Inhibitors

It has been shown that the acetamido methyl protons of N-acetyl-d-glucosamine undergo a chemical shift to higher fields in their proton magnetic resonance spectrum when the inhibitor is bound to lysozyme. The observed chemical shift in the presence of the enzyme is different for the agr- and ß-anomeric forms of 2-acetamido-2-deoxy-d-glucopyranose indicating either a difference in the affinity of the anomeric forms for lysozyme or different magnetic environments for the methyl protons in their enzyme-bound state. That the agr- and ß-anomeric forms of GlcAc bind to lysozyme in a competitive fashion was indicated by observing the proton magnetic resonance spectra in the presence of 2-acetamido-d3-2-deoxy-agr-d-glucopyranose. The methyl glycosides, methyl-agr-GlcAc and methyl-ß-GlcAc, were also shown to bind competitively with both anomers of GlcAc. Quantitative analysis of the chemical shift data observed for the association of GlcAc with lysozyme was complicated by the mutarotation of GlcAc between its agr- and ß-anomeric forms. However, in the case of the methyl glucosides, where the conformation of each anomer is frozen, it was possible to analyze the chemical shift data in a straightforward manner, and the dissociation constant as well as the chemical shift of the acetamido methyl protons of the enzyme-inhibitor complex was determined for both anomers. The results indicate that the two anomers of methyl-GlcAc bind to lysozyme with slightly different affinities but that the acetamido methyl groups of both anomers experience identical magnetic environments in the enzyme-inhibitor complex

Studies related to primitive chemistry. A proton and nitrogen-14 nuclear magnetic resonance amino acid and nucleic acid constituents and a and their possible relation to prebiotic

Preliminary proton nuclear magnetic resonance (NMR) studies were made to determine the applicability of this technique for the study of interactions between monomeric and polymeric amino acids with monomeric nucleic acid bases and nucleotides. Proton NMR results for aqueous solutions (D2O) demonstrated interactions between the bases cytosine and adenine and acidic and aromatic amino acids. Solutions of 5'-AMP admixed with amino acids exhibited more complex behavior but stacking between aromatic rings and destacking at high amino acids concentration was evident. The multisite nature of 5'-AMP was pointed out. Chemical shift changes for adenine and 5'-AMP with three water soluble polypeptides demonstrated that significant interactions exist. It was found that the linewidth-pH profile of each amino acid is unique. It is concluded that NMR techniques can give significant and quantitative data on the association of amino acid and nucleic acid constituents

Poisson noise induced switching in driven micromechanical resonators

We study Poisson-noise induced switching between coexisting vibrational states in driven nonlinear micromechanical resonators. In contrast to Gaussian noise induced switching, the measured logarithm of the switching rate is proportional not to the reciprocal noise intensity, but to its logarithm, for fixed pulse area. We also find that the switching rate logarithm varies as a square root of the distance to the bifurcation point, instead of the conventional scaling with exponent 3/2.Comment: accepted by PR

On the interactions of lipids and proteins in the red blood cell membrane

The effects of temperature and of the action of a purified phospholipase C enzyme preparation on human red blood cell membranes has been investigated by chemical analyses, circular dichroism, and proton magnetic resonance measurements. The results indicate that a substantial fraction of the phospholipids and the proteins of the membranes can change structure independently of one another, suggesting a mosaic pattern for the organization of the lipids and proteins in membranes

More is Less: Perfectly Secure Oblivious Algorithms in the Multi-Server Setting

The problem of Oblivious RAM (ORAM) has traditionally been studied in a single-server setting, but more recently the multi-server setting has also been considered. Yet it is still unclear whether the multi-server setting has any inherent advantages, e.g., whether the multi-server setting can be used to achieve stronger security goals or provably better efficiency than is possible in the single-server case. In this work, we construct a perfectly secure 3-server ORAM scheme that outperforms the best known single-server scheme by a logarithmic factor. In the process, we also show, for the first time, that there exist specific algorithms for which multiple servers can overcome known lower bounds in the single-server setting.Comment: 36 pages, Accepted in Asiacrypt 201

Dynamic Set Intersection

Consider the problem of maintaining a family $F$ of dynamic sets subject to insertions, deletions, and set-intersection reporting queries: given $S,S'\in F$, report every member of $S\cap S'$ in any order. We show that in the word RAM model, where $w$ is the word size, given a cap $d$ on the maximum size of any set, we can support set intersection queries in $O(\frac{d}{w/\log^2 w})$ expected time, and updates in $O(\log w)$ expected time. Using this algorithm we can list all $t$ triangles of a graph $G=(V,E)$ in $O(m+\frac{m\alpha}{w/\log^2 w} +t)$ expected time, where $m=|E|$ and $\alpha$ is the arboricity of $G$. This improves a 30-year old triangle enumeration algorithm of Chiba and Nishizeki running in $O(m \alpha)$ time. We provide an incremental data structure on $F$ that supports intersection {\em witness} queries, where we only need to find {\em one} $e\in S\cap S'$. Both queries and insertions take O\paren{\sqrt \frac{N}{w/\log^2 w}} expected time, where $N=\sum_{S\in F} |S|$. Finally, we provide time/space tradeoffs for the fully dynamic set intersection reporting problem. Using $M$ words of space, each update costs $O(\sqrt {M \log N})$ expected time, each reporting query costs $O(\frac{N\sqrt{\log N}}{\sqrt M}\sqrt{op+1})$ expected time where $op$ is the size of the output, and each witness query costs $O(\frac{N\sqrt{\log N}}{\sqrt M} + \log N)$ expected time.Comment: Accepted to WADS 201

Energetic Components of Cooperative Protein Folding

A new lattice protein model with a four-helix bundle ground state is analyzed by a parameter-space Monte Carlo histogram technique to evaluate the effects of an extensive variety of model potentials on folding thermodynamics. Cooperative helical formation and contact energies based on a 5-letter alphabet are found to be insufficient to satisfy calorimetric and other experimental criteria for two-state folding. Such proteinlike behaviors are predicted, however, by models with polypeptide-like local conformational restrictions and environment-dependent hydrogen bonding-like interactions.Comment: 11 pages, 4 postscripts figures, Phys. Rev. Lett. (in press

Facile O-atom insertion into C-C and C-H bonds by a trinuclear copper complex designed to harness a singlet oxene

Two trinuclear copper [CuICuICuI(L)]1+ complexes have been prepared with the multidentate ligands (L) 3,3'-(1,4-diazepane-1,4-diyl)bis(1-((2-(dimethylamino)ethyl)(methyl)amino)propan-2-ol) (7-Me) and (3,3'-(1,4-diazepane-1,4-diyl)bis(1-((2-(diethylamino) ethyl)(ethyl) amino)propan-2-ol) (7-Et) as models for the active site of the particulate methane monooxygenase (pMMO). The ligands were designed to form the proper spatial and electronic geometry to harness a "singlet oxene," according to the mechanism previously suggested by our laboratory. Consistent with the design strategy, both [CuICuICuI(L)]1+ reacted with dioxygen to form a putative bis(µ3-oxo)CuIICuIICuIII species, capable of facile O-atom insertion across the central C-C bond of benzil and 2,3-butanedione at ambient temperature and pressure. These complexes also catalyze facile O-atom transfer to the C-H bond of CH3CN to form glycolonitrile. These results, together with our recent biochemical studies on pMMO, provide support for our hypothesis that the hydroxylation site of pMMO contains a trinuclear copper cluster that mediates C-H bond activation by a singlet oxene mechanism

Proton pumping in cytochrome c oxidase: The coupling between proton and electron gating

Comment on Bovine cytochrome c oxidase structures enable O2 reduction with minimization of reactive oxygens and provide a proton-pumping gate. [Proc Natl Acad Sci U S A. 2010