Extensive counter-ion interactions seen at the surface of subtilisin in an aqueous medium

The extent of protein and counter-ion interactions in solution is still far from being fully described and understood. In low dielectric media there is documented evidence that counter-ions do bind and affect enzymatic activity. However, published crystal structures of macromolecules of biological interest in aqueous solution often do not report the presence of any counter-ions on the surface. The extent of counter-ion interactions within subtilisin in an aqueous medium has been investigated crystallographically using CsCl soak and X-ray wavelength optimised anomalous diffraction at the Cs K-edge. Ten Cs+, as well as six Cl- sites, have been clearly identified, revealing that in aqueous salt solutions ions can bind at defined points around the protein surface. The counter-ions do not generally interact with formal charges on the protein; formally neutral oxygens, mostly backbone carbonyls, mostly coordinate the Cs+ ions. The Cl- ion sites are also found likely to be near positive charges on the protein surface. The presence of counter-ions substantially changes the protein surface electrical charge. The surface charge distribution on a protein is commonly discussed in relation to enzyme function. The correct identification of counter-ions associated with a protein surface is necessary for a proper understanding of an enzyme's function

GPCRTree: online hierarchical classification of GPCR function

Background: G protein-coupled receptors (GPCRs) play important physiological roles transducing extracellular signals into intracellular responses. Approximately 50% of all marketed drugs target a GPCR. There remains considerable interest in effectively predicting the function of a GPCR from its primary sequence. Findings: Using techniques drawn from data mining and proteochemometrics, an alignment-free approach to GPCR classification has been devised. It uses a simple representation of a protein's physical properties. GPCRTree, a publicly-available internet server, implements an algorithm that classifies GPCRs at the class, sub-family and sub-subfamily level. Conclusion: A selective top-down classifier was developed which assigns sequences within a GPCR hierarchy. Compared to other publicly available GPCR prediction servers, GPCRTree is considerably more accurate at every level of classification. The server has been available online since March 2008 at URL: http://igrid-ext.cryst.bbk.ac.uk/gpcrtree

Dalitz Plot Analysis of the Decay D^+ --> K^- pi^+ pi^+ and Indication of a Low-Mass Scalar K pi Resonance

We study the Dalitz plot of the decay D^+ --> K^- pi^+ pi^+ with a sample of 15090 events from Fermilab experiment E791. Modeling the decay amplitude as the coherent sum of known K pi resonances and a uniform nonresonant term, we do not obtain an acceptable fit. If we allow the mass and width of the K^*_0(1430) to float, we obtain values consistent with those from PDG but the chi^2 per degree of freedom of the fit is still unsatisfactory. A good fit is found when we allow for the presence of an additional scalar resonance, with mass 797 +/- 19 +/- 43 MeV/c^2 and width 410 +/- 43 +/- 87 MeV/c^2. The mass and width of the K^*_0(1430) become 1459 +/- 7 +/- 5 MeV/c^2 and 175 +/- 12 +/- 12 MeV/c^2, respectively. Our results provide new information on the scalar sector in hadron spectroscopy.Comment: Accepted for publication in Physical Review Letter

Search for the Flavor-Changing Neutral-Current Decays D+→π+μ+μ−D^+\to \pi^+ \mu^+ \mu^- and D+→π+e+e−D^+\to \pi^+ e^+ e^-

We report the results of a search for the flavor-changing neutral-current decays $D^+\rightarrow \pi^+ \mu^+ \mu^-$ and $D^+\rightarrow \pi^+ e^+ e^-$ in data from Fermilab charm hadroproduction experiment E791. No signal above background is found, and we obtain upper limits on branching fractions, $B(D^+\rightarrow \pi^+ \mu^+ \mu^-) < 1.8 \times 10^{-5}$ and $B(D^+\rightarrow \pi^+ e^+ e^-) < 6.6 \times 10^{-5}$, at the 90\% confidence level.Comment: nine pages with figures; compressed, uuencoded postscrip

Experimental evidence for a light and broad scalar resonance in D+→π−π+π+D^+\to \pi^-\pi^+\pi^+ decay

From a sample of $1172 \pm 61$ $D^+ \to \pi^- \pi^+ \pi^+$ decay, we find $\Gamma (D^+ \to \pi^- \pi^+ \pi^+) / \Gamma (D^+ \to K^- \pi^+ \pi^+) = 0.0311 \pm 0.0018 ^{+0.0016}_{-0.0026}$. Using a coherent amplitude analysis to fit the Dalitz plot of this decays, we find strong evidence that a scalar resonance of mass $478^{+24}_{-23} \pm 17$ MeV/$c^2$ and width $324^{+42}_{-40} \pm 21$ MeV/$c^2$ accounts for approximately half of all decays.Comment: 10 pages, 3 eps figure

Study of the Ds+→π−π+π+D^+_s \to \pi^- \pi^+ \pi^+ decay and measurement of f0f_0 masses and widths

From a sample of 848 $\pm$ 44 $D_s^+ \to \pi^- \pi^+ \pi^+$ decays, we find $\Gamma(D_s^+ \to \pi^- \pi^+ \pi^+) / \Gamma(D_s^+ \to \phi \pi^+) = 0.245 \pm 0.028^{+0.019}_{-0.012}$. Using a Dalitz plot analysis of this three body decay, we find significant contributions from the channels $\rho^0(770)\pi^+$, $\rho^0(1450)\pi^+$, $f_0(980)\pi^+$, $f_2(1270)\pi^+$, and $f_0(1370)\pi^+$. We present also the values obtained for masses and widths of the resonances $f_0(980)$ and $f_0(1370)$.Comment: 10 pages, 3 eps figure

Direct measurement of the pion valence quark momentum distribution, the pion light-cone wave function squared

We present the first direct measurements of the pion valence quark momentum distribution which is related to the square of the pion light-cone wave function. The measurements were carried out using data on diffractive dissociation of 500 GeV/c $\pi^-$ into di-jets from a platinum target at Fermilab experiment E791. The results show that the $|q\bar {q}>$ light-cone asymptotic wave function, which was developed using perturbative QCD methods, describes the data well for $Q^2 \sim 10 ~{\rm (GeV/c)^2}$ or more. We also measured the transverse momentum distribution of the diffractive di-jets.Comment: 13 pages, 4 figure

Asymmetries between the production of D+ and D- mesons from 500 GeV/c pi- nucleon interactions as a function of xF and pt**2

We present asymmetries between the production of D+ and D- mesons in Fermilab experiment E791 as a function of xF and pt**2. The data used here consist of 74,000 fully-reconstructed charmed mesons produced by a 500 GeV/c pi- beam on C and Pt foils. The measurements are compared to results of models which predict differences between the production of heavy-quark mesons that have a light quark in common with the beam (leading particles) and those that do not (non-leading particles). While the default models do not agree with our data, we can reach agreement with one of them, PYTHIA, by making a limited number of changes to parameters used

Branching Fractions for D0 -> K+K- and D0 -> pi+pi-, and a Search for CP Violation in D0 Decays

Using the large hadroproduced charm sample collected in experiment E791 at Fermilab, we have measured ratios of branching fractions for the two-body singly-Cabibbo-suppressed charged decays of the D0: (D0 -> KK)/(D0 -> Kpi) = 0.109 +- 0.003 +- 0.003, (D0 -> pipi)/(D0 -> Kpi) = 0.040 +- 0.002 +- 0.003, and (D0 -> KK)/(D0 -> pipi) = 2.75 +- 0.15 +- 0.16. We have looked for differences in the decay rates of D0 and D0bar to the CP eigenstates K+K- and pi+pi-, and have measured the CP asymmetry parameters A_CP(K+K-) = -0.010 +- 0.049 +- 0.012 and A_CP(pi+pi-) = -0.049 +- 0.078 +- 0.030, both consistent with zero.Comment: 10 Postscript pages, including 2 figures. Submitted to Phys. Lett.