768 research outputs found
Inductive effects in amino acids and peptides: Ionization constants and tryptophan fluorescence
Although inductive effects in organic compounds are known to influence chemical properties such as ionization constants, their specific contribution to the properties/behavior of amino acids and functional groups in peptides remains largely unexplored. In this study we developed a computationally economical algorithm for ab initio calculation of the magnitude of inductive effects for non-aromatic molecules. The value obtained by the algorithm is called the Inductive Index and we observed a high correlation (R2 = 0.9427) between our calculations and the pKa values of the alpha-amino groups of amino acids with non-aromatic side-chains. Using a series of modified amino acids, we also found similarly high correlations (R2 > 0.9600) between Inductive Indexes and two wholly independent chemical properties: i) the pKa values of ionizable side-chains and, ii) the fluorescence response of the indole group of tryptophan. After assessing the applicability of the method of calculation at the amino acid level, we extended our study to tryptophan-containing peptides and established that inductive contributions of neighboring side-chains are transmitted through peptide bonds. We discuss possible contributions to the study of proteins.Fil: Lara Popoca, Jesús. Universidad Nacional Autónoma de México; MéxicoFil: Thoke, Henrik S.. International and Interdisciplinary Research Network; DinamarcaFil: Stock, Roberto P.. Universidad Nacional Autónoma de México; MéxicoFil: Rudino Pinera, Enrique. Universidad Nacional Autónoma de México; MéxicoFil: Bagatolli, Luis Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigación Médica Mercedes y Martín Ferreyra. Universidad Nacional de Córdoba. Instituto de Investigación Médica Mercedes y Martín Ferreyra; Argentin
Deletion of DNA sequences of using a polymerase chain reaction based approach
We developed a simple, rapid and reliable method to delete DNA
fragments in plasmids using a polymerase chain reaction based
amplification of the circular DNA sequence that excludes the fragment
to be deleted. The primers are designed to contain a non-complementary
5' sequence consisting of a restriction enzyme target sequence.
Following PCR amplification, the plasmid is digested with Dpn I to
eliminate the template DNA, with the chosen restriction enzyme, and
ligated. The only limitation is the selection of the restriction enzyme
target sequence that must not be present in the original plasmid. The
method is straightforward in its execution and success relies on a
meticulous primer design that permits us obtain 100% of transformants
containing the desired mutation. The extraordinary simplicity of the
method makes it a valuable tool to generate DNA deletions in plasmids
and to study the effects of those deletions in protein function
The double-edged sword of CRISPR-Cas systems
A recent paper gives the details on how specific small RNAs can program a protein to cleave an undesired piece of DNA and to provide immunity to a microbial cell
Tale proteins bind to both active and inactive chromatin
TALE (transcription activator-like effector) proteins can be tailored to bind to any DNA sequence of choice and thus are of immense utility for genome editing and the specific delivery of transcription activators. However, to perform these functions, they need to occupy their sites in chromatin. In the present study, we have systematically assessed TALE binding to chromatin substrates and find that in vitro TALEs bind to their target site on nucleosomes at the more accessible entry/exit sites, but not at the nucleosome dyad. We show further that in vivo TALEs bind to transcriptionally repressed chromatin and that transcription increases binding by only 2-fold. These data therefore imply that TALEs are likely to bind to their target in vivo even at inactive loci
Search for the Higgs boson in events with missing transverse energy and b quark jets produced in proton-antiproton collisions at s**(1/2)=1.96 TeV
We search for the standard model Higgs boson produced in association with an
electroweak vector boson in events with no identified charged leptons, large
imbalance in transverse momentum, and two jets where at least one contains a
secondary vertex consistent with the decay of b hadrons. We use ~1 fb-1
integrated luminosity of proton-antiproton collisions at s**(1/2)=1.96 TeV
recorded by the CDF II experiment at the Tevatron. We find 268 (16) single
(double) b-tagged candidate events, where 248 +/- 43 (14.4 +/- 2.7) are
expected from standard model background processes. We place 95% confidence
level upper limits on the Higgs boson production cross section for several
Higgs boson masses ranging from 110 GeV/c2 to 140 GeV/c2. For a mass of 115
GeV/c2 the observed (expected) limit is 20.4 (14.2) times the standard model
prediction.Comment: 8 pages, 2 figures, submitted to Phys. Rev. Let
Observation of the Baryonic Flavor-Changing Neutral Current Decay Lambda_b -> Lambda mu+ mu-
We report the first observation of the baryonic flavor-changing neutral
current decay Lambda_b -> Lambda mu+ mu- with 24 signal events and a
statistical significance of 5.8 Gaussian standard deviations. This measurement
uses ppbar collisions data sample corresponding to 6.8fb-1 at sqrt{s}=1.96TeV
collected by the CDF II detector at the Tevatron collider. The total and
differential branching ratios for Lambda_b -> Lambda mu+ mu- are measured. We
find B(Lambda_b -> Lambda mu+ mu-) = [1.73+-0.42(stat)+-0.55(syst)] x 10^{-6}.
We also report the first measurement of the differential branching ratio of B_s
-> phi mu+ mu- using 49 signal events. In addition, we report branching ratios
for B+ -> K+ mu+ mu-, B0 -> K0 mu+ mu-, and B -> K*(892) mu+ mu- decays.Comment: 8 pages, 2 figures, 4 tables. Submitted to Phys. Rev. Let
Observation and Mass Measurement of the Baryon
We report the observation and measurement of the mass of the bottom, strange
baryon through the decay chain , where
, , and .
Evidence for observation is based on a signal whose probability of arising from
the estimated background is 6.6 x 10^{-15}, or 7.7 Gaussian standard
deviations. The mass is measured to be (stat.) (syst.) MeV/.Comment: Minor text changes for the second version. Accepted by Phys. Rev.
Let
Polarizations of J/psi and psi(2S) Mesons Produced in ppbar Collisions at 1.96 TeV
We have measured the polarizations of \jpsi and \psiprime mesons as
functions of their transverse momentum \pt when they are produced promptly in
the rapidity range with \pt \geq 5 \pgev. The analysis is performed
using a data sample with an integrated luminosity of about 800 \ipb collected
by the CDF II detector. For both vector mesons, we find that the polarizations
become increasingly longitudinal as \pt increases from 5 to 30 \pgev. These
results are compared to the predictions of nonrelativistic quantum
chromodynamics and other contemporary models. The effective polarizations of
\jpsi and \psiprime mesons from -hadron decays are also reported.Comment: 8 pages, 7 figures, published in Physical Review Letter
Search for the standard model Higgs boson decaying to a pair in events with no charged leptons and large missing transverse energy using the full CDF data set
We report on a search for the standard model Higgs boson produced in
association with a vector boson in the full data set of proton-antiproton
collisions at TeV recorded by the CDF II detector at the
Tevatron, corresponding to an integrated luminosity of 9.45 fb. We
consider events having no identified charged lepton, a transverse energy
imbalance, and two or three jets, of which at least one is consistent with
originating from the decay of a quark. We place 95% credibility level upper
limits on the production cross section times standard model branching fraction
for several mass hypotheses between 90 and . For a Higgs
boson mass of , the observed (expected) limit is 6.7
(3.6) times the standard model prediction.Comment: Accepted by Phys. Rev. Let
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