23 research outputs found
Hadamard magnetization transfers achieve dramatic sensitivity enhancements in homonuclear multidimensional NMR correlations of labile sites in proteins, polysaccharides and nucleic acids
EXSY, TOCSY and NOESY lie at the foundation of homonuclear NMR experiments in
organic and pharmaceutical chemistry, as well as in structural biology. Limited
magnetization transfer efficiency is an intrinsic downside of these methods,
particularly when targeting rapidly exchanging species such as labile protons
ubiquitous in polysaccharides, sidechains and backbones of proteins, and in
bases and sugars of nucleic acids: the fast decoherence imparted on these
protons through solvent exchanges, greatly reduces their involvement in
homonuclear correlation experiments. We have recently discussed how these
decoherences can be visualized as an Anti-Zeno Effect, that can be harnessed to
enhance the efficiency of homonuclear transfers within Looped PROjected
SpectroscopY (L-PROSY) leading to 200-300% enhancements in NOESY and TOCSY
cross-peaks for amide groups in biomolecules. This study demonstrates that even
larger sensitivity gains per unit time, equivalent to reductions by several
hundred-folds in the duration of experiments, can be achieved by looping
inversion or using saturation procedures. In the ensuing experiments a priori
selected frequencies are encoded according to Hadamard recipes, and
subsequently resolved along the indirect dimension via linear combinations.
Magnetization-transfer (MT) processes reminiscent of those occurring in CEST
provide significant enhancements in the resulting cross-peaks, in only a
fraction of acquisition time of a normal 2D experiment. The effectiveness of
the ensuing three-way polarization transfer interplay between water, labile and
non-labile protons was corroborated experimentally for proteins,
homo-oligosaccharides and nucleic acids. In all cases, cross-peaks barely
detectable in conventional 2D NMR counterparts, were measured ca. 10-fold
faster and with 200-600% signal enhancements by the Hadamard MT counterparts
Implicit Regularization and Renormalization of QCD
We apply the Implicit Regularization Technique (IR) in a non-abelian gauge
theory. We show that IR preserves gauge symmetry as encoded in relations
between the renormalizations constants required by the Slavnov-Taylor
identities at the one loop level of QCD. Moreover, we show that the technique
handles divergencies in massive and massless QFT on equal footing.Comment: (11 pages, 2 figures
On the equivalence between Implicit Regularization and Constrained Differential Renormalization
Constrained Differential Renormalization (CDR) and the constrained version of
Implicit Regularization (IR) are two regularization independent techniques that
do not rely on dimensional continuation of the space-time. These two methods
which have rather distinct basis have been successfully applied to several
calculations which show that they can be trusted as practical, symmetry
invariant frameworks (gauge and supersymmetry included) in perturbative
computations even beyond one-loop order.
In this paper, we show the equivalence between these two methods at one-loop
order. We show that the configuration space rules of CDR can be mapped into the
momentum space procedures of Implicit Regularization, the major principle
behind this equivalence being the extension of the properties of regular
distributions to the regularized ones.Comment: 16 page
Regularization Independent Analysis of the Origin of Two Loop Contributions to N=1 Super Yang-Mills Beta Function
We present a both ultraviolet and infrared regularization independent
analysis in a symmetry preserving framework for the N=1 Super Yang-Mills beta
function to two loop order. We show explicitly that off-shell infrared
divergences as well as the overall two loop ultraviolet divergence cancel out
whilst the beta function receives contributions of infrared modes.Comment: 7 pages, 2 figures, typos correcte
Direct Evidence for Hydrogen Bonding in Glycans: A Combined NMR and Molecular Dynamics Study
Direct Evidence for Hydrogen Bonding in Glycans : A Combined NMR and Molecular Dynamics Study
We introduce the abundant hydroxyl groups of glycans as NMR handle's and structural probes to expand the repertoire of tools for structure function studies on glycans in solution. To this end, we present the facile detection and assignment of hydroxyl groups in a Wide range of sample concentrations (0.5-1700 mM) and temperatures, ranging from -5 to 25 degrees C.,We then exploit this information to directly detect hydrogen bonds, well-known for their importance in molecular structural determination through NMR. Via HSQC-TOCSY, we were able to determine the directionality; of these hydrogen bonds in sucrose Furthermore, by means Of molecular dynamics simulations in conjunction with NMR, we establish that one Out of the three detected hydrogen bonds arises from intermolecular interactions. This finding may shed light on glycan glycan interactions and glycan recognition by proteins.AuthorCount:4;</p
Uncovering Nonconventional and Conventional Hydrogen Bonds in Oligosaccharides through NMR Experiments and Molecular Modeling: Application to Sialyl Lewis-X
Glycan OH Exchange Rate Determination in Aqueous Solution: Seeking Evidence for Transient Hydrogen Bonds
Hydrogen bonds (Hbonds)
are important stabilizing forces in biomolecules.
However, for glycans in aqueous solution, direct NMR detection of
Hbonds is elusive because of their transient nature. Here, we present
Isotope-based Natural-abundance TOtal correlation eXchange SpectroscopY
(INTOXSY), a new <sup>1</sup>Hâ<sup>13</sup>C heteronuclear
single quantum coherenceâtotal correlation spectroscopy based
method, to extract OH groupsâ exchange rate constants (<i>k</i><sub>ex</sub>) for molecules in natural <sup>13</sup>C
abundance and show that OH Hbonds can be inferred from âslowerâ
H/D <i>k</i><sub>ex</sub>. We evaluate <i>k</i><sub>ex</sub> measured with INTOXSY in light of those extracted with
line-shape analysis. Subsequently, we use a set of common glycans
to establish a <i>k</i><sub>ex</sub> reference basis set
and to infer the existence of transient Hbonds involving OH donor
groups. Then, we report <i>k</i><sub>ex</sub> values for
a series of mono- and disaccharides, as well as for oligosaccharides
sialyl Lewis X and ÎČ-cyclodextrin, and compare the results with
those from the reference set to extract Hbond information. Finally,
we utilize NMR experimental data in conjunction with molecular dynamics
simulations to establish donor and acceptor Hbond pairs. Our exchange
rate measurements indicate that OH/OD exchange rates, <i>k</i><sub>HD</sub>, values <10 s<sup>â1</sup> are consistent
with transient Hbond OH groups and potential acceptor groups can be
uncovered through MD simulations
Direct Evidence for Hydrogen Bonding in Glycans: A Combined NMR and Molecular Dynamics Study
We introduce the abundant hydroxyl
groups of glycans as NMR handles
and structural probes to expand the repertoire of tools for structureâfunction
studies on glycans in solution. To this end, we present the facile
detection and assignment of hydroxyl groups in a wide range of sample
concentrations (0.5â1700 mM) and temperatures, ranging from
â5 to 25 °C. We then exploit this information to directly
detect hydrogen bonds, well-known for their importance in molecular
structural determination through NMR. Via HSQC-TOCSY, we were able
to determine the directionality of these hydrogen bonds in sucrose.
Furthermore, by means of molecular dynamics simulations in conjunction
with NMR, we establish that one out of the three detected hydrogen
bonds arises from intermolecular interactions. This finding may shed
light on glycanâglycan interactions and glycan recognition
by proteins