pinecone/core-2020-05-10-deduplication huggingface dataset:
Identification of a novel bond between a histidine and the essential tyrosine in catalase HPII of Escherichia coli

8 pages, 7 figures, 1 table.-- PMID: 9144772 [PubMed].-- PMCID: PMC2143697.A bond between the N delta of the imidazole ring of His 392 and the C beta of the essential Tyr 415 has been found in the refined crystal structure at 1.9 A resolution of catalase HPII of Escherichia coli. This novel type of covalent linkage is clearly defined in the electron density map of HPII and is confirmed by matrix-assisted laser desorption/ionization mass spectrometry analysis of tryptic digest mixtures. The geometry of the bond is compatible with both the sp3 hybridization of the C beta atom and the planarity of the imidazole ring. Two mutated variants of HPII active site residues, H128N and N201H, do not contain the His 392-Tyr 415 bond, and their crystal structures show that the imidazole ring of His 392 was rotated, in both cases, by 80 degrees relative to its position in HPII. These mutant forms of HPII are catalytically inactive and do not convert heme b to heme d, suggesting a relationship between the self-catalyzed heme conversion reaction and the formation of the His-Tyr linkage. A model coupling the two processes and involving the reaction of one molecule of H2O2 on the proximal side of the heme with compound 1 is proposed.n. Thwiso rk was supported by an operating grant from the Natural Sciences and Engineering Research Council (NSERC (OGP9600) to P.C.L. and a postgraduate scholarship from NSERC to A.H. Work in Barcelona was supported by grants PB92-0707\ud
and PB95-0218 to I.F. J.B. was the recipient of a doctoral fellowship from the Generalitat de Catalunya. Data collection in Hamburg was supporbteyd the Human Capital Mobility Project on contract CHGE-CT93-0040Peer reviewe
Structures of adamalysin II with peptidic inhibitors. Implications for the design of tumor necrosis factor alpha convertase inhibitors

10 pages, 7 figures, 3 tables.-- PMID: 9521103 [PubMed].-- PMCID: PMC2143928.Crotalus adamanteus snake venom adamalysin II is the structural prototype of the adamalysin or ADAM family comprising proteolytic domains of snake venom metalloproteinases, multimodular mammalian reproductive tract proteins, and tumor necrosis factor alpha convertase, TACE, involved in the release of the inflammatory cytokine, TNFalpha. The structure of adamalysin II in noncovalent complex with two small-molecule right-hand side peptidomimetic inhibitors (Pol 647 and Pol 656) has been solved using X-ray diffraction data up to 2.6 and 2.8 A resolution. The inhibitors bind to the S'-side of the proteinase, inserting between two protein segments, establishing a mixed parallel-antiparallel three-stranded beta-sheet and coordinate the central zinc ion in a bidentate manner via their two C-terminal oxygen atoms. The proteinase-inhibitor complexes are described in detail and are compared with other known structures. An adamalysin-based model of the active site of TACE reveals that these small molecules would probably fit into the active site cleft of this latter metalloproteinase, providing a starting model for the rational design of TACE inhibitors.Financial support of NIH grant HL22996\ud
(L.F.K.), the Robert Welsh Foundation (A-328 to E.F.M.), Schering-Plough and Zeneca (E.F.M.), the Human Capital and Mobility Programme of the European Union (ERBCHRXCT9400535), and the Ministerio de Educación y Ciencia (grant EX9446121 143).Peer reviewe
Transition state in the folding of α-lactalbumin probed by the 6-120 disulfide bond

The guanidine hydrochloride concentration dependence of the folding and unfolding rate constants of a derivative of α-lactalbumin, in which the 6-120 disulfide bond is selectively reduced and S-carboxymethylated, was measured and compared with that of disulfide-intact α-lactalbumin. The concentration dependence of the folding and unfolding rate constants was analyzed on the basis of the two alternative models, the intermediate-controlled folding model and the multiple-pathway folding model, that we had proposed previously. All of the data supported the multiple-pathway folding model. Therefore, the molten globule state that accumulates at an early stage of folding of α-lactalbumin is not an obligatory intermediate. The cleavage of the 6-120 disulfide bond resulted in acceleration of unfolding without changing the refolding rate, indicating that the loop closed by the 6-120 disulfide bond is unfolded in the transition state. It is theoretically shown that the chain entropy gain on removing the cross-link from a random coil chain with helical stretches can be comparable to that from an entirely random chain. Therefore, the present result is not inconsistent with the known structure in the molten globule intermediate. Based on this result and other knowledge obtained so far, the structure in the transition state of the folding reaction of α-lactalbumin is discussed
The functional importance of structural differences between the mannitol-specific IIAmannitol and the regulatory IIAnitrogen

The three-dimensional structures of the IIA domain of the mannitol-specific phosphoenol-pyruvate dependent phosphotransferase system (PTS) of Escherichia coli and the regulatory IIAntr enzyme have been compared. The enzymes are 20% identical in sequence and contain the sequence motif specific for IIA proteins belonging to the mannitol-fructose family of the PTS. The fold of the enzymes is nearly identical, which confirms their evolution from a common ancestor. Moreover, the phosphorylation site of IIAmtl (His65) and one of the observed conformations of the active site Arg49 are extremely similar to their equivalents (His73 and Arg57) in IIAntr. In contrast, His120, the equivalent of the second active site His111 of IIAmtl, is not located in the active site of IIAntr but points into the solvent on the other side of the molecule. The different position of His120 makes it unlikely that this residue assists in phosphoryl transfer in the regulatory IIAntrs. As His120 is conserved in all IIAntr enzymes, it could have an essential role in the recognition of the target protein of IIAntr.
Single qubit estimation from repeated unsharp measurements

When estimating an unknown single pure qubit state, the optimum fidelity is
2/3. As it is well known, the value 2/3 can be achieved in one step, by a
single ideal measurement of the polarization along a random direction. I
analyze the opposite strategy which is the long sequence of unsharp
polarization measurements. The evolution of the qubit under the influence of
repeated measurements is quite complicated in the general case. Fortunately, in
a certain limit of very unsharp measurements the qubit will obey simple
stochastic evolution equations known for long under the name of time-continuous
measurement theory. I discuss how the outcomes of the very unsharp measurements
will asymptotically contribute to our knowledge of the original qubit. It is
reassuring that the fidelity will achieve the optimum 2/3 for long enough
sequences of the unsharp measurements.Comment: 8pp, 3 figures, talk at 9th Central European Workshop on Quantum
  Optic
The quantum way to diagonalize hermitean matrices

An entirely quantum mechanical approach to diagonalize hermitean matrices has
been presented recently. Here, the genuinely quantum mechanical approach is
considered in detail for (2x2) matrices. The method is based on the measurement
of quantum mechanical observables which provides the computational resource. In
brief, quantum mechanics is able to directly address and output eigenvalues of
hermitean matrices. The simple low-dimensional case allows one to illustrate
the conceptual features of the general method which applies to (NxN) hermitean
matrices.Comment: 7 page
Dipole-Dipole Coupling in the Presence of Dispersing and Absorbing
  Bodies

An effective Hamiltonian and equations of motion for treating both the
resonant dipole-dipole interaction between two-level atoms and the resonant
atom-field interaction are derived, which can suitably be used for studying the
influence of arbitrary dispersing and absorbing material surroundings on these
interactions. It is shown that the dipole-dipole interaction and the atom-field
interaction, respectively, are closely related to the real part and the
imaginary part of the (classical) Green tensor. The theory is applied to the
study of the transient behavior of two atoms that initially share a single
excitation, with special emphasis on the role of the two competing processes of
virtual and real photon exchange in the energy transfer between the atoms. To
illustrate the powerfulness of the theory, specific results for the case of the
atoms being near a dispersing and absorbing microsphere are presented. In
particular, the regimes of weak and strong atom-field coupling are addressed.Comment: 8 pages, 4 figs, proceedings of 9th Central-European Workshop on
  Quantum Optics, Szeged, 2002, to appear in Fortschritte der Physi
Entanglement and Properties

Various topics concerning the entanglement of composite quantum systems are
considered with particular emphasis concerning the strict relations of such a
problem with the one of attributing objective properties to the constituents.
In particular we will focus our attention to composite quantum systems composed
of identical constituents, with the purpose of dealing with subtle issues,
which have never been adequately discussed in the literature, originating from
the true indistinguishability of the subsystems involved.Comment: 10 pages, Latex, corrected typo
Rabi oscillations, Ramsey fringes and spin echoes in an electrical
  circuit

We present a superconducting tunnel junction circuit which behaves as a
controllable atom, and whose ground and first excited state form an effective
spin 1/2. By applying microwave pulses, we have performed on this circuit
experiments demonstrating the controlled manipulation of the spin : Rabi
precession, Ramsey interferences, and spin echoes.Comment: To be published in the proceedings of the conference "Quantum
  Interferometry IV" (Trieste, March 2002) in a special issue of Fortschritte
  der Physi
Entanglement at distance: qubits versus continuous variables

We consider the problem of obtaining maximally entangled photon states at
distance in the presence of loss. We compare the efficiency of two different
schemes in establishing $N$ shared ebits: i) $N$ single ebit states with the
qubit encoded on polarization; ii) a single continuous variable entangled state
(emode) assisted by optimal local operation and classical communication (LOCC)
protocol in order to obtain a $2^N$-dimensional maximally entangled state, with
qubits encoded on the photon number.Comment: 5 pages. 4 eps files. Use fortschritte.sty (included
Time Asymmetric Quantum Theory - II. Relativistic Resonances from
  S-Matrix Poles

Relativistic resonances and decaying states are described by representations
of Poincar\'e transformations, similar to Wigner's definition of stable
particles. To associate decaying state vectors to resonance poles of the
$S$-matrix, the conventional Hilbert space assumption (or asymptotic
completeness) is replaced by a new hypothesis that associates different dense
Hardy subspaces to the in- and out-scattering states. Then one can separate the
scattering amplitude into a background amplitude and one or several
``relativistic Breit-Wigner'' amplitudes, which represent the resonances per
se. These Breit-Wigner amplitudes have a precisely defined lineshape and are
associated to exponentially decaying Gamow vectors which furnish the
irreducible representation spaces of causal Poincar\'e transformations into the
forward light cone.Comment: 57 pages, 6 figure
Unitary Quantum Field Theory on the Noncommutative Minkowski space

This is the written version of a talk I gave at the 35th Symposium Ahrenshoop
in Berlin, Germany, August 2002. It is an exposition of joint work with S.
Doplicher, K. Fredenhagen, and Gh. Piacitelli [1]. The violation of unitarity
found in quantum field theory on noncommutative spacetimes in the context of
the so-called modified Feynman rules is linked to the notion of time ordering
implicitely used in the assumption that perturbation theory may be done in
terms of Feynman propagators. Two alternative approaches which do not entail a
violation of unitarity are sketched. An outlook upon our more recent work is
given.Comment: 6 pages. To appear in the proceedings of 35th International Symposium
  Ahrenshoop on the theory of Elementary Particles: Recent Developments in
  String / M Theory and Field Theory, Berlin, Germany, 26-30 Aug 2002 (special
  issue of the journal "Fortschritte der Physik") v2: minor addition to the
  abstrac
Intersecting Branes, Defect Conformal Field Theories and Tensionless
  Strings

The defect conformal field theory describing intersecting D3-branes at a
C^2/Z_k orbifold is used to (de)construct the theory of intersecting M5-branes,
as well as M5-branes wrapping the holomorphic curve xy=c. The possibility of a
't Hooft anomaly due to tensionless strings at the intersection is discussed.
This note is based on a talk given by Zachary Guralnik at the 35th
International Symposium Ahrenshoop on the Theory of Elementary Particles.Comment: latex, one figure, 9pages. Talk given by Z.G. at the 35th
  International Symposium Ahrenshoop on the Theory of Elementary Particle
Non--Commutative Field Theories beyond Perturbation Theory

We investigate two models in non-commutative (NC) field theory by means of
Monte Carlo simulations. Even if we start from the Euclidean lattice
formulation, such simulations are only feasible after mapping the systems onto
dimensionally reduced matrix models. Using this technique, we measure Wilson
loops in 2d NC gauge theory of rank 1. It turns out that they are
non-perturbatively renormalizable, and the phase follows an Aharonov-Bohm
effect if we identify \theta = 1/B. Next we study the 3d \lambda \phi^{4} model
with two NC coordinates, where we present new results for the correlators and
the dispersion relation. We further reveal the explicit phase diagram. The
ordered regime splits into a uniform and a striped phase, as it was
qualitatively conjectured before. We also confirm the recent observation by
Ambjorn and Catterall that such stripes occur even in d=2, although they imply
the spontaneous breaking of translation symmetry. However, in d=3 and d=2 we
observe only patterns of two stripes to be stable in the range of parameters
investigated.Comment: 8 pages, 8 figures, talk presented at 35th Ahrenshoop Symposiu
Nontrivial RR two-form field strength and SU(3)-structure

We discuss how in the presence of a nontrivial RR two-form field strength and
nontrivial dilaton the conditions of preserving supersymmetry on
six-dimensional manifolds lead to generalized monopole and Killing spinor
equations. We show that the manifold is K\"ahler in the ten-dimensional string
frame if F_0^{(1,1)}=0. We then determine explicitly the intrinsic torsion of
the SU(3)-structure on six-manifolds that result via Kaluza-Klein reduction
from seven-manifolds with G_2-structure of generic intrinsic torsion. Lastly we
give explicitly the intrinsic torsion of the SU(3)-structure for an N=1
supersymmetric background in the presence of nontrivial RR two-form field
strength and nontrivial dilaton.Comment: LaTeX, 8 pages, talk given at the 35th Symposium Ahrenshoop, enlarged
  version of the contribution to the proceeding
Solving String Field Equations: New Uses for Old Tools

It is argued that the (NS-sector) superstring field equations are integrable,
i.e. their solutions are obtainable from linear equations. We adapt the
25-year-old solution-generating "dressing" method and reduce the construction
of nonperturbative superstring configurations to a specific cohomology problem.
The application to vacuum superstring field theory is outlined.Comment: Talk presented by O.L. at the 35th International Symposium Ahrenshoop
  on the Theory of Elementary Particles, Berlin, Germany, 26-30 Aug 2002; v2:
  minor corrections, textheight adjuste
N=1 SUSY inspired Whitham prepotentials and WDVV

This brief review deals with prepotentials inspired by N=1 SUSY
considerations due to Cachazo, Intrilligator, Vafa. These prepotentials
associated with matrix models following Dijkgraaf and Vafa should be considered
as given on an enlarged moduli space that includes Whitham times (couplings of
the superpotential). This moduli space is nothing but the whole moduli space of
(decorated) hyperelliptic curves. Corresponding prepotentials are logarithms of
(quasiclassical) tau-functions and satisfy the WDVV equations.Comment: 7 pages, references added, based on talk presented at the 35th
  Symposium Ahrenshoo
Topological Transitions and Enhancon-like Geometries in Calabi-Yau
  Compactifications of M-Theory

We study the impact of topological phase transitions of the internal
Calabi-Yau threefold on the space-time geometry of five-dimensional extremal
black holes and black strings. For flop transitions and SU(2) gauge symmetry
enhancement we show that solutions can always be continued and that the
behaviour of metric, gauge fields and scalars can be characterized in a model
independent way. Then we look at supersymmetric solutions which describe naked
singularities rather than geometries with a horizon. For black strings we show
that the solution cannot become singular as long as the scalar fields take
values inside the Kahler cone. For black holes we establish the same result for
the elliptic fibrations over the Hirzebruch surfaces F_0, F_1, F_2. These three
models exhibit a behaviour similar to the enhancon, since one runs into SU(2)
enhancement before reaching the apparent singularity. Using the proper
continuation inside the enhancon radius one finds that the solution is regular.Comment: 7 page
Black Holes and Black Strings on Cylinders

We review the recently discovered ansatz that describes non-extremal charged
dilatonic branes of string/M-theory with a transverse circle. The ansatz
involves a new coordinate system that interpolates between the spherical and
cylindrical case, and reduces the equations of motion to a set of equations on
one unknown function of two variables. The function is independent of the
charge, so that the ansatz can also be used to construct neutral black holes on
cylinders and near-extremal charged dilatonic branes with a transverse circle.
The construction enables us to argue that, for sufficiently large mass, there
exists a neutral solution that breaks translational invariance in the circle
direction, and has larger entropy than that of the neutral black string of the
same mass.Comment: 7 pages, Talk presented by N.O. at the 35th International Symposium
  Ahrenshoop on the Theory of Elementary Particles, Berlin, Germany, 26-30 Aug
  200
Strings in Singular Time-Dependent Backgrounds

We review the construction of time-dependent backgrounds with space-like
singularities. We mainly consider exact CFT backgrounds. The algebraic and
geometric aspects of these backgrounds are discussed. Physical issues, results
and difficulties associated with such systems are reviewed. Finally, we present
some new results: a two dimensional cosmology in the presence of an Abelian
gauge field described within a family of (SL(2)xU(1))/(U(1)xZ) quotient CFTs.Comment: 22 pages, 4 figures, Contribution to the proceedings of Symposium
  Ahrenshoop, August 200
Production of Black Holes in TeV-Scale Gravity

Copious production of microscopic black holes is one of the least
model-dependent predictions of TeV-scale gravity scenarios. We review the
arguments behind this assertion and discuss opportunities to track the striking
associated signatures in the near future. These include searches at neutrino
telescopes, such as AMANDA and RICE, at cosmic ray air shower facilities, such
as the Pierre Auger Observatory, and at colliders, such as the Large Hadron
Collider.Comment: 8 pages, 10 figures, fortschritte.sty (included); talk presented at
  the 35th International Symposium Ahrenshoop on the Theory of Elementary
  Particles, Aug. 26-30, 2002, Berlin-Schmoeckwitz, German
Boundaries, defects and Frobenius algebras

The interpretation of D-branes in terms of open strings has lead to much
interest in boundary conditions of two-dimensional conformal field theories
(CFTs). These studies have deepened our understanding of CFT and allowed us to
develop new computational tools. The construction of CFT correlators based on
combining tools from topological field theory and non-commutative algebra in
tensor categories, which we summarize in this contribution, allows e.g. to
discuss, apart from boundary conditions, also defect lines and disorder fields.Comment: 7 pages. Contribution to the 35th International Symposium Ahrenshoop
  on the Theory of Elementary Particles (Berlin, August 2002) and to the
  International Conference on Theoretical Physics (UNESCO, Paris, July 2002).
  For related proceedings contributions see
  http://tpe.physik.rwth-aachen.de/schweigert/proceedings.htm
Form-field Gauge Symmetry in M-theory

We show how to cast an interacting system of M--branes into manifestly
gauge-invariant form using an arrangement of higher-dimensional Dirac surfaces.
Classical M--theory has a cohomologically nontrivial and noncommutative set of
gauge symmetries when written using a ``doubled'' formalism containing 3-form
and 6-form gauge fields. We show how the arrangement of Dirac surfaces allows
an integral subgroup of these symmetries to be preserved at the quantum level.
The proper context for discussing these large gauge transformations is relative
cohomology, in which the 3-form transformation parameters become exact when
restricted to the five-brane worldvolume. This structure yields the correct
lattice of M-theory brane charges.Comment: Contributed to 35th International Symposium Ahrenshoop on the theory
  of Elementary Particles: Recent Developments in String / M Theory and Field
  Theory, Berlin, Germany, 26-30 Aug 2002; 9pp, plain Late
The Tachyon does Matter

We review the concept of S-branes introduced by Gutperle and Strominger
hep-th/0202210. Using the effective spacetime description of the rolling
tachyon worldsheets discussed by Sen, we analyze the possibility that the
gravitational backreaction of tachyon matter is important in the time-dependent
process. We show that this is indeed the case in the example of the S0-brane in
4-dimensional Einstein-Maxwell theory. This talk is based on hep-th/0207235.Comment: 8 pages, Talk given at 35th Symposium Ahrenshoop, Contribution to the
  Proceeding
Effective Actions Near Singularities: The STU-Model

We derive the low energy effective action of the STU-model in four and five
dimensions near the line T=U, where SU(2) gauge symmetry enhancement occurs. By
`integrating in' the light W^{\pm} bosons together with their superpartners,
the quantum corrected effective action becomes non-singular at T=U and
manifestly SU(2) invariant. The four-dimensional theory is found to be
consistent with modular invariance and the five-dimensional decompactification
limit. This talk concisely summarizes results that have been obtained in
collaboration with J. Louis and T. Mohaupt.Comment: 6 pages, LaTeX. Contribution to the proceedings of the 35th Symposium
  Ahrenshoop, Berlin, Germany, August 2002. v2: reference corrected, paper
  format adjuste