1,915 research outputs found
Four-states phase diagram of proteins
A four states phase diagram for protein folding as a function of temperature
and solvent quality is derived from an improved 2-d lattice model taking into
account the temperature dependence of the hydrophobic effect. The phase diagram
exhibits native, globule and two coil-type regions. In agreement with
experiment, the model reproduces the phase transitions indicative of both warm
and cold denaturations. Finally, it predicts transitions between the two coil
states and a critical point.Comment: 7 pages, 5 figures. Accepted for publication in Europhysics Letter
Sequencing of folding events in Go-like proteins
We have studied folding mechanisms of three small globular proteins: crambin
(CRN), chymotrypsin inhibitor 2 (CI2) and the fyn Src Homology 3 domain (SH3)
which are modelled by a Go-like Hamiltonian with the Lennard-Jones
interactions. It is shown that folding is dominated by a well-defined
sequencing of events as determined by establishment of particular contacts. The
order of events depends primarily on the geometry of the native state.
Variations in temperature, coupling strengths and viscosity affect the
sequencing scenarios to a rather small extent. The sequencing is strongly
correlated with the distance of the contacting aminoacids along the sequence.
Thus -helices get established first. Crambin is found to behave like a
single-route folder, whereas in CI2 and SH3 the folding trajectories are more
diversified. The folding scenarios for CI2 and SH3 are consistent with
experimental studies of their transition states.Comment: REVTeX, 12 pages, 11 EPS figures, J. Chem. Phys (in press
Role of framework mutations and antibody flexibility in the evolution of broadly neutralizing antibodies
Eliciting antibodies that are cross reactive with surface proteins of diverse strains of highly mutable pathogens (e.g., HIV, influenza) could be key for developing effective universal vaccines. Mutations in the framework regions of such broadly neutralizing antibodies (bnAbs) have been reported to play a role in determining their properties. We used molecular dynamics simulations and models of affinity maturation to study specific bnAbs against HIV. Our results suggest that there are different classes of evolutionary lineages for the bnAbs. If germline B cells that initiate affinity maturation have high affinity for the conserved residues of the targeted epitope, framework mutations increase antibody rigidity as affinity maturation progresses to evolve bnAbs. If the germline B cells exhibit weak/moderate affinity for conserved residues, an initial increase in flexibility via framework mutations may be required for the evolution of bnAbs. Subsequent mutations that increase rigidity result in highly potent bnAbs. Implications of our results for immunogen design are discussed
Breit interaction correction to the hyperfine constant of an external s-electron in many-electron atom
Correction to the hyperfine constant of an external s-electron in
many-electron atom caused by the Breit interaction is calculated analytically:
. Physical mechanism for this correction is
polarization of the internal electronic shells (mainly shell) by the
magnetic field of the external electron. This mechanism is similar to the
polarization of vacuum considered by Karplus and Klein long time ago. The
similarity is the reason why in both cases (Dirac sea polarization and internal
atomic shells polarization) the corrections have the same dependence on the
nuclear charge and fine structure constant.
In conclusion we also discuss corrections to the parity violation
effects in atoms.Comment: 8 pages, 2 figure
Theory of Anomalous Hall Effect in a Heavy fermion System with a Strong Anisotropic Crystal Field
In a heavy fermion system, there exists the anomalous Hall effect caused by
localized -orbital freedom, in addition to the normal Hall effect due to the
Lorentz force. In 1994, we found that the Hall coefficient caused by the
anomalous Hall effect () is predominant and the relation ( is the electrical resistivity) holds at low
temperatures in many compounds. In this work, we study the system where the
magnetic susceptibility is highly anisotropic due to the strong crystalline
electric field on -orbitals. Interestingly, we find that is
nearly isotropic in general. This tendency is frequently observed
experimentally, which has casted suspicion that the anomalous Hall effect may
be irrelevant in real materials. Our theory corresponds to corrections and
generalizations of the pioneering work on ferromagnetic metals by Karplus and
Luttinger.Comment: 4 pages, revtex, to be published in J. Phys. Soc. Jpn. (No.8
Quantum Electrodynamics of the Helium Atom
Using singlet S states of the helium atom as an example, I describe precise
calculation of energy levels in few-electron atoms. In particular, a complete
set of effective operators is derived which generates O(m*alpha^6) relativistic
and radiative corrections to the Schr"odinger energy. Average values of these
operators can be calculated using a variational Schr"odinger wave function.Comment: 23 pages, revte
Dynamics of semiclassical Bloch wave - packets
The semiclassical approximation for electron wave-packets in crystals leads
to equations which can be derived from a Lagrangian or, under suitable
regularity conditions, in a Hamiltonian framework. In the plane, these issues
are studied %in presence of external fields using the method of the coadjoint
orbit applied to the ``enlarged'' Galilei group.Comment: 15 pages, Talk given at Nonlinear Physics. Theory and Experiment.
IV,Gallipoli (Lecce), Italy - June 22 - July 1, 200
Anomalous Hall Effect and Skyrmion Number in Real- and Momentum-space
We study the anomalous Hall effect (AHE) for the double exchange model with
the exchange coupling being smaller than the bandwidth for the
purpose of clarifying the following unresolved and confusing issues: (i) the
effect of the underlying lattice structure, (ii) the relation between AHE and
the skyrmion number, (iii) the duality between real and momentum spaces, and
(iv) the role of the disorder scatterings; which is more essential,
(Hall conductivity) or (Hall resistivity)? Starting from a generic
expression for , we resolve all these issues and classify the regimes
in the parameter space of (: elastic-scattering time), and
(length scale of spin texture). There are two distinct mechanisms
of AHE; one is characterized by the real-space skyrmion-number, and the other
by momentum-space skyrmion-density at the Fermi level, which work in different
regimes of the parameter space.Comment: 4 pages, 1 figure, REVTe
Conformations of Proteins in Equilibrium
We introduce a simple theoretical approach for an equilibrium study of
proteins with known native state structures. We test our approach with results
on well-studied globular proteins, Chymotrypsin Inhibitor (2ci2), Barnase and
the alpha spectrin SH3 domain and present evidence for a hierarchical onset of
order on lowering the temperature with significant organization at the local
level even at high temperatures. A further application to the folding process
of HIV-1 protease shows that the model can be reliably used to identify key
folding sites that are responsible for the development of drug resistance .Comment: 6 pages, 3 eps figure
- …