6,494 research outputs found
One way to Characterize the compact structures of lattice protein model
On the study of protein folding, our understanding about the protein
structures is limited. In this paper we find one way to characterize the
compact structures of lattice protein model. A quantity called Partnum is given
to each compact structure. The Partnum is compared with the concept
Designability of protein structures emerged recently. It is shown that the
highly designable structures have, on average, an atypical number of local
degree of freedom. The statistical property of Partnum and its dependence on
sequence length is also studied.Comment: 10 pages, 5 figure
Hopping conductivity in heavily doped n-type GaAs layers in the quantum Hall effect regime
We investigate the magnetoresistance of epitaxially grown, heavily doped
n-type GaAs layers with thickness (40-50 nm) larger than the electronic mean
free path (23 nm). The temperature dependence of the dissipative resistance
R_{xx} in the quantum Hall effect regime can be well described by a hopping law
(R_{xx} \propto exp{-(T_0/T)^p}) with p=0.6. We discuss this result in terms of
variable range hopping in a Coulomb gap together with a dependence of the
electron localization length on the energy in the gap. The value of the
exponent p>0.5 shows that electron-electron interactions have to be taken into
account in order to explain the occurrence of the quantum Hall effect in these
samples, which have a three-dimensional single electron density of states.Comment: 5 pages, 2 figures, 1 tabl
Quantum Hall Effect induced by electron-electron interaction in disordered GaAs layers with 3D spectrum
It is shown that the observed Quantum Hall Effect in epitaxial layers of
heavily doped n-type GaAs with thickness (50-140 nm) larger the mean free path
of the conduction electrons (15-30 nm) and, therefore, with a three-dimensional
single-particle spectrum is induced by the electron-electron interaction. The
Hall resistance R_xy of the thinnest sample reveals a wide plateau at small
activation energy E_a=0.4 K found in the temperature dependence of the
transverse resistance R_xx. The different minima in the transverse conductance
G_xx of the different samples show a universal temperature dependence
(logarithmic in a large range of rescaled temperatures T/T_0) which is
reminiscent of electron-electron-interaction effects in coherent diffusive
transport.Comment: 6 pages, 3 figures, 1 tabl
Origin of Scaling Behavior of Protein Packing Density: A Sequential Monte Carlo Study of Compact Long Chain Polymers
Single domain proteins are thought to be tightly packed. The introduction of
voids by mutations is often regarded as destabilizing. In this study we show
that packing density for single domain proteins decreases with chain length. We
find that the radius of gyration provides poor description of protein packing
but the alpha contact number we introduce here characterize proteins well. We
further demonstrate that protein-like scaling relationship between packing
density and chain length is observed in off-lattice self-avoiding walks. A key
problem in studying compact chain polymer is the attrition problem: It is
difficult to generate independent samples of compact long self-avoiding walks.
We develop an algorithm based on the framework of sequential Monte Carlo and
succeed in generating populations of compact long chain off-lattice polymers up
to length . Results based on analysis of these chain polymers suggest
that maintaining high packing density is only characteristic of short chain
proteins. We found that the scaling behavior of packing density with chain
length of proteins is a generic feature of random polymers satisfying loose
constraint in compactness. We conclude that proteins are not optimized by
evolution to eliminate packing voids.Comment: 9 pages, 10 figures. Accepted by J. Chem. Phy
Structural classification of proteins and structural genomics: new insights into protein folding and evolution
This review article surveys the protein structures determined by Joint Center for Structural Genomics and published in this special issue of Acta Crystallographica Section F
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Implications of the Orb2 Amyloid Structure in Huntington’s Disease
Huntington’s disease is a progressive, autosomal dominant, neurodegenerative disorder caused by an expanded CAG repeat in the huntingtin gene. As a result, the translated protein, huntingtin, contains an abnormally long polyglutamine stretch that makes it prone to misfold and aggregating. Aggregation of huntingtin is believed to be the cause of Huntington’s disease. However, understanding on how, and why, huntingtin aggregates are deleterious has been hampered by lack of enough relevant structural data. In this review, we discuss our recent findings on a glutamine-based functional amyloid isolated from Drosophila brain and how this information provides plausible structural insight on the structure of huntingtin deposits in the brain
Properties of contact matrices induced by pairwise interactions in proteins
The total conformational energy is assumed to consist of pairwise interaction
energies between atoms or residues, each of which is expressed as a product of
a conformation-dependent function (an element of a contact matrix, C-matrix)
and a sequence-dependent energy parameter (an element of a contact energy
matrix, E-matrix). Such pairwise interactions in proteins force native
C-matrices to be in a relationship as if the interactions are a Go-like
potential [N. Go, Annu. Rev. Biophys. Bioeng. 12. 183 (1983)] for the native
C-matrix, because the lowest bound of the total energy function is equal to the
total energy of the native conformation interacting in a Go-like pairwise
potential. This relationship between C- and E-matrices corresponds to (a) a
parallel relationship between the eigenvectors of the C- and E-matrices and a
linear relationship between their eigenvalues, and (b) a parallel relationship
between a contact number vector and the principal eigenvectors of the C- and
E-matrices; the E-matrix is expanded in a series of eigenspaces with an
additional constant term, which corresponds to a threshold of contact energy
that approximately separates native contacts from non-native ones. These
relationships are confirmed in 182 representatives from each family of the SCOP
database by examining inner products between the principal eigenvector of the
C-matrix, that of the E-matrix evaluated with a statistical contact potential,
and a contact number vector. In addition, the spectral representation of C- and
E-matrices reveals that pairwise residue-residue interactions, which depends
only on the types of interacting amino acids but not on other residues in a
protein, are insufficient and other interactions including residue
connectivities and steric hindrance are needed to make native structures the
unique lowest energy conformations.Comment: Errata in DOI:10.1103/PhysRevE.77.051910 has been corrected in the
present versio
Universal flow diagram for the magnetoconductance in disordered GaAs layers
The temperature driven flow lines of the diagonal and Hall magnetoconductance
data (G_{xx},G_{xy}) are studied in heavily Si-doped, disordered GaAs layers
with different thicknesses. The flow lines are quantitatively well described by
a recent universal scaling theory developed for the case of duality symmetry.
The separatrix G_{xy}=1 (in units e^2/h) separates an insulating state from a
spin-degenerate quantum Hall effect (QHE) state. The merging into the insulator
or the QHE state at low temperatures happens along a semicircle separatrix
G_{xx}^2+(G_{xy}-1)^2=1 which is divided by an unstable fixed point at
(G_{xx},G_{xy})=(1,1).Comment: 10 pages, 5 figures, submitted to Phys. Rev. Let
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