963 research outputs found
Path Integral Approach to Strongly Nonlinear Composite
We study strongly nonlinear disordered media using a functional method. We
solve exactly the problem of a nonlinear impurity in a linear host and we
obtain a Bruggeman-like formula for the effective nonlinear susceptibility.
This formula reduces to the usual Bruggeman effective medium approximation in
the linear case and has the following features: (i) It reproduces the weak
contrast expansion to the second order and (ii) the effective medium exponent
near the percolation threshold are , , where is the
nonlinearity exponent. Finally, we give analytical expressions for previously
numerically calculated quantities.Comment: 4 pages, 1 figure, to appear in Phys. Rev.
Statics, metastable states and barriers in protein folding: A replica variational approach
Protein folding is analyzed using a replica variational formalism to
investigate some free energy landscape characteristics relevant for dynamics. A
random contact interaction model that satisfies the minimum frustration
principle is used to describe the coil-globule transition (characterized by
T_CG), glass transitions (by T_A and T_K) and folding transition (by T_F).
Trapping on the free energy landscape is characterized by two characteristic
temperatures, one dynamic, T_A the other static, T_K (T_A> T_K), which are
similar to those found in mean field theories of the Potts glass. 1)Above T_A,
the free energy landscape is monotonous and polymer is melted both dynamically
and statically. 2)Between T_A and T_K, the melted phase is still dominant
thermodynamically, but frozen metastable states, exponentially large in number,
appear. 3)A few lowest minima become thermodynamically dominant below T_K,
where the polymer is totally frozen. In the temperature range between T_A and
T_K, barriers between metastable states are shown to grow with decreasing
temperature suggesting super-Arrhenius behavior in a sufficiently large system.
Due to evolutionary constraints on fast folding, the folding temperature T_F is
expected to be higher than T_K, but may or may not be higher than T_A. Diverse
scenarios of the folding kinetics are discussed based on phase diagrams that
take into account the dynamical transition, as well as the static ones.Comment: 41 pages, LaTeX, 9 EPS figure
Protein design in a lattice model of hydrophobic and polar amino acids
A general strategy is described for finding which amino acid sequences have
native states in a desired conformation (inverse design). The approach is used
to design sequences of 48 hydrophobic and polar aminoacids on three-dimensional
lattice structures. Previous studies employing a sequence-space Monte-Carlo
technique resulted in the successful design of one sequence in ten attempts.
The present work also entails the exploration of conformations that compete
significantly with the target structure for being its ground state. The design
procedure is successful in all the ten cases.Comment: RevTeX, 12 pages, 1 figur
Modeling study on the validity of a possibly simplified representation of proteins
The folding characteristics of sequences reduced with a possibly simplified
representation of five types of residues are shown to be similar to their
original ones with the natural set of residues (20 types or 20 letters). The
reduced sequences have a good foldability and fold to the same native structure
of their optimized original ones. A large ground state gap for the native
structure shows the thermodynamic stability of the reduced sequences. The
general validity of such a five-letter reduction is further studied via the
correlation between the reduced sequences and the original ones. As a
comparison, a reduction with two letters is found not to reproduce the native
structure of the original sequences due to its homopolymeric features.Comment: 6 pages with 4 figure
Architecture of Pol II(G) and molecular mechanism of transcription regulation by Gdown1.
Tight binding of Gdown1 represses RNA polymerase II (Pol II) function in a manner that is reversed by Mediator, but the structural basis of these processes is unclear. Although Gdown1 is intrinsically disordered, its Pol II interacting domains were localized and shown to occlude transcription factor IIF (TFIIF) and transcription factor IIB (TFIIB) binding by perfect positioning on their Pol II interaction sites. Robust binding of Gdown1 to Pol II is established by cooperative interactions of a strong Pol II binding region and two weaker binding modulatory regions, thus providing a mechanism both for tight Pol II binding and transcription inhibition and for its reversal. In support of a physiological function for Gdown1 in transcription repression, Gdown1 co-localizes with Pol II in transcriptionally silent nuclei of early Drosophila embryos but re-localizes to the cytoplasm during zygotic genome activation. Our study reveals a self-inactivation through Gdown1 binding as a unique mode of repression in Pol II function
Steric constraints in model proteins
A simple lattice model for proteins that allows for distinct sizes of the
amino acids is presented. The model is found to lead to a significant number of
conformations that are the unique ground state of one or more sequences or
encodable. Furthermore, several of the encodable structures are highly
designable and are the non-degenerate ground state of several sequences. Even
though the native state conformations are typically compact, not all compact
conformations are encodable. The incorporation of the hydrophobic and polar
nature of amino acids further enhances the attractive features of the model.Comment: RevTex, 5 pages, 3 postscript figure
Comparative analysis of homology models of the Ah receptor ligand binding domain: Verification of structure-function predictions by site-directed mutagenesis of a nonfunctional receptor
The aryl hydrocarbon receptor (AHR) is a ligand-dependent transcription factor that mediates the biological and toxic effects of a wide variety of structurally diverse chemicals, including the toxic environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). While significant interspecies differences in AHR ligand binding specificity, selectivity, and response have been observed, the structural determinants responsible for those differences have not been determined, and homology models of the AHR ligand-binding domain (LBD) are available for only a few species. Here we describe the development and comparative analysis of homology models of the LBD of 16 AHRs from 12 mammalian and nonmammalian species and identify the specific residues contained within their ligand binding cavities. The ligand-binding cavity of the fish AHR exhibits differences from those of mammalian and avian AHRs, suggesting a slightly different TCDD binding mode. Comparison of the internal cavity in the LBD model of zebrafish (zf) AHR2, which binds TCDD with high affinity, to that of zfAHR1a, which does not bind TCDD, revealed that the latter has a dramatically shortened binding cavity due to the side chains of three residues (Tyr296, Thr386, and His388) that reduce the amount of internal space available to TCDD. Mutagenesis of two of these residues in zfAHR1a to those present in zfAHR2 (Y296H and T386A) restored the ability of zfAHR1a to bind TCDD and to exhibit TCDD-dependent binding to DNA. These results demonstrate the importance of these two amino acids and highlight the predictive potential of comparative analysis of homology models from diverse species. The availability of these AHR LBD homology models will facilitate in-depth comparative studies of AHR ligand binding and ligand-dependent AHR activation and provide a novel avenue for examining species-specific differences in AHR responsiveness. © 2013 American Chemical Society
A review on hierarchical routing protocols for wireless sensor networks
The routing protocol for Wireless Sensor Networks (WSNs) is defined as the manner of data dissemination from the network field (source) to the base station (destination). Based on the network topology, there are two types of routing protocols in WSNs, they are namely flat routing protocols and hierarchical routing protocols. Hierarchical routing protocols (HRPs) are more energy efficient and scalable compared to flat routing protocols. This paper discusses how topology management and network application influence the performance of cluster-based and chain-based hierarchical networks. It reviews the basic features of sensor connectivity issues such as power control in topology set-up, sleep/idle pairing and data transmission control that are used in five common HRPs, and it also examines their impact on the protocol performance. A good picture of their respective performances give an indication how network applications, i.e whether reactive or proactive, and topology management i.e. whether centralized or distributed would determine the network performance. Finally, from the ensuring discussion, it is shown that the chain-based HRPs guarantee a longer network lifetime compared to cluster-based HRPs by three to five times
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