1,549 research outputs found
How Accurate Must Potentials Be for Successful Modeling of Protein Folding?
Protein sequences are believed to have been selected to provide the stability
of, and reliable renaturation to, an encoded unique spatial fold. In recently
proposed theoretical schemes, this selection is modeled as ``minimal
frustration,'' or ``optimal energy'' of the desirable target conformation over
all possible sequences, such that the ``design'' of the sequence is governed by
the interactions between monomers. With replica mean field theory, we examine
the possibility to reconstruct the renaturation, or freezing transition, of the
``designed'' heteropolymer given the inevitable errors in the determination of
interaction energies, that is, the difference between sets (matrices) of
interactions governing chain design and conformations, respectively. We find
that the possibility of folding to the designed conformation is controlled by
the correlations of the elements of the design and renaturation interaction
matrices; unlike random heteropolymers, the ground state of designed
heteropolymers is sufficiently stable, such that even a substantial error in
the interaction energy should still yield correct renaturation.Comment: 28 pages, 3 postscript figures; tared, compressed, uuencode
Freezing Transition of Random Heteropolymers Consisting of an Arbitrary Set of Monomers
Mean field replica theory is employed to analyze the freezing transition of
random heteropolymers comprised of an arbitrary number () of types of
monomers. Our formalism assumes that interactions are short range and
heterogeneity comes only from pairwise interactions, which are defined by an
arbitrary matrix. We show that, in general, there exists a
freezing transition from a random globule, in which the thermodynamic
equilibrium is comprised of an essentially infinite number polymer
conformations, to a frozen globule, in which equilibrium ensemble is dominated
by one or very few conformations. We also examine some special cases of
interaction matrices to analyze the relationship between the freezing
transition and the nature of interactions involved.Comment: 30 pages, 1 postscript figur
Prevalence of malnutrition and intestinal parasites in preschool slum children in Lucknow
Objective: To assess the point prevalence of intestinal parasites and their association with nutritional parameters. Setting: Anganwadi centers under the Integrated Child Development Scheme (ICDS) in Lucknow, North India. Design: Cross-sectional survey. Methods: By random draw, 32 out of 153 Anganwadi centers were selected. All eligible subjects registered with the Anganwadi worker were enrolled. These were 1061 children (48.3% girls and 51.7% boys) between the ages of 1.5 to 3.5 years. Results: Of these, 67.6% were underweight (weight for age <- 2 SD), 62.8% were stunted (height for age <-2 SD) and 26.5% were wasted (weight for height <-2 SD). Parasites were detected in 17.5% (95% CI 15.3%-19.9%) children by a single direct fecal smear examination. Of these, Ascaris lumbricoides was found in 124 (68.1%) and Giardia lamblia in 60 (32.9%). There was no association between weight or height and parasite positivity. The mean hemoglobin levels for children who were smear positive versus smear negative for ascaris or giardia were 9.1 g/dl and 9.6 g/dl, respectively (p<0.0001). Conclusion: In the urban slums the point prevalence of intestinal parasites is 17.5% in the preschool children. Malnutrition and low hemoglobin levels are also widely prevalent. Urgent remedial steps are needed on community basis to improve their nutritional status and control parasitic infestation
Reductive Biotransformation of Ethyl Acetoacetate: A Comparative Studies using Free and Immobilized Whole Yeast Cells
Bioreduction of ethyl acetoacetate with free and immobilized yeast whole cell was achieved by using water and sucrose combination. After detachment from immobilized beads under basic condition, the corresponding ethyl(S)-(+)-3-hydroxybutanoate was isolated with 98 to 100% yield. Immobilized beads of yeast whole cell were prepared at different temperature which affects the morphology and physiology of the beads for the diffusion of the enzyme, which shown the maximum conversion of the substrate to products as compared to the free yeast whole cell
Is Heteropolymer Freezing Well Described by the Random Energy Model?
It is widely held that the Random Energy Model (REM) describes the freezing
transition of a variety of types of heteropolymers. We demonstrate that the
hallmark property of REM, statistical independence of the energies of states
over disorder, is violated in different ways for models commonly employed in
heteropolymer freezing studies. The implications for proteins are also
discussed.Comment: 4 pages, 3 eps figures To appear in Physical Review Letters, May 199
Free Energy Self-Averaging in Protein-Sized Random Heteropolymers
Current theories of heteropolymers are inherently macrpscopic, but are
applied to folding proteins which are only mesoscopic. In these theories, one
computes the averaged free energy over sequences, always assuming that it is
self-averaging -- a property well-established only if a system with quenched
disorder is macroscopic. By enumerating the states and energies of compact 18,
27, and 36mers on a simplified lattice model with an ensemble of random
sequences, we test the validity of the self-averaging approximation. We find
that fluctuations in the free energy between sequences are weak, and that
self-averaging is a valid approximation at the length scale of real proteins.
These results validate certain sequence design methods which can exponentially
speed up computational design and greatly simplify experimental realizations.Comment: 4 pages, 3 figure
Two State Behavior in a Solvable Model of -hairpin folding
Understanding the mechanism of protein secondary structure formation is an
essential part of protein-folding puzzle. Here we describe a simple model for
the formation of the -hairpin, motivated by the fact that folding of a
-hairpin captures much of the basic physics of protein folding. We argue
that the coupling of ``primary'' backbone stiffness and ``secondary'' contact
formation (similar to the coupling between the ``secondary'' and ``tertiary''
structure in globular proteins), caused for example by side-chain packing
regularities, is responsible for producing an all-or-none 2-state
-hairpin formation. We also develop a recursive relation to compute the
phase diagram and single exponential folding/unfolding rate arising via a
dominant transition state.Comment: Revised versio
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