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Stirred spin glass models of in vivo protein folding
No full text"The similarity between spin glasses and proteins is that both have complex energy landscapes with multiple energy minima and barriers. The approach to equilibrium in such systems has been previously studied. We present here a ""stirred"" spin glass whose equilibrium is constantly being perturbed by a possibility for effectively leaving and reentering the system. Our results indicate that such stirring causes a spread in the equilibrium occupancy of energy levels and, probably lower or abolish the freezing temperature of the system."We used this stirred spin-glass picture to analyze in vivo protein folding. The statistical energy landscape picture of protein folding has led to the understanding that a necessary condition for in vitro foldability is the presence of some sort of guiding forces in the energy landscape leading to folding funnels. Chaperone molecules which are the important actors in in vivo protein folding are known to act basically by repeated binding and unbinding to partially unfolded protein molecules. I describe how this binding and unbinding is equivalent to leaving and re-entering the system and thus to a stirred spin glass. I describe a model of chaperone action based on this repetitive binding, giving rise to a possibility of kinetic proofreading. I also studied models where chaperone binding is locally biased depending upon the similarity to the native state. Our results show that the presence of guiding forces in the energy landscape is necessary for folding within the Levinthal time in vitro. While unbiased binding can help folding modestly, the results show that biased chaperone binding can form the nonequilibrium analog of a folding funnel and dramatically improve yields and shorten timescales.Made available in DSpace on 2011-05-07T12:10:21Z (GMT). No. of bitstreams: 2
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Physical models of protein folding within the energy landscape theory
No full textThe energy landscape theory of protein fol9.ing is based on a statistical description of
a protein's complex potential energy surface. Individual folding events are sampled
from an ensemble of possible routes on the landscape. The theory suggests that the
landscape of a protein can be described as that of a partially random heteropolymer
with a rugged, yet funnelled landscape towards the native structure. The quantitative
aspects of folding are developed using tools from the statistical mechanics of disordered
systems, polymers, and phase transitions of finite systems. The theory provides an
interpretation of results from fast folding experiments as well as minimalist models
used in computer simulations.Submitted by William Weathers ([email protected]) on 2012-05-15T16:19:13Z
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Glassy models of protein folding
No full textIn this thesis we have used concepts from the physics of disordered
materials to study protein folding. The first chapter consists of a general
introduction to proteins and protein folding. In Chapter Two we develop a
simple protein folding model and use a random energy approximation to
calculate its equilibrium properties. The model has unfolded, folded and
glassy phases. In Chapter Three we investigate the dynamics of the model.
The model has many metastable states and the distribution of the lifetimes of
these states is log-normal at high temperatures and becomes much broader in
the glassy phase. Also, we calculate the folding time by deriving a
generalization of transition state theory that takes into account some of the
glassy behavior of our model. The results for the folding time are physically
reasonable. In Chapter Four we combine the ideas of the preceding chapters
with the theory of polymer collapse. First we study the collapse of random
hetropolymers and find that hetropolymers have a frozen collapsed phase that
does not occur in homopolymers. Then we study the equilibrium properties
and folding time of a model of protein folding that incorporates some features
of polymer collapse. The properties of this model are found to be qualitatively
similar to those of our earlier model. We also find that in this new model the
rate limiting step in folding occurs after much of the native structure has been
formed, which agrees with experiments.Submitted by William Weathers ([email protected]) on 2012-04-19T20:21:06Z
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Chain dynamical theories of protein folding
No full textCompletely microscopic theories of protein folding must take into account chain dynamics. The
energy landscape description of protein folding accommodates two rather distinct behaviors of the
polypeptide chain: the glassy dynamics expected for heteropolymers with random interactions and
the organized dynamics expected for minimally frustrated proteins that fold rapidly on a funneled
landscape. The chain dynamical phenomena relevant to both these extremes are studied in this
thesis. First, we derive a mode-coupling theory for the dynamics of a random heteropolymer and
study the dynamical glass transition signaled by a violation of the fluctuation-dissipation theorem.
Next, we develop a variational theory for the smooth free energy surface of minimally frustrated
proteins. In this theory, ensembles of structures along an average folding route (identified by the
stationary points in the free energy surface) are characterized by the local Debye-Waller factor
for each residue about its native position. The description of the folding dynamics of minimally
frustrated proteins is completed by considering the chain dynamics of crossing barriers on the
resulting free energy profile. We choose the λ-repressor protein as a specific example to illustrate
the model, but address the interesting polymer physics that influence free energy profiles and
barrier crossing dynamics. Direct observation of chain dynamics experimentally involves measuring
the fluorescence quenching between individual pairs of monomers. As a first step to providing
the theory for this, a variational formalism is developed to study diffusion influenced reactions
(easily extended to model intrachain quenching in polymers) and applied to simple one-dimensional
problems in order to evaluate the method. Lastly, we investigate how functioning proteins that
bind from the unfolded state exploit protein folding to speed their function.Submitted by William Weathers ([email protected]) on 2012-05-30T20:52:33Z
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Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
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