389 research outputs found
Single-molecule fluorescence studies of intrinsically disordered proteins and liquid phase separation
Intrinsically disordered proteins (IDPs) are ubiquitous in proteomes and serve in a range of cellular functions including signaling, regulation, transport and enzyme function. IDP misfunction and aggregation are also associated with several diseases including neurodegenerative diseases and cancer. During the past decade, single-molecule methods have become popular for detailed biophysical and structural studies of these complex proteins. This work has included recent applications to cellular liquid-liquid phase separation (LLPS), relevant for functional dynamics of membraneless organelles such as the nucleolus and stress granules. In this concise review, we cover the conceptual motivations for development and application of single-molecule fluorescence methods for such IDP studies. We follow with a few key examples of systems and biophysical problems that have been addressed, and conclude with thoughts for emerging and future directions
Mean first passage time analysis reveals rate-limiting steps, parallel pathways and dead ends in a simple model of protein folding
We have analyzed dynamics on the complex free energy landscape of protein
folding in the FOLD-X model, by calculating for each state of the system the
mean first passage time to the folded state. The resulting kinetic map of the
folding process shows that it proceeds in jumps between well-defined, local
free energy minima. Closer analysis of the different local minima allows us to
reveal secondary, parallel pathways as well as dead ends.Comment: 7 page
Origins of Chevron Rollovers in Non-Two-State Protein Folding Kinetics
Chevron rollovers of some proteins imply that their logarithmic folding rates
are nonlinear in native stability. This is predicted by lattice and continuum
G\=o models to arise from diminished accessibilities of the ground state from
transiently populated compact conformations under strongly native conditions.
Despite these models' native-centric interactions, the slowdown is due partly
to kinetic trapping caused by some of the folding intermediates' nonnative
topologies. Notably, simple two-state folding kinetics of small single-domain
proteins are not reproduced by common G\=o-like schemes.Comment: 10 pages, 4 Postscript figures (will appear on PRL
Folding, Design and Determination of Interaction Potentials Using Off-Lattice Dynamics of Model Heteropolymers
We present the results of a self-consistent, unified molecular dynamics study
of simple model heteropolymers in the continuum with emphasis on folding,
sequence design and the determination of the interaction parameters of the
effective potential between the amino acids from the knowledge of the native
states of the designed sequences.Comment: 8 pages, 3 Postscript figures, uses RevTeX. Submitted to Physical
Review Letter
On the statistical mechanics of prion diseases
We simulate a two-dimensional, lattice based, protein-level statistical
mechanical model for prion diseases (e.g., Mad Cow disease) with concommitant
prion protein misfolding and aggregation. Our simulations lead us to the
hypothesis that the observed broad incubation time distribution in
epidemiological data reflect fluctuation dominated growth seeded by a few
nanometer scale aggregates, while much narrower incubation time distributions
for innoculated lab animals arise from statistical self averaging. We model
`species barriers' to prion infection and assess a related treatment protocol.Comment: 5 Pages, 3 eps figures (submitted to Physical Review Letters
Statistical mechanics of secondary structures formed by random RNA sequences
The formation of secondary structures by a random RNA sequence is studied as
a model system for the sequence-structure problem omnipresent in biopolymers.
Several toy energy models are introduced to allow detailed analytical and
numerical studies. First, a two-replica calculation is performed. By mapping
the two-replica problem to the denaturation of a single homogeneous RNA in
6-dimensional embedding space, we show that sequence disorder is perturbatively
irrelevant, i.e., an RNA molecule with weak sequence disorder is in a molten
phase where many secondary structures with comparable total energy coexist. A
numerical study of various models at high temperature reproduces behaviors
characteristic of the molten phase. On the other hand, a scaling argument based
on the extremal statistics of rare regions can be constructed to show that the
low temperature phase is unstable to sequence disorder. We performed a detailed
numerical study of the low temperature phase using the droplet theory as a
guide, and characterized the statistics of large-scale, low-energy excitations
of the secondary structures from the ground state structure. We find the
excitation energy to grow very slowly (i.e., logarithmically) with the length
scale of the excitation, suggesting the existence of a marginal glass phase.
The transition between the low temperature glass phase and the high temperature
molten phase is also characterized numerically. It is revealed by a change in
the coefficient of the logarithmic excitation energy, from being disorder
dominated to entropy dominated.Comment: 24 pages, 16 figure
Ensino e Aprendizagem de Matemática Através da Resolução de Problemas Como Prática Sociointeracionista
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
Role of Secondary Motifs in Fast Folding Polymers: A Dynamical Variational Principle
A fascinating and open question challenging biochemistry, physics and even
geometry is the presence of highly regular motifs such as alpha-helices in the
folded state of biopolymers and proteins. Stimulating explanations ranging from
chemical propensity to simple geometrical reasoning have been invoked to
rationalize the existence of such secondary structures. We formulate a
dynamical variational principle for selection in conformation space based on
the requirement that the backbone of the native state of biologically viable
polymers be rapidly accessible from the denatured state. The variational
principle is shown to result in the emergence of helical order in compact
structures.Comment: 4 pages, RevTex, 4 eps figure
Protein structures and optimal folding emerging from a geometrical variational principle
Novel numerical techniques, validated by an analysis of barnase and
chymotrypsin inhibitor, are used to elucidate the paramount role played by the
geometry of the protein backbone in steering the folding to the correct native
state. It is found that, irrespective of the sequence, the native state of a
protein has exceedingly large number of conformations with a given amount of
structural overlap compared to other compact artificial backbones; moreover the
conformational entropies of unrelated proteins of the same length are nearly
equal at any given stage of folding. These results are suggestive of an
extremality principle underlying protein evolution, which, in turn, is shown to
be associated with the emergence of secondary structures.Comment: Revtex, 5 pages, 5 postscript figure
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