12,590 research outputs found
End-to-End Optimized Pipeline for Prediction of Protein Folding Kinetics
Protein folding is the intricate process by which a linear sequence of amino
acids self-assembles into a unique three-dimensional structure. Protein folding
kinetics is the study of pathways and time-dependent mechanisms a protein
undergoes when it folds. Understanding protein kinetics is essential as a
protein needs to fold correctly for it to perform its biological functions
optimally, and a misfolded protein can sometimes be contorted into shapes that
are not ideal for a cellular environment giving rise to many degenerative,
neuro-degenerative disorders and amyloid diseases. Monitoring at-risk
individuals and detecting protein discrepancies in a protein's folding kinetics
at the early stages could majorly result in public health benefits, as
preventive measures can be taken. This research proposes an efficient pipeline
for predicting protein folding kinetics with high accuracy and low memory
footprint. The deployed machine learning (ML) model outperformed the
state-of-the-art ML models by 4.8% in terms of accuracy while consuming 327x
lesser memory and being 7.3% faster.Comment: Accepted for presentation at the 22nd International Conference on
Machine Learning and Application
Transition states in protein folding kinetics: Modeling Phi-values of small beta-sheet proteins
Small single-domain proteins often exhibit only a single free-energy barrier,
or transition state, between the denatured and the native state. The folding
kinetics of these proteins is usually explored via mutational analysis. A
central question is which structural information on the transition state can be
derived from the mutational data. In this article, we model and structurally
interpret mutational Phi-values for two small beta-sheet proteins, the PIN and
the FBP WW domain. The native structure of these WW domains comprises two
beta-hairpins that form a three-stranded beta-sheet. In our model, we assume
that the transition state consists of two conformations in which either one of
the hairpins is formed. Such a transition state has been recently observed in
Molecular Dynamics folding-unfolding simulations of a small designed
three-stranded beta-sheet protein. We obtain good agreement with the
experimental data (i) by splitting up the mutation-induced free-energy changes
into terms for the two hairpins and for the small hydrophobic core of the
proteins, and (ii) by fitting a single parameter, the relative degree to which
hairpin 1 and 2 are formed in the transition state. The model helps to
understand how mutations affect the folding kinetics of WW domains, and
captures also negative Phi-values that have been difficult to interpret.Comment: 27 pages, 6 pages, 3 tables; to appear in Biophys.
The Energy Landscape, Folding Pathways and the Kinetics of a Knotted Protein
The folding pathway and rate coefficients of the folding of a knotted protein
are calculated for a potential energy function with minimal energetic
frustration. A kinetic transition network is constructed using the discrete
path sampling approach, and the resulting potential energy surface is
visualized by constructing disconnectivity graphs. Owing to topological
constraints, the low-lying portion of the landscape consists of three distinct
regions, corresponding to the native knotted state and to configurations where
either the N- or C-terminus is not yet folded into the knot. The fastest
folding pathways from denatured states exhibit early formation of the
N-terminus portion of the knot and a rate-determining step where the C-terminus
is incorporated. The low-lying minima with the N-terminus knotted and the
C-terminus free therefore constitute an off-pathway intermediate for this
model. The insertion of both the N- and C-termini into the knot occur late in
the folding process, creating large energy barriers that are the rate limiting
steps in the folding process. When compared to other protein folding proteins
of a similar length, this system folds over six orders of magnitude more
slowly.Comment: 19 page
Pathways and kinetic barriers in mechanical unfolding and refolding of RNA and proteins
Using self-organized polymer models, we predict mechanical unfolding and
refolding pathways of ribo-zymes, and the green fluorescent protein. In
agreement with experiments, there are between six and eight unfolding
transitions in the Tetrahymena ribozyme. Depending on the loading rate, the
number of rips in the force-ramp unfolding of the Azoarcus ribozymes is between
two and four. Force-quench refolding of the P4-P6 subdomain of the Tetrahymena
ribozyme occurs through a compact intermediate. Subsequent formation of
tertiary contacts between helices P5b-P6a and P5a/P5c-P4 leads to the native
state. The force-quench refolding pathways agree with ensemble experiments. In
the dominant unfolding route, the N-terminal a helix of GFP unravels first,
followed by disruption of the N terminus b strand. There is a third
intermediate that involves disruption of three other strands. In accord with
experiments, the force-quench refolding pathway of GFP is hierarchic, with the
rate-limiting step being the closure of the barrel.Comment: 33 pages 7 figure
- …