4,273 research outputs found
Topological entropy and secondary folding
A convenient measure of a map or flow's chaotic action is the topological
entropy. In many cases, the entropy has a homological origin: it is forced by
the topology of the space. For example, in simple toral maps, the topological
entropy is exactly equal to the growth induced by the map on the fundamental
group of the torus. However, in many situations the numerically-computed
topological entropy is greater than the bound implied by this action. We
associate this gap between the bound and the true entropy with 'secondary
folding': material lines undergo folding which is not homologically forced. We
examine this phenomenon both for physical rod-stirring devices and toral linked
twist maps, and show rigorously that for the latter secondary folds occur.Comment: 13 pages, 8 figures. pdfLaTeX with RevTeX4 macro
Estimating topological entropy from the motion of stirring rods
Stirring a two-dimensional viscous fluid with rods is often an effective way
to mix. The topological features of periodic rod motions give a lower bound on
the topological entropy of the induced flow map, since material lines must
`catch' on the rods. But how good is this lower bound? We present examples from
numerical simulations and speculate on what affects the 'gap' between the lower
bound and the measured topological entropy. The key is the sign of the rod
motion's action on first homology of the orientation double cover of the
punctured disk.Comment: 10 pages, 20 figures. IUTAM Procedia style (included). Submitted to
volume "Topological Fluid Dynamics II.
Loop-closure principles in protein folding
Simple theoretical concepts and models have been helpful to understand the
folding rates and routes of single-domain proteins. As reviewed in this
article, a physical principle that appears to underly these models is loop
closure.Comment: 27 pages, 5 figures; to appear in Archives of Biochemistry and
Biophysic
Macromolecular crowding modulates folding mechanism of alpha/beta protein apoflavodoxin
Protein dynamics in cells may be different from that in dilute solutions in
vitro since the environment in cells is highly concentrated with other
macromolecules. This volume exclusion due to macromolecular crowding is
predicted to affect both equilibrium and kinetic processes involving protein
conformational changes. To quantify macromolecular crowding effects on protein
folding mechanisms, here we have investigated the folding energy landscape of
an alpha/beta protein, apoflavodoxin, in the presence of inert macromolecular
crowding agents using in silico and in vitro approaches. By coarse-grained
molecular simulations and topology-based potential interactions, we probed the
effects of increased volume fraction of crowding agents (phi_c) as well as of
crowding agent geometry (sphere or spherocylinder) at high phi_c. Parallel
kinetic folding experiments with purified Desulfovibro desulfuricans
apoflavodoxin in vitro were performed in the presence of Ficoll (sphere) and
Dextran (spherocylinder) synthetic crowding agents. In conclusion, we have
identified in silico crowding conditions that best enhance protein stability
and discovered that upon manipulation of the crowding conditions, folding
routes experiencing topological frustrations can be either enhanced or
relieved. The test-tube experiments confirmed that apoflavodoxin's
time-resolved folding path is modulated by crowding agent geometry. We propose
that macromolecular crowding effects may be a tool for manipulation of protein
folding and function in living cells.Comment: to appear in Biophysical Journal (2009). to appear in Biophysical
Journal (2009
A simple measure of native-state topology and chain connectivity predicts the folding rates of two-state proteins with and without crosslinks
The folding rates of two-state proteins have been found to correlate with
simple measures of native-state topology. The most prominent among these
measures is the relative contact order (CO), which is the average CO or
'localness' of all contacts in the native protein structure, divided by the
chain length. Here, we test whether such measures can be generalized to capture
the effect of chain crosslinks on the folding rate. Crosslinks change the chain
connectivity and therefore also the localness of some of the the native
contacts. These changes in localness can be taken into account by the
graph-theoretical concept of effective contact order (ECO). The relative ECO,
however, the natural extension of the relative CO for proteins with crosslinks,
overestimates the changes in the folding rates caused by crosslinks. We suggest
here a novel measure of native-state topology, the relative logCO, and its
natural extension, the relative logECO. The relative logCO is the average value
for the logarithm of the CO of all contacts, divided by the logarithm of the
chain length. The relative log(E)CO reproduces the folding rates of a set of 26
two-state proteins without crosslinks with essentially the same high
correlation coefficient as the relative CO. In addition, it also captures the
folding rates of 8 two-state proteins with crosslinks.Comment: 13 pages, 2 tables, and 2 figure
Protein folding in high-dimensional spaces:hypergutters and the role of non-native interactions
We explore the consequences of very high dimensionality in the dynamical
landscape of protein folding. Consideration of both typical range of
stabilising interactions, and folding rates themselves, leads to a model of the
energy hypersurface that is characterised by the structure of diffusive
"hypergutters" as well as the familiar "funnels". Several general predictions
result: (1) intermediate subspaces of configurations will always be visited;
(2) specific but non-native interactions are important in stabilising these
low-dimensional diffusive searches on the folding pathway; (3) sequential
barriers will commonly be found, even in "two-state"proteins; (4) very early
times will show charactreristic departures from single-exponential kinetics;
(5) contributions of non-native interactions to phi-values are calculable, and
may be significant. The example of a three-helix bundle is treated in more
detail as an illustration. The model also shows that high-dimensional
structures provide conceptual relations between the "folding funnel",
"diffusion-collision", "nucleation-condensation" and "topomer search" models of
protein folding. It suggests that kinetic strategies for fast folding may be
encoded rather generally in non-native, rather than native interactions. The
predictions are related to very recent findings in experiment and simulation.Comment: Submitted to Biophys.
How native state topology affects the folding of Dihydrofolate Reductase and Interleukin-1beta
The overall structure of the transition state and intermediate ensembles
experimentally observed for Dihydrofolate Reductase and Interleukin-1beta can
be obtained utilizing simplified models which have almost no energetic
frustration. The predictive power of these models suggest that, even for these
very large proteins with completely different folding mechanisms and functions,
real protein sequences are sufficiently well designed and much of the
structural heterogeneity observed in the intermediates and the transition state
ensembles is determined by topological effects.Comment: Proc. Natl. Acad. Sci. USA, in press (11 pages, 4 color PS figures)
Higher resolution PS files can be found at
http://www-physics.ucsd.edu/~cecilia/pub_list.htm
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