skip to main content
US FlagAn official website of the United States government
dot gov icon
Official websites use .gov
A .gov website belongs to an official government organization in the United States.
https lock icon
Secure .gov websites use HTTPS
A lock ( lock ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

Attention:

The NSF Public Access Repository (PAR) system and access will be unavailable from 10:00 PM to 12:00 PM ET on Tuesday, March 25 due to maintenance. We apologize for the inconvenience.


Title: Uncovering the folding mechanism of pertactin: A comparative study of isolated and vectorial folding
Award ID(s):
1806833
PAR ID:
10459165
Author(s) / Creator(s):
; ;
Date Published:
Journal Name:
Biophysical Journal
Volume:
122
Issue:
14
ISSN:
0006-3495
Page Range / eLocation ID:
2988 to 2995
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. Self-folding origami, structures that are engineered flat to fold into targeted, three-dimensional shapes, have many potential engineering applications. Though significant effort in recent years has been devoted to designing fold patterns that can achieve a variety of target shapes, recent work has also made clear that many origami structures exhibit multiple folding pathways, with a proliferation of geometric folding pathways as the origami structure becomes complex. The competition between these pathways can lead to structures that are programmed for one shape, yet fold incorrectly. To disentangle the features that lead to misfolding, we introduce a model of self-folding origami that accounts for the finite stretching rigidity of the origami faces and allows the computation of energy landscapes that lead to misfolding. We find that, in addition to the geometrical features of the origami, the finite elasticity of the nearly-flat origami configurations regulates the proliferation of potential misfolded states through a series of saddle-node bifurcations. We apply our model to one of the most common origami motifs, the symmetric “bird's foot,” a single vertex with four folds. We show that though even a small error in programmed fold angles induces metastability in rigid origami, elasticity allows one to tune resilience to misfolding. In a more complex design, the “Randlett flapping bird,” which has thousands of potential competing states, we further show that the number of actual observed minima is strongly determined by the structure's elasticity. In general, we show that elastic origami with both stiffer folds and less bendable faces self-folds better. 
    more » « less
  2. How knotted proteins fold has remained controversial since the identification of deeply knotted proteins nearly two decades ago. Both computational and experimental approaches have been used to investigate protein knot formation. Motivated by the computer simulations of Bölinger et al. [Bölinger D, et al. (2010)PLoS Comput Biol6:e1000731] for the folding of the 6 1 -knotted α-haloacid dehalogenase (DehI) protein, we introduce a topological description of knot folding that could describe pathways for the formation of all currently known protein knot types and predicts knot types that might be identified in the future. We analyze fingerprint data from crystal structures of protein knots as evidence that particular protein knots may fold according to specific pathways from our theory. Our results confirm Taylor’s twisted hairpin theory of knot folding for the 3 1 -knotted proteins and the 4 1 -knotted ketol-acid reductoisomerases and present alternative folding mechanisms for the 4 1 -knotted phytochromes and the 5 2 - and 6 1 -knotted proteins. 
    more » « less
  3. Prediction of RNA structure is an important problem in understanding biological processes in living organism. Computational models have been created to study the processes with the aim of unravelling the RNA structure. In this work, a novel formalism for formal analysis of RNA structure prediction is described. A graph rewriting system is formalized to represent structural dynamics of RNA structure under uncertainty. Probabilistic model checking is performed on queries seeking structural properties in RNA. Experiments were conducted to evaluate the computational feasibility of the model. 
    more » « less
  4. null (Ed.)