Force-Extension Curve of an Entangled Polymer Chain: A Superspace Approach

Author(s):  
Huan Gong ◽  
Jian-Feng Li ◽  
Hong-Dong Zhang ◽  
An-Chang Shi
2019 ◽  
Vol 116 (39) ◽  
pp. 19500-19505 ◽  
Author(s):  
Matthew T. J. Halma ◽  
Dustin B. Ritchie ◽  
Tonia R. Cappellano ◽  
Krishna Neupane ◽  
Michael T. Woodside

Specific structures in mRNA can stimulate programmed ribosomal frameshifting (PRF). PRF efficiency can vary enormously between different stimulatory structures, but the features that lead to efficient PRF stimulation remain uncertain. To address this question, we studied the structural dynamics of the frameshift signal from West Nile virus (WNV), which stimulates −1 PRF at very high levels and has been proposed to form several different structures, including mutually incompatible pseudoknots and a double hairpin. Using optical tweezers to apply tension to single mRNA molecules, mimicking the tension applied by the ribosome during PRF, we found that the WNV frameshift signal formed an unusually large number of different metastable structures, including all of those previously proposed. From force-extension curve measurements, we mapped 2 mutually exclusive pathways for the folding, each encompassing multiple intermediates. We identified the intermediates in each pathway from length changes and the effects of antisense oligomers blocking formation of specific contacts. Intriguingly, the number of transitions between the different conformers of the WNV frameshift signal was maximal in the range of forces applied by the ribosome during −1 PRF. Furthermore, the occupancy of the pseudoknotted conformations was far too low for static pseudoknots to account for the high levels of −1 PRF. These results support the hypothesis that conformational heterogeneity plays a key role in frameshifting and suggest that transitions between different conformers under tension are linked to efficient PRF stimulation.


2005 ◽  
Vol 873 ◽  
Author(s):  
Jason T. Roland ◽  
Dora Guzman ◽  
Jane Bai ◽  
Zhibin Guan

AbstractNative load-bearing proteins, such as the muscle protein titin, exhibit a remarkable degree of combined toughness, strength, and elasticity which have yet to be matched by synthetic materials.Single molecule nanomechanical studies on titin and other modular proteins suggest that these exceptional properties arise from a modular elongation mechanism. The sequential unfolding allows modular biopolymers to sustain a large force over the whole extension of the chain, which makes the polymer strong, along with a large area under the force-extension curve, making it tough as well. In addition, when the external force is removed, the unfolded domains of modular proteins will refold automatically, making them elastic. Inspired by nature, one research effort in my group is aimed at designing synthetic macromolecules that form high order structures by programming non-covalent interactions into polymer chain. The goal is to achieve synthetic biomaterials with combined strength, toughness and elasticity. Three classes of well-defined modular polymers have been synthesized in our laboratory: (1) using quadruple hydrogen-bonding motif 2-ureidon-4-pyrimidone (Upy) to direct the formation loops along a polymer chain (J. Am. Chem. Soc.2004, 126, 2058); (2) using a peptidomimetic beta-sheet based double-closed loop (DCL) as module (J. Am. Chem. Soc.2004, 126, 14328); and (3) an engineered protein G domain III as module. Single molecule force-extension experiments revealed the sequential unfolding of the loops or domains as these modular polymers are stretched, resulting in sawtooth-patterned curves similar to those seen in titin and other biopolymers. In this paper, we will discuss our designs, syntheses and single-molecule studies of polymers having modular domain structures.


1999 ◽  
Vol 145 (2) ◽  
pp. 215-223 ◽  
Author(s):  
Bahram Houchmandzadeh ◽  
Stefan Dimitrov

Chromosome condensation is one of the most critical steps during cell division. However, the structure of condensed mitotic chromosomes is poorly understood. In this paper we describe a new approach based on elasticity measurements for studying the structure of in vitro assembled mitotic chromosomes in Xenopus egg extract. The approach is based on a unique combination of measurements of both longitudinal deformability and bending rigidity of whole chromosomes. By using specially designed micropipettes, the chromosome force–extension curve was determined. Analysis of the curvature fluctuation spectrum allowed for the measurement of chromosome bending ridigity. The relationship between the values of these two parameters is very specific: the measured chromosome flexibility was found to be 2,000 times lower than the flexibility calculated from the experimentally determined Young modulus. This requires the chromosome structure to be formed of one or a few thin rigid elastic axes surrounded by a soft envelope. The properties of these axes are well-described by models developed for the elasticity of titin-like molecules. Additionally, the deformability of in vitro assembled chromosomes was found to be very similar to that of native somatic chromosomes, thus demonstrating the existence of an essentially identical structure.


2010 ◽  
Vol 36 (3) ◽  
pp. 221-228 ◽  
Author(s):  
Hamid Dalir ◽  
Takasi Nisisako ◽  
Yasuko Yanagida ◽  
Takeshi Hatsuzawa

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