A revised worm‐like chain model for elasticity of polypeptide chains

Abstract

The elasticity of polypeptide chains is usually characterized by the worm‐like chain model that was proposed first to describe the elasticity of double‐stranded DNA. However, the molecular dynamics simulation data on the elasticity of the polypeptide chains are deviated significantly away from the theoretical data obtained based on the worm‐like chain model. Here, we provide a revised worm‐like chain model by considering entropic, enthalpic, and hydrophobic effects and the effect of the compressing force applied to the polypeptide chains. The theoretical data obtained based on the revised model are in good agreement with the molecular dynamics simulation data. Additionally, we reveal that, besides the positive‐force regime in the elasticity of polypeptide chains, the negative‐force regime also plays important roles in the biological functions of proteins. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2018, 56, 297–307

The hierarchical emergence of worm-like chain behaviour from globular domain polymer chains

“…This dependence of L p on L c was implicitly noted by Kellermeyer in a study of the biopolymer titin 21 , who noted the 'apparent' persistence length changed as certain titin subdomains unfolded under experimental conditions. Further, Fu et al introduced the idea of a 'natural length' for a polymer 22 , termed L n , representing the end-to-end distance of the polymer at zero external force. Yet if the lengths of the polymeric structure change as a function of applied force, this leaves the contour length L c acting as a fitting parameter with a somewhat loose physical interpretation, rather than explicitly defining the polymeric structure as we might assume.…”

Tracking the Single-Carbon-Dot Transmembrane Transport by Force Tracing Based on Atomic Force Microscopy

“…To understand the dynamic transporting process in-depth, another key parameter, the average speed during the process of CDs transmembrane transporting was calculated (displacement divided by duration). Figure displays that the displacement ( D ) of CD transporting includes the bending distance of the AFM tip cantilever ( d ) and the stretching length of the PEG linker ( Q ), as expressed by the following equation. According to the relationship between PEG stretching behavior and the force, the value of Q could be obtained by the extended worm-like chain (WLC) model: Where L p is the persistence length, k B stands for the Boltzmann constant, T refers to the absolute temperature, the extension of the PEG linker is Q , L 0 is the contour length, and k 0 presents the enthalpic correction. Referring to the literature, , the persistence L p is 3.8 ± 0.02 Å, and k 0 is 1561 ± 33 pN.…”

Energy/entropy partition of force at DNA stretching

“…The thermoelastic relation Equation (9) implies that f = f U at T = 0. Thus, the extrapolation of the function f (T) to T = 0 should provide the energy contribution f U.…”

“…The analytical WLC model has been powerful in the interpretation of the tensile nanomechanics of a wide range of semiflexible polymers under weak and moderate tensile forces. [3][4][5][6][8][9][10] The popularity of the model is in part bound to the availability of the closedform force-extension relationship f(R) due to Marko and Siggia (MS). [3] However, the polymers under strong forces in experiments can be stretched above their contour length L o .…”