相关论文: Role of pulling direction in understanding the ene…
Single molecule manipulation techniques reveal that the mechanical resistance of a protein depends on the direction of the applied force. Using a lattice model of polymers, we show that changing the pulling direction leads to different…
In recent years single molecule force spectroscopy has opened a new avenue to provide profiles of the complex energy landscape of biomolecules. In this field, quantitative analyses of the data employing sound theoretical models, have played…
A simple lattice model, recently introduced as a generalization of the Wako--Sait\^o model of protein folding, is used to investigate the properties of widely studied molecules under external forces. The equilibrium properties of the model…
In recent years, single molecule force techniques have opened a new avenue to decipher the folding landscapes of biopolymers by allowing us to watch and manipulate the dynamics of individual proteins and nucleic acids. In single molecule…
Mechanical unfolding of polyproteins by force spectroscopy provides valuable insight into their free energy landscapes. Most phenomenological models of the unfolding process are two-state and/or one dimensional, with the details of the…
A theoretical analysis of the unfolding pathway of simple modular proteins in length- controlled pulling experiments is put forward. Within this framework, we predict the first module to unfold in a chain of identical units, emphasizing the…
Single molecule force spectroscopy reveals unfolding of domains in titin upon stretching. We provide a theoretical framework for these experiments by computing the phase diagrams for force-induced unfolding of single domain proteins using…
In the current AFM experiments the distribution of unfolding times, P(t), is measured by applying a constant stretching force f_s from which the apparent unfolding rate is obtained. To describe the complexity of the underlying energy…
Single molecule mechanical unfolding experiments are beginning to provide profiles of the complex energy landscape of biomolecules. In order to obtain reliable estimates of the energy landscape characteristics it is necessary to combine the…
An Ising--like model of proteins is used to investigate the mechanical unfolding of the Green Fluorescent Protein along different directions. When the protein is pulled from its ends, we recover the major and minor unfolding pathways…
The understanding, and even the description of protein folding is impeded by the complexity of the process. Much of this complexity can be described and understood by taking a statistical approach to the energetics of protein conformation,…
We study the geometric properties of the energy landscape of coarse-grained, off-lattice models of polymers by endowing the configuration space with a suitable metric, depending on the potential energy function, such that the dynamical…
We review theoretical approaches, experiments and numerical simulations that have been recently proposed to investigate the folding problem in single-domain proteins. From a theoretical point of view, we emphasize the energy landscape…
With the help of force spectroscopy, several analytical theories aim at estimating the rate coefficient of folding for various proteins. Nevertheless, a chief bottleneck lies in the fact that there is still no perfect consensus on how does…
This review is a tutorial for scientists interested in the problem of protein structure prediction, particularly those interested in using coarse-grained molecular dynamics models that are optimized using lessons learned from the energy…
We discuss recent theoretical developments in the study of simple lattice models of proteins. Such models are designed to understand general features of protein structures and mechanism of folding. Among the topics covered are (i) the use…
The folding dynamics of proteins at the single molecule level has been studied with single-molecule force spectroscopy (SMFS) experiments for twenty years, but a common standardized method for the analysis of the collected data and for the…
We study folding dynamics of protein-like sequences on square lattice using physical move set that exhausts all possible conformational changes. By analytically solving the master equation, we follow the time-dependent probabilities of…
Biological forces govern essential cellular and molecular processes in all living organisms. Many cellular forces, e.g. those generated in cyclic conformational changes of biological machines, have repetitive components. However, little is…
The dependence of the unfolding pathway of proteins on the pulling speed is investigated. This is done by introducing a simple one-dimensional chain comprising $N$ units, with different characteristic bistable free energies. These units…