Related papers: New method for deciphering free energy landscape o…
We present a Monte Carlo study of a model protein with 54 amino acids that folds directly to its native three-helix-bundle state without forming any well-defined intermediate state. The free-energy barrier separating the native and unfolded…
We have developed a new extended replica exchange method to study thermodynamics of a system in the presence of external force. Our idea is based on the exchange between different force replicas to accelerate the equilibrium process. We…
We present an efficient method to compute transition rates between states for a two-state system. The method utilizes the equivalence between steady-state flux and mean first passage rate for such systems. More specifically, the procedure…
The experimental calorimetric two-state criterion requires the van't Hoff enthalpy $\Delta H_{\rm vH}$ around the folding/unfolding transition midpoint to be equal or very close to the calorimetric enthalpy $\Delta H_{\rm cal}$ of the…
The present work shows that the free energy landscape associated with alanine dipeptide isomerization can be effectively represented by specific interatomic distances without explicit reference to dihedral angles. Conventionally, two stable…
Within the frame of an effective, coarse-grained hydrophobic-polar protein model, we employ multicanonical Monte Carlo simulations to investigate free-energy landscapes and folding channels of exemplified heteropolymer sequences, which are…
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,…
Under certain conditions, the dynamics of coarse-grained models of solvated proteins can be described using a Markov state model, which tracks the evolution of populations of configurations. The transition rates among states that appear in…
Energy landscape theory describes how a full-length protein can attain its native fold by sampling only a tiny fraction of all possible structures. Although protein folding is now understood to be concomitant with synthesis on the ribosome,…
We describe a two-step approach for combining interactive molecular dynamics in virtual reality (iMD-VR) with free energy (FE) calculation to explore the dynamics of biological processes at the molecular level. We refer to this combined…
In experiments and in simulations, the free energy of a state of a system can be determined from the probability that the state is occupied. However, it is often necessary to impose a biasing potential on the system so that high energy…
Understanding the differentiation, a biological process from a multipotent stem or progenitor state to a mature cell is critically important. We develop a theoretical framework to quantify the underlying potential landscape and biological…
Most single-molecule studies derive the kinetic rates of native, intermediate, and unfolded states from equilibrium hopping experiments. Here, we apply Kramers kinetic diffusive model to derive the force-dependent kinetic rates of…
Developing accurate and efficient coarse-grained representations of proteins is crucial for understanding their folding, function, and interactions over extended timescales. Our methodology involves simulating proteins with molecular…
The Metropolis Monte Carlo (MC) method is used to extract reaction kinetics from a given equilibrium distribution of states of a complex system. The approach is illustrated by the folding/unfolding reaction for two proteins - a model…
Jarzynski's equality [1] allows us to investigate free energy landscapes (FELs) by constructing distributions of work performed on a system from an initial ensemble of states to final states. This work is experimentally measured by…
Free energy landscapes encode the kinetics, intermediates, and transition states that govern molecular processes and are thus a key target of single biomolecule research. Typical approaches to deriving optimal, error-minimizing,…
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…
We investigate the mechanical unfolding of the tenth type III domain from fibronectin, FnIII10, both at constant force and at constant pulling velocity, by all-atom Monte Carlo simulations. We observe both apparent two-state unfolding and…
Protein folding is analyzed using a replica variational formalism to investigate some free energy landscape characteristics relevant for dynamics. A random contact interaction model that satisfies the minimum frustration principle is used…