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Themed collection The free energy landscape: from folding to cellular function

21 items
Editorial

A second molecular biology revolution? The energy landscapes of biomolecular function

This themed issue showcases a collection of work from leading scientists, demonstrating the significance of the free energy landscape in the field of physiochemical biology.

Graphical abstract: A second molecular biology revolution? The energy landscapes of biomolecular function
Perspective

Protein conformation as a regulator of cell–matrix adhesion

Conformational changes within proteins play key roles in the regulation of cell–matrix adhesion. We discuss the mechanisms involved in conformational regulation, including mechanical signals, posttranslational modifications and intrinsically disordered proteins.

Graphical abstract: Protein conformation as a regulator of cell–matrix adhesion
Perspective

The free energy landscape in translational science: how can somatic mutations result in constitutive oncogenic activation?

The free energy landscape theory has transformed the field of protein and related it to function.

Graphical abstract: The free energy landscape in translational science: how can somatic mutations result in constitutive oncogenic activation?
Perspective

The binding mechanisms of intrinsically disordered proteins

Intrinsically disordered protein domains display a range of binding mechanisms, from apparent two-state to multistate.

Graphical abstract: The binding mechanisms of intrinsically disordered proteins
Paper

Fast recovery of free energy landscapes via diffusion-map-directed molecular dynamics

An adaptive sampling algorithm is proposed to rapidly reconstruct free-energy landscapes of macromolecular systems.

Graphical abstract: Fast recovery of free energy landscapes via diffusion-map-directed molecular dynamics
Paper

From structure to function: the convergence of structure based models and co-evolutionary information

A combination of physical models and co-evolutionary information helps to improve our understanding of biomolecular structure and function.

Graphical abstract: From structure to function: the convergence of structure based models and co-evolutionary information
Paper

Predicted disorder-to-order transition mutations in IκBα disrupt function

Single predicted disorder-to-order mutations impair the ability of IκBα to dissociate NFκB from the DNA.

Graphical abstract: Predicted disorder-to-order transition mutations in IκBα disrupt function
Paper

NMR mapping of protein conformational landscapes using coordinated behavior of chemical shifts upon ligand binding

The CONCISE statistical analysis of chemical shifts measures the population shifts and collectiveness of protein response associated with ligand titrations.

Graphical abstract: NMR mapping of protein conformational landscapes using coordinated behavior of chemical shifts upon ligand binding
Paper

Diffuse transition state structure for the unfolding of a leucine-rich repeat protein

Φ-value analysis of the folding mechanism of the leucine-rich repeat domain from TAP reveals a diffusely structured transition state.

Graphical abstract: Diffuse transition state structure for the unfolding of a leucine-rich repeat protein
Paper

Exploring multi-dimensional coordinate-dependent diffusion dynamics on the energy landscape of protein conformation change

Two-dimensional diffusion coefficiencies on the free energy landscape.

Graphical abstract: Exploring multi-dimensional coordinate-dependent diffusion dynamics on the energy landscape of protein conformation change
Paper

A hybrid MD-kMC algorithm for folding proteins in explicit solvent

We present a novel hybrid MD-kMC algorithm and apply it to the folding of the Trp-Cage protein. The algorithm presented not only captures experimentally observed folding intermediates and kinetics, but yields insights into the relative roles of local and global interactions in determining folding mechanisms and rates.

Graphical abstract: A hybrid MD-kMC algorithm for folding proteins in explicit solvent
Paper

Effects of desolvation barriers and sidechains on local–nonlocal coupling and chevron behaviors in coarse-grained models of protein folding

Coarse-grained protein chain models with desolvation barriers or sidechains lead to stronger local–nonlocal coupling and more linear chevron plots.

Graphical abstract: Effects of desolvation barriers and sidechains on local–nonlocal coupling and chevron behaviors in coarse-grained models of protein folding
Paper

Equilibrium thermodynamics and folding kinetics of a short, fast-folding, beta-hairpin

Equilibrium thermodynamics of a short beta-hairpin are studied using unbiased all-atom replica exchange molecular dynamics simulations in explicit solvent.

Graphical abstract: Equilibrium thermodynamics and folding kinetics of a short, fast-folding, beta-hairpin
Open Access Paper

Free energy landscape of G-protein coupled receptors, explored by accelerated molecular dynamics

G-protein coupled receptors (GPCRs) mediate cellular responses to various hormones and neurotransmitters and are important targets for treating a wide spectrum of diseases.

Graphical abstract: Free energy landscape of G-protein coupled receptors, explored by accelerated molecular dynamics
Paper

The energy landscape of a protein switch

Protein switches are made of highly similar sequences that fold to dramatically different structures.

Graphical abstract: The energy landscape of a protein switch
Paper

The kinetics of folding of frataxin

The role of the denatured state in protein folding represents a key issue for the proper evaluation of folding kinetics and mechanisms.

Graphical abstract: The kinetics of folding of frataxin
Paper

Conformational flexibility of loops of myosin enhances the global bias in the actin–myosin interaction landscape

Increase in the compaction–expansion fluctuation of loop 2, the stronger binding of myosin to actin, and the biased Brownian motion of myosin S1 are coupled with each other and should take place in a concurrent way.

Graphical abstract: Conformational flexibility of loops of myosin enhances the global bias in the actin–myosin interaction landscape
Paper

A kinetic study of domain swapping of Protein L

NMR real-time kinetic experiments show that domain swapping of Protein L proceeds through a compact transition state.

Graphical abstract: A kinetic study of domain swapping of Protein L
Paper

Sequence-dependent folding landscapes of adenine riboswitch aptamers

Multi-scale simulations show that a point mutation eliminates the differences in the folding landscapes of pbuE and add A-riboswitches.

Graphical abstract: Sequence-dependent folding landscapes of adenine riboswitch aptamers
Paper

Exploring the electrostatic energy landscape for tetraloop–receptor docking

It has long been appreciated that Mg2+ is essential for the stabilization of RNA tertiary structure.

Graphical abstract: Exploring the electrostatic energy landscape for tetraloop–receptor docking
Paper

Effect of interactions with the chaperonin cavity on protein folding and misfolding

Attractive interactions between a substrate protein can modulate the folding rate and stability, and help to prevent domain-swapped misfolding.

Graphical abstract: Effect of interactions with the chaperonin cavity on protein folding and misfolding
21 items

About this collection

This themed issue showcases a collection of work from leading scientists, demonstrating the significance of the free energy landscape in the field of physiochemical biology.

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