ABSTRACT
The interconversion between inactive and active protein states, traditionally described by two static structures, is at the heart of signalling. However, how folded states interconvert is largely unknown due to the inability to experimentally observe transition pathways. Here we explore the free energy landscape of the bacterial response regulator NtrC by combining computation and nuclear magnetic resonance, and discover unexpected features underlying efficient signalling. We find that functional states are defined purely in kinetic and not structural terms. The need of a well-defined conformer, crucial to the active state, is absent in the inactive state, which comprises a heterogeneous collection of conformers. The transition between active and inactive states occurs through multiple pathways, facilitated by a number of nonnative transient hydrogen bonds, thus lowering the transition barrier through both entropic and enthalpic contributions. These findings may represent general features for functional conformational transitions within the folded state.
Subject(s)
Bacterial Proteins/metabolism , PII Nitrogen Regulatory Proteins/metabolism , Bacterial Proteins/chemistry , Entropy , Hydrogen Bonding , Kinetics , Magnetic Resonance Spectroscopy , Markov Chains , Models, Molecular , Molecular Dynamics Simulation , PII Nitrogen Regulatory Proteins/chemistry , Protein Structure, Tertiary , Signal Transduction , ThermodynamicsABSTRACT
We analyze a model of mutually propelled filaments suspended in a two-dimensional solvent. The system undergoes a mean-field isotropic-nematic transition for large enough filament concentrations, and the nematic order parameter is allowed to vary in space and time. We show that the interplay between nonuniform nematic order, activity, and flow results in spatially modulated relaxation oscillations, similar to those seen in excitable media. In this regime the dynamics consists of nearly stationary periods separated by "bursts" of activity in which the system is elastically distorted and solvent is pumped throughout. At even higher activity, the dynamics becomes chaotic.
Subject(s)
Liquid Crystals/chemistry , Hydrodynamics , Stress, Mechanical , SuspensionsABSTRACT
We report on the construction of colloidal stars: 1 microm polystyrene beads grafted with a dense brush of 1 microm long and 10 nm wide charged semiflexible filamentous viruses. The pair interaction potentials of colloidal stars are measured using an experimental implementation of umbrella sampling, a technique originally developed in computer simulations in order to probe rare events. The influence of ionic strength and grafting density on the interaction is measured. Good agreements are found between the measured interactions and theoretical predictions based upon the osmotic pressure of counterions.
Subject(s)
Bacteriophage M13/chemistry , Capsid Proteins/chemistry , Colloids/chemistry , Polystyrenes/chemistry , Algorithms , Colloids/chemical synthesis , Computer Simulation , Fluorescence , Gold/chemistry , Microscopy, Electron, Transmission , Osmolar ConcentrationABSTRACT
Generation of nanomechanical cantilever motion from biomolecular interactions can have wide applications, ranging from high-throughput biomolecular detection to bioactuation. Although it has been suggested that such motion is caused by changes in surface stress of a cantilever beam, the origin of the surface-stress change has so far not been elucidated. By using DNA hybridization experiments, we show that the origin of motion lies in the interplay between changes in configurational entropy and intermolecular energetics induced by specific biomolecular interactions. By controlling entropy change during DNA hybridization, the direction of cantilever motion can be manipulated. These thermodynamic principles were also used to explain the origin of motion generated from protein-ligand binding.
