Kinetics and statistical distributions of single-molecule conformational dynamics

Qiang Lu1, Jin Wang

  • 1Department of Chemistry, Physics and Applied Mathematics, State University of New York at Stony Brook, Stony Brook, New York 11790, USA.

Summary

We modeled adenylate kinase protein dynamics, revealing two conformational states (open and closed) connected by distinct pathways. Kinetic analysis showed non-exponential behavior and memory effects, consistent with experimental observations.

Related Concept Videos

Distribution of Molecular Speeds01:27

Distribution of Molecular Speeds

The motion of molecules in a gas is random in magnitude and direction for individual molecules, but a gas of many molecules has a predictable distribution of molecular speeds. This predictable distribution of molecular speeds is known as the Maxwell-Boltzmann distribution. The distribution of molecular speeds in liquids is comparable to that of gases but not identical and can help to understand the phenomenon of the boiling and vapor pressure of a liquid. Consider that a molecule requires a...
¹H NMR of Conformationally Flexible Molecules: Temporal Resolution00:52

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

At room temperature, the chair conformer of cyclohexane undergoes rapid ring flipping between two equivalent chair conformers at a rate of approximately 105 times per second. These two chair conformers are in equilibrium. The rapid ring flipping results in the interconversion of the axial proton to an equatorial proton and an equatorial to the axial proton. Such interconversions are too rapid and cannot be detected on the NMR timescale. Hence, the NMR spectrometer cannot distinguish between the...
The Kinetic Model of Gases01:24

The Kinetic Model of Gases

The kinetic model of gases explains the properties of a perfect gas using three main assumptions: molecules move in ceaseless random motion, their size is negligible compared to the distances between them, and they do not interact except during perfectly elastic collisions. The total energy of a gas is the sum of the kinetic energies of all its constituent molecules. The pressure exerted by the gas arises from the continual bombardment of the container walls by billions of colliding molecules.
Kinetic Molecular Theory: Molecular Velocities, Temperature, and Kinetic Energy03:07

Kinetic Molecular Theory: Molecular Velocities, Temperature, and Kinetic Energy

The kinetic molecular theory qualitatively explains the behaviors described by the various gas laws. The postulates of this theory may be applied in a more quantitative fashion to derive these individual laws.
Molecular Kinetic Energy01:21

Molecular Kinetic Energy

The word "gas" comes from the Flemish word meaning "chaos," first used to describe vapors by the chemist J. B. van Helmont. Consider a container filled with gas, with a continuous and random motion of molecules. During collisions, the velocity component parallel to the wall is unchanged, and the component perpendicular to the wall reverses direction but does not change in magnitude. If the molecule’s velocity changes in the x-direction, then its momentum is changed. During the short time of the...
Maxwell-Boltzmann Distribution: Problem Solving01:20

Maxwell-Boltzmann Distribution: Problem Solving

Individual molecules in a gas move in random directions, but a gas containing numerous molecules has a predictable distribution of molecular speeds, which is known as the Maxwell-Boltzmann distribution, f(v).
This distribution function f(v) is defined by saying that the expected number N (v1,v2) of particles with speeds between v1 and v2 is given by