An intuitive approach to steady state kinetics

Raines, Ronald T.; Hansen, David E.

doi:10.1021/ed065p757

Cited by 24 publications

(23 citation statements)

References 9 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…78 for instance), Eq. (7) recovers the average rate constant of the steady-state approximation, where the assumption that k c + k − k + is used, giving the more familiar expression: k 2 = k + k c /(k c + k − ).…”

Section: Conversion Of Micellesmentioning

confidence: 99%

Mechanisms and rates of nucleation of amyloid fibrils

Lee

Terentjev

2017

The Journal of Chemical Physics

View full text Add to dashboard Cite

The classical nucleation theory finds the rate of nucleation proportional to the monomer concentration raised to the power, which is the 'critical nucleaus size', n c . The implicit assumption, that amyloids nucleate in the same way, has been recently challenged by an alternative two-step mechanism, when the soluble monomers first form a metastable aggregate (micelle), and then undergo conversion into the conformation rich in β-strands that are able to form a stable growing nucleus for the protofilament. Here we put together the elements of extensive knowledge about aggregation and nucleation kinetics, using a specific case of Aβ 1−42 amyloidogenic peptide for illustration, to find theoretical expressions for the effective rate of amyloid nucleation. We find that at low monomer concentration in solution, and also at low interaction energy between two peptide conformations in the micelle, the nucleation occurs via the classical route. At higher monomer concentration, and a range of other interaction parameters between peptides, the two-step 'aggregation-conversion' mechanism of nucleation takes over. In this regime, the effective rate of the process can be interpreted as a power of monomer concentration in a certain range of parameters, however, the exponent is determined by a complicated interplay of interaction parameters and is not related to the minimum size of the growing nucleus (which we find to be ∼ 7-8 for Aβ 1−42 ).

show abstract

Section: Conversion Of Micellesmentioning

confidence: 99%

Mechanisms and rates of nucleation of amyloid fibrils

Lee

Terentjev

2017

The Journal of Chemical Physics

View full text Add to dashboard Cite

show abstract

“…With three-state kinetics, one has to make approximations to find an analytic expression for the rate constant. We choose to follow the steady-state approximation 29 , where the intermediate state is assumed to be in equilibrium with the native state, and transitions to the extended state are assumed to be permanent (no refolding). In this approximation, the rate constant is expressed as…”

Section: B Jump Before the Barriermentioning

confidence: 99%

Non-exponential kinetics of unfolding under a constant force

Bell

Terentjev

2016

The Journal of Chemical Physics

View full text Add to dashboard Cite

We examine the population dynamics of naturally folded globular polymers, with a super-hydrophobic "core" inserted at a prescribed point in the polymer chain, unfolding under an application of external force, as in AFM force-clamp spectroscopy. This acts as a crude model for a large class of folded biomolecules with hydrophobic or hydrogen-bonded cores. We find that the introduction of super-hydrophobic units leads to a stochastic variation in the unfolding rate, even when the positions of the added monomers are fixed. This leads to the average non-exponential population dynamics, which is consistent with a variety of experimental data and does not require any intrinsic quenched disorder that was traditionally thought to be at the origin of non-exponential relaxation laws.

show abstract

“…5. If QSSA is applicable, accurate rate equations can rapidly be obtained using linear algebraic manipulation (27,36). 6.…”

Section: The Partition Between Intermediates and Other Speciesmentioning

confidence: 99%