Molecular dynamics study of unbinding of the avidin-biotin complex

Abstract

We report molecular dynamics simulations that induce, over periods of 40-500 ps, the unbinding of biotin from avidin by means of external harmonic forces with force constants close to those of AFM cantilevers. The applied forces are sufficiently large to reduce the overall binding energy enough to yield unbinding within the measurement time. Our study complements earlier work on biotin-streptavidin that employed a much larger harmonic force constant. The simulations reveal a variety of unbinding pathways, the role of key residues contributing to adhesion as well as the spatial range over which avidin binds biotin. In contrast to the previous studies, the calculated rupture forces exceed by far those observed. We demonstrate, in the framework of models expressed in terms of one-dimensional Langevin equations with a schematic binding potential, the associated Smoluchowski equations, and the theory of first passage times, that picosecond to nanosecond simulation of ligand unbinding requires such strong forces that the resulting protein-ligand motion proceeds far from the thermally activated regime of millisecond AFM experiments, and that simulated unbinding cannot be readily extrapolated to the experimentally observed rupture.

A nanomechanical interface to rapid single-molecule interactions

“…In addition to the evidence provided for an additional energy barrier, the data also provide experimental evidence that the forces can be as high as that predicted by MD simulations 14 . Those calculations identified several unbinding paths for avidin-biotin complex, with rupture forces between 650 and 800 pN.…”

“…Consequently, the slow mechanical interface to single-molecule processes makes it difficult to access short-lived single-molecule events 12 . For example, a comparison of experiments and molecular dynamics (MD) simulations of the well-studied biotin-avidin complex shows that these molecules have a potential to supply forces much larger than that encountered in experiments [13][14][15] . The larger forces will emerge only if bound molecules are pulled apart on a shorter timescale.…”

Single-molecule force spectroscopy: Practical limitations beyond Bell’s model

“…We now illustrate the findings from sections III B and III C. To avoid uncontrollable experimental inaccuracies and uncertainties regarding the "true" model and the "true" model parameters µ 0 , we numerically generated synthetic rupture data f by "simulating" an idealized experiment on the computer according to the probabilistic "laws" (28), (29) with given parameters µ = µ 0 . Hence all remaining uncertainties are statistical finite N effects.…”

“…2. However, in view of the fact that the escape rate depends on the energy difference at two force-dependent extrema, this problem does not have a unique solution [28]. Therefore, one may start with some model energy landscape, and try to deduce its global features, such as barrier height in the absence of the force and dissociation length (the distance between potential well and barrier without bias force, cf.…”

Liaisons « accrocheuses » et mécanique moléculaire

“…Les expériences que nous venons de décrire présentent un double intérêt: d'une part, elles montrent qu'une analyse plus approfondie des mécanismes des interactions moléculaires permet de comprendre des phénomènes expérimen-taux jusque-là inexplicables [8]. D'autre part, nous abordons maintenant une étape nouvelle de la compréhension des relations entre la structure et la fonction des macromolécules: les structures cristallographiques des couples ligand-récepteur étudiés étant connues, il est possible de simuler la rupture des complexes au moyen de techniques de «dynamique moléculaire» [28]. Il sera ainsi possible de tester expérimentale-ment tous les outils développés par les chimistes théoriciens pour prédire le «paysage énergétique» décrivant l'interaction d'un complexe ligand/récep-teur.…”