Filamentous biopolymers on surfaces: atomic force microscopy images compared with Brownian dynamics simulation of filament deposition

• Published in: PloS one Vol. 4; no. 11; p. e7756
• Main Authors: Mücke, Norbert, Klenin, Konstantin, Kirmse, Robert, Bussiek, Malte, Herrmann, Harald, Hafner, Mathias, Langowski, Jörg
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 04.11.2009; Public Library of Science (PLoS)
• Subjects: Adsorption; Aluminum Silicates - chemistry; Atomic force microscopy; Balancing; Biochemistry/Experimental Biophysical Methods; Biochemistry/Macromolecular Assemblies and Machines; Biochemistry/Theory and Simulation; Biophysics; Biophysics/Experimental Biophysical Methods; Biophysics/Macromolecular Assemblies and Machines; Biophysics/Theory and Simulation; Biopolymers; Biopolymers - chemistry; Brownian motion; Cancer; Comparative analysis; Computational Biology/Macromolecular Structure Analysis; Computer Simulation; Deoxyribonucleic acid; DNA; Electrolytes; Energy (Physics); Filaments; Flexibility; Glass; Humans; Image Processing, Computer-Assisted - methods; Intermediate filament proteins; Intermediate filaments; Medical research; Microscopy; Microscopy, Atomic Force - methods; Models, Statistical; Models, Theoretical; Nanotechnology - methods; Physics; Polymers; Polymers - chemistry; Proteins; Recombinant Proteins - chemistry; Simulation; Surface chemistry; Surface Properties; Thermal energy; Trapping; Vimentin; Vimentin - chemistry; Vimentin - genetics; Germany
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0007756

Nanomechanical properties of filamentous biopolymers, such as the persistence length, may be determined from two-dimensional images of molecules immobilized on surfaces. For a single filament in solution, two principal adsorption scenarios are possible. Both scenarios depend primarily on the interaction strength between the filament and the support: i) For interactions in the range of the thermal energy, the filament can freely equilibrate on the surface during adsorption; ii) For interactions much stronger than the thermal energy, the filament will be captured by the surface without having equilibrated. Such a 'trapping' mechanism leads to more condensed filament images and hence to a smaller value for the apparent persistence length. To understand the capture mechanism in more detail we have performed Brownian dynamics simulations of relatively short filaments by taking the two extreme scenarios into account. We then compared these 'ideal' adsorption scenarios with observed images of immobilized vimentin intermediate filaments on different surfaces. We found a good agreement between the contours of the deposited vimentin filaments on mica ('ideal' trapping) and on glass ('ideal' equilibrated) with our simulations. Based on these data, we have developed a strategy to reliably extract the persistence length of short worm-like chain fragments or network forming filaments with unknown polymer-surface interactions.