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AFM Force Spectroscopy and Steered Molecular Dynamics Simulation of Protein Contactin 4

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Strzelecki J.

Acta Physica Polonica A

2009

vol. 116

issue S

S-156-S-159

We use a single molecule atomic force spectroscopy combined with the steered molecular dynamics simulation to determine a mechanical behavior of neural cell adhesion protein contactin during its unfolding. Force curves typical for modular proteins were observed, showing at most four unfolding peaks. The analysis of force spectra performed within worm-like chain model of polymer elasticity showed the presence of three unfolding lengths. Small plateaus, most likely resulting from forced transitions within domains were observed for the first time. Steered molecular dynamics simulations help to determine atomistic picture of domain unfolding.

Dynamics of Protein Elements of Hybrid Nanostructures - Molecular Dynamics Simulations of Light Harvesting Peridinin-Chlorophyll a-Protein Model

100%

Jasiński A., Mikulska K., Krajnik B., Mackowski S., Nowak W.

Acta Physica Polonica A

2012

vol. 122

issue 2

284-288

Hybrid nanostructures are often composed of inorganic parts and "biological" ones. Optimized through million years of evolution light harvesting proteins are hard to mimic synthetically. Promising strategy in search for efficient solar cells is an attachment of selected natural protein systems to inorganic quantum dots. Such experimental hybrid structures should have improved charge separation properties. Among the most promising proteins is peridinin-chlorophyll-protein from Amphidinium carterae (PCP). It has a wide absorption spectrum (420-550 nm), optimized for sunlight. The dynamics of this protein, used in modern nanotechnology has been not addressed yet. In this work we present results of PCP computer modeling using a well established molecular dynamics methodology. The CHARMM27 force field parameters were prepared for this protein and all chromophore components. The system was embedded in a box of water, with proper counter ions, and a number of 10 ns molecular dynamics simulations were run using the NAMD code. It has been found that peridinine chromophores exhibit substantial orientational flexibility but a pair Per612 and Per613 is more rigid than the remaining two carotenoids. Orientation and dynamics of absorption and emission electric dipole moments have been also analyzed. Apparently, the architecture of PCP is not optimized for efficient Per-Chl a energy transfer by the Förster mechanism. Several practical issues related to molecular dynamics simulation of similar hybrid nanostructures are discussed.

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2 Acta Physica Polonica A

1 2012

1 2009

1 Jasiński A.

1 Krajnik B.

1 Mackowski S.

1 Mikulska K.

1 Nowak W.

1 Strzelecki J.

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AFM Force Spectroscopy and Steered Molecular Dynamics Simulation of Protein Contactin 4

Dynamics of Protein Elements of Hybrid Nanostructures - Molecular Dynamics Simulations of Light Harvesting Peridinin-Chlorophyll a-Protein Model