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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.

AFM Investigation of Biological Nanostructures

86%

Strzelecki J., Dąbrowski M., Strzelecka J., Tszydel M., Mikulska K., Nowak W., Balter A.

Acta Physica Polonica A

2012

vol. 122

issue 2

329-332

Nanostructures created by living organisms, optimized through millions of years of evolution, can be a valuable inspiration for nanotechnology. We employ atomic force microscopy to examine such structures in materials created by common organisms - caddisfly and diatoms. Caddisfly larvae are well known for their ability to spin silk, which serves as an "adhesive tape" to glue various materials and collect food in aqueous environment. Atomic force microscopy imaging of caddisfly silk, performed for the first time by our team, has shown that its surface is patterned with 150 nm extensions - a feature related to its exceptional underwater sticking abilities. Results of force spectroscopy of protein structures found on the surface are also shown. A characteristic feature of diatoms is that they are encased within a unique silica cell wall called frustules, patterned with 200 nm pores, which allow cellular interaction with the environment. We perform atomic force microscopy imaging of frustules in living diatoms as well as adhesion measurements inside pores.

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2 Acta Physica Polonica A

2 2012

2 Mikulska K.

2 Nowak W.

1 Balter A.

1 Dąbrowski M.

1 Jasiński A.

1 Krajnik B.

1 Mackowski S.

1 Strzelecka J.

1 Strzelecki J.

1 Tszydel M.

Search results

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

AFM Investigation of Biological Nanostructures