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Viral Protein Nano-Actuators, Computational Studies of Bio-nanomachines

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Encyclopedia of Complexity and Systems Science

Definition of the Subject

In this paper, we describe computational aspects of an initiative to create a nanodevice for chemo‐mechanical energy conversion based on a biological system. We provide insights into the available methods and their applications to gain knowledge about whether a given molecule is suitable to function as a nanoactuator. The field of bio‐nanotechnology is new and it is developing fast. Noticeably, its roots go back decades of studies in the fields of biophysics, biochemistry and engineering. These disciplines can now come together to create useful and controllable devices at the nano-scale thereby adding another dimension to human scientific capabilities. Their applications in the fields of medicine, space exploration and colonization, and military are very promising.

Introduction

There is a persistent need of miniaturization of machines and energy conversion devices for various engineering applications. A great part of modern research is shifting from macro to...

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Abbreviations

Nanodevice:

A Device with size dimensions of the order of the nanometer (10\( { ^{-9} } \) m)

Actuator:

A device used to generate motion by converting some form of energy (such as chemical or light energy) into mechanical energy.

ATP:

Adenosine Triphosphate molecule used by living organisms to store and transport energy.

End‐effector:

The last link in a robotic assembly that performs the desired tasks by the robot by interacting with or acting upon the elements outside the robot.

Retrovirus:

A type of virus that has a protein envelope around it, stores its genetic information in an RNA molecule instead of double stranded DNA and transcripts its genome into DNA which integrates into the chromosome of the infected cell thereby replicating the virus when the cell replicates.

Glycoprotein:

A protein molecule which has a carbohydrate attached to it.

Membrane fusion:

A process when viral and hose cellular membranes fuse together during infection.

Hemagglutinin:

A type of protein on the surface of the influenza virus.

Fusogenic:

The unit that facilitates or takes part in membrane fusion.

Disulfide bond:

A sulfur–sulfur atomic bond which typically joins two biological segments such as protein chains.

Proteolytic cleavage:

A process of breaking the peptide bond between amino acids in a protein chain.

Endosome:

Intracellular vesicle formed by the outer cell membrane used to transport material inside the animal cell.

Endocytosis:

The process of encapsulation of an external element by the cell membrane and subsequent formation of an endosome for transport within the cell.

Nucleocapsid:

The genome of a virus enclosed in a protein coat.

α-Helix:

A secondary structure of protein molecules characterized by a helical shape and a specific pitch and stabilized by hydrogen bonds along the length of the helix.

β-Sheet:

A secondary structure of protein molecules where two or more chains are interconnected by hydrogen bonds forming a sheet-like structure.

Titin:

A big filamentous protein used by muscles.

Holonomic constraint:

A constraint that puts a restriction on the motion of a system by the use of integrable system of differential equations.

Chymotrypsin:

An enzyme in the pancreas which is involved in the catalysis of hydrolysis of proteins in the small intestine.

PDB:

The protein data bank which contains structural and other information about a large number of protein molecules. http://www.rcsb.org/pdb/home/home.do

Implicit solvation:

A technique used in molecular simulation which allows for a potential function to be used in place of explicit solvent molecules surrounding the molecule of interest.

Protonation:

The process of accepting a positively charged hydrogen ion or a proton by an amino acid.

Helicity:

The measure of the helical content of a given peptide molecule.

Denaturation:

Process of loss of secondary structure of a peptide molecule, which can happen for example due to heating beyond a certain level.

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Acknowledgments

The authors gratefully acknowledge support of the National Science Foundation (Grant NSF NIRT #0303950).

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Authors and Affiliations

  1. Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, USA

    Atul Dubey & M. Silvina Tomassone

Authors
  1. Atul Dubey
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  2. M. Silvina Tomassone
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Editor information

Editors and Affiliations

  1. RAMTECH LIMITED, 122 Escalle Lane, Larkspur, CA, 94939, USA

    Robert A. Meyers Ph. D. (Editor-in-Chief) (Editor-in-Chief)

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© 2009 Springer-Verlag

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Dubey, A., Tomassone, M.S. (2009). Viral Protein Nano-Actuators, Computational Studies of Bio-nanomachines. In: Meyers, R. (eds) Encyclopedia of Complexity and Systems Science. Springer, New York, NY. https://doi.org/10.1007/978-0-387-30440-3_577

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