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

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 Triphosphatemolecule 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 transportmaterial 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. -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. ˇ-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 bankwhich 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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