Peptides integration

Figure 12 TEM micrographs of Au nanoparticle synthesis mediated hy an HRE peptide integrated heat shock protein (Hsp 60) from Sulfolobus shibatae. (a) TEM of Au /(HRE)-Hsp complex prepared from addition of AuCLt , reduced hy citrate, and negatively stained hy uranyl acetate, (b) TEM of An /(HRE)-Hsp prepared from insoluble An precursor of AuClP(CH3)3 and reduced by borohydride (unstained)...

Aguilera, T. A., Olson, E. S., Timmers, M. M., Jiang, T., Tsien, R. Y. (2009). Systemic in vivo distribution of activatable cell penetrating peptides is superior to that of cell penetrating peptides. Integrative Biology (Cambridge), 1(5-6), 371-381. 

P. Derreumaux and T. Schlick. Long-time integration for peptides by the dynamics driver approach. Proteins Struc. Pune. Gen., 21 282-302, 1995. 

It is important to notice that the united-atom simplification cannot be applied to functional hydrogens which are involved in the formation of a hydrogen hond or a salt bridge. This would destroy interactions important for the structural integrity of the protein. Removing the hydrogen at the u-carbon of the peptide backbone is also dangerous, because it prevents racemization of the amino acid. 

One important class of integral equation theories is based on the reference interaction site model (RISM) proposed by Chandler [77]. These RISM theories have been used to smdy the confonnation of small peptides in liquid water [78-80]. However, the approach is not appropriate for large molecular solutes such as proteins and nucleic acids. Because RISM is based on a reduction to site-site, solute-solvent radially symmetrical distribution functions, there is a loss of infonnation about the tliree-dimensional spatial organization of the solvent density around a macromolecular solute of irregular shape. To circumvent this limitation, extensions of RISM-like theories for tliree-dimensional space (3d-RISM) have been proposed [81,82],... 

Complex II is perhaps better known by its other name—succinate dehydrogenase, the only TCA cycle enzyme that is an integral membrane protein in the inner mitochondrial membrane. This enzyme has a mass of approximately 100 to 140 kD and is composed of four subunits two Fe-S proteins of masses 70 kD and 27 kD, and two other peptides of masses 15 kD and 13 kD. Also known as flavoprotein 2 (FP2), it contains an FAD covalently bound to a histidine residue (see Figure 20.15), and three Fe-S centers a 4Fe-4S cluster, a 3Fe-4S cluster, and a 2Fe-2S cluster. When succinate is converted to fumarate in the TCA cycle, concomitant reduction of bound FAD to FADHg occurs in succinate dehydrogenase. This FADHg transfers its electrons immediately to Fe-S centers, which pass them on to UQ. Electron flow from succinate to UQ,... 

Dey S., Alpha Helical Peptide Nucleic Acids (Alpha PNAs) - Integration of Protein Structure and Nucleic Acid Function. PhD thesis. Case Western Reserve University, Cleveland, OH, January 2001. 

Adamantane can be used to construct peptidic scaffolding and synthesis of artificial proteins. It has been introduced into different types of synthetic peptidic macrocycles, which are useful tools in peptide chemistry and stereochemistry studies and have many other applications as well. Introduction of amino acid-functionalized adamantane to the DNA nanostmctures might lead to construction of DNA-adamantane-amino acid nanostmctures with desirable stiffness and integrity. Diamondoids can be employed to constmct molecular rods, cages, and containers and also for utilization in different methods of self-assembly. In fact, through the development of self-assembly approaches and utilization of diamondoids in these processes, it would be possible to design and constmct novel nanostmctures for effective and specific carriers for each dmg. 

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