Direct proteins

Nucleic acids are the molecules of the genetic apparatus. They direct protein biosynthesis in the body and are the raw materials of genetic technology (see Genetic engineering). Most often polynucleotides are synthesized microbiologicaHy, or at least enzymatically, but chemical synthesis is possible. 

These predictive methods are very useful in many contexts for example, in the design of novel polypeptides for the identification of possible antigenic epitopes, in the analysis of common motifs in sequences that direct proteins into specific organelles (for instance, mitochondria), and to provide starting models for tertiary structure predictions. 

H Translation is the process by which mRNA directs protein synthesis. Each mRNA is divided into codons, ribonucleotide triplets that are recognized by small amino acid-carrying molecules of transfer RNA (tRNA), which deliver the appropriate amino acids needed for protein synthesis. 

Translation (Section 28.5) The process by which the genetic information transcribed from DNA onto mRNA is read by tRNA and used to direct protein synthesis. 

Table 46-4. Some sequences or compounds that direct proteins to specific organelles.

Yuan, L., Kurek, I., English, J. and Keenan, R. (2005) Laboratory-directed protein evolution. Microbiology and Molecular Biology Reviews, 69, 373-392. 

Geddie, M.L., Rowe, L.A., Alexander, O.B. and Matsumura, I. (2004) High throughput microplate screens for directed protein evolution. Methods in Enzymology, 388, 134-145. 

The potential of live cell imaging to address mechanisms of cellular biology is ever expanding. Directed protein-tagging techniques have been used to visualize nascent versus mature protein in vivo (Rodriguez et al., 2006). This technique involves the use of arsenic-based dyes, such as FiAsH or ReAsH, which bind to tetracysteine (TC) tags (Zhang et al, 2002). In addition, photo-activatable variants of GFP have been shown to determine the kinetics of protein movement in live cells (Patterson and Lippincott-Schwarz, 2002). Furthermore, techniques such as FRET and the... 

DIRECTIONALITIES in the flow of information from DNA to RNA to protein. All new DNA or RNA chains grow by adding new nucleotides to a free 3 end so that the chain lengthens in the 5 to 3 direction. Protein is made by reading the RNA template starting at the 5 end and making the protein from the N to the C terminus. 

Two general mechanisms have been considered by which a depleted intracellular Ca2+ pool might communicate with the plasma membrane [4]. There is evidence that the IP3 receptor is associated with the cytoskeleton, and this association may tether the IP3 receptor to the plasma membrane. Depletion of intracellular calcium stores might cause a conformational change in the IP3 receptor, which could be conveyed to the plasma membrane via the cytoskeleton or by a more direct protein-protein interaction. Alternatively, signaling could occur... 

The nucleus is surrounded by the nuclear envelope, which takes on a lumenal structure connected to the endoplasmic reticulum. The transport of proteins into (and out of) the nucleus occurs through the nuclear pore complex (NPC), a large complex composed of more than 100 different proteins (Talcott and Moore, 1999). Because NPC forms an aqueous pore across the two membranes, small proteins less than 9 nm in diameter can pass through it simply by diffusion. However, most of the transports of both proteins and RNAs are mediated by an active transport mechanism. It is now clear that there is heavy traffic through the NPC in both directions. Proteins are not only imported into the nucleus but also actively exported from it as well. There are many reasons for nuclear export. One reason is to send some shuttle proteins back after their import another is for some viral proteins to export their replicated genomes outside the nucleus. 

Fig. 1. The generalized protein-protein interaction network that includes (A) direct protein-protein interactions such as in the signal transduction pathway, (B) enzyme-enzyme relations in the metabolic pathway, and (C) transcription factor-expressed gene product relations in the gene regulatory pathway. The interactions in (B) and (C) are termed indirect protein-protein interactions.

Protein-protein relation Sequence similarity/orthology Enzyme-enzyme relation by successive reactions Transcription factor-transcribed gene product relation Direct protein-protein interaction... 

Nickel W (2005) Unconventional secretory routes direct protein export across the plasma membrane of mammalian cells. Traffic 6 607-614... 

The activated glucocorticoid receptor inhibits the transcription factor T-bet by direct protein-protein interaction. 

Yamauchi E, Kiyonami R, Kanai M, Taniguchi H. 1998. The C-terminal conserved domain of MARCKS is phosphory-lated in vivo by praline-directed protein kinase. Application of ion trap mass spectrometry to the determination of protein phosphorylation sites. J Biol Chem 273 4367. 

J. Ladd, C. Boozer, Q. Yu, S. Chen, J. Homola, and S. Jiang, Langmuir, "DNA-Directed Protein Immobilization on Mixed Self-Assembled Monolayers via a Streptavidin Bridge," The A CS Journal of Surfaces and Colloids 20, 8090 - 8095 (2004). 

In each of these cases, the gradient is utilized by an ATP synthase (4) to form ATP. ATP synthases consist of two components—a proton channel (Fq) and an inwardly directed protein complex (Fi), which conserves the energy of back-flowing protons through ATP synthesis (see p. 142). 

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