Template helical protein

Traditional methods for fabricating nano-scaled arrays are usually based on lithographic techniques. Alternative new approaches rely on the use of self-organizing templates. Due to their intrinsic ability to adopt complex and flexible conformations, proteins have been used to control the size and shape, and also to form ordered two-dimensional arrays of nanopartides. The following examples focus on the use of helical protein templates, such as gelatin and collagen, and protein cages such as ferritin-based molecules. 

We often think of chromosomes as being flat with little or no geographical topology because the sheet of paper or screen we view them on is flat. However, it is the three-dimensional structure that assists the various genes to perform their function in designing the necessary proteins. The secondary structure of these features is more or less helical, with the different clefts causing the DNA to have these varying structures. The transfer of information from the DNA template to protein, and less so RNA, synthesis is described in Section 10.4. 

Figure 8 Template approach to de novo heme protein design using metalloporphyrins as templates, (a) helichrome (b) tetraphilins (c) artificial membrane proteins. (Reprinted with permission from Ref. 22. 2001 the American Chemical Society) (d) helical proteins based on Cys-containing cyclic peptide. (Reprinted with permission from H.K. Ran, N. DeJonge, and W. Haehnel, Proc. Natl. Acad. Sci. U.S.A., 1998, 95, 11526. 1998 National Academy of Sciences, USA)...

Figure 17.10 Construction of a two helix truncated Z domain, (a) Diagram of the three-helix bundle Z domain of protein A (blue) bound to the Fc fragment of IgG (green). The third helix stabilizes the two Fc-binding helices, (b) Three phage-display libraries of the truncated Z-domaln peptide were selected for binding to the Fc. First, four residues at the former helix 3 interface ("exoface") were sorted the consensus sequence from this library was used as the template for an "intrafece" library, in which residues between helices 1 and 2 were randomized. The most active sequence from this library was used as a template for five libraries in which residues on the Fc-binding face ("interface") were randomized. Colored residues were randomized blue residues were conserved as the wild-type amino acid while yellow residues reached a nonwild-type consensus, [(b) Adapted from A.C. Braisted and J.A. Wells,...

If the sequence of a protein has more than 90% identity to a protein with known experimental 3D-stmcture, then it is an optimal case to build a homologous structural model based on that structural template. The margins of error for the model and for the experimental method are in similar ranges. The different amino acids have to be mutated virtually. The conformations of the new side chains can be derived either from residues of structurally characterized amino acids in a similar spatial environment or from side chain rotamer libraries for each amino acid type which are stored for different structural environments like beta-strands or alpha-helices. 

Although biologically active helical y-peptides have not been reported so far, the striking structural similarities (polarity and helicity) between the a-helix of L-a-peptides and the (P)-2.6i4-hehx of y-peptides suggest that the 2.614-helical backbone might prove useful as a template for elaborating functional mimetics of a-helical surfaces and intervening in protein-protein interactions. 

Fig. 4. Schematic representation of template-assembled synthetic proteins. The conforma-tionally restricted template can be orthogonally protected and sequentially linked to helical segments to form a large variety of functionalized TASP proteins. Flexible spacers that connect the folded peptide segments and the template provide the necessary conformational freedom that will allow the hydrophobic residues to find their optimum orientations for packing the core...

The two major types of nucleic acids are DNA and RNA. Nucleic acids are polyphosphate esters containing the phosphate, sugar, and base moieties. Nucleic acids contain one of five purine or pyrimidine bases that are coupled within double-stranded helices. DNA, which is an essential part of the cell s chromosome, contains the information for the synthesis of protein molecules. For double-stranded nucleic acids, as the two strands separate, they act as a template for the construction of a complementary chain. The reproduction or duplication of the DNA chains is called replication. The DNA undergoes semiconservative replication where each of the two new strands contains one of the original strands. 

Ahmad M, Grancher N, Heil M et al 2002 Action spectrum for cryptochrome-dependent hypocotyl growth inhibition in A-rabidopsis. Plant Physiol 129 774—785 Baldwin JM, Schertler GF, Unger VM 1997 An alpha-carbon template for the transmembrane helices in the rhodopsin family of G-protein-coupled receptors. J Mol Biol 272 144—164 Batni S, Scalzetti L, Moody S A, Knox BE 1996 Characterization of the Xenopus rhodopsin gene. J Biol Chem 271 3179-3186... 

RGURE 8-27 Base-paired helical structures in an RNA. Shown here is the possible secondary structure of the M1 RNA component of the enzyme RNase P of coli, with many hairpins RNase R which also contains a protein component (not shown), functions in the processing of transfer RNAs (see Rg. 26-23). The two brackets indicate additional complementary sequences that may be paired in the three-dimensional structure. The blue dots indicate non-Watson-Crick G=U base pairs (boxed inset). Note that G=U base pairs are allowed only when presynthesized strands of RNA fold up or anneal with each other. There are no RNA polymerases (the enzymes that synthesize RNAs on a DNA template) that insert a U opposite a template G, or vice versa, during RNA synthesis... 

If the rate-controlling step in the addition of each monomer to agrowing chain is, in all cases, assumed to be an enzymatically catalyzed chemical event rather than, for example, the unraveling of double helical template structure (in advance of the growing-chain end) where such exists, then the syntheses of DNA, RNA, and protein would, at first sight, all seem to represent similar, one-dimensional, stochastic processes. However, even... 

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