Template protein

Foo CWP, Huang J, Kaplan DL (2004) Lessons from seashells silica mineralization via protein templating. Trends Biotechnol 22 577-585... 

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. 

The concept is extendable to templated sensors made of protein templated xerogels in which a luminescent reporter group is further added in close proximity to the template site so as to effectively transduce the protein-molecularly imprinted polymer binding event (Figure 6.12).11... 

Solution-precipitation methods, e.g., those with use of strong borohydride reductors Sol-gel technologies Reverse-micelle synthesis Polymer-mediated synthesis Protein-templated methods... 

Lipmann, F., Gevers, W., Kleinkauf, H., and Roskoski, R. Jr. (1971). Polypeptide synthesis on protein templates the enzymatic synthesis of gramicidin S and tyrocidine. Adv. Enzymol. Relat. Areas Mol. Biol. 35, 1-34. 

The inner surface of the silicalemma, i.e., the limiting membrane within which silica deposition occurs549 consists of a protein template enriched in serine and threonine. This protein will present a layer of hydroxyl groups which can undergo condensation reaction with silicic acid molecules with a consequent loss of water (Fig. 48). As a result, the initial layer of condensed silicic acid will be held fixed to the protein template of silicic acid (Fig. 49). Such a situation is kinetically more favorable than simply allowing the silicic acid molecules to come together by random collision. 

Fig. 48. Proposed condensation reaction between silicic acid and serine on the protein template of the silicalemma (Hecky et a/.548 )...

Fig. 2. Schematic of the synthesis of nanostructured metals and alloys in varying grain sizes supported on hollow, highly oriented protein templates (Behrens, Dinjus, and Unger, 1999 Behrens et al., 2000).

A crystalline bacterial surface layer with a well defined geometry of Sporosarcina ureae (so-called S layer) is used as a protein template (unit cell 13.2 nm x 13.2 nm) on a cell membrane. Noble metal nanoclusters (Pt or Pd) are deposited chemically to produce nanostructures. The spatial distribution of noble metal nanoclusters is characterized by transmission electron microscopy (TEM). 

Figure 11 Strategy for nanoparticle rnclusion/release by chaper-onin protein templates, (a) Structural representation of chaperonin proteins, GroEL, and T. th cpn. (b) Scheme depicting inclusion of CdS nanoparticles within chaperonin cavity and their triggered release from the cavity hy ATP. (Reproduced hy permission of Nature Puhlishing Group (www.nature.com))...

The catalytic mechanisms and molecular recognition properties of peptide synthetases have been studied for several decades [169]. Nonribosomal peptides are assembled on a polyenzyme-protein template, first postulated by Lipmann [170]. The polyenzyme model was refined into the thiotemplate mechanism (Fig. 11) in which the amino acid substrates are covalently bound via thioester linkages to active site sulfhydryls of the enzyme and condensed via a processive mechanism involving a 4 -phosphopantetheine carrier [171-173].The presence of a covalently attached pantetheine cofactor was first established in a cell-free system that catalyzed enzymatic synthesis of the decapeptides gramicidin S and tyrocidine. As in the case of fatty acid synthesis, its role in binding and translocating the intermediate peptides was analyzed [174,175]. 

Arnold and co-workers attempted to prepare imprinted metal-coordinating polymers for proteins [25]. For this purpose, efforts were made to prepare metalcoordinating molecularly patterned surfaces in mixed monolayers spread at the air-water interface or liposomes. This approach was termed as molecular printing and is illustrated in Fig. 6.6. In this process, a protein template is introduced into the aqueous phase, which imposes a pattern of functional amphiphiles in the surfactant monolayer via strong interactions with metal-chelating surfactant head groups. The pattern is then fixed by polymerising the surfactant tails. The technique has also been employed for two dimensional crystallisation of proteins [26]. 

Pair potentials vs contact capacity potentials a) a pair potential attributes an energetic contribution to each pair of amino acids a, and aj that are mapped by a sequence-structure alignment onto locations of the amino acids b and b/ of the protein template structure. The contribution depends on the types of residues a, and aj as well as on geometric features of their locations b/, and b/, such as their distance in space or in sequence. Often, only certain pairs of amino acid residues are scored, such as those that are contacting or close in space. The total energy is computed as the sum of all pair contributions, b) a contact capacity potential rates the energetic contribution of an amino acid a, from the protein target... 

Nair, D.T., Johnson, R.E., Prakash, L., Prakash, S., and Aggarwal, A.K. (2008) Protein-template-directed synthesis across an acrolein-derived DNA adduct by yeast Revl DNA polymerase. Structure, 16, 239-245. 

Eukaryotes - In eukaryotes, the mRNA is produced in the nucleus and must be exported into the cytosol for translation. Furthermore, the initial product of transcription (pre-mRNA) may include introns, which must be removed before translation can occur. There is no ribosomal attachment sequence like the Shine - Dalgamo sequence in prokaryotes. For all these reasons, eukaryotic mRNA requires extensive processing before it can be used as a protein template. This processing takes place while mRNA is still in the nucleus. 

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