Protein scaffolds

Development of methodologies for protein self-assembly into a predesigned three-dimensional protein lattice carries potential for the construction of protein scaffolds, offering potential applications such as platforms for the ordered positioning of other proteins via protein fusion or of organic molecules by specific binding. 

Figure 48-1. Molecular features of collagen structure from primary sequence up to the fibril. (Slightly modified and reproduced, with permission, from Eyre DR Collagen Molecular diversity in the body s protein scaffold.Science 1980 207 1315. Copyright 1980 by the American Association for the Advancement of Science.)...

The role of the enzyme s protein scaffold is to hold the zinc ion, coenzyme, and substrate in the three-dimensional array required to lower the energy of the transition state. 

Peptide and protein scaffolds offer a means to influence coenzyme reactivity without some of the Hmitations of the host organic scaffolds described above. Both proteins and peptides can be used to generate complex chemical environments. Existing proteins, which already contain structural complexity, can be... 

Work in the Imperiali laboratory has also focused on exploring the ability of minimal peptide scaffolds to augment the rate of coenzyme-mediated transaminations [22-25]. To accomplish this, a strategy has been developed in which the core functionality of the coenzyme is incorporated as an integral constituent of an unnatural coenzyme amino acid chimera construct. Thus, non-cova-lent binding of the coenzyme to the peptide or protein scaffold is unnecessary. Both the pyridoxal and pyridoxamine analogs have been synthesized in a form competent for Fmoc-based solid phase peptide synthesis (SPPS) (Fig. 7) [23,24]. 

Two reports in 1994 began to develop the concepts of coordination chemistry based self-assembly of heme into designed protein scaffolds. In collaborative work, the laboratories of DeGrado and Dutton provided two related architectures for de novo heme protein design... 

Monomeric hemes possess a mirror plane and are hence achiral (151). Incorporation of the heme macrocycle into the anisotropic protein matrix distorts the heme environment, inducing a circular dichroism spectrum (57, 152, 153). From the design standpoint, the presence of an induced heme CD spectrum qualitatively confirms intimate communication between the heme and the surrounding protein matrix, which indicates the heme is most likely specifically bound. This spectroscopic signature serves as a first indication that the heme resides within the designed protein scaffold and has been used by various groups to... 

The first general principle is that the type of metalloporphyrin incorporated into a designed protein or natural cytochrome offers a method to adjust the reduction potential of the heme. Sharp et al. (149) have demonstrated that a synthetic heme, l-methyl-2-oxomesoheme XIII, incorporated into a designed heme protein has a reduction potential 90 mV higher than the same protein with heme b. Additionally, Gib-ney et al. (148) have illustrated that heme a has a reduction potential 160 mV higher than heme b in the identical protein scaffold. This heme-dependent effect provides protein designers with a predictable modulation of the heme reduction potential in a synthetic protein. 

Cellular membranes function as selective barriers and integral membrane protein scaffolds. Membranes allow the compartmentalization of cells, and individual organelles within cells, and are critical in energy transduction and cell signaling. In vivo membranes contain hundreds to thousands of lipid types, making characterization of particular lipid-lipid interactions challenging. 

Since the protein scaffold is commonly not very stable, many methods have been used for stabilization presence of additives, immobilization by multiple-point attachment, stabilization by chemical or biochemical modification and by protein engineering, and several others. 

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