Domains in proteins

The methods involved in the production of proteins in microbes are those of gene expression. Several plasmids for expression of proteins having affinity tails at the C- or N-terminus of the protein have been developed. These tails are usefiil in the isolation of recombinant proteins. Most of these vectors are commercially available along with the reagents that are necessary for protein purification. A majority of recombinant proteins that have been attempted have been produced in E. Coli (1). In most cases these recombinant proteins formed aggregates resulting in the formation of inclusion bodies. These inclusion bodies must be denatured and refolded to obtain active protein, and the affinity tails are usefiil in the purification of the protein. Some of the methods described herein involve identification of functional domains in proteins (see also Protein engineering). 

Janin, J., Chothia, C. Domains in proteins definitions, location and structural principles. Methods Enzymol. 115 420-430, 1985. 

III PEG MPD Steric exclusion Repulsion from charges To hydrophobic regions Good precipitants stabilizers of native structure at low temp., unfolded structure at high temp. stabilizers and solubilizers of hydrophobic domains in proteins... 

The first major grouping of structures contains domains that are essentially all a-helical. Since there is relatively little other structure besides the helices, the simplest ways of connecting them involve predominantly antiparallel helix interactions, and that is in fact what is observed for these proteins. This category corresponds to Levitt and Chothia s all-a category, but it has more members both because of a number of new structures and because of helical domains in proteins they classified as a + /3 (such as thermolysin). 

The calponin homology (CH) domain has been identified in many molecules of differing function. However, its presence usually signifies an interaction of some sort with the actin cytoskeleton via an association with F-actin. The domain was initially identified as a 100-residue motif found at the N-terminus of the smooth muscle regulatory protein calponin and, hence, was termed the CH domain (Castresana and Saraste, 1995). The refinement of algorithms for the identification of distinct protein motifs has allowed the identification of CH domains in proteins that range... 

Fariselli, P. Casadio, R. (1996). HTP a neural network-based method for predicting the topology of helical transmembrane domains in proteins. Comput Appl Biosci 12,41-8. 

Skrynnikov, N. R., Goto, N. K., Yang, D., Choy, W. Y, Tolman, J. R., Mueller, G. A., and Kay, L. E. (2000). Orienting domains in proteins using dipolar couplings measured by liquid-state NMR Differences in solution and crystal forms of maltodextrin binding protein loaded with beta-cyclodextrin. J. Mol. Biol. 295, 1265-1273. 

Association between elements of the secondary structure form structural domains with properties determined both by the chiral properties of the polypeptide chain and by the packing requirements which effectively minimize the molecule s hydrophobic surface area. Association of domains in proteins results in the formation of the protein s tertiary structure. Furthermore, protein subunits can pack together to form quaternary structure, which can either serve a structural role or provide a structural basis for modification of the protein s functional properties [132]. 

Sequence analysis has become a powerful tool in identifying functional domains in proteins. One such tool is the Evolutionary Trace (ET) method as developed and implemented by Lichtarge et One such study was on the... 

Liebman, M. Quantitative analysis of structural domains in proteins. Biophys. J. 32, 213-215 (1980). 

Janin, J. and Wodak, S. Y. (1983) Structural Domains in Proteins and Their Role in the Dynamics of Protein Function, Prog. Biophys. Mol. Biol. 42, 21-78. 

T. Pizytycka, R. Srinivasan and G. D. Rose. Recursive domains in proteins. Protein Science, 2 (2002), 409. 

Watson, J. D. (1976). Molecular Biology of the Gene. Menlo Park, CA W. A. Benjamin. Wernisch, L. and Wodak, S. J. (2003). Identifying structural domains in proteins. In... 

Wootton, J. C. (1994) Non-globular domains in protein sequences automated segmentation using complexity measures. Comput Chem. 18, 269-285. 

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