Protein folding amino acid substitution

Protein stability is the free energy difference (AG) between the folded and unfolded states at physiological conditions, and it is in the range of 5-25 kcal/mol. Site-directed mutagenesis experiments provided a wealth of data for understanding the importance of chemical interactions for the stability of proteins during amino acid substitutions. Protein stability is experimentally measured with differential scanning calorimetry, circular dichroism, fluorescence spectroscopy, and so forth. The availability of such data in an electronically accessible database would be a valuable resource for the analysis and prediction of protein mutant stability. 

Although all constituent amino acids of a protein may be considered important for the maintenance of an optimally folded native structure, some residues have been found to be struaurally and functionally more important than others. Residues that are directly involved in essential structure and/or function of a protein are among the most conserved, and their modifications or replacements usually result in a drastic decrease in the activity of the protein. In contrast, nonessential residues can be replaced by other amino acids and sections of polypeptides can even be removed without large negative effects on the stability of a protein. Proteins tolerate amino acid substitutions by various mechanisms (83) (a) some substitutions preserve critical interactions, (b) some interactions apparently do not make large contributions to stability, and (c) conformational adjustments occur to compensate for the changes in primary structure. 

This chapter aims to summarize our efforts to investigate the effects of fluorinated amino acid substitutes on the interactions with natural protein environments. In addition to a rather specific example concerning the interactions of small peptides with a proteolytic enzyme, we present a simple polypeptide model that aids for a systematic investigation of the interaction pattern of amino acids that differ in side chain length as well as fluorine content within both a hydrophobic and hydrophilic protein environment. Amino acid side chain fluoiination highly affects polypeptide folding due to steric effects, polarization, and fluorous interactions. 

J. Overingon, D. Donnelly, M. S- Johnson, A. Sali. and T. L, Blundell. Environment-specific amino acid substitution tables tertiary templates and prediction of protein folds. Protein Set. 7 216-226 (1992). 

DNA shuffling improves the search of local fold space via a random yet correlated combination of homologous coding fragments that contain limited numbers of beneficial amino acid substitutions. As in experimental evolutions (Stemmer, 1994 Crameri et al., 1998 Zhang et al, 1997 Moore et al, 1997), the simulated shuffling improved protein function significantly better than did point mutation alone (see Table III and Fig. 6b). However, local... 

A comprehension of how a channel structure is formed and how its structure affects the function of ion transport across membranes requires knowledge of many facets of this relationship. One must understand the interaction between a specific peptide or protein and the membrane environment which ultimately determines the folded structure that forms a channel. Single amino acid substitution in the sequence of the peptide or protein can be used to investigate the very delicate balance of forces that must exist between side-chains of the residues and the membrane environment to maintain a stable folded structure. The structure of these peptide or protein analogues in a membrane environment must be obtained to determine if there are structural differences that might... 

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