Principles of Protein Structure

Proteins are linear polymers (polypeptides) with the amino acids as the monomer units. The molecular weight of a protein is typically in the range of 10000-100000 for a single chain. Higher molecular weights occur by the association of several protein chains. There are 20 amino acids commonly associated in proteins. The general formula of an amino acid is as follows  

The arrangement of the four different groups about the a-carbon atom can be either left- (laevo, L) or right- (dextro, D) handed. Only L-amino acids are constituents of natural proteins. 

In proteins, the a-carboxyl group of one amino acid is joined to the a-amino group of another amino acid by a peptide bond. The formation of a dipeptide from two amino acids follows the reaction  

The particular sequence of side chains or amino acids along the polypeptide backbone is known as the primary structure. This structure is determined by a particular sequence of nucleic acids in the gene the relationship between a nucleic acid sequence and an amino acid sequence is known as the genetic code (see section 3.2). 

Proteins have well-defined three-dimensional structures in their functional form. It is possible, under extreme conditions of acid or heat, to denature a protein, i.e. for the molecule to lose its specific shape and also then its function. Conversely by returning to mild conditions the linear chain refolds to a specific three-dimensional structure. Generally speaking, therefore, it is apparent that a particular primary sequence contains 

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Ithough knowledge-based potentials are most popular, it is also possible to use other types potential function. Some of these are more firmly rooted in the fundamental physics of iteratomic interactions whereas others do not necessarily have any physical interpretation all but are able to discriminate the correct fold from decoy structures. These decoy ructures are generated so as to satisfy the basic principles of protein structure such as a ose-packed, hydrophobic core [Park and Levitt 1996]. The fold library is also clearly nportant in threading. For practical purposes the library should obviously not be too irge, but it should be as representative of the different protein folds as possible. To erive a fold database one would typically first use a relatively fast sequence comparison lethod in conjunction with cluster analysis to identify families of homologues, which are ssumed to have the same fold. A sequence identity threshold of about 30% is commonly... 

Pemtz M 1992. Protein Structure. New Approaches to Disease And Therapy. New York, W H Freeman. Schulz G E and R H Schirmer 1979. Principles of Protein Structure. New York, Springer-Verlag. 

The first six chapters of this book deal with the basic principles of protein structure as we understand them today, and examples of the different major classes of protein structures are presented. Chapter 7 contains a brief discussion on DNA structures with emphasis on recognition by proteins of specific nucleotide sequences. The remaining chapters illustrate how during evolution different structural solutions have been selected to fulfill particular functions. 

Schulz, G.E., Schirmer, R.H. Principles of Protein Structure. New York Springer, 1979. 

Schulz, G. E., and Schirmer, R. H. (1979). Principles of Protein Structure. Springer-Verlag, New York. 

The fundamental principles of protein structure and function are available in modern biochemistry textbooks6 7). The current edition of Stryer is particularly recommended 7). The books by Dickerson and Geis 6,9) are excellent tutorials on the fundamental principles of protein structure. The modern text by Schulz and Schir-mer8), Principles of Protein Structure, is outstanding. In addition, modern physical... 

Schultz GE, Schirmer RH (1979) Principles of protein structure. Springer, Berlin Heidelberg New York... 

Thus, rather than trial-and-error development of functionality, it should be possible to design functionality based on the principles of protein structure and function and the specificities of the enzymes used for modification. Use of immobilized exo- and endopeptidases in such technology could be especially attractive for the reasons listed in Table I, particularly since problems associated with autolysis would be eliminated and the extent of proteolytic reactions could be controlled with some precision. 

The JHE model was constructed in order to better test hypotheses of catalytic activity, substrate preference and protein uptake. It will also allow us to improve our ability to rationally design modified forms of JHE as a biologically based insecticide. This model was built using both acetylcholinesterase from T californica and lipase from G. candidum as templates and is consistent with the principles of protein structure. 

Schulz, G.E. and Schirmer, R.H. (1979). "Principles of protein structure". Springer-Vedag, New York-NY. Schulz, G.E. (1987). Anrr. Rev. Biophys. Biophys. Chem.,M, 1-21. 

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