Local secondary structure

The rapid and reversible formation of local. secondary. structures... 

On a larger scale, the unique folding and structure of one complete polypeptide chain is termed the tertiary structure of protein molecules. The difference between local secondary structure and complete polypeptide tertiary structure is arbitrary and sometimes of little practical difference. 

Figure 8 Superposition of the T. thermophilus NAD-IMDH binary complex with NAD (gray) on the E. coli NADP-IDH binary complex with NADP (black). NADP-IDH numbering is used throughout. It is noted that due to the difference of the local secondary structures, the NAD-IMDH does not have the counterpart of the Arg395 found in the NADP-IDH.

This reaction is frequently useful in resolving pile-ups caused by regions of local secondary structure in the copied DNA (cf section 4.7). 

We also used CD to ascertain the effects on structure and stability of the ZDD domain upon removal of the labile-bound RING finger zinc ion. In this case, the CD spectrum shows a 36% loss in molar ellipticity at 204 nm as compared to the native domain, indicating partial unfolding upon release of the metal ion from the labile site (shown in Figure 2A). These observations support the conclusion that the labile zinc plays an important role in the determination and stabilization of the local secondary structure in the RING finger subdomain. 

In an aqueous environment, the component polypeptides of a protein tend to fold in a characteristic fashion to form localized secondary structures i.e. pleated sheet, -turns, or random coil (6). The integrity and stabilization of secondary, tertiary, and quaternary structures of a given protein are dependent on different forces. An understanding of the various forces responsible for the native structure of proteins is fundamental in comprehending how they affect the conformation and functional properties of proteins (1). 

Figure 5. Stereo diagram of the Serratia nuclease active site. The a-carbon tracing identifies local secondary structure and displays the side chains of residues thought to be catalytically important...

The a-helix peptide structure consists of a spiral chain of amino acids interacting via hydrogen bonding between the backbone NH and CO groups along the peptide chain itself, and therefore is a local secondary structure. The structure was first discovered by Pauling, Corey, and Crick in the... 

Huang B, Prantil MA, Gustafson TL, Parquette JR (2003) The effect of global ctunpactitm on the local secondary structure of folded dendrimers. J Am Chem Soc 125 14518-14530... 

The structure of a protein is generally understood in terms of an organizational hierarchy that consists of protein sequence, local secondary structure, tertiary stmcture, and finally quaternary structure. The study of protein structure in these terms has led to a greater understanding of... 

The information on local secondary structures (a helix and /3 sheet) is usually obtained by using spectroscopic methods such as NMR, ORD, and/or CD. However, secondary structures can be best derived from the tertiary structural information. 

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