Secondary structure of proteins

Because proteins consist of long chains of amino acids strung together, one might think that their shapes are rather amorphous, or floppy and ill-defined. This is incorrect. Many proteins have been isolated in pure crystalline form and are polymers with well-defined shapes. Indeed, even in solution, the shapes seem to be quite regular. Let us examine some of the structural features of peptide chains that are responsible for their definite shapes. 

Two protein chains bound together in the pleated-sheet secondary structure. Each sphere represents an amino acid. 

One type of secondary protein structure is like a spiral staircase and is called the a-hellx. The circles represent individual amino acids. 

The protein myoglobin. Note that the secondary structure is basically a-helical except at the bends. The tertiary structure is globular. 

So far we have considered the primary structure of proteins—the order of amino acids in the chain as shown below. 

A second level of stmcture in proteins is the arrangement in space of the chain of the long molecule. This is called the secondary structure of the protein. 

Silk has this arrangement of proteins, making its fibers flexible but very strong and resistant to stretching. The pleated sheet is also found in muscle fibers. 

What is it about a pleated sheet arrangement that makes it suitable for muscle fibers  

The two main types of secondary structural arrangements are the a-helix and the P-pleated sheet. Generally, these conformations generate the secondary structure of proteins. 

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Plenary 2. S A Asher et al, e-mail address asher ,vms.cis.pitt.edu/asher+ (RRS, TRRRS). UV RRS is used to probe methodically the secondary structure of proteins and to follow unfolding dynamics. Developing a library based approach to generalize the mediod to any protein. 

The cylinder model is used to characterize the helices in the secondary structure of proteins (see the helices in Figure 2-124c),... 

Chou P Y and G D Fasman 1978. Prediction of the Secondary Structure of Proteins from Tlieir Amino Acid Sequence. Advances in Enzymology 47 45-148. 

Section 27 19 Two secondary structures of proteins are particularly prominent The pleated sheet is stabilized by hydrogen bonds between N—H and C=0 groups of adjacent chains The a helix is stabilized by hydrogen bonds within a single polypeptide chain... 

PY Chou, CD Easman. Prediction of the secondary structure of proteins from their ammo acid sequence. Adv Enzymol Relat Areas Mol Biol 47 45-148, 1978. 

Figure 26.5 (a) The o-helical secondary structure of proteins is stabilized by hydrogen bonds between the N—H group of one residue and the C=0 group four residues away, (b) The structure of myoglobin, a globular protein with extensive helical regions that are shown as coiled ribbons in this representation. 

Propiolactone is one example. It will alkylate amino, imino, hydroxyl and carboxyl groups, all of which occur in proteins, and react also with thiol and disulphide groups responsible for the secondary structure of proteins and the activity of some enzymes. 

In proteins in particular the peptide bonds contribute to the CD-spectra of the macromolecule. Here, CD-spectra reflect the secondary structure of proteins, which are derived from CD-spectra of model macromolecules with only one defined secondary structure (like poly-L-lysine at given pH values) or based on spectra of proteins with known structures (e.g.,from X-ray crystallography). The amount of a-helices or -sheets in the unknown structure is calculated by linear combination of the reference spectra [150,151]. 

Figure 11.2 The secondary structure of proteins. The simplest spatial arrangement of amino acids in a polypeptide chain is as a fully extended chain (a) which has a regular backbone structure due to the bond angles involved and from which the additional atoms, H and O, and the amino acid residues, R, project at varying angles. The helical form (b) is stabilized by hydrogen bonds between the —NH group of one peptide bond and the —CO group of another peptide bond. The amino acid residues project from the helix rather than internally into the helix.

HSSP Homology-derived secondary structure of proteins database (HSSP)... 

These model experiments involving e.e. amplification of amino adds during polymerization admittedly need prebiotically unrealistic substrates as well as carefully contrived experimental conditions. Nevertheless, it is noteworthy that both secondary structures of proteins, a-helices, and P-sheets have been found capable of acting stereoselectively to provide e.e. enhancements during these model polymerizations. 

Noncovalent interactions play a key role in biodisciplines. A celebrated example is the secondary structure of proteins. The 20 natural amino acids are each characterized by different structures with more or less acidic or basic, hydrophilic or hydrophobic functionalities and thus capable of different intermolecular interactions. Due to the formation of hydrogen bonds between nearby C=0 and N-H groups, protein polypeptide backbones can be twisted into a-helixes, even in the gas phase in the absence of any solvent." A protein function is determined more directly by its three-dimensional structure and dynamics than by its sequence of amino acids. Three-dimensional structures are strongly influenced by weak non-covalent interactions between side functionalities, but the central importance of these weak interactions is by no means limited to structural effects. Life relies on biological specificity, which arises from the fact that individual biomolecules communicate through non-covalent interactions." " Molecular and chiral recognition rely on... 

Figure 13.1 Secondary structure of proteins hydrogen bonding in 3-sheets ...

Fourier transform infrared/photoacoustic spectroscopy (FT-IR/PAS) can be used to evaluate the secondary structure of proteins, as demonstrated by experiments on concanavalin A, hemoglobin, lysozyme, and trypsin, four proteins having different distributions of secondary... 

In amides, the lone electron pair on the nitrogen atom promotes resonance stabilization of the carbonyl region (see Figure 9-14). This stabilization is important not only to amides, but also to the secondary structure of proteins. 

Circular dichroism Secondary structure of proteins, interaction between ligands and proteins, binding of metals at active sites in enzymes 1 )... 

Heat, strong acids or bases, ethanol, or heavy-metal ions irreversibly alter the secondary structure of proteins (see below). This process, known as denaturation, is exemplified by the heat-induced coagulation and hardening of egg white (albumin). Denaturation destroys the physiological activity of proteins. 

The wavelengths of IR absorption bands are characteristic of specific types of chemical bonds. In the past infrared had little application in protein analysis due to instrumentation and interpretation limitations. The development of Fourier transform infrared spectroscopy (FUR) makes it possible to characterize proteins using IR techniques (Surewicz et al. 1993). Several IR absorption regions are important for protein analysis. The amide I groups in proteins have a vibration absorption frequency of 1630-1670 cm. Secondary structures of proteins such as alpha(a)-helix and beta(P)-sheet have amide absorptions of 1645-1660 cm-1 and 1665-1680 cm, respectively. Random coil has absorptions in the range of 1660-1670 cm These characterization criteria come from studies of model polypeptides with known secondary structures. Thus, FTIR is useful in conformational analysis of peptides and proteins (Arrondo et al. 1993). 

Johson, W.C. (1988). Secondary structure of proteins through circular dichroism spectroscopy. Ann. Rev. Biophys. Biophys. Chem., 17 145-166. 

The knowledge of amino acid sequences of proteins may provide their three-dimensional structures if CD predictions are valid. However, the CD prediction for the secondary structure of a given protein, especially having (3-sheet structures, is not valid enough to probe the structure-function relationships in native proteins. We are awaiting the development of a more precise prediction method for secondary structures of proteins. 

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