Protein! s secondary

A protein s secondary structure arises from the formation of intra- and inter-molecular hydrogen bonds. All carboxyl group oxygens and amine hydrogens of a polypeptide participate in H-bonding. Protein secondary structure also derives from the fact that although all C-N bonds in peptides have some double bond character and cannot rotate, rotation about the Co-N and Ca-C bonds is possible and is... 

The polypeptide chains of proteins do not remain in a flat plane. Instead, as a protein is formed, the polypeptide chain starts to twist and curl up. It folds and coils like a rope that can be bundled in many different shapes. This coiling and folding determines the protein s secondary structure. The secondary structure is maintained by chemical bonds between the carboxyl groups and the amino groups in the polypeptide backbone. There are many secondary structure patterns, but the two most common are the a-helix, and the p-sheet. 

Combined SAXS/Circular dichroism beamline. Biological macromolecules, such as proteins, carbohydrates and nucleic acids, are composed of many optically active or chiral units that exhibit large Circular Dichroism (CD) signals. CD spectroscopy has therefore been used extensively in the study of proteins, where asymmetric carbon atoms in their amino acid backbone give rise to a CD spectrum. The shape of the spectrum depends on the protein s secondary structure content and allows the proportions of helix, beta structure, turns and random to be determined. 

While the information contained in one primary sequence alone seems to be insufficient to predict a protein s secondary structure, multiply aligned sequences (see below) offer a means to push the limits of the prediction. Originally due to Zvelebil et al. [26] this line of attack on the problem is the basis of the PHD method by Rost and Sander [27]. The PHD method takes as input a multiple alignment of a set of homologous protein sequences and... 

For each polypeptide chain that an organism produces, there exists a corresponding gene. The nucleotide sequence in that gene dictates the amino acid sequence of the protein which, in turn, defines the protein s secondary, tertiary, and quaternary structures. 

Ans. This involves the reaction of the sulfhydryl side groups of cysteine residues. Two sulfhydryl groups, either on the same polypeptide chain or different chains, react with one Pb ion to alter the protein s secondary, tertiary, and quaternary structures, and cause precipitation of the protein ... 

The tertiary structure describes the complete three-dimensional stmcture of the whole polypeptide chain. It includes the relationship of different domains formed by the protein s secondary structure and the interactions of the amino acid substituent -R groups. An example of a protein chain with a-helices and /3-folding, the enzyme ribonuclease, is shown in Fig. 1.17. The specific folding of a protein is only thermodynamically stable within a restricted range of environmental parameters, i.e. the right temperature, pH and ionic strength. Outside of this range, the protein could unfold and lose its activity. 

Proteins in living organisms are not simply long, flexible chains with totally random shapes. Rather, the chains self-assemble into structures based on the intermolecular forces we learned about in Chapter 11. This self-assembling leads to a protein s secondary structure, which refers to how segments of the protein chain are oriented in a regular pattern, as seen in FIGURE 24.20. 

In addition to X-ray crystallography, a number of other techniques have demonstrated the existence of intramolecular hydrogen bonds in the polypeptide chain. Hydrogen bonds form between the carbonyl and amide groups of nearly all the polypeptide chains. They are responsible for the secondary structure of proteins. Thus, intramolecular interactions (hydrogen bonds and others—see below) impose a new superstructure upon the primary structure of the polypeptide, and this first level of suprastructure is referred to as the protein s secondary structure. 

The two geometrical parameters of greatest interest are the C—N—C —C and N—C —C—N torsions, known respectively as and tl . The series ot j> and values for each residue in a protein ultimately describes that protein s secondary and tertiary structures. Table 4 contains the < ) and values for the... 

Fig. 5.5 To the left of the arrow are shown the differences in size between HCAI (represented by a ribbon structure) and the different patticles (lepiesented by gray spheres) in a 2D plane. To the right of the arrow is a schematic illustration of the effect of the particle curvatures on the protein s secondary structure...

FIGURE 6 Far-UV CD spectra of an a-helical protein. Fai UV circular dichroism (CD) is a convenient method to assess a protein s secondary structure in solution. The spectra are of the folded and unfolded states or the protein. 

The spectra of proteins found in cells have a strong amide I band near 1650cm" ( 6.06 im). This band is affected by the environment of the peptide linkage and the protein s secondary amine. The amide II band occurs near 1530 cm" ( 6.54pm) and the amide III band occurs near 1245 cm" ... 

Denaturation refers to the loss of a protein s secondary and tertiary structures. 

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