Proteomics - Challenges in Delivery of Therapeutic Genomics and Proteomics - page 405

and structure of a protein due to change in the dielectric constant, leading to overall
change in the stability of the protein molecule under consideration. The addition of
reducing agents and materials like guanidine results in a reduction of disulfide link-
ages that are responsible for maintaining three-dimensional structures of proteins.
Reduction of disulfide linkages results in increased intrinsic viscosity, suggesting
that globular proteins are unfolding to loose, expanding random coil chains. This
process is called denaturation.
The definition of denaturation is the nonproteolytic modification in a struc-
ture of a natural/native protein, leading to sea change in its physical, chemical, and
ultimately biological activity. Protein denaturation is confirmed and assessed by a
number of techniques, such as determination of intrinsic viscosity, optical rotation
ultraviolet differential spectroscopy, and others. Protein denaturation finally results
in disruption of disulfide bridges and separation of protein or peptide chains.
8.5.2 Methods of Protein Structure Prediction
It has always been a matter of interest and importance to develop specific and sen-
sitive methods for the prediction of protein structure. This is particularly useful in
determining the structure of antigens and epitopes that are responsible for diseases
like AIDS. Structural models currently used by scientists facilitate easy structural
prediction. Some of the popular and widely adopted methodologies for structural
prediction of proteins are discussed here.
The availability of state-of-the-art facilities and techniques like X-ray crystallog-
raphy enables scientists to determine the conformational arrangements of proteins.
These techniques can be applied to new proteins where the secondary structures are
not completely elucidated.
8.5.2.1 Prediction of Hydrophobicity and Hydrophilicity
Hydrophobicity is a major catalyst for the arrangement of different sections of pep-
tide sequence in different parts of protein. Hence, prediction of hydrophobicity may
act as a handy tool for determining secondary protein structure. Nozaki and Tanford
[38] were pioneers in establishing a hydrophobicity scale based on solubility of
amino acid in aqueous ethanol and dioxane solutions.
�.5.2.1.1 Applications of Predicted Hydrophobicity and Secondary
Structure
Hydrophilicity and hydrophobicity data are instrumental in predicting the antigenic
determinants. Despite the ability to use conformational techniques, these techniques
have also been widely adopted to predict hydrophobicity and secondary structure,
to fold new protein sequences into globular structure. If the novel protein bears a
sequence analogous to a protein having known X-ray crystal structure, it may be quite
easy to predict the real structure due to the concordance of the secondary structures to
the original ones. This method was used for the structural prediction of renin.