advances-in-protein-chemistry

Protein Characterization
using Modern Biophysical
Techniques
Shuja Shafi Malik 1 * and Tripti Shrivastava 2
1
Department of Biochemistry and Molecular Biology, School of
Medicine University of Maryland, USA
2
Translational Health Science and Technology Institute, India
*Corresponding author: Shuja Shafi Malik, Department of
Biochemistry and Molecular Biology, School of Medicine University
of Maryland, Baltimore, USA; E-mail: shujasmalik@gmail.com
Introduction
Proteins are an important class of macromolecules in living systems that form observable outcome of genetic
inheritance or to say are manifestation of genome. They function in different forms, at varied levels and in diverse ways
like structural components of cells and cellular organelles, catalyze biochemical reactions in enzymatic pathways, serve as
signaling molecules, receive and respond to stimulus or function as one of the most important components of immune
system in form of antibodies. It is through proteins that life expresses itself and this importance of proteins in maintaining
life becomes more obvious in conditions of disease, disorder or unfavorable living conditions. Even a small change in
protein sequence or structure can have detrimental outcome, like sickle cell anemia, which is caused by single amino
acid substitution of glutamic acid by valine. It is by changing or shuffling composition of their proteins that certain living
systems circumvent hostile atmospheres to make their survival possible and sustainable. The human immunodeficiency
virus (HIV) is one such pathogen that evades host immune system by mutating its own envelope protein. Opportunistic
pathogens like Mycobacterium tuberculosis survive within hosts for infinitely longer durations of their life by switching
over to alternate modes of metabolism i.e. use different set of proteins other than their regular life-cycle proteins that help
them survive in these non-favorable environments. In short it is the protein molecules that act as harbinger of life. Berzelius
justifiably called these molecules proteins. The term ‘protein’ has its origin Greek word ‘proteois’ which means ‘primary’ or
‘standing in front’ [1].
Looking at important roles proteins play in living system it is but natural for human interest to delve into exploring
structure, function, working, mechanisms and other aspects related to these biological entities. Besides these reasons,
studying proteins becomes important for fact that in almost all cases of disease and disorder they are targets for different
therapies and interventions. Therefore methods and approaches for studying proteins have kept on evolving both in terms
of multitude of techniques applied and in terms of bettering approaches within individual techniques. Proteins can be
characterized by exploiting diverse structural, biochemical, electromagnetic, spectroscopic and thermodynamic properties
that are bestowed on them by virtue of their composition. But in spite of this diversity the fundamental biochemical
composition and rules governing protein architecture are same. Isolation of proteins and their subsequent functional and
structural characterization utilizes cumulative knowledge from basic common composition and the diversity accorded by
that composition. This chapter is discussed in three subsections divided on basis of biochemical and biophysical properties
of proteins viz. mass and size, electromagnetic properties and thermodynamic characteristics.
Methods Based on Mass and Size
Proteins like other molecular entities have mass and size and information about these fundamental characteristics holds
an important step in protein characterization. Proteins are polymers formed by the association of fundamental structural
unit, the amino acid. Simplest of proteins in terms of composition and oligomeric nature are monomers. There are proteins
which are formed by association of identical or non-identical monomeric subunits giving rise to formation of what are
called homomeric or heteromeric oligomers. Likewise oligomeric proteins differ in the number of subunits from a simple
dimeric state to more than decameric composition of assemblies like chromatin remodelers and proteasomes. While as
mass is directly proportional to the number of amino acids in a protein, its size is determined by other factors as well,
like how amino-acids in a monomeric protein interact or in what manner subunits in multi-subunit protein cooperate
determines the shapes proteins take like globular, fibrous etc. Therefore knowledge about mass and size of proteins holds an
important key into elucidating information about proteins and this information can be exploited further in studying and
understanding their different structural and functional characteristics.
Mass Spectrometry
Mass spectrometry is one of the highly recognized techniques used in eliciting information about molecular masses of
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