advances-in-protein-chemistry

than ten thousand unique structures of soluble proteins only few of them have been studied at atomic resolution/level. The complete
understanding of the structure and function of membranous proteins is crucial for designing better therapeutical molecules.
Plasma membrane: A complex lipid-protein compound
Plasma membrane consists of lipids with highest percentage (60-70%) followed by the protein with lesser in percentage (30-40%). In
a few percentage cholesterol and other molecules are also present in plasma membrane. In the complex structure of plasma membrane
the mobility and diffusion of protein become irregular with respect to diffusion coefficient and showing lower value as compared to
the artificial membrane systems. Probably, all this happens due to interaction of protein molecules with other molecules, cytoskeleton
interaction and presence of sterol and sphingolipid enriched domains known as lipid rafts [3-7].
Figure 5: Protein Diffusion in Cell is affected by Multiple Biological Processes.
Particularly three techniques are used for analyzing dynamics in proteins including fluorescence recovery after photo bleaching,
fluorescence correlation spectroscopy and single particle tracking. Moreover, physical models are engaged in analyzing the data for
protein dynamics that represents extraordinary features of the biophysical nature regarding protein dynamics and membrane domains
in membranes. Up till now, there remain considerable unknown information among cholesterol dependent lipid micro-domains, protein
interactions, and cause of the underlying cytoskeleton. Innovative techniques of microscopy may provide better sequential and spatial
resolution ensuing in more perfect identification and recognition of proteins as well as its dynamics in biological system. The kinetic
aspects of protein in a membrane and the types of motion that it contain go through by the lateral organization of cellular boundary. Fluid
mosaic model given by Singer and Nicolson projected that the cell membrane contains membrane-associated proteins which can diffuse
(spread) liberally with Brownian movement [8] and randomly distributed on the cellular surface.
Importance of Dynamics in Proteins
The dynamic behavior of proteins is distinguished to play significant role in protein function. Diverse characteristics of protein
function are influenced by dynamics of protein. For example, protein to protein identification [9], protein-DNA associations [10] and
enzyme-substrate bonding and activity of enzymes [11-13] are all resolute by the structural flexibility of the protein molecule and side
chains, resulting into characterizing not only the structure, but also dynamic properties as well. On a wide variety of time scales, the
dynamics of proteins are thoroughly related to function of protein. Fast as well as moderately fast fluctuations of protein structure
facilitate a protein to sample a complex conformational-energy landscape. Such motions of atoms or residues give rise to the slower
processes associated with protein function. Molecular dynamics (MD) simulations have shown that a protein can sample thousands of
conformations within a very short time. Determination of protein dynamics by X-ray, NMR and other experimental techniques and
theory helped in understanding the dynamics that provides an important connection between protein function and protein structure [14].
Dynamics of proteins and mRNA
mRNA and protein molecules are dynamic entities, and their presence in the cell is the outcome of contrasting processes that bring
about their biosynthesis or destruction. The abundance-weighted total of all proteins in a cell or sub-cellular space is also dynamic.
The amount of a true intracellular protein in a cell is the result of the opposing processes of protein synthesis and protein degradation.
However, for extracellular proteins, it has to factor in the irreversible loss due to secretion. If a protein decreases in amount in a cell, this
can be a consequence of a reduction of mRNA, or of a decrease in ribosomal activity or translation initiation. Equally possible it could be
the consequence of enhanced degradation of the protein.
Protein Motions
Proteins are composed of multiple domains, whose flexibility and mobility lead to a great deal of versatility in their function. Protein
dynamics, at the domain level, is a controlling influence in the allosteric formation of protein complexes, in catalysis, in cell signaling and
regulation, in cellular locomotion and in metabolic transport.
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