This discussion is focused on the nature, structure and functions of proteins, how these are formed and the role played by folding and aggregation in protein and the various interactions that are part of protein functions.
Proteins are a class of macromolecules, also described as polymers of amino acids present in all biological organisms and made up of carbon, hydrogen, nitrogen and oxygen…
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The three dimensional structures of proteins aid in delineating protein functions at a molecular level and the structure of proteins are determined usually with X ray crystallography, NMR spectroscopy etc. Some structural features of proteins would be necessary to perform certain biochemical functions although multifunctional and structural proteins may have higher number of residues than the average of 300 residues. Large aggregates are formed as a result of folding from protein subunits and actin molecules also assemble into actin filaments.
The protein structure has four distinct features including amino acid sequence of peptide chains as seen in a primary structure, secondary structures which are regular sub structures, such as strands of beta sheet, tertiary structure as seen in the three dimensional structure of a single protein molecule and quaternary structure which represents a complex of polypeptide chains and protein molecules (Copley, 1997; Berg, 2002). Proteins tend to transition between structures to perform the biological functions and this would be known as conformational changes.
The primary structure of proteins with amino acid sequences would be held together by covalent peptide bonds and the extremities of the amino acid chains are known as carboxy terminus (C - terminus) and amino terminus ( N -terminus).
The secondary structures are defined by their patterns of hydrogen bonds between the peptide groups although these bonds are generally not too stable except in conditions when the water concentration is low as in molten globule or fully folded states (Urbanc et al, 2006). The non specific interactions and propensities of amino acids would lead to the formation of molten globules. The tertiary structure shows structurally specific interactions within the protein domain with side chains and hydrogen bonds. The disulfide bonds tend to stabilize the tertiary structures of extra cellular proteins and reduce entropy in an unfolded state. The 4 levels of protein structure are given diagrammatically as follows -
Figure I - From Columbia.edu, biology courses, 2005 handouts
The formation of proteins could be explained as the combination of two amino acids in a condensation reaction and long chains of residues such as amino acids in peptide bond. The sequence of amino acids forms the primary structure of the peptide or protein and is determined by a gene. Within the primary structure, a sequence of nucleotides in DNA is transcribed into mRNA and this is translated by a ribosome and the sequence tends to define the structure and functions of the protein and would be unique to any specific protein. Determining the sequence of nucleotides within the primary structure would actually help in defining the protein (Berg, 2002; Copley, 1997). In the secondary structure, alpha helix and beta sheet saturate the peptide and secondary structures tend to occur most frequently in most proteins. The secondary structure elements tend to have a regular geometry with specific values and are usually folded into a shape with loops and turns (Berg, 2002, Copley, 1997). Tertiary structures are formed with interactions such as hydrogen bonding and ionic interactions and
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11 7. - Tools of the Trade; X-ray Crystallography and NMR. p.13 - Summary p. 16 References. p. 17 Abstract: A meta-analysis covering sixty years of biochemical research into the history and evolution of both the study and reality of proteins was conducted.
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