structural organisation of protiens
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Submitted By Vikas C J
ORGANISATION OF PROTEINS
CONTENTS INTRODUCTION CLASSIFICATION OF PROTEINS STRUCTURAL ORGANISATION OF
PROTEINS CONCLUSION REFERENCE
INTRODUCTION Proteins are polymers of 20 different amino acids
joined by peptide bonds. The proteins we observe in nature have evolved,
through selective pressure, to perform specific functions.
The functional properties of proteins depend upon their three-dimensional structures.
The three-dimensional structure arises because particular sequences of amino acids in polypeptide chains fold to generate, from linear chains, compact domains with specific three-dimensional structures
Proteins are polypeptide chains
Amino acids are joined end-to-end during protein synthesis by the formation of peptide bonds.
carboxyl group of one amino acid condenses with the amino group of the next to eliminate water.
CLASSIFICATION OF AMINO ACIDS BY R GROUP
The amino acids are classified into five main classes based on the properties of
their R groups. These are: Non-polar, Aliphatic R Group Aromatic R Group Polar, Uncharged R Group Positively Charged R Group Negatively Charged R group
There are 20 different types of amino acids.
Nonpolar,aliphatic R groups
Aromatic R groups
Polar,uncharged R groups
Positively charged R groups (Basic)
Negatively charged R groups (Acidic)
STRUCTURAL ORGANIZATION OF PROTEINSThe structural and functional features of proteins and protein
complexesare addressed at four levels of hierarchal organization. These
are:1. Primary structure (1o-Structure)2. Secondary structure (2o-Structure)3. Tertiary structure (3o-Structure)4. Quaternary structure (4o-Structure)
PRIMARY STRUCTURE Primary structure refers to amino acid linear
sequence of polypeptide bonds. The primary structure is held together
by covalent or peptide bond , which are made during the process of protein biosynthesis or translation.
The two ends of the polypeptide chains are referred to as the C-terminal (Carboxyl) and the N-terminal (amino) based on the nature of the free group on each extremity.
Here the chain is connected by disulphide linkage
Eg : insulin
SECONDARY STRUCTURE Localized arrangement of adjacent amino acids formed as the
polypeptide chain folds. it consists of alpha helix and beta pleated sheets
Linus Pauling proposed some essential features of peptide units and polypeptide backbone. They are:
The amide group is rigid and planar as a result of resonance. So rotation about C-N bond is not feasible.
Rotation can take place only about N- Cα and Cα – C bonds. Trans configuration is more stable than cis for R grps at Cα
From these conclusions Pauling postulated 2 ordered structures α helix and β sheet
RAMACHANDRAN PLOT• The angle pairs ф and Ѱ are usually plotted against each other
in a diagram called a Ramachandran plot after the Indian biophysicist G.N. Ramachandran who first made calculations of sterically allowed regions.
• Regions in the Ramachandran plot are named after the conformation that results in a peptide if the corresponding ф and Ѱ angles are repeated in successive amino acids along the chain.
• The major allowed regions are the right-handed α helical cluster in the lower left quadrant; The broad region of extended β strands of both parallel and antiparallel β structures in the upper left quadrant; and the small, sparsely populated left-handed α -helical region in the upper right quadrant.
• Left-handed α helices are usually found in loop regions or in small single-turn a helices.
RAMACHANDRAN PLOT
A Ramachandran plot (also known as Ramachandran diagram or a [φ,ψ] plot), originally developed in 1963 by G. N. Ramachandran
Yellow areas : outer limit
White regions : Sterically disallowed for all amino acids except glycine.
Red regions : allowed regions namely the a-helical and b-sheet conformations.
Yellow areas : outer limit
The alpha (α) helix is an important element of secondary structure Alpha helices in proteins are found when a stretch
of consecutive residues all have ф and Ѱ angle pair approximately -60° and -50°, corresponding to the allowed region in the bottom left quadrant of the Ramachandran plot
The α helix is right-handed The α helix has 3.6 residues per turn and a pitch(the
distance the helix rises along its axis per turn) of 5.4 Å.
The a helices of proteins have an average length of ,12 residues, which corresponds to over three helical turns, and a length of ,18 Å.
the backbone hydrogen bonds are arranged such that the peptide C=O bond of the nth residue points along the helix axis toward the peptide N-H group of the (n+4)th residue.
α Keratin—A Coiled Coil It is the principal component of their
horny outer epidermal layer and its related appendages such as hair, horn, nails, and feathers
The conformation of keratin’s coiled coil is a consequence of its primary structure
the two keratin helices are inclined about 18° relative to one another, resulting in the coiled coil arrangement
The central ,310-residue segment of each polypeptide chain has a 7-residue pseudo repeat, a-b-c-d-e-f-g, with non polar residues predominating at positions a and d
Since an helix has 3.6 residues per turn, keratin’s a and d residues line up along one side of each helix
The hydrophobic strip along one helix associates with the hydrophobic strip on another helix.
Because the 3.5-residue repeat in keratin is slightly smaller than the 3.6 residues per turn of a standard helix.
β Sheets
In β sheets hydrogen bonding occurs between neighboring polypeptide chains rather than within one as in an α helix.
Sheets come in two varieties: The antiparallel β sheet, in which neighboring hydrogen-
bonded polypeptide chains run in opposite directions . The parallel β sheet, in which the hydrogen-bonded
chains extend in the same direction• Successive side chains of a polypeptide chain in
a β sheet extend to opposite sides of the sheet with a two-residue repeat distance of 7.0 Å
Fibroin—A β Sheet Insects and arachnids (spiders)
produce various silks to fabricate structures such as cocoons, webs, nests, and egg stalks
Fibroin consist of series of following residues
(-Gly-Ser-Gly-Ala-Gly-Ala-)n The bsheets stack to form a
microcrystalline array in which layers of contacting Gly side chains from neighboring sheets alternate with layers of contacting Ser and Ala side chains
Super secondary structure - collagen
Its strong, insoluble fibers are the major stress-bearing components of connective tissues such as bone, teeth, cartilage, tendon, and the fibrous matrices of skin and blood vessels
A single collagen molecule consists of three polypeptide chains
Collagen has a distinctive amino acid composition. Nearly one-third of its residues are Gly; another 15 to 30% of its residues are Pro
Tertiary Structure The tertiary structure describes the folding of
secondary structures and pack together in part to bury the hydrophobic side chains, forming a compact molecule with very little empty space in the interior
The interactions hold together are polar interactions between hydrophilic groups and van der Waals interaction between nonpolar groups
Factors influencing tertiary structure include
Hydrophobic/hydrophilic interactions
Hydrogen bonding Disulfide linkages Folding by chaperone proteins
The globin fold is present in myoglobin
The first protein X-ray structure, that of myoglobin, was elucidated in the late 1950s by John Kendrew and co-workers
The major types of secondary structural elements, α helices and pleated sheets, commonly occur in globular proteins
The tertiary structure of myoglobin is that of a typical water soluble globular protein
myoglobin, consist only of α helices spanned by short connecting links that have coil conformations
This protein binds and stores oxygen in muscle. It consists of 153 amino acids, which fold into 8 α-helices of differing lengths
Myoglobin A myoglobin polypeptide is
comprised of 8 separate right handed α-helices, designated A through H, that are connected by short non helical regions.
The interior consists almost entirely of nonpolar residues including leucine, valine, methionine, and phenylalanine
two histidines are the only polar residues which play an integral role in the binding of heme oxygen
Quaternary structure The quaternary structure of a protein describes the
interactions between different peptide chains that make up the protein
The forces that hold different chains together are the same that hold the tertiary structure together, hydrogen bonding between polar R-groups, ionic bonds between charged R-groups, hydrophobic interactions
between nonpolar R-groups, and disulfide bonds
Allostery in Haemoglobin Allosteric regulation is the regulation of an enzyme or
other protein by binding an effector molecule at the protein's allosteric site.
Haemoglobin is an allosteric protein- binding of oxygen to one of the subunits is affected by its interactions with the other subunits
binding of oxygen to haemoglobin is said to be cooperative degree of saturation of myoglobin is always higher than
haemoglobin Myoglobin therefore has a higher affinity for oxygen than
does haemoglobin
REFERENCE David Hames and Nigel Hooper. Instant
notes on biochemistry. Third edition. David L Nelson and Michael M Cox.
Lehninger principles of biochemistry. Fourth edition.
U Sathyanarayana. U Chakrapani. Biochemistry
Richard A Harvey. Biochemistry. Fifth edition.
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