proteins. proteins? what is its how does it how is its how does it how is it where is it what are...
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Proteins
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Proteins?
What is its What is its How does it How does it How is its How does it How is it Where is it What are its
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H2N
R1
O
O
H
C
C
N
H
H
C
R2
C
O
OH
HH
O
H
H
H2N
R1
O
C
C
N
H
C
R2
C
O
OH
HH
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Peptide bond formation
Condensation reaction forms a peptide bond.
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The peptide bond
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Peptide
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The planar peptide bond
Three bonds separate sequential carbons in a polypeptide chain. The N—C and C—C bonds can rotate, described by dihedral angles designated and , respectively. The C—N peptide bond is not free to rotate.
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• Rotation around the peptide bond is not permitted
• Rotation around bonds connected to the alpha carbon is permitted• (phi): angle around the -carbon—amide nitrogen bond• (psi): angle around the -carbon—carbonyl carbon bond• In a fully extended polypeptide, both and are 180°
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Steric Hindrance
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While many angles of rotation are possible, only a few are energetically favorable
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Ramchandran plot
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• Some f and y combinations are very unfavorable because of steric crowding ofbackbone atoms with other atoms in the backbone or side-chains• Some f and y combinations are more favorable because of chance to formfavorable H-bonding interactions along the backbone• Ramachandran plot shows the distribution of f and y dihedral angles thatare found in a protein• shows the common secondary structure elements• reveals regions with unusual backbone structure
While many angles of rotation are possible only a few are energetically favorable
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Rotation
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Alpha helix
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• The backbone is more compact with the dihedral (N–C—C–N) in the range ( 0° < < -70°)
• Helical backbone is held together by hydrogen bonds between the nearby backbone amides
• Right-handed helix with 3.6 residues (5.4 Å) per turn
• Peptide bonds are aligned roughly parallel with the helical axis
• Side chains point out and are roughlyperpendicular with the helical axis
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Left and right handedness
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• Not all polypeptide sequences adopt a helical structures
• Small hydrophobic residues such as Ala and Leu are strong helix formers
• Pro acts as a helix breaker because the rotation around the N-Ca bond is impossible
• Gly acts as a helix breaker because the tiny R group supports other conformations
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Peptide dipole
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• The backbone is more extended with the dihedral(N–C—C–N) in the range ( 90° < < 180°)• The planarity of the peptide bond and tetrahedral geometry of the -carbon create a pleated sheetlike structure• Sheet-like arrangement of backbone is held together by hydrogen bonds between the more distal backbone amides• Side chains protrude from the sheet alternating in up and down direction
• Parallel or antiparallel orientation of two chains within a sheet are possible• In parallel sheets the H-bonded strands run in the same direction• In antiparallel sheets the H-bonded strands run in opposite directionsBeta strand is an extended structure… 3.5 A between R groups in sheetcompared to 1.5 in alpha helix
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Beta Sheet
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Anti‐parallel B sheetR‐groups spaced at 3.5 ADistanceR groups alternate aboveand below plane of sheet
Parallel B sheetR‐groups spaced at 3.25 AdistanceR groups alternate above andbelow plane of sheet
Parallel and antiparallel
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• -turns occur frequently whenever strands in sheets change the direction• The 180° turn is accomplished over four amino acids• The turn is stabilized by a hydrogen bond from a carbonyl oxygen to amide proton three residues down the sequence• Proline in position 2 or glycine in position 3 are common in -turns
The Beta turn
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The Beta turn
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Cis and Trans proline
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Tertiary Structures
• Tertiary structure refers to the overall spatial arrangement of atoms in a polypeptide chain or in a protein• One can distinguish two major classes– fibrous proteinstypically insoluble; made from a single secondary structure– globular proteins water-soluble globular proteins lipid-soluble membrane proteins
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Fibrous Proteins
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Keratin
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Hair
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Collagen
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Collagen
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Silk
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Silk
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Globular Proteins
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Myoglobin Tertiary
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A simple motif
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An elaborate motif
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X-ray diffraction
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NMR (1D)
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NMR (2D)
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Constructing large motifs
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Quaternary structure
• Quaternary structure is formed by spontaneous assemblyof individual polypeptides into a larger functional cluster
• Oligomeric Subunits are arranged in Symmetric Patterns
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Hemoglobin
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Rotational symmetry
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Dihedral symmetry
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Protein Denaturation
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Protein Denaturation
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Protein Renaturation
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Protein folding
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Folding pathway
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Molten globules
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Chaperones
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