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Published byAden Thistlethwaite Modified over 9 years ago
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The amino acids in their natural habitat
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Topics: Hydrogen bonds Secondary Structure Alpha helix Beta strands & beta sheets Turns Loop Tertiary & Quarternary Structure Protein Domains
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Hydrogen Bonds A hydrogen bond is a type of attractive (dipole-dipole) interaction between an electronegative atom and a hydrogen atom bonded to another electronegative atom. Hydrogen Bond Donors (D): Nitrogene.g. N-H amide in peptide bond Oxygene.g. O-H sidechain of Ser Hydrogen Bond Acceptors (A): Oxygene.g. C=O carbonyl in peptide bond Distance: H-A 2.5 Å; D-A 3.5 Å; also dependent on angle D-H … A
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Hydrogen Bonds (2)
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Secondary structure The amino acids form four different secondary structure elements: α-helices β-strands Turns Loops
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Secondary structure: the -helix hydrogen bond between backbone O (from C=O) of residue i and backbone H (from N-H) of residue i+4: O(i) – N(i+4) 3.6 residues per turn right-handed helix
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The -helix
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Helix
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Helix dipole All peptide unit planes are roughly parallel to the helix axis Each peptide bond is a small dipole The dipoles within the helix are aligned, i.e. all C=O groups point in the same direction and all N-H groups point the other way The helix becomes a net dipole with +0.5 charge units at the N-terminal and – 0.5 at the C-terminal By convention the dipole points from negative to positive
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Helix summary Hydrophobicity distribution Hydrogen bond between O (i) and N (i+4) Helix dipole
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Secondary structure – β -strand A β-sheet consists of at least two β-strands interact with each other Anti-parallelParallel
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-strands and -sheets Backbone adopts an “extended” conformation: -strand The -strands are arranged side by side; adjacent -strands can be parallel or anti-parallel Backbone hydrogen bonding between adjacent -strands; formation of a -sheet R-groups extend below and above the sheet, perpendicular to the plane of the H-bonds The strand is twisted
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Residue direction in -sheets R-groups of neighbouring residues within one -strand point in opposite directions. R-groups of neighbouring residues on adjacent -strands point in the same direction
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Antiparallel -sheet N -> C C <- N
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Parallel -sheet N -> C
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Bulge An irregularity in antiparallel structures Hydrogen-bonding of two residues from one strand with one residue from the other in antiparallel sheets
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Strand summary Multiple strands form a sheet Hydrophobicity distribution alternating Parallel and anti-parallel strands & hydrogen bonding patterns Bulges are irregularities
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Secondary structure – Turn Turns connect the secondary structure elements
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Turns Specialized secondary structures that allow for chain reversal without violating conformational probabilities Nearly one-third of the amino acids in globular proteins are found in turns. Most turns occur at the surface of the molecule. A specific subclass is the -turn, a region of the polypeptide of 4 amino acids (i, i+1, i+2, i+3, between two -strands) having a hydrogen bond from O(i) to N(i+3).
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-Hairpin Widespread in globular proteins. One of the simplest super-secondary structures
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Turn summary A turn sits between two ‘things’ A -turn sits between two -strands There are many types of -turn Nearly all -turns contain at least one Gly or Pro
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Secondary structure - Loop A loop is everything that has no defined secondary structure
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Tertiary structure The secondary structure elements interact to form the structured protein
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Quaternary structure Some proteins can interact with each other to form dimers or multimers The individual chains are callled subunits or monomers
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Protein domains - definitions Group of residues with high contact density, number of contacts within domains is higher than the number of contacts between domains. A stable unit of protein structure that can fold autonomously A rigid body linked to other domains by flexible linkers. A portion of the protein that can be active on its own if you remove it from the rest of the protein.
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Protein Domains Domains can be 25 to 500 amino acids long; most are less than 200 amino acids The average protein contains 2 or 3 domains The same or similar domains are found in different proteins. “Nature is a ‘tinkerer’ and not an inventor” (Jacob, 1977). “Nature is smart but lazy” Usually, each domain plays a specific role in the function of the protein.
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Protein Domains - an alphabet of functional modules WD40WWSH2SH3 14-3-3 ANK3 ARM BH1C1C2 CARD EHEVHFYVEPDZDeathDEDEFH PHPTBSAM From: Bioinformatics.ca
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Domain Database InterPro InterPro - protein sequence analysis & classification InterPro provides functional analysis of proteins by classifying them into families and predicting domains and important sites. Interpro combines protein signatures from a number of member databases into a single searchable resource, capitalising on their individual strengths to produce a powerful integrated database and diagnostic tool
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Summary 3D, 4D & domains Proteins are folded up in 3D Protein subunits can fold up to form a quarternary structure Sometimes monomer is not active, but quarternary structure is Protein domains “independent units” with own function& structure Average size 100-150 aa Lego blocks of nature Look in Interpro to find info about domains in your protein
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