supersecondary structures. supersecondary structures motifs motifs or folds, are particularly stable...
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Supersecondary structures
Supersecondary structures motifs
• motifs or folds, are particularly stable arrangements of several elements of the secondary structure.
• Supersecondary structures are usually produced by packing side chains from adjacent secondary structural elements close to each other.
Rules for secondary structure.• Hydrophobic side groups must be buried inside the
folds, therefore, layers must be created ( - - ; -b a b aa).
• a-helix and b-sheet, if occur together, are found in different structural layers.
• Adjacent polypeptide segments are stacked together.• Connections between secondary structures do not
form knots.• The b-sheet is the most stable.
Motif
• Secondary structure composition,e.g. all , all , segregated +, mixed /
• Motif = small, specific combinations of secondary structure elements,
e.g. -- loop
Supersecodary Structures (Motifs)
Serum albumin Ferritin
α-amylase inhibitorImmunoglobulin
Pilin
Tertiary protein structure
• Secondary structures fold and pack together to form tertiary
structure– Usually globular shape
• Tertiary structure stabilised by bonds between R groups (i.e.
side chains)
• Intracellular protein tertiary structures mostly held together
by weak forces. Extracellular tertiary structures stabilised by
disulfide (covalent) bonds.
Three-dimensional structure of proteins
• Three-dimensional structure of proteins is determined by it amino acid sequence.
• Function of the protein depends on its structure.• Each protein has a unique or nearly unique structure.• Non-covalent interactions are the most important
forces stabilizing the three dimensional structure of the protein.
• There common structural patterns in vast protein architecture.
• Native structure is the natural 3-dimensional structure of a protein.
Domains
• Domains are the fundamental functional and three-dimensional structural units of polypeptides
• Polypeptide chains that are greater than 200 amino acids in length generally consist of two or more domains
• The core of a domain is built from combinations of supersecondary structural elements (motifs)
• Folding of the peptide chain within a domain usually occurs independently of folding in other domains
• Therefore, each domain has the characteristics of a small, compact globular protein that is structurally independent of the other domains in the polypeptide chain.
Interactions stabilizing tertiary structure :
1.Disulfide bonds: These strong, covalent bonds help stabilize the structure of proteins, and prevent them from becoming denatured in the extracellular environment.
2.Hydrophobic interactions
3.Hydrogen bonds
4. Ionic interactions
Tertiary structure - disulfide bond– Covalent bond
between sulfur atoms on two cysteine amino acids
• H bonds weak allowing to be broken and reformed easily– Allows structural
change• produces ‘functional’
molecules
Hydrogen bond
Tertiary structure - H bond
• Ions on R groups form salt bridges through ionic bonds
Tertiary structure - hydrophobic forces
• Close attraction of non-polar
R groups through dispersion
forces
• Very weak but collective
interactions over large area
stabilise structure
• Repel polar and charged
molecules/particles
Tertiary Structure
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Tertiary Structure
• The interactions of the R groups give a protein its specific three-dimensional tertiary structure.
Tertiary Structure
• non-linear• 3 dimensional• global but restricted to the amino
acid polymer• formed and stabilized by
hydrogen bonding, covalent (e.g. disulfide) bonding, hydrophobic packing toward core and hydrophilic exposure to solvent
• A globular amino acid polymer folded and compacted is somewhat functional (catalytic) and energetically favorable interaction!
Quaternary Structure of Proteins
Many proteins consist of a single polypeptide chain, and are defined as monomeric proteins.
others may consist of two or more polypeptide chains that may be structurally identical or totally unrelated.
The arrangement of these polypeptide subunits is called the quaternary structure of the protein.
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Quaternary Structure of Proteins
• The biological function of some molecules is determined by multiple polypeptide chains – multimeric proteins
• Two kinds of quaternary structures: both are multi-subunit proteins.
• Homotypic: association between identical polypeptide chains.
• Heterotypic: interactions between subunits of very different structures.
• The interactions within multimers is the same as that found in tertiary and secondary structures
Quarternary Structure• This structure for proteins that have more than one
polypeptide chains.
• It is the arrangement of protein subunits (protein that has more than one polypeptide chain) in three dimensional complex.
• The interaction between subunits are stabilized by:• hydrogen bonds
• electrostatic bonds
• hydrophobic bonds
• e.g. of proteins having quaternary structure:• Lactate dehydrogenase enzyme: (4 subunits), hemoglobin (4
subunits)
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Summary of Structural Levels