M2C: Protein Structure 1

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Proteins Do:

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1. Enzymes
2. Hormones and hormone receptors
3. Transport molecules like O2 and metals
4. Generate mechanical motion
5. Antibodies
6. Replicate and fix DNA
7. Important in disease
6.

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Primary protein structure

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Amino Acid code

Beginning = N-terminus.
End = C-terminus

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Secondary protein structure

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"Initial folding" of a protein. Alpha helices, beta sheets, turns, loops.

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Alpha Helices

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Carbonyl groups H-bond with Nitrogen to form helical structure.

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Beta Sheets

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Oxygen on carbonyl group H-bonds with H of Nitrogen group causing "pleating" of proteins.

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Alpha helices and beta sheets. Why they are common.

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Satisfy all H-bonding potential of backbone O and N in proteins.

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Turns

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Reverse direction of protein. Small loops. <4 residues long.

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Loops

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Irregular structure in protein. >4 residues in length.

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Tertiary protein structure

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Particular shape of protein. Determined by aa sequence. Globular, Fibrous, and integral membrane proteins.

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Globular proteins

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Compact, spherical, non-repetative sequence.
Hydrophobic residues found on interior, polar on exterior.
Fairly rigid due to tightly packed aa side-chains.
O and N on inside are intra-H-bonding. On outside, interacting with water.

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Fibrous proteins

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Highly elongated structures. Repetitive sequences.
Structural materials physically stabilize biological structures. Used in skin, muscle, bone, tendon, etc.
Have motile utility.
Collagen is most common in vertebrates. Has great tensile strength.

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Fibrous protein example: Explanation for Scurvy

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Repeats of Gly-X-Y where x usually = Pro and Y = Hyp. Pro is converted to Hyp by enzyme Prolyl Hydroxylase. Enzyme uses vitamin C as a co-factor. Hyp is crucial to stability of collagen, and therefore, with lack of vit C, weakening of collagen, and therefore scurvy.

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Membrane Proteins

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Associated with membranes. Either peripheral or integral to membranes.

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Peripheral membrane proteins

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Found on outside of membranes. Same idea as globular proteins.

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Integral membrane proteins

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Inbedded in membranes. Outer residues are often hydrophobic instead of usual polar.

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Porin proteins

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Type of integral membrane protein. Allows nutrients in and out of cell. Hydrophobic residues touch membrane. Hydrophillic (polar) inside "hole".

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Quaternary structure of proteins

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Complexes of poly-peptides create functional proteins.

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Protein to protein interactions

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Hydrogen bonding is key. Some components must be soluble without counterparts.

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Multi-domain proteins

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Evolution uses pre-existing domains to create new proteins using flexible linkers to connect pre-existing domains.

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Disulfide bonds

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Covalent bonds existing between two cystines. Used in tertiary as well as quaternary structures. More stable in an oxidizing environment. Often found in extra-cellular space.

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Post-translational modifications

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Further modification after creation to make a protein functional. Includes proteolytic modification, phosphorylation, methylation, hydroxylation, glycosylation.

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Proteolytic modification

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Cleaving by proteases create active form of a protein. Insulin is a good example.

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Phosphorylation

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Often associated with a conformational change. Used to activate signaling proteins. Involves adding a phosphate to the oxygen on Ser, Tyr, and Thr)

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Methylation

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Addition of a methyl group to an aa, usually Lys. Helps regulate histones in DNA packaging.

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Hydroxylation

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Adding OH group to C. Important in structure of collagen. (Think Scurvy).

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Glycosylation

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Addition of a carbohydrate to protein. Stabilizes relationship between membrane and membrane protein.

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Conformational change

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Substrate can determine shape of protein and active vs. inactive state. Conformational change can also allow or disallow substrate interaction.

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Determining structure of a protein

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x-ray crystallography or Nuclear Magnetic Resonance (NMR).

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X-ray crystallography

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Crystal of protein is required. Wavelength is at same measurement as protein. Are crystal structures relevant to what occurs in solution?

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NMR

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Nuclear Magnetic Resonance. Can only be used on small proteins.