Lecture 6: Structure Determines Function

three common themes in 3d protein structure

• Flexible enough to function properly

  • flexible to move into move stable form; or to change conformation according to their environment

• Stable enough that it will not change to another conformation

• Exposed amino acids are compatible with the environments where the protein will function

  • So that they are stable in that environment for it to function

Conformation in protein structure and function

• general types of protein function

  • Three main kinds

• conformation a predict the protein function

• General types of protein structures

  • Globular proteins

    • found in aqueous environment

    • DNA binding proteins - bind to DNA (e..g. TATA binding protein) and need

  • Fibrous proteins

    • long structural solid proteins

    • very stable (e.g. actin) compared to other proteins

  • Transmembrane proteins

    • found in more hydrophobic environments

    • Works with the phospholipid bilayer

Hemoglobin: O2 transport

• type of general protein

• Adult ver. called a ____

• What does each subunit contain

  • Explain its characteristic and what it does

• What happens when O2 binds

• a globular protein found in the cytoplasm of red blood cells

• Adult protein is a heterotetramer (different polypeptides)

  • 4 polypeptides

    • 2 is a globin subunits

    • 2 is b-globin subunits

• Each subunit contains a cofactor

  • Heme group (iron-containing porphyrin ring - prosthetic group - not going to dissociate - binds forever with the protein)

  • Able to bind to O2 and deliver

• Binding to O2 causes conformational changes in the protein

  • Make it more easier for O2 to bind

Binding of O2 with hemoglobin

• when bind to o2

• When releasing o2

• Binding of irons with the heme group makes a conformational change, making the O2 easier to bind

• release of o2, making another reverse conformational change for other o2 to be easier to release

hemoglobin -. sickle-cell phenotype

• how did this occur - what type of change on which subunit of the hemoglobin

• Unaltered blood cell is very flexible and move across tight spaces in the capillaries

• singular amino acid change (GLU6Val) on the surface of the b-globin protein

  • A conformational change

Hemoglobin - explain why the change of glutamate amino acid to valine changes the hemoglobin (the red blood cells)

• Increase hydrophobicity promotes protein-protein interactions

• Creates sticks of proteins

• Cannot change shape easily

• Red blood cells bursts and releases these sticks

Antibodies

• what type of general protein

• What cells are they produced by

• Were does it get released into

• Characteristic of an anitbody

  • How can you determine the difference between different antibodies within the same category?

• How is it held together

• how does it elicit an immune response

• More linkers = more flexibility = very useful

  • Each polypeptide

• globular protein

• Produced by B cells

• released into the blood

• a hetero-tetramer - only these can be altered (these specific regions only)

  • 2 light chains

  • 2 heavy chains

• Determined the difference by primary sequence

• Held together by disulphide bonds

• Binding to complementary antigens to elicit an immune response

Glucose transporters

• what do they do

• bind to the glucose found outside the cell

  • Glucose is very polar

• mediate transport into the cell, through the non-polar plasma membrane

• Changes conformational shape

  • From V to A, changing the opening regions of the transmembrane protein

What if proteins do not fold correctly?

• what happens to the proteins themselves

• What happens to the over cell/human body

• proteins gets degraded by the proteasome or lysosome

  • Half life typically 7 hours

  • However, half life depends on the type of cell

• Can aggregate (harder to break down; cell is harder to function because they are in the way of other functions in the cell) and result in Diseases

  • Cystic fibrosis

  • Parkinson’s disease

  • Alzheimer’s disease

  • Huntinton’s diseas

  • Huntinton’s disease

  • Cancer

  • Prions - associated with mad cow’s disease (neural disease)

The Prion protein

• cells it is located in

• Normal conformation

• Misfolded conformation

• Interactions (it is kinda bad)

• located in all cells (most also expressed in few) - a gene that Encodes the prion protein

• Normal conformation: PrP^C - cellular forms

  • Mostly a-helical

• Misfolded conformation: PrP^SC - scrappy form

  • Mostly B-strands

  • Results in being able to form stable intermolecular interactions

• When SC interacts with C, C will undergo refolding into SC conformation (BAD)

Why would a-helices convert to aligomers of B-sheets

• undergo a conformational change with more presence of B-sheets if under certain unique conditions

  • misfolding

  • PTM

  • Mutation

  • Ligand-binding

Using protein structure for drug design

• why is knowing the structure important

  • What types of molecules can be made/types of drugs

• understanding the protein structure can help in designing molecules that can help alter the proteins function by altering the proteins structure

• Types of drugs that can be made

  • Enzyme inhibitors: blocking substrate binding through the blockage of the enzyme active site

  • Molecular glues: drug that can help bind two proteins to each other - and perhaps change their functions

  • Receptor activators: A ligand that activates a signally pathway in a cell better than the native ligand