Biology 3601 Fall 2013

Organic Cofactors

Vitamins and Minerals

Vitamin A

Organic pigment

Cofactor for light

sensitive proteins

for vision

Vitamin A

for growth and

differentiation

Pellagra

Symptoms:

Sensitivity to sunlight

Dermatitis, alopecia, skin lesions

Tongue inflammation

Diarrhea

Cardiomyopathy

General Weakness

Aggressive Behavior

Emotional Disturbances

Disorientation

Dementia

Death

Niacin deficiency in corn-dominated diets

Nicotonic Acid and NAD+

Niacin (Nicotinic Acid)

NAD+ cofactor: “biological battery”

Cobalamin (Vitamin B12)

corrin molecule (hetercyclic ring)

+ nucleotide derivative (below)

Pyridoxal (dietary Vitamin B6)

Pyridoxal-5-Phosphate (PLP)

plays a significant role in transamination, racemization (synthesis of D-amino acids) and decarboxylation reactions; a cofactor in the synthesis of heme and neurotransmitters, and in the metabolism of glucose and lipids

Transamination reaction

Protein Interactions

Proteins interact with:

Protomers (to form complexes) & other Proteins

Organic and Inorganic Cofactors and Ligands

Substrates (as enzymes)

Proteins are Never Alone

http://www.topsan.org/@api/deki/files/596

https://upload.wikimedia.org/wikipedia/commons/3/3d/1GZX_Haemoglobin.png

dimer

tetramer

trimer

filament

capsid

complex

Protein – Protein Interactions

Protein interaction map of baker’s yeast shows how proteins interact with one another. Every spot corresponds to a protein and a line between them means that they two proteins bind to or interact with one another.

Protein – Protein Interactions

Pyruvate Dehydrogenase Complex

Bacterial Flagellum Complex

functionally obligatory

not obligatory but highly beneficial

Carbamoyl phosphate synthetase

Glutamine (green)

ATP (blue) and bicarbonate

ADP (red)

Channeling

Benefits of

channeling

• Efficiency
• Isolation

The Equilibrium Constant

A + B  C

Keq = [C]/[A][B]

for transient (temporary) associations

Proteins and Ligands

ligand/substrate

receptor complex

association

dissociation

hydrogen bonding

hydrophobic interactions

electrostatic interactions

KA low

KA high

Association Constant KA

Protein- Ligand Interactions

Productive Interactions between proteins and their ligands requires the ligand to be present at concentrations ~ Kd.

To increase the fraction of saturated proteins, either the amount of ligand must increase, or the volume of the cell/compartment must decrease.

This places a strict limit on the size of the cell / compartment. Small cells use proteins and their ligands more efficiently!

Electrophoretic Mobility Shift Assay (EMSA)

saturation point

Association Constant and Occupancy q

association, not acid

General expression:

Ka = [P:L]/[P][L]

Occupancy:

q = [P1:L]/([P1:L] + [P1])

q = [L]/([L] + 1/Ka)



When q = 0.5, [L] = 1/Ka

L

L

L

L

Association and Dissociation

association, not acid

L

L

L

L

L

L

L

L

when q = 0.5, [L] = 1/Ka = Kd

Graphical Representation of Ligand Binding

Saturation Curve

http://elte.prompt.hu/sites/default/files/tananyagok/IntroductionToPracticalBiochemistry/images/m420bfb8b.jpg

q

Specificity

X

X

http://2012books.lardbucket.org/books/principles-of-general-chemistry-v1.0m/section_28/2ddb1976eb93d821f1871a1bc7d91e6e.jpg

Chirality

Structural/Functional Homology

Lactate dehydrogenase

Malate dehydrogenase

Structural Homology

Human Triosephosphate Isomerase (4POC)

Vicia Narbonin

(1NAR)

an enzyme

plant seed protein storage

Functional Homology

Subtilisin (1GNS)

Chymotrypsin (1SBC)

http://cbc.arizona.edu/classes/bioc462/462a/NOTES/ENZYMES/catalytic_triad.gif

catalytic triad common in serine proteases

Quaternary Structure