9.5 Protein-Ligand Interactions

Function of hemoglobin

transports molecular oxygen from lung to tissue, then transports CO2 from tissue to lung

Function of myoglobin

stores molecular oxygen in tissue

Similarities of Myoglobin and Hemoglobin in structures

similar tertiary structure but different primary structures

Myoglobin and hemoglobin are what kind of proteins that bind to…

heme-proteins; oxygen

Protoporphyrin

Organic ring structure bound to Fe²⁺ (Binds to O₂)

Where are the 6 bonds with Fe in protoporphyrin

4 from main structure, 2 from perpendicular structure; proximal His and O₂

Fe²⁺ vs Fe³⁺

Binds O₂ vs irreversibly; some small molecules can bind to Fe²⁺ with greater affinity (CO & NO)

Myoglobin and each hemoglobin monomer is a

single polypeptide composed of 8 helices (Called globin fold)

In each polypeptide chain, a heme group is bound between helix (Include which His)

E7 (His 64) and F8 (His 93)

4 types of globin in mammals

Myo, hemo, neuro (Stores O₂ for brain), cyto (Regulates NO); All monomeric (Except hemo which is tetrameric)

Myoglobin is a single polypeptide chain of ___ amino acid residues

153

Tertiary structure of 8 right-handed a-helices with a hydrophobic pocket, which forms a

protective sheath for a heme group with iron atom in the middle

CO binds to heme ______ times better because it binds to heme _________ to plane

20,000x; perpendicular

Heme iron bonded to HIs on helix _, with an open O2 binding site between iron and His on helix _

E7; F8

Monomeric heme protein found mainly in ____ tissue; serves as

muscle; an intracellular storage site for oxygen

Each heme contains

one central, coordinately bound, iron atom that is normally in the Fe2+, or ferrous oxidation state

Oxygen carried by heme-proteins (both myoglobin and hemoglobin) is bound directly to

ferrous iron atom of the heme prosthetic group

Heme groups is located in a crevice between

E and F helices, except for non-polar R groups surround the heme

Fe2+ covalently bonded to the

imidazole group of histidine 93 (F8)

O2 is held on the other side by

histidine 64 (E7)

Heme protein conjugate is strongly stabilized by

hydrophobic interactions between the heme tetrapyrrole ring system and hydrophobic R groups on the interior of the cleft in the protein

Heme protein conjugate is stabilized further by

coordination of the iron atom with the nitrogen atom of the histidine R group, located above the plane of the heme ring on the F-helix

In oxygen-bound myoglobin (oxy-Mb) or oxygen-bound hemoglobin (oxy-HB), the remaining bonding site on the iron (6th coordinate position) is occupied by

the oxygen O2

O2 binding is stabilized by ________________ on the E-helix

second histidine residue (distal His)

Heme and protein protect Fe2+ from

irreversible oxidation to Fe3+

T/F Carbon monoxide binds to heme iron more strongly than oxygen

TRUE

Preferential binding of carbon monoxide to heme iron is largely responsible for

the asphyxiation in carbon monoxide poisoning

O2 binds to free heme at ____, but CO binds to free heme ____ to the heme plane

an angle; perpendicular

When O2 binds to the heme in Mb or Hb, binds at _____ ________, because the perpendicular arrangement is blocked by ___ ___

slight angle; His E7

Hemoglobin is tetramer of

four polypeptide chains

Hemoglobin consists of two identical a chains (___ AA residues) and two idential B chains (___ AA residues)

141, 146

Each chain has a ___ group, hence ___ O2 can bind to each Hb

heme, four

Each subunit of a hemoglobin tetramer has a

heme prosthetic group identical to that described for myoglobin

The quaternary structure of hemoglobin leads to physiologically important ____ interactions between the subunits. Property lacking in monomeric myoglobin, which is otherwise very similar to a subunit of hemoglobin

allosteric

α₁β₁ (and α₂β₂) interface involves ______ residues

α₁β₂ (and α₂β₁) interface involves ______ residues

> 30; 19

T state is stabilized by many _______ pairs. When it switches to R state, some of them break, a ______ in subunits occur, and new ______ pairs are formed

ion, shift, ion

Two conformations of hemoglobin

R (relaxed) and T (Tense) state; Higher affinity for O₂ vs lower affinity

What causes the switch from T to R Hb state

O₂ binding causes conformational change to R state, weaker interactions shift and certain areas narrows/rotate; O₂ causes Fe²⁺ to pull into plane of heme

_______ binds cooperatively to O₂

Hemoglobin; Is able to transition from high to low affinity states

Hb also carries end products of ________ _________

Cellular respiration; H+ and CO₂; T state favors these end products

Bohr Effect

Describes the affect of pH and CO₂ on the binding and release of O₂ by Hb

Effect of pH on O₂ binding

High pH: O₂ binds more, H+ released; Low pH: O₂ released, H+ binds more

CO₂ binding to Hb is ________ related to binding of O₂

Inversely

How does CO₂ bind to Hb

To the N-term of a residue rather than the Fe⁺²

BPG

2,3-bisphosphoglycerate; heterotrophic allosteric modulation; binds to site distant from O₂ site; reduces affinity for O₂ (Oxygen releases faster); Stabilizes T state

Sickle Cell Anemia

glu is changed to val; produces hydrophobic patch on Hb; causes Hbs to aggregate and create polymers; makes it harder to travel through capillaries

Hill Plot

Measures cooperativity; No cooperativity means plot shows 1 (ex. Mb); Only tells you if it’s cooperative, it doesn’t tell you about amount of subunits or binding spots