BB ch5,p1

Reversible protein–ligand binding

A non-covalent interaction between a protein and a ligand that can readily associate and dissociate.

Ligand

Any molecule that specifically binds to a protein’s binding site.

Complementary interactions

Precise structural and chemical matching between a protein surface and its ligand that enables selective binding.

Immune system (protein context)

Defense network that relies on highly specific protein–ligand recognition such as antibody–antigen binding.

Chemical-energy-driven protein interaction

Association of proteins powered by ATP or other energy sources, exemplified by muscle contraction.

Heme

Iron-porphyrin prosthetic group that reversibly binds O2 in globins.

Prosthetic group

A non-protein component permanently attached to a protein and essential for its function.

Myoglobin

17-kDa monomeric globin in muscle that stores and transports oxygen.

Hemoglobin

Tetrameric blood protein that transports O2, H+ and CO2 between lungs and tissues.

Proximal histidine (His F8)

Histidine residue directly coordinated to the heme iron in globins.

Distal histidine (His E7)

Histidine that stabilizes bound O2 and hinders perpendicular CO binding in globins.

Porphyrin ring

Tetrapyrrole macrocycle that chelates Fe2+ in heme.

Oxygen transport

Delivery of O2 from lungs to tissues via hemoglobin.

Oxygen storage

Temporary retention of O2 in muscle, primarily by myoglobin.

Binding-site occupancy (θ)

Fraction of total protein binding sites that are occupied by ligand.

Dissociation constant (Kd)

Ligand concentration at which half of the binding sites are occupied; inverse measure of affinity.

Association rate constant (ka)

Kinetic constant for formation of the protein–ligand complex.

Dissociation rate constant (kd)

Kinetic constant for disassembly of the protein–ligand complex.

Rectangular hyperbola

Plot shape of θ versus [L] for simple, non-cooperative binding.

Avidin–biotin interaction

Exceptionally tight binding pair with Kd ≈ 10⁻¹⁵ M, often treated as irreversible.

High-affinity binding

Protein–ligand interaction characterized by very low Kd values.

Low-affinity binding

Interaction with high Kd values, indicating weak binding strength.

Steric hindrance in ligand binding

Restriction of ligand approach caused by spatial crowding within a protein.

Carbon monoxide (CO) binding to heme

Interaction where CO binds Fe2+ in heme, typically more strongly than O2.

Hyperbolic binding curve

Saturation curve without cooperativity, exemplified by myoglobin.

P50

Partial pressure of O2 at which a globin is 50 % saturated.

Cooperative binding

Ligand binding phenomenon where affinity changes with occupancy, common in multi-subunit proteins.

Sigmoid binding curve

S-shaped saturation plot indicative of cooperative ligand binding.

T state of hemoglobin

Low-affinity, deoxygenated conformation stabilized by ion pairs.

R state of hemoglobin

High-affinity, oxygen-bound conformation of hemoglobin.

α1β1 interface

Contact surface between one α and one β subunit that changes little during O2 binding.

α1β2 interface

Subunit contact area that undergoes significant rearrangement during the T→R transition.

Hill equation

Mathematical expression log(θ/1-θ) = n log[L] – log Kd describing cooperative binding.

Hill coefficient (nh)

Slope of the Hill plot reflecting degree, not number, of cooperativity.

Positive cooperativity

Condition where binding of the first ligand increases affinity for subsequent ligands.

Negative cooperativity

Condition where initial ligand binding decreases affinity at remaining sites.

Allosteric protein

Protein whose ligand binding sites influence one another via conformational changes.

Bohr effect

Inverse relationship between hemoglobin’s O2 affinity and pH/CO2 levels.

Carbaminohemoglobin

Hemoglobin form with CO2 covalently attached to its α-amino termini.

Carbonic anhydrase

Enzyme that catalyzes CO2 + H2O ↔ HCO3⁻ + H⁺ in red blood cells.

Proton transport

Movement of H⁺ from tissues to lungs facilitated by hemoglobin.

CO2 transport

Carriage of carbon dioxide in blood by hemoglobin and as bicarbonate.

2,3-Bisphosphoglycerate (BPG)

Negatively charged effector that lowers hemoglobin’s O2 affinity by stabilizing the T state.

Heterotropic allosteric regulation

Modulation of protein function by a ligand different from the primary ligand.

High-altitude adaptation

Physiological increase in BPG that maintains O2 delivery despite reduced atmospheric O2.

Fetal hemoglobin

Hemoglobin variant with higher O2 affinity due to weaker BPG interaction, aiding placental oxygen uptake.

Sickle-cell anemia

Genetic blood disorder caused by mutant hemoglobin that deforms erythrocytes.

Hemoglobin S

Mutant hemoglobin containing a Glu6Val substitution in each β chain.

Glu6Val mutation

Replacement of glutamate by valine at position 6 of β globin, creating hydrophobic surface.

Hydrophobic patch

Non-polar surface region that promotes abnormal aggregation in Hb S.

Insoluble aggregates

Fibrous polymers of deoxygenated Hb S that distort red blood cells.

Deoxyhemoglobin

Hemoglobin lacking bound O2, predominantly in the T state.

Oxygenated hemoglobin

Hemoglobin with O2 bound, predominantly in the R state.

Cooperative allosteric transition

Concerted shift of hemoglobin subunits from T to R or vice versa.

β subunit of hemoglobin

One of two types of globin chains forming the adult hemoglobin tetramer.

α subunit of hemoglobin

Globin chain that pairs with β chains in adult hemoglobin.

Globin fold

Conserved eight-α-helix structural motif shared by hemoglobin and myoglobin.

Primary structure similarity

Sequence conservation observed among different globins.

Secondary structure (α-helix)

Right-handed helical conformation prevalent in globin proteins.

Helix F

Sixth α-helix in globins that shifts upon O2 binding to flatten the heme.

O2 binding pocket

Hydrophobic cavity between the E and F helices where the heme resides.

His HC3

Histidine at β-chain C-terminus involved in T-state salt bridges.

Asp FG1

Aspartate that forms an ion pair with His HC3 in T-state hemoglobin.

Lys C5

Lysine participating in intersubunit salt bridges that stabilize the T state.

Carbon monoxide poisoning

Toxic condition where CO occupies hemoglobin sites, blocking O2 transport.

Carboxyhemoglobin

Complex of hemoglobin with CO bound to heme iron.

PDB ID 1MBO

Protein Data Bank identifier for sperm whale myoglobin structure.

PDB ID 1HGA

Protein Data Bank identifier for human hemoglobin β-subunit structure.

Prosthetic group binding

Covalent or tight non-covalent attachment of a cofactor such as heme to a protein.

Ligand-induced conformational change

Structural alteration in a protein upon ligand binding that can affect function.

Cooperative oxygen delivery

Enhanced release of O2 due to hemoglobin’s sigmoid binding behavior.

Sequence-specific protein–DNA interaction

High-affinity binding of proteins to particular nucleotide sequences in DNA.

Calmodulin

Calcium-binding messenger protein with multiple Kd values for its four Ca²⁺ sites.

Nickel-binding protein

E. coli protein that sequesters Ni²⁺ ions with micromolar affinity.

Insulin receptor

Membrane receptor that binds insulin with a Kd around 10⁻¹⁰ M.

Antibody–antigen interaction

Highly specific binding between an immunoglobulin and its foreign target.

Binding affinity

Quantitative strength of a protein–ligand interaction, commonly expressed by Kd.

T → R transition

Cooperative conformational shift of hemoglobin from low to high O2 affinity.

Beta chains of hemoglobin

The two β globin polypeptides that, with two α chains, form adult hemoglobin.

Myoglobin P50 value

0.26 kPa partial pressure of O2 required for half-saturation of myoglobin.

Lung pO₂ (13 kPa)

High oxygen partial pressure that loads hemoglobin with O2.

Tissue pO₂ (4 kPa)

Lower oxygen partial pressure that promotes O2 release from hemoglobin.

Sigmoid vs. hyperbolic curve

Comparison of cooperative (sigmoid) versus independent (hyperbolic) binding profiles.

CO binding affinity to hemoglobin (250×)

Carbon monoxide binds hemoglobin about 250 times more tightly than oxygen.

Bohr effect equation

HbH⁺ + O₂ ↔ HbO₂ + H⁺, illustrating proton release upon O2 binding.

Carbamate formation

Covalent attachment of CO₂ to the α-amino termini of globin chains releasing H⁺.

Salt bridge

Electrostatic bond between charged residues that stabilizes specific protein states.

BPG binding site

Positively charged cavity between β subunits where BPG stabilizes the T state.

α-amino terminus

Free amino group at the N-end of a polypeptide, site for carbamate formation.

CO₂ solubility

Limited dissolution of carbon dioxide in water, enhanced by carbonic anhydrase.

Cooperative ligand model

Conceptual framework explaining interdependent binding sites in oligomeric proteins.

Hill plot

Graph of log(θ/1-θ) versus log[L] used to determine nh and Kd.

Positive allosteric modulator

Molecule that increases a protein’s affinity for its primary ligand.

Negative allosteric modulator

Molecule that decreases a protein’s affinity for its main ligand, e.g., BPG for Hb.

Tense state stabilization

Factors such as salt bridges or BPG that favor hemoglobin’s low-affinity conformation.

Relaxed state stabilization

Binding of O2 or other effectors that favor hemoglobin’s high-affinity conformation.

O2 saturation

Fractional occupancy of hemoglobin binding sites by oxygen.

Multi-subunit protein

Protein composed of more than one polypeptide chain, enabling cooperative behavior.