Why Proteins Know Their Ligands Flashcards

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Ligand

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A ligand is a molecule that binds reversibly to a biomolecule to form a complex and perform a biological function. Ligands are typically small molecules and bind via noncovalent interactions such as hydrogen bonds, van der Waals, hydrophobic, and ionic interactions. The binding site on the protein that recognizes a ligand is called the binding site.

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Induced fit

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Induced fit describes how both ligand and protein can change conformation upon binding to achieve tighter complementarity. This conformational adaptation often increases binding affinity and can be important for enzyme catalysis and specificity. The model contrasts with a rigid "lock-and-key" view.

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Cooperativity

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Cooperativity occurs when binding of a ligand at one site on a multi-subunit protein affects the affinity at other sites, producing non-hyperbolic (often sigmoid) binding curves. Positive cooperativity means the first binding increases affinity at remaining sites; negative cooperativity means it decreases affinity. Hemoglobin is a classic example of positive cooperativity for $O_2$ binding.

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Allosteric regulation

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Allosteric regulation is when binding of a ligand at one site modulates binding or activity at a different site on the same protein. It can be homotropic (the normal ligand is the regulator) or heterotropic (a different ligand regulates the normal ligand). Cooperativity is a special case of positive homotropic allosteric regulation.

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Heme

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Heme is a porphyrin-based prosthetic group containing an iron atom in the ferrous state ($Fe^{2+}$) coordinated to the porphyrin ring. Protein-bound heme enables reversible binding of diatomic gases like $O_2$ while reducing reactivity that free iron would otherwise cause. The iron has six coordination positions, four in the plane of the porphyrin and two perpendicular.

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Myoglobin

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Myoglobin is a monomeric, globular protein that stores $O_2$ in muscle and contains one heme group. It binds $O_2$ with a high, essentially non-cooperative affinity and is described by a hyperbolic binding curve. Myoglobin's binding is often expressed in terms of partial pressure ($pO_2$).

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Hemoglobin

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Hemoglobin is a tetrameric protein (α2β2) that transports $O_2$ in blood and binds oxygen cooperatively, producing a sigmoidal binding curve. Conformational changes between the tense (T) and relaxed (R) states underlie its cooperative behavior and regulation by pH, $CO_2$, and $2,3$-BPG. Hemoglobin also transports $H^+$ and $CO_2$ to help maintain acid–base balance.

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Bohr effect

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The Bohr effect is the pH- and $CO_2$-dependent decrease in hemoglobin $O_2$ affinity that facilitates $O_2$ release in metabolically active tissues. Increased $H^+$ and $CO_2$ (lower pH) stabilize the T state by protonation of residues such as His146 and formation of carbamates, shifting the equilibrium toward $O_2$ release. This effect enhances oxygen delivery where it is most needed.

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2,3-BPG

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$2,3$-BPG is a negative heterotropic regulator of hemoglobin that binds the central cavity of deoxyhemoglobin and stabilizes the T state. By lowering hemoglobin affinity for $O_2$, it promotes $O_2$ release to tissues and plays a role in altitude adaptation. The binding pocket for $2,3$-BPG disappears upon oxygenation (T→R transition).

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Carbon monoxide

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Carbon monoxide ($CO$) is a diatomic gas that binds heme much more tightly than $O_2$ and competes for the same binding site. Protein environments reduce $CO$ affinity relative to free heme, but $CO$ still binds about 250-fold tighter to myoglobin and blocks $O_2$ transport, making it highly toxic. Binding geometry and distal His interactions partly explain the difference.

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Soret band

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The Soret band is a strong absorption feature of the heme chromophore in the blue region of the visible spectrum used to monitor oxygen binding. The ferrous ($Fe^{2+}$) deoxy form has a Soret peak near 429 nm that shifts to about 414 nm upon oxygenation. UV–Vis spectroscopy of the Soret band thus reports heme electronic and ligation state.

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Sickle-cell mutation

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Sickle-cell anemia arises from a single point mutation in the β chain of hemoglobin, Glu6→Val (E6V), which creates a hydrophobic patch on deoxyhemoglobin S. This patch promotes polymerization into long fibers that distort erythrocytes into a sickle shape, causing hemolysis and vaso-occlusion. Heterozygotes gain malaria resistance while homozygotes suffer severe disease.

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Peptide bond

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The peptide bond is a planar, partially double-bonded amide linkage between amino acids with significant resonance stabilization. This resonance restricts rotation about the C–N bond and gives the backbone predictable geometry important for secondary structure formation. The trans configuration is strongly favored except in some proline-containing sites.

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Phi/Psi angles

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Phi ($\phi$) and psi ($\psi$) are the backbone dihedral angles around the $\alpha$-carbon that determine polypeptide conformation. Steric constraints and favorable hydrogen bonding restrict $\phi$ and $\psi$ to characteristic regions, which are visualized in a Ramachandran plot. Secondary structures like $\alpha$-helices and $\beta$-sheets correspond to preferred $\phi$/$\psi$ values.

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Alpha helix

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The $\alpha$ helix is a right-handed helix stabilized by hydrogen bonds between the backbone $N$–H and $C=O$ groups of residues $i$ and $i+4$. It has 3.6 residues per turn and a rise of about 5.4 Å per turn, with side chains projecting outward. The helix has a macroscopic dipole that often influences the location of charged residues.

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Beta sheet

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$\beta$ sheets are formed by hydrogen bonding between backbone segments (strands) that can be parallel or antiparallel. Side chains alternate above and below the sheet plane, producing a pleated appearance. Antiparallel sheets have straighter, stronger hydrogen bonds compared with parallel sheets.

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Ramachandran plot

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A Ramachandran plot maps allowed and observed $\phi$ and $\psi$ angles for amino acid residues in proteins and highlights favored regions corresponding to common secondary structures. Glycine often populates otherwise disallowed regions due to its flexibility, while proline is more restricted. The plot is a diagnostic of backbone geometry and model quality.

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Anfinsen experiment

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Anfinsen’s experiments on ribonuclease A showed that the amino acid sequence alone determines the protein’s native conformation, as the protein refolded and reformed correct disulfide bonds after denaturation and removal of denaturants. This work established that the native state is thermodynamically most stable under physiological conditions. It earned the 1972 Nobel Prize in Chemistry.

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Levinthal paradox

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Levinthal’s paradox states that a polypeptide cannot sample all possible conformations randomly to reach the native state in biologically relevant times. Protein folding therefore proceeds via directed pathways or funnels rather than exhaustive search. Models such as hierarchical folding and the folding funnel resolve this paradox.

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Molecular chaperone

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Molecular chaperones are proteins that assist folding of other proteins by preventing misfolding and aggregation, often using ATP-dependent mechanisms. Chaperonins like GroEL/GroES provide an isolated chamber for a polypeptide to fold. Chaperones are crucial for proteostasis in the cell.