March 20
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Introduction to Protein Structures
Globular Proteins
Definition: Proteins that are folded into a more or less spherical shape.
Solubility: Tend to be soluble in water or salt solutions.
Polar vs Nonpolar Chains:
Most polar side chains are located on the outside, interacting with the aqueous environment through hydrogen bonding and ion-dipole interactions.
Most nonpolar side chains are buried inside the protein structure.
Secondary Structures: Globular proteins primarily contain substantial sections of α-helix and β-sheet.
Examples: Myoglobin (Mb) and Hemoglobin (Hb).
Fibrous Proteins
Definition: Proteins with polypeptide chains organized parallel to a single axis, forming long fibers or sheets.
Properties:
Mechanically strong.
Insoluble in water and dilute salt solutions.
Play structural roles in nature.
Examples:
Keratin: Found in hair and wool.
Collagen: Found in connective tissues (e.g., skin, bones, teeth, cartilage, blood vessels).
Structure, Composition, and Function of Collagen
Characteristics of Fibrous Proteins
Each fibrous protein has a unique secondary structure.
Collagen is a prominent example of fibrous proteins and constitutes 25% to 35% of the total protein in mammals.
Structure: Collagen consists of three helical polypeptide chains (about 800 residues in length) wrapped around each other in a triple helix.
Tropocollagen: The triple helical molecule, measuring 300 nm long and 1.5 nm in diameter.
Amino Acid Sequence in Collagen
The amino acid sequence includes repeating units such as:
Proline-Glycine-X (where X can be any amino acid).
Hydroxyproline-Glycine-X (where X can also be any amino acid).
Approximately every third amino acid in collagen is glycine. High abundance of proline and hydroxyproline residues contributes to stability through hydrogen bonding within the triple helix.
Role of Vitamin C in Collagen Function
Hydroxylation of proline into hydroxyproline is catalyzed by an enzyme requiring ascorbic acid (Vitamin C).
Deficiency of Vitamin C: Leads to weakened collagen fibers and the development of scurvy, characterized by lesions in skin and gums, and weak blood vessels.
Protein Folding and Stability
Factors Guiding Protein Folding
Disulfide Bonds: Formation of covalent bonds between side chains of cysteines contributes to structural integrity.
Noncovalent Interactions:
Hydrogen bonds between polar side chains (e.g., serine and threonine).
Electrostatic attractions and repulsions among charged side chains (e.g., leucine with glutamine and arginine).
Hydrophobic interactions between nonpolar side chains (e.g., valine and isoleucine).
Myoglobin Overview
Location: Found in high concentration in cardiac and skeletal muscle.
Structural Discovery: First protein for which a complete 3-D structure was determined using X-ray crystallography.
Function: Responsible for oxygen storage in mammalian muscle and comprises a single polypeptide chain of 153 amino acids.
Myoglobin Structure Details
Contains a single heme group (protoporphyrin IX complexed with iron) located in a hydrophobic pocket.
Comprised of 8 regions of α-helix labeled from A to H, no regions of β-sheet present.
Most polar side chains are located on the surface, while nonpolar side chains are folded to the interior.
Denaturation of Proteins
Definition and Process
Denaturation: Refers to the loss of structural order (secondary, tertiary, or quaternary structures) that leads to a protein's loss of biological activity, while the primary structure remains intact.
Causes of Denaturation:
Temperature Changes: Disruption of weak hydrogen bonds leads to protein unfolding; most proteins have melting points below 100°C.
High Pressure.
Ultraviolet Light (UV).
Strong Acidic or Basic Conditions: Alters the charges of amino acid side chains, breaking ionic bonds that maintain 3-D structure.
Chemical Denaturants: Such as urea (8M) and guanidinium chloride (5M), disrupt hydrogen bonding and hydrophobic interactions.
Detergents: Such as SDS, which disrupt hydrophobic interactions.
Reducing Agents: Such as mercaptoethanol which reduce disulfide bonds to sulfhydryl groups.
Denaturation Results
Physical Properties: Includes changes in viscosity and loss of solubility.
Biological Properties: Results in the loss of biological activity, specific for enzymes and other proteins.
Renaturation
Definition: The process whereby denatured proteins regain their native structure and biological activity upon removal of denaturing agents.
Protein Folding and Chaperones
Role of Chaperones in Protein Folding
Chaperones: Proteins found in all organisms that assist in the folding process of nascent proteins.
Molecular Chaperones: Prevent aggregation until proteins reach their functional forms.
Chaperonins: Assist incorrect or premature folding.
Stress Response: Chaperone synthesis is increased under stress conditions (e.g., heat-shock proteins hsp60 and hsp70). They are produced as temperature increases.
Quaternary Structure of Proteins
Definition and Basic Concepts
Quaternary Structure: Involves multiple polypeptide chains (oligomers) interacting through weak interaction forces (H-bonds, Van der Waals forces, ionic interactions, hydrophobic interactions, and disulfide bonds).
Protein Interfaces: In aqueous proteins, hydrophobic amino acids often comprise the interfaces between subunits; in membrane-bound proteins, hydrophilic amino acids are common.
Hemoglobin Structure
Comprised of 4 polypeptide chains:
2 identical alpha-subunits (HbA) and 2 identical beta-subunits (HbB).
Each subunit binds its own heme group, enabling the binding of oxygen.
Structural similarity of Hb to Mb is significant, although their binding dynamics differ.
Oxygen Binding Dynamics
Binding Mechanism:
O2 binding to the heme group involves several key amino acid residues surrounding the heme: Phe 43, His 64, Val 68, and His 93. These create a hydrophobic environment to secure the heme.
Oxygen binding triggers changes in conformation that affect further binding—this is a hallmark of cooperative binding seen in Hb.
Cooperative Binding of O2 to Hemoglobin
Definition: This refers to the increased affinity of hemoglobin for oxygen as more molecules of O2 bind.
Dynamics:
Initially, at low O2 concentrations, Hb shows minimal binding. Suddenly, once a threshold concentration is exceeded, hemoglobin rapidly saturates.
Bohr Effect: The physiological phenomenon whereby the release of O2 from hemoglobin is enhanced in lower pH conditions, facilitated by increased CO2 concentration. The binding equilibrium showing:
2,3-Bisphosphoglycerate (2,3-BPG) Role
Function: Induces O2 dissociation by binding to hemoglobin, exhibiting electrostatic interactions with positively charged chains (Lys, Arg).
Fetal vs Adult Hb: Fetal hemoglobin does not bind 2,3-BPG and therefore shows higher O2 affinity than adult hemoglobin.
Abnormal Hemoglobins and Their Effects
Pathological Variations
Sickle Cell Disease (Hb S)
Mutation: Substitution of valine for glutamic acid at position 6 in b-subunit results in decreased oxygen affinity and increased aggregation propensity.
Phenotype: Sickled erythrocytes are elongated and rigid, causing obstructions in capillaries, leading to severe health issues.
Hemoglobin C (Hb C)
Mutation: Glutamic acid at position 6 is mutated to lysine, leading to crystallization without sickling.
Thalassemias
Definition: Hereditary diseases caused by reduced synthesis of normal a-globin or b-globin chains of hemoglobin (predominantly in specific demographics infected with malaria).
Protein Misfolding and Prion Diseases
General Concepts
Protein Misfolding: Incorrect folding of proteins can lead to various diseases, notably neurodegenerative disorders such as Alzheimer’s, Parkinson’s, and Creutzfeldt-Jakob disease.
Prions: Misfolded proteins that aggregate and are infectious, leading to diseases such as mad cow disease in cattle and similar conditions in humans.
Mechanism of Prion Disease
Example: In Creutzfeldt-Jakob disease, the misfolded form of the prion protein (PrP) aggregates and induces structural misfolding in other proteins, leading to the degeneration of brain functionality and neuronal death.
Aggregates: Typically rich in beta-pleated sheets leading to the formation of amyloid fibers causing severe neurological impact.