Protein 3D Structure & Function

• Study notes on the three-dimensional structure of proteins

Protein Structure and Function

• Plants primarily use cellulose for structure.
• Animals mainly use structural proteins as the chief constituents of their skin, bones, hair, and nails.
• Collagen and keratin are two important structural proteins.
• Enzymes are essential for catalysis as their absence would cause reactions to occur too slowly.
• Muscle movement relies on expansion and contraction involving protein molecules like myosin and actin.
• Hemoglobin is a blood protein that transports oxygen from the lungs to cells and carbon dioxide from cells back to the lungs.
• Insulin, erythropoietin, and human growth hormone are examples of protein hormones.
• Antibodies are proteins produced by the body to counteract foreign proteins or substances (antigens).
• Blood clotting, a protective function, is carried out by the protein fibrinogen.
• Casein in milk and ovalbumin in eggs serve as storage proteins, providing nutrients for newborns.
• Ferritin, located in the liver, acts as a storage protein for iron.
• Some proteins regulate gene expression, controlling the types of proteins synthesized in a cell and the timing of their production.

Levels of Protein Structure

• The spatial arrangement of atoms in a protein is called its conformation.
• Protein conformations can be achieved without breaking covalent bonds, such as through rotation around single bonds.
• Only a few conformations usually dominate under biological conditions, despite the numerous possibilities.
• These existing conformations are usually thermodynamically stable, possessing the lowest Gibbs free energy (G).
• Folded, functional conformations of proteins are called native proteins.
• Fibrous proteins are insoluble in water and have structural roles.
• Globular proteins are generally water-soluble and have nonstructural roles.
• Proteins have four levels of structure: Primary, Secondary, Tertiary, and Quaternary.
• The primary structure is the amino acid sequence.
• The secondary structure describes the regular pattern of peptide backbone orientation.
• The tertiary structure describes the overall three-dimensional shape of the protein molecule as it coils.
• The quaternary structure describes how multiple polypeptide chains come together to form large aggregate structures.
• The primary structure is determined by sequencing the protein.
• The secondary, tertiary, and quaternary structures are determined by NMR or X-ray crystallography.

Primary Structure of Proteins

• The primary structure consists of the sequence of amino acids in the chain.
• The total number of possible peptides or proteins for a chain of n amino acids is calculated as 20^n.
• The hormone insulin consists of two polypeptide chains (51 amino acids): A and B, held together by two disulfide cross-bridges.
• A table shows amino acid sequence differences for human, bovine, hog, and sheep insulin.
• The amino acid sequence differences influence the activity of hormone insulin.
• Hemoglobin in adult humans is made of four globin chains: two identical α chains (141 amino acid residues), and two identical β chains (146 residues).
• Each globin chain surrounds an iron-containing heme unit.
• The globin chains are amino acid portions while the heme chains are prosthetic groups.
• Minor changes in only one amino acid in the chains can produce hemoglobin (HbS), which can cause fatal sickle cell anemia.

Secondary Structure of Proteins

• The secondary structure is the hydrogen-bonded arrangement of the protein's backbone, specifically the polypeptide chain.
• Within each amino acid residue, there are two bonds with free rotation: the bond between the α-carbon and the amino nitrogen, and the bond between the α-carbon and the carboxyl carbon.
• Side chains also have an impact on a proteins' three-dimensional shape; however, only the backbone is considered in the secondary structure.
• Resonance gives each peptide bond a certain double-bond character which prevents rotation.
• Rotation is permitted around the N—Cα and the Cα—C bonds.
• The angles Φ (phi) and Ψ (psi), called Ramachandran angles, are used to designate rotations around the N—Cα and C—Cα bonds, respectively.
• The values of Φ and Ψ for each residue from -180° to 180° specify a protein backbone's conformation.
• Two commonly occurring secondary structures in proteins are the repeating α-helix and β-pleated sheet (or β-sheet).
• The Φ and Ψ angles repeat themselves in contiguous amino acids in regular secondary structures.
• Alpha-helices and Beta-sheets are only one of the possible types of secondary structure.
• A peptide-chain backbone can be visualized as a series of playing cards, each representing a planar peptide group.
• The cards are linked at opposite corners by swivels, representing the bonds about which there is freedom of rotation.
• A Ramachandran plot displays ψ-angles as a function of φ-angles.
• Areas shaded dark blue indicate allowed conformations with no steric overlap, medium blue indicates conformations at extreme limits, and light blue reflects conformations permissible with flexibility in bond angles.
• The asymmetry of the plot results from L stereochemistry of amino acid residues.
• The a-helix forms when a peptide chain twists into a right-handed or clockwise spiral.
• Hydrogen bonds parallel to the helix axis stabilize the alpha-helix within the backbone of a single polypeptide chain.
• Counting from the N-terminal end, the C=O group is hydrogen bonded to the N-H group of the amino acid four residues earlier in the covalently bonded sequence.
• The helical conformation allows a linear arrangement of atoms involved in hydrogen bonds, making the helical conformation very stable.
• There are 3.6 residues for each turn of the helix, and the pitch of the helix is 5.4 Å.
• There are 3.6 amino acids at each turn of the helix.
• All N-H and C=O bonds point along the axis of the helix in opposite directions.
• The C=O group of one amino acid is hydrogen bonded to the N-H group four residues farther along the chain, so the same chain has hydrogen bonding.
• R groups of amino acids extend outward from the helix's core.
• The amino acid proline creates a bend in the backbone because of its cyclic structure.
• Proline cannot fit into the alpha-helix because of a severely restricted bond and its inability to participate in intrachain hydrogen bonding.
• Localized factors include strong electrostatic repulsion owing to proximity of charged groups such as lysine and arginine residues, or glutamate and aspartate residues.
• Another source comes from crowding (steric repulsion) from several bulky side chains; there is no room for them if the alpha-carbon is directly bound to two atoms other than hydrogen, like in valine, isoleucine, and threonine.

Beta-Pleated Sheets

• In beta-sheets the peptide backbone is almost completely extended.
• Hydrogen bonds can form between different parts of a single chain (intrachain bonds) or among different chains (interchain bonds).
• If the peptide chains run in the same direction (N-terminal to C-terminal), a parallel pleated sheet is formed.
• When alternating chains run in opposite directions, an antiparallel pleated sheet is formed.
• The hydrogen bonding between peptide chains gives rise to a repeated zigzag structure.

Irregularities in Regular Structures

• The 3.6^13 helix is the most common conformation and is known as the a-helix, having 3.6 amino acid residues per turn and 13 atoms in the ring formed by making the hydrogen bond.
• 3^10, 2^7, and 4.4^16 helices are irregular helical structures often found in shorter stretches that may break up the regularity of an a-helix.
• The most common irregular helix is the 3^10 helix (3 amino acid residues per turn and 10 atoms in the ring forming the hydrogen bond).
• Other common irregular helices include the 2^7 helix (2 amino acid residues per turn and 7 atoms in the ring) and the 4.4^16 helix (4.4 amino acid residues per turn and 16 atoms in the ring).
• Beta-bulges are common non-repetitive irregularities found in antiparallel ß-sheets and occur between two normal ß structure hydrogen bonds.
• Beta turns (or reverse turns) are where protein folding requires that the peptide backbones and secondary structures are able to change directions, and often mark the transition between one secondary structure and another.
• Glycine is frequently encountered in reverse turns at which the polypeptide chain changes direction.
• Prolines, with their cyclic structure, have the correct geometry for a reverse turn, and are often encountered in such turns.
• Beta turns are common in proteins and connects the ends of two adjacent segments of an antiparallel sheet.
• Typically, the beta turn structure is a 180 turn that consists of four amino acid residues, with the alpha-carbon oxygen of the first residue forming a hydrogen bond in combination with the amino hydrogen of the fourth.
• The two peptide groups of the central two residues do not partake in any inter-residue hydrogen bonding.
• Glycine (Gly) and Proline (Pro) residues feature often in turns because Gly is small and flexible and because peptide bonds composed of the imino nitrogen of proline may readily use the cis configuration.

Supersecondary Structures and Domains

• The combination of alpha- and beta-strands produces supersecondary structures in proteins.
• The most common feature is the βαβ unit, (two parallel strands of β-sheet connected by a stretch of a-helix ).
• An αα unit (helix-turn-helix) consists of two antiparallel a-helices.
• In a β-meander, an antiparallel sheet is formed via a series of tight reverse turns that act as connectors for the stretches of the polypeptide chain.
• Another type of antiparallel sheet is formed when the polypeptide chain doubles back on itself in a pattern as the Greek key.
• A motif (module) is a repetitive structure.
• ẞ-meanders and Greek keys are frequently located within a ẞ-barrel in the tertiary structure of the protein.

Collagen Triple Helix

• Collagen, a most abundant protein, makes up bone and connective tissue and fibrous parts of a vertebrate.
• A collagen fiber is made of three polypeptide chains as they are wrapped around each other, that makes a triple helix.
• The three chains consist, depending on boundaries, of a repeating sequence of three amino acid residues, X — Pro — Gly or X — Hyp — Gly, the position designated with X indicates that those may be substituted with any amino acid.
• Constituting 30% of residue in collagen are proline and hydroxyproline; the action of hydroxylating enzymes upon amino acids form hydroxyproline as the enzymes link them; collagen also is constructed and contains hydroxylysine.
• The triple helix aligns so every third residue contained within each chain is inside the helix.
• Glycine alone has the capacity to fit inside the free space available because of its small size.
• The three individual collagen chains are themselves helices that differ from the alpha-helix.
• They are twisted around each other inside of a superhelical arrangement with the plan to develop a stiff rod.
• Tropocollagen can then be constructed to generate the same features that triple coil forms to produce a collagen helix with a specific size, or 300 nm (3000 Å) tall and a diameter ranging 1.5 nm (15 Å).
• The weight distribution stands from nearly 300,000, in 800 amino acid ranges.
• A bond links the three strands; hydrogen assists in the support for both the hydroxyproline and the hydroxylysine residue.
• Cross-linking bonds composed of histidine and lysine attach both in an intercellular form while still developing collagen.
• The amount of linking tissue increases as age increases.
• Symptoms of the ailment Scurvy come from poor state for both normal function and high levels of stability inside of non-hydroxylated hydroxyproline as that is the process.
• Enzyme (Hydroxylating) triggers with Vitamin C help to maintain the normal level of function in the state of proline and the Scurvy is linked and triggered by diet.

Tertiary Structure of Proteins

• Arrangement every atom has within the molecules is the tertiary structure in the arrangement, excluding the secondary structure, due to its inclusion of both interaction and the side chain process that is separate from the backbone peptide.
• The 5 categories of stabilized structures are as follows: 1-Disulfide bridging through Covalent bonding 2- Hydrogen Bonding 3-Salt Bridges 4-Hydrophobic Interactions(effects) 5-Metal Ion Coordination
• As a protein, Chaperone's features allow for the collection and building to other proteins, as well enables their confirmation from an original, active conformation.
• Prions act as small protein agents found in the location of nerve structures, while the function stays unknown.
• Prions undergo conformational change to enable illnesses to take hold with the characteristics found in scraping and in the brain.
• It forms the allosteric tertiary structure of a-lactalbumin.

Quaternary Structure of Proteins

• The quaternary structure involves both a spatial relationship in combination with more subunits than a polypetide chain; there needs to be more chains, with the chains either acting different or identical.
• Dimers, trimers and tetramers comprise with differing arrangement of two, three, or four polypeptide types.
• The generic term for these types form a molecule that makes as an oligomer.
• Subunits connect for the construction of the same, in order to develop the bonds, between a structure in subtle stages and with properties for the protein material, while affecting far distances.
• Allosteric proteins that show differing variations comprise the bonds in subunits.
• Hemoglobin has a quartenary structure that makes adult Humans with the chains known as globins.
• All chains have two forms called α and β chains that contain 141 for the α and 146 in the secondary chain.
• Both of the designations a and β come with no similarity, yet are still related.
• An example of collagen, with its features forming higher sets of groups with subunits being able to be located within the structures and collagen groups.
• Integral parts are inside with parts for membrane and polypeptide chains by bilayer formation.
• A third of protein (calculated into parts) measures how many transmembrane polypeptide components are located inside that amount. In order for stability with both a no polar range that has to have an outer layer or surface, two structures are known in the form that (1) 6 or 10 alpha will cross, and (2) Alpha contains forms made of between 8-18 anti parts.

Denaturing Proteins

• In their native states, secondary and tertiary structures, and also in the binding of subunits through quaternary structure, cause for proteins to be in a conformation that are consistent.
• Whatever agent or structure that will disrupt or destroy may change the proteins in relation.
• Denaturation (unfolding) occurs when the protein's quaternary and tertiary structures are destroyed by either chemical or physical events while leaving the initial compound unaltered.
• Recovering may be possible under testing environments, through process of Refolding and development.
• Reversing types in structural patterns forms with various types.