Protein Structure Notes

Protein Structure

Protein structure is organized into four levels, with three being complex. Primary structure is the sequence of individual amino acids, which differ in their side chains, influencing protein folding. Non-covalent forces also play a role in holding the structure together.

Prosthetic Groups

These can be inorganic, such as metals like iron or zinc, or organic. Prosthetic groups are essential components of some proteins and are crucial for their function. They expand the functional diversity of proteins by providing chemical functionalities beyond those available from amino acid side chains alone.

Conformation vs. Configuration

Conformation refers to the spatial arrangement and temporary 3D shape of a molecule related to the rotation of bonds. Configuration, on the other hand, involves stereoisomers, where changing from one isomer to another requires breaking bonds.

Conformation

Conformation is due to the rotation of bonds. It is responsible for protein folding.

Configuration

Changes in configuration, such as cis-trans isomerization (catalyzed by enzymes), are rare. An example might involve an amino acid switching from L to D form, but this is uncommon.

Consider saturated fats.

Saturated Fats

Saturated fats pack more tightly and require more energy to melt, making them solid at room temperature.

Unsaturated Fats

Unsaturated fats have double bonds, causing them to be kinked and liquid at room temperature.

In the food industry, hydrogenation adds hydrogen to double bonds, sometimes creating trans bonds not found in nature. Peptide bonds are planar and often in the trans configuration. When amino acids condense into a polypeptide chain, it's another instance of change in configuration. Protein structure mainly involves conformation changes.

Visualizing Protein Structures

Protein structures are complex, making it hard to interpret structures showing every atom. Simplified representations help emphasize specific features.

Representations of Liquidin

Liquidin, a 76-amino acid protein involved in protein degradation and signaling, can be represented in different ways:

• Cartoon Model: Useful for showing secondary structure, such as alpha helices (teal) and beta sheets.
• Stick Model: Shows individual atoms with different colors for carbon (green), etc. Allows analysis of hydrogen bonding and distances.
• Surface Model: Displays the protein's surface, useful for visualizing substrate binding to an enzyme active site.
• Electrostatic Surface Model: Shows positive and negative charges on the protein surface.

Primary Structure

Primary structure is the amino acid sequence linked by covalent peptide bonds. The amino acid sequence determines the 3D structure of a protein, which in turn determines its function. Altering the primary structure can change the protein's function.

Example: Sickle Cell Anemia

A mutation (E to V) causes mutant hemoglobin to aggregate into fibers, distorting red blood cell shape. Primary structure includes disulfide bridges between cysteines.

Health Effects

Sickle cell anemia reduces oxygen transport efficiency. Despite its negative effects, it persists due to a survival advantage in malaria-prone regions.

Malaria Resistance

Heterozygous individuals with sickle cell trait are resistant to malaria.

Peptide Bond Formation

Peptide bonds have direct consequences for secondary structure. Amino acids are connected through peptide bonds between the carboxyl and amino groups of two individual amino acids ($NH_3$, $C=OH$).

Condensation/Dehydration Reaction

Peptide bond formation involves a condensation or dehydration reaction where a water molecule is lost.

$H_2O$ is lost in the formation of the peptide bond, which is why amino acids in a polypeptide chain are referred to as residues.

Polypeptide Terminology

• Dipeptide: Two amino acids joined.
• Tripeptide: Three amino acids joined.
• Oligopeptide: Multiple amino acids joined.
• Polypeptide: Many amino acids joined.

Tetrapeptide Example

A tetrapeptide has three peptide bonds. Protein sequences are given in the N-to-C direction, reflecting the polypeptide chain's growth direction.

Main Chain vs. Side Chain

The main chain of amino acids is repetitive and constant, while the side chain (R-group) is variable and differs among the 20 amino acids. This directionality is crucial.

Properties of the Peptide Bond

The peptide bond has three features that influence protein folding: it is planar, rigid, and in the trans configuration.

• Planar: All atoms exist in one plane with no rotation.
• Rigid: Resonance gives it partial double bond character.
• Trans Configuration: R-groups of adjacent amino acids are on opposite sides of the bond.

Resonance

Resonance gives the peptide bond partial double bond character, making it planar and rigid. Pi bonds exist in the peptide bond.

The planar, rigid character of the peptide bond impacts polypeptide chain folding.

Disulfide Bonds

Some proteins have disulfide bonds, formed when two cysteines are oxidized to form a cystine. A complete primary structure description includes the positions of these bonds. Disulfide bonds can be intramolecular or intermolecular.

Disulfide Example

A protein made of two polypeptides can have disulfide bonds between chains. Cysteines forming disulfide bridges are in close proximity in 3D space but not necessarily in the primary sequence.

Secondary Structure

Secondary structure involves the local conformation of the backbone atoms. Hydrogen bonding is repetitive, leading to repetitive backbone conformations. Common secondary structures include alpha helices and beta sheets.

Types of Helices

• Alpha Helix: Right-handed, about 5 angstroms wide.
• Polyproline II Helix: Left-handed, similar to collagen helix.
• 310 Helix: Right-handed, more compact than alpha helix.

Other irregular secondary structures include reverse turns and loops, which lack repeating hydrogen bonding patterns but are stabilized by hydrogen bonds.

The cartoon model is useful for showing secondary structure elements. Protein may contain around 60% regular secondary structure elements.

Beta Lactamase

Secondary structure folding is spontaneous, driven by peptide bond properties and steric hindrance between side chains and the backbone.

Proline's Influence

Proline restricts backbone movement because its side chain is covalently bonded with the backbone. It often appears between secondary structure elements, breaking bonds.

Torsion Angles

You can rotate on two of the bonds within the backbone. Bulky amino acids restrict rotation more than smaller ones like glycine. Proline is the most restricted amino acid.

All systems move to a state of lower energy.

Peptide Bond Configuration

The peptide bond is planar and rigid due to its partial double bond character, so rotation around that bond is not possible. Polypeptide chain behaves like a series of rectangular plates.

Rotation

There is rotation around the psi bonds. Rotation is not completely unrestricted due to inherent hindrance of the R groups.

Specific confirmations of the side and side angles are possible, depending on which particular amino acids.

I Bond Exceptions

The orientation of peptide bonds is important for creating and stabilizing secondary structure.

Alpha Helix Details

An alpha helix is made from a single polypeptide chain. Peptide bonds point in the same N-to-C direction, parallel to the axis of the helix.

Hydrogen Bonding

Residue $i$ hydrogen bonds with residue $i+4$. For example, residue one hydrogen bonds with residue five, two with six, and so on.

Characteristics

Side chains are on the outside of the helix. Side chains of residues $i$, $i+3$, and $i+4$ are close in space. How they interact influences secondary structure. Their interaction with each other can stabilize or destabilize the structure. If these guys are positively interacting with each other, the protein can adopt a different secondary structure if it's energetically more favorable. Residues close in sequence may not be close in physical space.

Width of the helix (backbone) is about 5 angstroms.

Membrane Channel Proteins

Alpha helices in membrane channels have hydrophobic outsides and hydrophilic insides. Alpha helices that form membrane channels tend to be amphipathic. Amphipathic helices can form a coiled-coil structure. Alpha helices in keratin are key structural proteins in hair, skin, and nails.

Beta Sheet

Made up of multiple beta strands lined up next to each other. Backbone resembles a series of rotated plates, forming kinks instead of coiling.

Key Features

• Stretched Out: Polypeptide chain is stretched out and extended.
• Hydrogen Bonds: In beta sheets, hydrogen bonds are between the NH and CO of neighboring strands, not within the same strand as in alpha helices.
• Side Chains: Side chains are above and below the plane of the sheet.

Beta sheets can grow infinitely large, with strands bonding between each other.

Strands can be from the same protein chain or different proteins. Data sheets can also be anti classic.

Amphipathic Features

Side chains of $i$ and $i+2$ are on the same side of the sheet. Amphipathic beta sheets have hydrophilic and hydrophobic sides, with an alternating pattern of hydrophilic and hydrophobic residues.

Irregular Secondary Structure

With irregular secondary structure, polypeptide chains change direction. Beta turns connect antiparallel beta strands. Beta turns consist of four amino acids: $i$, $i+1$, $i+2$, $i+3$ and makes a U-turn.

Loops

Loops are similar to beta turns, are irregular, and are found on the surfaces of proteins but tend to be longer.

Glycines

Glycines lack steric hindrance, allowing for sharp turns. Proline forces the backbone.

In beta turns, middle residues do not participate in hydrogen bonding with other backbone atoms, making them more flexible to hydrogen bond with water.

Summary of Protein Structure

• Primary Structure: Amino acid sequence held together by peptide bonds, including descriptions of cysteines forming disulfide bonds.
• Secondary Structure: Local conformation of backbone peptide bonds held together by hydrogen bonding, forming elements like alpha helices and beta sheets. The elements occur because of restrictions on back bone conformation because restrictions on side chain confirmations.
• Irregular Elements: Loops and turns that connect strands and helices at the protein surface.