Structure of Proteins PDF

# STRUCTURE OF PROTEIN ## Protein * Proteins are the most abundant organic molecules in living systems * They constitute about 50% of the cellular dry weight. * They constitute the fundamental basis of structure and function of life. * In 1839, Dutch chemist G.J. Mulder was the first to describe...

# STRUCTURE OF PROTEIN ## Protein * Proteins are the most abundant organic molecules in living systems * They constitute about 50% of the cellular dry weight. * They constitute the fundamental basis of structure and function of life. * In 1839, Dutch chemist G.J. Mulder was the first to describe proteins. * The term protein is derived from the Greek *proteios*, meaning "first place". * Proteins are macromolecules composed of many amino acids. ## AMINO ACIDS * Amino acids are a group of organic compounds containing two functional groups: **amino** and **carboxyl**. * The **amino** group (-NH₂) is basic, while the **carboxyl** group (-COOH) is acidic. * There are about 300 amino acids found in nature, but only 20 of them occur in proteins. ## Structure of amino acids * Each amino acid has 4 different groups attached to an **α-carbon** (the carbon atom next to COOH): 1. amino groups, 2. COOH group, 3. hydrogen, and 4. side chain (R). ## Amino acids groups | Group | Characteristics | Names | Example (-Rx) | | :-------- | :------------------------------- | :--------------------------------------------------------------------------- | :------------------------------------ | | non-polar | hydrophobic | Ala, Val, Leu, Ile, Pro, Phe, Trp, Met | CH₃-CH-CH₂-CH₃ (Leu) | | polar | hydrophilic (non-charged) | Gly, Ser, Thr, Cys, Tyr, Asn, Gln | OH-CH-CH₃ (Thr) | | acidic | negatively charged | Asp, Glu | O-C-CH₂ (Asp) | | basic | positively charged | Lys, Arg, His | NH₃⁺-CH₂-CH₂-CH₂-CH₂ (Lys) | ## Peptide Bond Formation * The α-carboxyl group of one amino acid (with a side chain R1) forms a covalent peptide bond with an α-amino group of another amino acid (with a side chain R2) by the removal of a water molecule. This results in a **dipeptide**. * Dipeptides can then form a second peptide bond with a third amino acid (with a side chain R3) to give a **tripeptide**. * Repetition of this process generates a **polypeptide** or **protein** of specific amino acid sequences. * The peptide bond has 40% double bond character, caused by resonance. ## Formation of peptide bond A diagram depicts the formation of a peptide bond from two amino acids with the removal of water. ## Polypeptide Backbone * The **polypeptide backbone** is a repeating sequence of the structure N-C-C-N-C-C.. in the peptide bond. * Side chains (or R groups) are not part of the polypeptide backbone or the peptide bond. ## Overview of Protein Structure * **Configuration:** The geometric relationship between a given set of atoms. For example, a configuration defines the difference between L-amino acids and D-amino acids. * **Conformation:** The spatial arrangement of atoms in a protein. * Thermodynamically, the most stable conformations exist. * Stability is stabilized largely by weak interactions. * **Stability:** The tendency to maintain a native conformation. * **Native confirmation:** The native confirmation of a protein is stabilized by a. disulfide bonds and b. non-covalent forces. ## Structure of Proteins Proteins have different levels of organization: * **Primary Structure:** The sequence of amino acids in a protein chain. * **Secondary Structure:** Regular sub-structures include: * α-helix: A right-handed spiral structure where the side chains extend outwards. * β-sheet: A sheet-like structure that consists of two or more extended polypeptide chains (β-strands) that are held together by hydrogen bonds. * **Tertiary Structure:** The three-dimensional structure of a protein. * **Quaternary Structure:** The arrangement of multiple polypeptide chains (subunits) in a protein complex. ## What forces determine the structure? * **Primary Structure:** Covalent bonds. * **Secondary, Tertiary, Quaternary Structure:** Weak forces. ## Protein Structure A diagram shows the levels of protein structure (primary, secondary, tertiary, quaternary) with a focus on the process (assembly, folding, packing, and interaction). ## Primary Structures * The primary structure of a protein refers to the sequence of amino acids present in the polypeptide chain. * Amino acids are covalently linked by peptide bonds (or covalent bonds). * Each component amino acid in a polypeptide is called a **residue** or **moiety**. * By convention, the primary structure of a protein starts from the **amino terminal** (N) and ends in the **carboxyl terminal** (C). ## Secondary Structure * A **secondary structure** is a local, regularly occurring structure found in proteins. * Secondary structures are mainly formed through **hydrogen bonds** between backbone atoms. * Pauling & Corey studied secondary structures and proposed 2 conformations: * **α-helix** * **β-sheet** ## Alpha Helix * **α-helix:** A right-handed spiral structure. * Side chains extend outwards * Stabilized by hydrogen bonding between the carbonyl oxygen (nth residue) and amide hydrogen (n+4 th residue). * Amino acids per turn: 3.6 * Pitch: 5.4 Å * Length: ~12 residues and ~3 helical turns. * **Phi:** -60 degrees. **Psi:** -45 degrees * Alpha helical segments are found in many globular proteins, such as myoglobin and troponin C. ## Types of Helix * **α-helix:** Also called the 3.6₁₂ helix * **π-helix:** Very loosely coiled hydrogen-bonded pattern (n+5). Found rarely in nature. * **3₁₀-helix:** Very tightly coiled hydrogen-bonded pattern (n+3). Found rarely in nature. ## Beta Pleated Sheet * **β-sheet:** Formed when 2 or more polypeptides line up side by side. * The individual polypeptide chains are called **β-strands**. * Each β-strand is fully extended. * Stabilized by hydrogen bonding between N-H and carbonyl groups of adjacent chains. * **β-sheets** come in two varieties: * **Antiparallel β-sheet:** Neighboring hydrogen bonded polypeptide chains run in the *opposite* direction. * **Parallel β-sheet:** Hydrogen bonded chains extend in the *same direction*. * The connection between two antiparallel strands can be just a small loop, but the link between tandem parallel strands must be a crossover connection that is out of the plane of the β-sheet. ## Polypeptide Chain Conformations * The **backbone** or **main chain** of a protein refers to the atoms that participate in peptide bonds, ignoring the side chains of the amino acid residues. * The only reasonable free movements are rotations around the **C_α-N** bond (measured as **Φ**) and the **C_α-C** bond (measured as **Ψ**). * These angles are defined as 180° when the polypeptide chain is in a **full conformation**. * The conformation of the polypeptide chain is described by the **torsion angles (dihedral angles or rotational angles)**. ## Protein Folding * The **peptide bond** allows for rotation, enabling proteins to fold and orient the R groups in favorable positions. * **Weak non-covalent interactions** hold the protein in its functional shape. These are weak and require many interactions to maintain the final form. * Protein folding occurs in the **cytosol**. ## 2 Regular Folding Patterns * **α-helix:** Protein turns like a spiral. Found in fibrous proteins (like hair, nails, and horns). * **β-sheet:** Protein folds back on itself as in a ribbon. Found in globular proteins. ## Turns and Loops * In addition to **α-helices** and **β-strands**, a folded polypeptide chain contains two other types of secondary structures: **loops** and **turns**. * **Loops and turns** connect **α-helices** and **β-strands**. * The most common types of turns and loops cause a change in the direction of the polypeptide chain, allowing it to fold back on itself to create a more compact structure. * **Loops** have **hydrophilic residues** and are found on the surface of a protein. * **Turns** have **only 4 or 5 amino acid residues** and are often called **turns** when they have internal hydrogen bonds. * **Reverse turns** are a form of tight turn in which the polypeptide chain makes a 180° change in direction. * **Reverse turns** are also called β **turns** because they usually connect adjacent β strands in a β-sheet. ## Beta Turns * Also known as β-bends or tight turns. * In a β-turn, a tight loop is formed when the carbonyl oxygen of one residue forms a hydrogen bond with the amide proton of an amino acid three residues down the chain. This hydrogen bond stabilizes the β-bend structure. * **Proline and Glycine** are frequently found in β-turns: * **Proline** because its cyclic structure is well-suited for the β-turn; * **Glycine** because of its small side chain, making it the most sterically flexible amino acid. * A β-turn is a means by which a protein can reverse the direction of its peptide chain. * β-turns often promote the formation of antiparallel β-sheets. ## Tertiary Structure of Proteins * The **tertiary structure** defines the specific overall 3-D shape of a protein. * The tertiary structure is based on various types of interactions between the side-chains of the peptide chain: a. **hydrophobic interactions**, b. **hydrophilic interactions** (including hydrogen bonding), c. **disulfide bonds**, d. **salt bridges**, and e. **ionic bonds**. ## Tertiary Structure Stabilization * **Globular proteins:** Tertiary interactions are frequently stabilized by the sequestration of hydrophobic amino acid residues in the protein core. This results in an enrichment of charged or hydrophilic residues on the protein's waters-exposed surface. * **Secreted proteins:** **Disulfide bonds** between cysteine residues are important for maintaining tertiary structure. ## Interactions Stabilizing Tertiary Structure * **Disulfide bonds** * **Hydrophobic interactions** * **Hydrogen bonds** * **Ionic interactions** * **Vander Waals force**. ## Tertiary Structure - Disulfide Bond * **Disulfide bonds** are covalent bonds between sulfur atoms on two cysteine residues. ## Tertiary Structure - H Bond * **Hydrogen bonds** are weak bonds that can easily be broken and reformed. * **Hydrogen bonds** allow for structural change and produce functional molecules. ## Salt Bridges * **Salt bridges** are electrostatic bonds between oppositely charged groups. * The strength of a salt bridge is usually 4 - 7 kcal/mol. * **Ions** on R groups form salt bridges through ionic bonds. * **NH₃⁺** and **COO^-** areas of the protein attract and form ionic bonds. ## Tertiary Structure - Hydrophobic Forces * **Hydrophobic forces** result from a close attraction of non-polar R groups through dispersion forces. * These are not true attractive interactions but arise from the inability of water to form hydrogen bonds with certain side chains. * **Hydrophobic interactions** are very weak, but their combination over large areas can stabilize protein structure. * **Hydrophobic interactions** repel polar and charged molecules/particles. ## Stabilizing Interactions of Tertiary Structures A table describes the nature of bonding and provides an example for each type of bonding (hydrophobic interactions, hydrophilic interactions, salt bridge, hydrogen bonds, disulfide bonds). ## Globular Proteins * **Globular proteins** fold up into compact, spherical shapes. * **Globular proteins** function in biosynthesis, transport, and metabolism. * For example, **myoglobin** is a globular protein that stores oxygen in muscles. * Myoglobin consists of a single peptide chain that is mostly α-helix. * **Myoglobin's oxygen-binding pocket** is formed by a **heme group** and specific amino acid side chains that come into position by the tertiary structure. ## Fibrous Proteins * **Fibrous proteins** consist of long fibers and are mainly structural proteins. * **Examples of fibrous proteins**: * **α-keratins** make *hair, fur, nails, and skin*: * Hair is made of twined fibrils, which are braids of three α-helices. This structure is similar to the triple helix structure of collagen. * Disulfide bonds hold the α-helices together. * **β-keratins** are found in *feathers and scales* and are made up mostly of β-pleated sheets. ## Supersecondary Structure * **Supersecondary structures** are associations of secondary structures. * **Types:** * β-sheet supersecondary structure * α-helix supersecondary structure * Mixed supersecondary structure * **Examples of supersecondary structures:** * βαβ-unit * 4-α-helix * β-meander * Greek key * coiled helices * β-barrel * zinc finger * leucine zipper ## Domains * A **domain** is a basic structural unit of a protein structure that is distinct from the conformations. * **Domains** can fold into a stable structure *independently*. * **Domains** can impart different functions in proteins. * Proteins can have *one to many domains* depending on their size. ## Myoglobin * **Myoglobin** is a small monomeric protein that serves as an intracellular oxygen storage site. * **Myoglobin** is found in abundance in the skeletal muscle of vertebrates and is responsible for the characteristic red color of muscle tissue. * **Myoglobin** is closely related to **hemoglobin**, which consists of four myoglobin-like subunits that form a tetramer and are responsible for carrying oxygen in blood. ## Quaternary Structure of Protein * The **quaternary structure** of a protein refers to the arrangement of several individual polypeptide chains (subunits) within a protein complex. * A variety of bonding interactions, including hydrogen bonding, salt bridges, and disulfide bonds, hold the subunits in a particular geometry. * **Two types of quaternary structures:** * **Homodimer:** Association of two identical polypeptide chains. * **Heterodimer:** Association of two different polypeptide chains. * The interactions within multisubunits are the same as those found in tertiary and secondary structures. ## Quaternary Structure and Stability * **Quaternary structure** adds stability by decreasing the surface/volume ratio of the smaller subunit. * **Quaternary structure** simplifies the construction of large complexes, such as viral capsids and proteasomes. ## Quaternary Structure Diagram A diagram depicts two proteins that associate to form a bigger protein with a more stable quaternary structure. ## Subunits are Symmetrically Arranged * Proteins cannot have inversion or mirror symmetry because it would require converting chiral L-residues to D-residues. Thus, proteins can only have *rotational symmetry*. * **Cyclic symmetry:** Two or more subunits are related by a single axis of rotation. * Two types of cyclic symmetry: * Twofold symmetry (C₂) * Threefold symmetry (C₃) * **Dihedral symmetry** is a more complicated type of rotational that results from an intersection of an "n-fold" rotation axis with a "2-fold rotation axis" at right angles. * **D₂** symmetry is, by far, the most common type of dihedral symmetry in proteins. ## Haemoglobin * **Haemoglobin** is a globular protein with 4 polypeptide chains bonded together. It is classified as a **quaternary structure**. * **Haemoglobin** contains 4 heme groups each containing iron. * Each heme group can carry one molecule of oxygen. * The four polypeptide chains consist of two alpha and two beta chains. ## Key Concepts * **Tertiary and quaternary structures** result from folding of the primary structure and secondary structural elements in 3 dimensions. * **Tertiary structure:** * Most proteins' tertiary structures are combinations of α-helices, β-sheets, and loops and turns. * Larger proteins often have multiple folding domains. * Folding of water-soluble, globular proteins into their native structures follows some basic rules/principles: * Minimization of solvent-accessible surface area (burying hydrophobic groups). * Maximization of intraprotein hydrogen bonds. * Chirality (right-handed twist and connectivity) of the polypeptide backbone. * **Quaternary structure:** * Some proteins have multiple polypeptide chains (quaternary structure). * The arrangement of polypeptides in multimeric proteins is generally symmetrical. * Quaternary structure can play important functional roles for multi-subunit proteins, especially in regulation. ## Summary of Structural Levels | Structural Level | Characteristics | | :--------------- | :-------------------------------------------------------------------------------------------------- | | Primary | The sequence of amino acids. | | Secondary | The coiled α-helix, β-pleated sheet, or a triple helix formed by hydrogen bonding between peptide bonds. | | Tertiary | Folding of the protein into a compact, three-dimensional shape, stabilized by interactions. | | Quaternary | A combination of two or more protein subunits to form a larger, biologically active protein. | ## THANK YOU