Lecture 4: 8/26 CHAPTER 4 Protein Three Dimensional Structure
Summary of the Lecture 3 There are 20 amino acids and only the L isomer amino acid exist in proteins Each amino acid consists of a central alpha carbon that is bonded by an amino group, a carboxyl group, a hydrogen atom and distinctive side chain or R group Amino acid can be classified based on the chemical properties of the side chains: 1. Hydrophobic amino acids 2. Polar amino acids 3. Positively charged amino acids 4. Negatively charged amino acids Essential amino acids (9 of them) must be obtained through diet and they are required for healthy growth and development 8/24/2016 2
Chapter 4 Outline
Polypeptides consist of amino acids linked by a peptide bond. The peptide bond is also called an amide bond. Each amino acid in a protein is called a residue.
Peptide bond formation The linking of two amino acids is accompanied by the loss of a molecule of water
A polypeptide bond has directionality. The amino terminal end is taken as the beginning of the polypeptide chain. The carboxyl terminal end is the end of the polypeptide chain. The primary structure is always written from the amino terminal to the carboxyl terminal, or left to right.
Amino acid sequences have direction Pentapeptide: Tyr Gly Gly Phe Leu (YGGFL) This pentapeptide, Leu enkephalin, is an opioid peptide that modulates the perception of pain.
The polypeptide consist of a repeating part called the main chain or backbone and a variable part consisting of the distinctive amino acid side chains. The backbone has hydrogen bonding potential because of the carbonyl groups and hydrogen atoms that are bonded to the nitrogen of the amine group. Most proteins consist of 50 to 2000 amino acids. The mean molecular weight for an amino acid is 110 g mol 1.
Components of a polypeptide chain A polypeptide chain consists of a constant backbone (shown in black) and variable side chains (shown in green). Can you identify peptide bound in this polypeptide?
In some proteins, the polypeptide chain can be cross linked by disulfide bonds. Disulfide bonds form by the oxidation of two cysteines. The resulting unit of two linked cysteines is called cystine.
Cross links between two cysteine amino acids The formation of a disulfide bond between two cysteine residues is an oxidation reaction
Amino acid sequence of bovine insulin Genes specify or code amino acid sequences in proteins (hint: central dogma)
Quick Quiz What is the amino terminus of a tripeptide Gyl Ala Asp? What is the approximate molecular weight of a protein composed of 300 amino acids? Approximately how many amino acid are required to form a protein with a molecular weight of 10,000?
Polypeptide Chains Are Flexible Yet Conformationally Restricted The peptide bond is essentially planar. Six atoms (C α, C, O, N, H, and C α ) lie in a plane. The peptide bond has partial double bond character because of resonance, and thus rotation about the bond is prohibited. Peptide bonds are planar The peptide bond is uncharged.
Typical bond lengths within a peptide unit
Polypeptide Chains Are Flexible Yet Conformationally Restricted Most peptide bonds are in the trans configuration so as to minimize steric clashes between neighboring R groups.
Polypeptide Chains Are Flexible Yet Conformationally Restricted Rotation is permitted about the N C α bond (the phi (Φ )bond) and about C α carbonyl bond (the psi ( ψ) bond.) The rotation about the Φ and ψ bonds, called the torsion angle, determines the path of the polypeptide chain. Not all torsion angles are permitted.
Rotation about bonds in a polypeptide
A Ramachandran diagram showing the values of Φ and ψ
Secondary structure is the three dimensional structure formed by hydrogen bonds between peptide NH and CO groups of amino acids that are near one another in the primary structure. The α helix, β sheets and turns are prominent examples of secondary structure.
The Alpha Helix Is a Coiled Structure Stabilized by Intrachain Hydrogen Bonds The α helix is a tightly coiled rod like structure, with the R groups bristling out from the axis of the helix. All of the backbone CO and NH groups form hydrogen bonds except those at the end of the helix. Essentially all α helices found in proteins are right handed.
The structure of the a helix
The hydrogen bonding scheme for an α helix In the α helix, the CO group of residue i forms a hydrogen bond with the NH group of residue i + 4.
Schematic views of a helices (A) A ribbon depiction. (B) A cylindrical depiction.
A largely α helical protein Ferritin, an iron storage protein, is built from a bundle of α helices.
Beta Sheets Are Stabilized by Hydrogen Bonding Between Polypeptide Strands The β sheet is another common form of secondary structure. Beta sheets are formed by adjacent β strands. In contrast to an α helix, the polypeptide in a β strand is fully extended.
The structure of a strand The side chains (green) are alternatively above and below the plane of the strand. The bar shows the distance between two residues.
Beta Sheets Are Stabilized by Hydrogen Bonding Between Polypeptide Strands Hydrogen bonds link the strands in a β sheet. The strands of a β sheet may be parallel, antiparallel, or mixed. β sheets may be flat or adopt a twisted conformation.
Antiparallel and parallel β sheets Antiparallel β sheets Antiparallel β sheets Parallel β sheets
Antiparallel β sheets Adjacent β strands run in opposite directions. Hydrogen bonds (green dashes) between NH and CO groups connect each amino acid to a single amino acid on an adjacent strand, stabilizing the structure.
Parallel β sheets Adjacent β strands run in the same direction. Hydrogen bonds connect each amino acid on one strand with two different amino acids on the adjacent strand.
The structure of a mixed β sheets
A twisted β sheet (A) A schematic model. (B) The schematic view rotated by 90 degrees to illustrate the twist more clearly.
A protein rich in β sheet The structure of a fatty acid binding protein
Polypeptide Chains Can Change Direction by Making Reverse Turns and Loops The structure of a reverse turn A) The CO group of residue i of the polypeptide chain is hydrogen bonded to the NH group of residue i + 3 to stabilize the turn. B) (B) A part of an antibody molecule has surface loops (shown in red).
Fibrous Proteins Provide Structural Support for Cells and Tissues α Keratin, a structural protein found in wool and hair, is composed of two right handed α helices intertwined to form a left handed super helix called a coiled coil. The helices interact with ionic bonds or van der Waals interactions. α Keratin is a member of a superfamily of structural proteins called coiled coil proteins. Other members of the family include some cytoskeleton proteins and muscle proteins.
An α helical coiled coil (A) Space filling model. (B) Ribbon diagram. The two helices wind around each other to form a superhelix. Such structures are found in many proteins, including keratin in hair, quills, claws, and horns.
Fibrous Proteins Provide Structural Support for Cells and Tissues Collagen is a structural protein that is a component of skin, bone, tendons, cartilage, and teeth. Collagen consists of three intertwined helical polypeptide chains that form a superhelical cable. The helical polypeptide chains of collagen are not α helices. Glycine appears at every third residue and the sequence gly pro pro is common.
The amino acid sequence of a part of a collagen chain Every third residue is glycine. Proline and hydroxyproline also are abundant.
The conformation of a single strand of a collagen triple helix
Fibrous Proteins Provide Structural Support for Cells and Tissues The helices in collagen are not stabilized by hydrogen bonds. Rather, they are stabilized by steric repulsion of the pyrrolidine rings of proline. The three intertwined chains interact with one another with hydrogen bonds. The interior of the superhelical cable is crowded, and only glycine can fit in the interior.
The structure of the protein collagen Space filling model of collagen Cross section of a model of collagen
Osteogenesis imperfecta, or brittle bone disease, occurs if a mutation results in the substitution of another amino acid in place of glycine.
Hydroxyproline, a modified version of proline in which a hydroxyl group replaces a hydrogen, is important for the stabilization of collagen. Vitamin C is required for the formation of hydroxyproline. A lack of vitamin C results in scurvy.
Tertiary structure refers to the spatial arrangement of amino acids that are far apart in the primary structure and to the pattern of disulfide bond formation.
Myoglobin Illustrates the Principles of Tertiary Structure Globular proteins, such as myoglobin, form complicated three dimensional structures. Globular proteins are very compact. There is little or no empty space in the interior of globular proteins. The interior of globular proteins consists mainly of hydrophobic amino acids. The exterior of globular proteins consists of charged and polar amino acids.
The three dimensional structure of myoglobin A ribbon diagram A space filling model
The Tertiary Structure of Many Proteins Can Be Divided into Structural and Functional Units Motifs, or supersecondary structure, are combinations of secondary structure that are found in many proteins. Some proteins have two or more similar or identical compact structures called domains.
The helix turn helix motif, a supersecondary structural element Helix turn helix motifs are found in many DNA binding proteins
Protein domains The cell surface protein CD4 consists of four similar domains.
Many proteins are composed of multiple polypeptide chains called subunits. Such proteins are said to display quaternary structure. Quaternary structure can be as simple as two identical polypeptide chains or as complex as dozens of different polypeptide chains.
Quaternary structure The Cro protein of bacteriophage λ is a dimer of identical subunits.
The 2 β 2 tetramer of human hemoglobin The ribbon diagram shows that they are composed mainly of helices. The space filling model illustrates the close packing of the atoms and shows that the heme groups (gray) occupy crevices in the protein.
Christian Anfinsen placed the enzyme ribonuclease, which degrades RNA, in a solution containing urea and β mercaptoethanol. Urea destroyed all noncovalent bonds, while the β mercaptoethanol destroyed the disulfide bonds. The ribonuclease was denatured. The enzyme displayed no enzymatic activity and existed only as a random coil. When the urea and β mercaptoethanol were slowly removed, the enzyme regained its structure and its activity. Ribonuclease was renatured and attained its normal or native state. These results demonstrated that the information required for a polypeptide chain to fold into a functional protein with a defined threedimensional structure is inherent in the primary structure.
Amino acid sequence of bovine ribonuclease The four disulfide bonds are shown in color
The role of β mercaptoethanol in reducing disulfide bonds As the disulfides are reduced, the β mercaptoethanol is oxidized and forms dimers
The reduction and denaturation of ribonuclease
Proteins Fold by the Progressive Stabilization of Intermediates Rather Than by Random Search A monkey randomly poking at a key board could type a sentence from Shakespeare in a few thousand keystrokes if the correct letters are retained, a process called cumulative selection.
Proteins Fold by the Progressive Stabilization of Intermediates Rather Than by Random Search Protein folding is often represented as a folding funnel. The protein has maximum entropy and minimal structure at the top of the funnel. The folded protein exists at the bottom of the funnel. Folding funnel: The folding funnel depicts the thermodynamics of protein folding
Some Proteins Are Inherently Unstructured and Can Exist in Multiple Conformations Intrinsically unstructured proteins (IUP) do not have a defined structure under physiological conditions until they interact with other molecules. Metamorphic proteins exist in an ensemble of structures of approximately equal energies that are in equilibrium. Lymphotactin exists in two conformations, which are in equilibrium
Amyloidoses are diseases that result from the formation of protein aggregates, called amyloid fibrils or plaques. Alzheimer disease is an example of an amyloidosis. PET scan of the brain of a normal person PET scan of the brain of Alzheimer patient Colored positron emission tomography (PET) scans of the brain of a normal person (left) and that of a patient who has Alzheimer disease (right). Color coding: high brain activity (red and yellow); low activity (blue and black). The Alzheimer patient s scan shows severe deterioration of brain activity.
Some infectious neurological diseases are caused by infectious proteins called prions. Prions exist in two states, one α helix rich (PrP) and the other β sheet rich (PrP SC ). PrP SC forms aggregates that disrupt cell function. The protein only model for prion disease transmission A nucleus consisting of proteins in an abnormal conformation grows by the addition of proteins from the normal pool.
Summary of the Lecture 4 Primary structure: Amino acids (aa) are linked by peptide bond or amide bond to form polypeptide chains Peptide bonds form between the carboxyl group (the H bond acceptor) of one aa and the amino group (the H bond donor) of the next aa. Significance: (a) Peptide bond is resistant to hydrolysis, and thus proteins are remarkably stable. (b) Each polypeptide bond has both a H bond donor (the NH group) and a H bond acceptor (the CO group) Proteins are sequence of amino acids and the sequences are written from the amino (NH) to the carboxyl (CO) terminus Secondary Structure: Polypeptide can fold into regular structures The a helix and b strand are the two major elements of the secondary structure. In the helix, polypeptide chain twists into tightly packed rod. Within the a helix, the CO group of each aa is H bonded to the NH group of the aa In the b strand, the polypeptide chain is nearly fully extended. Two or more b strand connected by NH to CO hydrogen bond come together to form b sheets. The strand of b sheets can be parallel, antiparallel, or mixed
Summary of the Lecture 4 (Continued) Tertiary structure: Water soluble proteins fold into compact structure. Amino acids with hydrophobic side chains are located in interior of the structure. Amino acids with hydrophilic side chains are largely located in surface of the structure and interact with aqueous environment The driving force of the formation of tertiary structure of water soluble proteins is the hydrophobic interaction between the interior residues Quaternary Structure: two or more polypeptide chains can assemble into a single protein. Each individual polypeptide is called a subunit. Subunit held together by noncovalent bonds The amino acid sequence of a protein determines its 3 D structure. The sequences of the bases in a DNA molecules determine the aa sequence of a protein Proper folding of a protein is important its intended function. Improper proper protein folding can cause diseases such Alzheimer disease