Protein Structure - PDB-101 PDF

pdb101.rcsb.org This presentation accompanies a video available at pdb101.rcsb.org > Learn > Videos The Building Blocks of Proteins pdb101.rcsb.org All proteins are made out of 21 building blocks, called amino acids. The Building Blocks of Proteins...

pdb101.rcsb.org This presentation accompanies a video available at pdb101.rcsb.org > Learn > Videos The Building Blocks of Proteins pdb101.rcsb.org All proteins are made out of 21 building blocks, called amino acids. The Building Blocks of Proteins pdb101.rcsb.org Amino acids are made of carbon, oxygen, nitrogen, and hydrogen, and some contain sulfur atoms. Selenocysteine is the only standard amino acid that contains a selenium atom. The Building Blocks of Proteins pdb101.rcsb.org The atoms of each amino acid form an amino group, a carboxyl group, and a side chain attached to a central carbon atom.  The Building Blocks of Proteins pdb101.rcsb.org Hydrophobic Hydrophilic or polar Charged No side chain The side chain is the only part that varies from amino acid to amino acid and determines its properties. The Building Blocks of Proteins pdb101.rcsb.org Hydrophobic amino acids have carbon-rich side chains, which don’t interact well with water. The Building Blocks of Proteins pdb101.rcsb.org Hydrophilic or polar amino acids interact well with water. The Building Blocks of Proteins pdb101.rcsb.org Charged amino acids interact with oppositely charged amino acids or other molecules. Protein Structure: Primary Structure pdb101.rcsb.org The primary structure of a protein is the linear sequence of amino acids as encoded by DNA. Protein Structure: Primary Structure pdb101.rcsb.org PEPTIDE BOND The amino acids are joined by peptide bonds, which link an amino group and a carboxyl group. A water molecule is released each time a bond is formed. Protein Structure: Primary Structure pdb101.rcsb.org The linked series of carbon, nitrogen, and oxygen atoms make up the protein backbone. Protein Structure: Secondary Structure pdb101.rcsb.org The protein chains often fold into two types of secondary structures: alpha helices, or beta sheets. Protein Structure: Secondary Structure pdb101.rcsb.org Hydrogen Bond An alpha helix is a right-handed coil stabilized by hydrogen bonds between the amine and carboxyl groups of nearby amino acids Protein Structure: Secondary Structure pdb101.rcsb.org Hydrogen Bond Beta-sheets are formed when hydrogen bonds stabilize two or more adjacent strands. Protein Structure: Tertiary Structure pdb101.rcsb.org The tertiary structure of a protein is the three-dimensional shape of the protein chain. This shape is determined by the characteristics of the amino acids making up the chain.  Protein Structure: Tertiary Structure pdb101.rcsb.org Many proteins form globular shapes with hydrophobic Membrane-bound proteins have hydrophobic residues side chains sheltered inside, away from the clustered together on the outside, so that they can interact surrounding water. with the lipids in the membrane. Charged amino acids allow proteins to interact with molecules that have complementary charges. Protein Structure: Tertiary Structure pdb101.rcsb.org The functions of many proteins rely on their three-dimensional shapes. For example, hemoglobin forms a pocket to hold heme, a small molecule with an iron atom in the center that binds oxygen. Protein Structure: Quaternary Structure pdb101.rcsb.org Two or more polypeptide chains can come together to form one functional molecule with several subunits. For example, the four subunits of hemoglobin cooperate so that the complex can pick up more oxygen in the lungs and release it in the body. Protein Representation pdb101.rcsb.org Different visual representations of proteins can give us visual clues about the protein structure and function. The space filling diagram shows all atoms that are making up this protein. The ribbon or cartoon diagram shows the organization of the protein backbone and highlights the alpha helices. The surface representation shows the areas that are accessible to water molecules. Protein Size pdb101.rcsb.org Most proteins are smaller than the wavelength of light. For example, the hemoglobin molecule is about 6.5 nanometers in size. Hemoglobin is found in high concentration in red blood cells. A typical red blood cell contains about 280 million hemoglobin molecules. Shape and Function: DEFENSE pdb101.rcsb.org The flexible arms of antibodies protect us from disease by recognizing and binding to pathogens such as viruses, and targeting them for destruction by the immune system.  Shape and Function: COMMUNICATION pdb101.rcsb.org 1 The hormone insulin (yellow) is a small, stable protein that can easily maintain its shape while traveling through the blood to regulate the blood glucose level. 2 3 Insulin binds to the insulin receptor (navy blue) and As a result, the glucose transporter (aqua) comes to the cell triggers an intracellular signaling pathway. surface creating a channel for glucose (white) to enter the cell. Shape and Function: ENZYMES pdb101.rcsb.org Alpha Amylase (turquoise) is an enzyme that begins digestion of starches in our saliva. It binds to a carbohydrate chain (yellow) and breaks it into smaller pieces with two or three glucose units. Shape and Function: TTRANSPORT pdb101.rcsb.org 1 The calcium pump reduces the calcium level in the muscle cell by transporting calcium ions back to the sarcoplasmic reticulum after each muscle contraction. Magnesium primes the pump for calcium intake and two atoms enter the pump. 2 3 The ATP causes a change in shape of the After the calcium atoms are released to the lumen of the transmembrane part of the pump, allowing the calcium sarcoplasmic reticulum, the whole cycle begins again. atoms to be pushed further down the channel. Shape and Function: STORAGE pdb101.rcsb.org Ferritin stores iron. It is a spherical protein with channels that allow the iron atoms to enter and exit depending on the organism’s needs. On the inside, ferritin forms a hollow space with the iron atoms attached to the inner wall. Ferritin stores iron in the non-toxic form.  Shape and Function: STRUCTURE pdb101.rcsb.org Collagen forms a strong triple helix 1 that is used throughout the body for structural support. 2 3 Collagen molecules can form elongated fibrils. The fibrils aggregate to form collagen fibers. This type of collagen is found in skin and tendons.