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This 5 page Class Notes was uploaded by Udbluehen03 on Saturday September 10, 2016. The Class Notes belongs to BISC401 at University of Delaware taught by Lachke,Salil in Fall 2016. Since its upload, it has received 12 views. For similar materials see Molecular Biology of the Cell in Biology at University of Delaware.
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Date Created: 09/10/16
Class 3 – 9/6/2016, Protein Structure and Function Dr. Salil Lachke Molecular Cell Biology, 8 edition – Lodish Secondary Structure – The Beta (β) Sheet - Consists of literally packed β strands - Pleated structure - Each β strand is a short (5-8 residues) polypeptide segment - Hydrogen bonds in the β sheet occur between backbone atoms in separate. - They are oriented perpendicularly to the chains of backbone atoms - Beta-sheets can form structural motifs called as Beta barrels o Beta-barrels are found in membrane-spanning proteins. o The interior of the barrel is hydrophilic while the exterior is hydrophobic. - Common amino acids in β-sheet o Isoleucine o Valine o Phenylalanine α-helix β-sheet bonds occur in closely located amino acids H bonds occur between adjacent Beta strands 30 residues Each β-strand is 5-8 residues Spiral structure Sheet structure Side chains outside Side chains above or below the plain Hydrophobic or Hydrophilic Parallel or anti-parallel Within same polypeptide β-strands from single or multiple polypeptides can form β-sheets Proline not found β-Turn - Composed of four residues - Located on the surface of a protein, forming sharp bends that reverse the direction of the polypeptide backbone. - Stabilized by a hydrogen bond between their end residues - Glycine and Proline are commonly found in β-turns - Help long polypeptides fold into highly compact structures Class 3 – 9/6/2016, Protein Structure and Function Dr. Salil Lachke Molecular Cell Biology, 8 edition – Lodish Proline and Glycine are found in β-turns - Type I o Proline reside is at position n+1 o The type I turn is stabilized by a hydrogen bond between the carbonyl oxygen of the first N-terminal residue (Phenylalanine) and the amide hydrogen of the fourth residue (Glycine) - Type II o Glycine residue is at position n+2 o The type II turn is stabilized by a hydrogen bond between the carbonyl oxygen of the N-terminal residue (Valine) and the amide hydrogen of the fourth residue (Asparagine) α-helices, β sheets, turns and loops combine to make a protein structure Tertiary structure - Three-dimensional arrangement of all the atoms in a protein - Not rigidly fixed because the stabilizing interactions are often weak - Undergoes continual minute fluctuations - Amino acids that are far apart in the polypeptide sequence and reside in different types of secondary structure may interact when the protein is folded - Primary forces that stabilize protein 3D structure o Sequestration of hydrophobic amino acids away from water (e.g. in the interior of water-soluble proteins) o Maximizing van der Waals contacts in the interior of proteins (minimizing open space) o Maximizing hydrogen bonds (e.g. in α helices or ß sheets) o Ion pairing between oppositely charged amino acids (e.g. Arginine and Glutamate) Quaternary Structure - Quaternary structure of a protein is the level of organization concerned with subunit interactions and assembly Class 3 – 9/6/2016, Protein Structure and Function Dr. Salil Lachke Molecular Cell Biology, 8 edition – Lodish - There are 2 types of globin o Alpha o Beta - Hemoglobin o 2 alpha globin subunits o 2 beta globin subunits Secondary structure Tertiary structure Stretches of polypeptide that form alpha Full 3-D organization of a polypeptide chain helix and Beta sheet constitute the protein’s secondary structure Determined by the short-range structural Determined by the long-range aspects of the relationship of amino acid residues amino acid sequence Stabilized only by hydrogen bonds Stabilized by hydrogen bonds, hydrophobic effect, ionic interactions, and van der Waals interactions, covalent bonds (disulfide linkages) Structural Motif - A combination of two or more secondary structures that forms a distinct three dimensional structure - Protein motifs are small structurally stable polypeptide folds - Motifs are also defined as small folded peptide regions that can exist stably in solution by themselves - Some Structural Motif when isolated from the rest of a protein, are stable, and are called structural domain - Three types o Coiled coil o EFhand/helix-loop-helix o Zinc-finger motif Class 3 – 9/6/2016, Protein Structure and Function Dr. Salil Lachke th Molecular Cell Biology, 8 edition – Lodish - Coiled coil motif o α-helices from two, three or even four separate polypeptide chain coil about one another – resulting in a coil of coils o the individual helices bind tightly to one another because each helix has a strip of aliphatic (hydrophobic but not aromatic) side chains running along one side of the helix that interacts with a similar strip in the adjacent helix - EFhand/helix-loop-helix o Binding of Ca2+ changes protein conformation and alters its activity o Calcium concentrations can control proteins structures and function - Zinc-finger motif o Contains 3 secondary structures An α-helix and two β strands with an antiparallel orientation o Forms a finger link bundle held together by a zinc ion o Help regulate transcription Domains with Proteins - distinct region of protein structure made with combinations of several motifs. - There are three types - 1. Functional domain – exhibits a particular activity, even in isolation - 2. Structural domain – >40 a.a. in length, stable distinct structure o 75% of the protein in eukaryotes have multiple structural domains o E.g. Epidermal growth factor (EGF) EGF is a small peptide hormone that binds to cells and causes them to divide - 3. Topological domain – regions of proteins that have distinctive spatial relationship to the rest of the protein - Structural and Functional domains are often re-used/shuffled to generate proteins having novel function - Immunoglobulin o Immunoglobulin molecules consist of 4 chains, each having several domains o 2 identical light chains o 2 identical heavy chains o Linked by disulfide bonds Class 3 – 9/6/2016, Protein Structure and Function Dr. Salil Lachke Molecular Cell Biology, 8 edition – Lodish Proteins - Different proteins have different shapes and sizes - Proteins are not rigid “lumps” - Proteins have precise moving parts whose mechanical actions are coupled to chemical events - Theoretically, if the angles between peptide group planes were limited to just 8 possibilities for n a n=10 amino acid-long polypeptide, it will still result in 8 combinations or 8.6 million residues! - However, proteins adopt only one or just a few very closely related conformations called the native state o most stably folded form of the molecule that allows it to be functional o in thermodynamic terms, the native state is usually the conformation with the lowest free energy (G) - Proteins fold along one or relatively few pathways - Proteins need the help of molecular chaperones for proper folding - Chaperone proteins facilitate proper folding of nascent proteins o For example, Hsp70 Interaction of a non-properly folded protein with Hsp70 allows it to be correctly folded. Hsp70 function involves ATP hydrolysis o Co-chaperone accessory proteins DnaJ/Hsp40 GrpE/BAG1