05 ProteinStructure - Protein Structure Investigation Due...

Info icon This preview shows page 1. Sign up to view the full content.

View Full Document Right Arrow Icon
This is the end of the preview. Sign up to access the rest of the document.

Unformatted text preview: Protein Structure Investigation Due: Fri April 15th, at 11:59pm: uploaded to Gradescope.com • Search the Protein databank for structure information • Visualize protein structures in pymol • Analyze secondary structure content • Visualize molecules bound to proteins. • Measure distances of stabilizing structures Protein Structure: Learning Objectives • Define and give examples of the four different levels of protein structure – Explain what interactions stabilize each and their general features • Diagram the known secondary structures and the forces that stabilize these structures. • Explain how all levels of protein structure are determined by the gene sequence(s). • Explain the potential effects of mutations on protein structure and function. DIFFERENT WAYS TO REPRESENT PROTEIN STRUCTURE Ribbon diagram: Just the backbone atoms, emphasizes 2˚ structure Surface Contour + side chains No defined 2˚ structure Space Filling: All atoms as spheres Composition of Some Proteins less than 30 - too hard for protein to fold Table 5-1 Types of Proteins • Simple Proteins single subunit • Oligomeric Proteins – more than one polypeptide chain • Conjugated Proteins – Cofactors Organic Cofactor be released after assistance of protein Transiently Associated Permanently stay with protein Associated Classes of Structure • Globular Proteins – Spherical – Soluble • Hydrophobic core, polar surface – Dynamic Function • e.g. catalysis (enzymes) • Fibrous Proteins – Rod-like – Insoluble – Structural • Can form fibers and matrices • Membrane Proteins inserted into membranes must interact with hydrophobic and aqueous part of protein 1˚ Protein Structure: sequence of amino acids Primary Structure Insulin ProInsulin: Signal sequence tells where protein is suppose to go and is then removed Chain B MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGER C Peptide removed from final polypeptide GFFYTPKTRREAEDLQVGQVELGGGPGAGSLQPLALEGSLQKR Chain A GIVEQCCTSICSLYQLENYCN Insulin: 3 disulfide bonds Chain A: 10 20 Gly-Ile-Val-Glu-Gln-Cys-Cys-Thr-Ser-Ile-Cys-Ser-Leu-Tyr-Gln-Leu-Glu-Asn-Tyr-Cys-Asn Chain B: 10 20 Phe-Val-Asn-Gln-His-Leu-Cys-Gly-Ser-His-Leu-Val-Glu-Ala-Leu-Tyr-Leu-Val-Cys-Gly-GluArg-Gly-Phe-Phe-Tyr-Thr-Pro-Lys-Thr Primary Sequence determines structure fully unfolded polypeptide; no activity Unfolding (Denaturation) Refolding (Renaturation) Primary sequence information is essential for understanding protein function • Determines 3D structure, and therefore function From alignments of multiple sequences • Variants from Humans – Identify mutations that result in diseases • diagnosis and effective therapies • Homologues from different species – protein function – molecular mechanism of action – evolutionary relationships Mutations don’t always affect structure one single primary structure will lead to one tertiary structure but you can have different primary structures that will lead to the same tertiary structures higher numbers = not so important to protein function Table 5-5 part 1 All look like this we can find positions that have a 1 at the bottom column, which means that every single organism has the same amino acid in that position, which means that if there was ever an amino acid in that position that got mutated to another one, that organism did not survive AMINO ACID IN THIS POSITION IS ESSENTIAL TO PROTEIN FUNCTION Sequence Determination: • Nucleotide sequence – Account for untranslated regions – Check final protein sequence for posttranslational processing • Mass Spectrometry – Determine mass of whole peptide – Break up peptide into different fragments – Mass differences represent amino acids that were removed. – Can also detect posttranslational modifications Which of the following has the most significant influence on the characteristics of an individual protein? A) the amino-acid sequence B) the amino-acid composition C) the location of its encoding gene within the genome D) the stereochemistry at the a-carbon 2˚ Protein Structure: Folding of the polypeptide backbone 2 structure describes the conformation of backbone atoms the peptide bond and anything in the same plane as the peptide bond so basically everything except the amino acid functional groups Peptide Bonds are always Trans: (almost) Ala-Phe trans Ala-Pro cis ‘steric clash’ trans keeps amino acid side chains as far apart from each other as possible trans cis preptide bonds that involve proline: in the cis conformation there is no steric clash; adopts cis conformation about 10 % of the time Constraints to Secondary Structure • Lack of Rotation around peptide Bond – Planar peptide bond with R groups in trans • Constraints to rotation from side chains – Steric handrance: Bulky R groups – Electrostatic Repulsion: Similar charge on R groups – Proline Potential Protein Hydrogen Bonds polypeptide backbone primarily consist of peptide bonds which have two permanent dipoles H N H O C C O H N O H Water Peptides Carbonyl Oxygen: Hydrogen Acceptor Amide Nitrogen: Hydrogen Donor α-Helix Top view Side view Side-chains all amino acids face outwards no space in the middle of the alpha helix because all of the backbone atoms are crushed into each other Properties of the Helix residues = amino acids C • 3.6 residues per turn • Hydrogen bonds 9 – between C=O of nth residue and N–H of (n + 4)th residue – Linear and parallel to the direction of chain 5 • Side Chain Interactions – Between nth and (n + 3 or4)th residue Text 1 N hydrogen bonds satisfied between neighboring strands neighboring amino acids point in opposite directions of sheet β-Sheet Anti - Parallel Parallel C N N C C N N P N P stronger hydrogen bonds top of sheet = nonpolar; bottom of sheet = nonpolar depending on the alternate characteristics of amino acids in the primary structure N P N P each of the neighboring strands are going in the same direction; no hydrogen bonding for carbonyl bonding directly so has to bend to get hydrogen bonding so parallel beta sheets are slightly weaker Side Chain Locations: (amphipathic structures) alternating polar and nonpolar amino aicd pointing up and down so one side is polar and other side is nonpolar Helix Figure 6-26 Pleated Sheet Connections between Adjacent secondary structures loops/turns to help protein fold together Figure 6-13 β-Turns in Polypeptide Chains Figure 6-14 Secondary structure predictions • Constraints on α-helix formation – Prolines and glycines • Amino acid propensity – Leu favors α-helix, Ile favors β-strands – Glu favors α-helix, Asp favors turns • Predict 2⁰ structure/motif - loop -hairpin predict family/functions HelixLoopHelix- Greek Key MCAT (old): Parallel and anti-parallel beta-pleated sheets are stabilized by which of the following interactions? A. B. C. D. Covalent bonds Electrostatic interactions Hydrogen bonds Hydrophilic interactions 3˚ & 4˚ Protein Structure: Interactions of Amino Acid Side chains Native 3-D Confirmation • Determines function • From tertiary structure we can gain valuable functional information – Active site composition/organization – Analog binding can show how an enzyme catalyzes a reaction – Design inhibitors (Pharmaceuticals) • Rational Design of Inhibitors of Ras guanine nucleotide exchange factor SOS1 most stabilizing for tertiary and quatenary in this order: 1. london dispersion 2. hydrogen bond/dipole-dipole 3. ionic interactions Relevant Interactions ionic more common in quatenary structure bonds between cysteine residues; S—S disulfide more often in tertiary structure 3 uncommon in tertiary structure 2 1 most significant role in determining structure and stabilizing protein: LD forces/hydrophobic interactions LD forces are the weakest force BUT theres so many of them in the core of the protein Table 2-1 Side Chain Distribution in Horse Heart Cytochrome c Figure 6-27 Proteins can be broadly classified based on their secondary structure content An all protein An all protein any of these combinations can make up the tertiary structure an ‘ / ’ protein The components of a tertiary structure Protein structure levels: 1⁰ structure } 2⁰ structure } motifs } domains} 3⁰ structures (be careful when talking about these as a hierarchy of structures; an entire protein can be 1 motif, or 1 motif or more can make up a domain) Motifs: recognizable arrangement of secondary domains can stably fold on their own; motifs cannot structure motifs/domains- specific combinations of secondary structures that have been identified over and over again and are associated with certain functions 4-helix bundle - loop Domains: an independently stable portion of the protein Nuclease domain -barrel Linker dsRNA binding motif (it is also a domain) Quaternary Structure Specific association of polypeptide chains (Subunits) Efficient means of producing highly complex proteins α1 β2 β1 α2 Which of the following series of amino acids is MOST likely to be at the surface of a watersoluble globular protein? A. ……..met-phe-pro-ile-leu…….. B. ……..tyr-phe-gly-asn-leu……... C. ……..glu-asn-ser-thr-arg……… D. ……..val-ala-val-glu-val……… E. ……..met-cys-pro-ala-tyr……... has all polar amino acids Which of the following could contribute to quaternary structure? A) charge-charge interaction between arginine and glutamic acid B) disulfide bond C) hydrogen bond between threonine hydroxyl group and imidazole ring of histidine D) hydrophobic interaction between phenylalanine and tryptophan E) all of the above secondary determinant primary determinant...
View Full Document

{[ snackBarMessage ]}

What students are saying

  • Left Quote Icon

    As a current student on this bumpy collegiate pathway, I stumbled upon Course Hero, where I can find study resources for nearly all my courses, get online help from tutors 24/7, and even share my old projects, papers, and lecture notes with other students.

    Student Picture

    Kiran Temple University Fox School of Business ‘17, Course Hero Intern

  • Left Quote Icon

    I cannot even describe how much Course Hero helped me this summer. It’s truly become something I can always rely on and help me. In the end, I was not only able to survive summer classes, but I was able to thrive thanks to Course Hero.

    Student Picture

    Dana University of Pennsylvania ‘17, Course Hero Intern

  • Left Quote Icon

    The ability to access any university’s resources through Course Hero proved invaluable in my case. I was behind on Tulane coursework and actually used UCLA’s materials to help me move forward and get everything together on time.

    Student Picture

    Jill Tulane University ‘16, Course Hero Intern