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Structure and Function of Proteins Ora Schueler-Furman 2009-2010 1 How to open an EKMD account ? Open this website: http://agcc.ekmd.huji.ac.il/ekmd.asp You’ll need The 1st 8 digits of your ID number 4 digit code Follow the instructions… Website Information http://courses.md.huji.ac.il/81817 https://eduportal.ekmd.huji.ac.il/courses/81817 Contact us: – Ora Schueler-Furman 87094 (02-6757094) E-mail: [email protected] – Sivan Pearl 85471 E-mail: [email protected] - Miriam Oxsman 88337 E-mail: [email protected] 3 PROTEINS From the Greek word proteio “Proteios” - first rank, most important Play central roles in all biological processes 4 Introduction into Protein Structure • The chemical nature of polypeptides • Forces that determine protein structure 5 The 4 Hierarchical Levels of Protein Structure 6 Primary Structure: Sequence 7 Formation of a Peptide Bond H +H N 3 Ca O C O- R cpk colors O - oxygen H - hydrogen N - nitrogen C - carbon 8 Dihedral Angles F and define Backbone Geometry w F The peptide bond w is planar and polar 9 Basic Facts Polypeptide chain: But also >20000 aa: 50-10’000 aa 34’350 aa (Titin) Average MW of aa : 110 daltons Average MW of a protein of length n aa: n X110 Distance (Cai – Cai+1) <=3.63Ǻ aa – amino acid 10 Basic Terms Main chain, backbone, side chain, residue bb sc Peptide: a small # of connected aa Polypeptide: a longer chain of aa Protein: polypeptide chain with defined aa sequence & conformation 11 The Protein Alphabet: 20 letters A C D E F G H I K L Ala Cys Asp Glu Phe Gly His Ile Lys Leu Alanine Cysteine Aspartate Glutamate Phenylalanine Glycine Histidine Isoleucine Lysine Leucine M N P Q R S T V W Y Met Asn Pro Gln Arg Ser Thr Val Trp Tyr Methionine Aspargine Proline Glutamine Arginine Serine Threonine Valine Tryptophane Tyrosine amino acids vary in: volume, shape, chemical nature (charge, hydrogen bonding capability, etc.) 12 Special Amino Acids CO N C H H H • The simplest aa • No sc • Very flexible bb CO N C H2C CH2 H • Cyclic aa • sc Connects bb N • Very constrained bb CH2 13 Aliphatic Amino Acids • sc contains only carbon and hydrogen atoms • hate water 14 Amino Acids with Hydroxyl Group 15 Negatively Charged Amino Acids different size → different tendency for 2. structure 16 Amide Amino Acids 17 Positively Charged Amino Acids • pKa 11.1 • pKa 12 • large sc 18 Aromatic Amino Acids • pKa 7 • benzene ring • sc contains aromatic ring 19 Amino Acids with Sulfur 20 Cystine Oxidation of Sulfur atoms creates covalent disulfide bond (S-S bond) between two cysteines 21 S-S Bonds Stabilize the Protein A chain s s GIVEQCCASVCSLYQLENENYCN s s B chain s s F V N Q H L C G S H L V E A L Y L V C G E R G F.. N C A chain Insulin B chain 22 Post-Translational Modifications • Processing (proinsulin/insulin) – control of protein activity • Glycosylation – protein trafficking • Phosphorylation (Tyr, Ser, Thr) – regulation of signaling • Methylation, Acetylation – histone tagging 23 Metal Binding Proteins • aa: HCDE • Fe, Zn, Mg, Ca • Fe – blood: red hemoglobin – electro-transfer: cytochrome c • Zn – in DNA-binding “Zn-finger” proteins – Alcohol dehydrogenase: oxidation of alcohol 24 Forces that Determine Protein Structure 25 Non-Covalent Forces Add up Each bond is weak Large number of bonds From: the Molecular Biology of the Cell, 4th ed. 26 E(r) = K/rp p=1: Coulomb interaction between two charges E(r) – energy of attraction Attractions between molecules p=1 p=6 r – distance between molecules p>1: delocalized charges – weaker interactions p=6: interaction between neutral molecules Short-range interactions: p>=3 27 1. Van der Waals Interactions (Lennard Jones Potential) Attractive: weak, due to transient dipoles rij Repulsive: Atoms do not penetrate each others → spheres (VdW-radii) 1Ǻ = 0.1nm 0.5-1kcal/mol From: the Molecular Biology of the Cell, 4th ed. 28 2. Hydrogen Bonds d H N O C Donor Acceptor Hydrogen “shared” between two electronegative atoms Important for 2nd struct. Interaction with water 1-3kcal/mol From: the Molecular Biology of the Cell, 4th ed. 29 3. Electrostatic Forces (Salt Bridges) Coulomb’s law: E = kqAqB/Dr qA, qB : point charges r: distance k=332 (for units of kcal/mol) D: dielectric constant (water:80; protein: ~4) Solvent screening: D’ = DrAB qA qB r 3Ǻ: ~1.4 kcal/mol 30 4. Aromatic Rings: p-p and Cation-p Interactions Aromatic ring: cloud of p electrons: negative charge From: wikipedia. Can interact with • positive charge of Lys, Arg, His • edge of other aromatic ring 31 5. Water • polar • cohesive •competes with interactions in the protein (Hb, SB) • high D – reduces electrostatic forces • hydrophobic effect • explicit modeling difficult From: the Molecular Biology of the Cell, 4th ed. 32 Accessible Surface Area Van der Waals surface • Roll ball (radius = 1.4Ǻ; H2O) over molecule • polar vs apolar: well solvated protein – polar atoms at surface, apolar atoms in the core 33 Non-Covalent Forces: Summary • VdW: Many small contributions sum up to significant energy • Salt bridges and hydrogen bonds: polar interactions are reduced by competing water at the surface • Surface of protein: hydrophobic atoms should be all buried 34