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Structure and Function of Proteins Ora Schueler-Furman 2009-2010 1.

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1 Structure and Function of Proteins Ora Schueler-Furman 2009-2010 1

2 How to open an EKMD account ? http://agcc.ekmd.huji.ac.il/ekmd.asp Open this website: You’ll need  The 1 st 8 digits of your ID number  4 digit code Follow the instructions…

3 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: oraf@ekmd.huji.ac.il –Sivan Pearl 85471 E-mail: sivan.pearl@mail.huji.ac.il -Miriam Oxsman 88337 E-mail: miriam.oxsman@mail.huji.ac.il 3

4 PROTEINS From the Greek word  “Proteios” - first rank, most important Play central roles in all biological processes 4

5 Introduction into Protein Structure The chemical nature of polypeptides Forces that determine protein structure 5

6 The 4 Hierarchical Levels of Protein Structure 6

7 Primary Structure: Sequence 7

8 Formation of a Peptide Bond O - oxygen N - nitrogen O-O- +H3N+H3N R H CC O C || H - hydrogen C - carbon cpk colors 8

9  Dihedral Angles  and  define Backbone Geometry   The peptide bond  is planar and polar 9

10 Basic Facts Polypeptide chain: 50-10’000 aa But also >20000 aa: 34’350 aa (Titin) Average MW of aa : 110 daltons Average MW of a protein of length n aa: n X110 Distance (C  i – C  i+1 ) <=3.63Ǻ aa – amino acid 10

11 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

12 The Protein Alphabet: 20 letters AAlaAlanine CCysCysteine DAspAspartate EGluGlutamate FPhePhenylalanine GGlyGlycine HHisHistidine IIleIsoleucine KLysLysine LLeuLeucine MMetMethionine NAsnAspargine PProProline QGlnGlutamine RArgArginine SSerSerine TThrThreonine VValValine WTrpTryptophane YTyrTyrosine amino acids vary in: volume, shape, chemical nature (charge, hydrogen bonding capability, etc.) 12

13 The simplest aa No sc Very flexible bb Special Amino Acids Cyclic aa sc Connects bb N Very constrained bb N CO CH HH N CH CH 2 H2CH2C 13

14 Aliphatic Amino Acids sc contains only carbon and hydrogen atoms hate water 14

15 Amino Acids with Hydroxyl Group 15

16 Negatively Charged Amino Acids different size → different tendency for 2. structure 16

17 Amide Amino Acids 17

18 Positively Charged Amino Acids large sc pK a 11.1 pK a 12 18

19 Aromatic Amino Acids sc contains aromatic ring pK a 7 benzene ring 19

20 Amino Acids with Sulfur 20

21 Cystine Oxidation of Sulfur atoms creates covalent disulfide bond (S-S bond) between two cysteines 21

22 S-S Bonds Stabilize the Protein A chain G I V E Q C C A S V C S L Y Q L E N E N Y C N s s s s B chain F V N Q H L C G S H L V E A L Y L V C G E R G F.. s s Insulin A chain N C B chain 22

23 Post-Translational Modifications Processing (pro- insulin/insulin) –control of protein activity Glycosylation –protein trafficking Phosphorylation (Tyr, Ser, Thr) –regulation of signaling Methylation, Acetylation –histone tagging …. 23

24 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

25 Forces that Determine Protein Structure 25

26 Non-Covalent Forces Add up Each bond is weak Large number of bonds From: the Molecular Biology of the Cell, 4 th ed. 26

27 Attractions between molecules E(r) = K/r p p=1: Coulomb interaction between two charges p>1: delocalized charges – weaker interactions p=6: interaction between neutral molecules Short-range interactions: p>=3 p=1 p=6 r – distance between molecules E(r) – energy of attraction 27

28 1. Van der Waals Interactions (Lennard Jones Potential) From: the Molecular Biology of the Cell, 4 th ed. r ij Attractive: weak, due to transient dipoles Repulsive: Atoms do not penetrate each others → spheres (VdW-radii) 0.5-1kcal/mol 1Ǻ = 0.1nm 28

29 2. Hydrogen Bonds Hydrogen “shared” between two electronegative atoms Important for 2 nd struct. Interaction with water 1-3kcal/mol N H OC d   Acceptor Donor From: the Molecular Biology of the Cell, 4 th ed. 29

30 3. Electrostatic Forces (Salt Bridges) Coulomb’s law: E = kq A q B /Dr q A, q B : point charges r: distance k=332 (for units of kcal/mol) D: dielectric constant (water:80; protein: ~4) Solvent screening: D’ = Dr AB qBqB qAqA r 3Ǻ: ~1.4 kcal/mol 30

31 4. Aromatic Rings:  and Cation-  Interactions Aromatic ring: cloud of  electrons: negative charge Can interact with positive charge of Lys, Arg, His edge of other aromatic ring From: wikipedia. 31

32 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, 4 th ed. 32

33 Accessible Surface Area Roll ball (radius = 1.4Ǻ; H 2 O) over molecule polar vs apolar: well solvated protein – polar atoms at surface, apolar atoms in the core Van der Waals surface 33

34 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

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