Summary of protein structure/function

Summary of protein structure/function 1. The 20 common aa s have different R groups. 2. Amino acids are linked by peptide bonds to form polypeptides & proteins. 3. Proteins are often large & have complex native (d) structures, but patterns do exist: 1, 2, 3, & 4 structures (also motifs, etc.) 4. Native protein structure is maintained by: peptide bonds (1 ), weak interactions (2, 3, & 4 ), and disulfide bonds ( 3 & 4 ). 5. Protein function depends on native structure. 1

Amino acids & Protein Structure 1. Most jobs (except information storage) in cells are performed by proteins. 2. Proteins usually have only a few possible stable conformations. ow does a protein get from one conformation to another? Mostly by rotation about single bonds. 3. Specific protein conformation (structure) is required to maintain function. 2

I. Functions of Proteins See Biochemistry II. The "-amino acids (aa) A. Name comes from the structure: The "- atom is next to the ' (carbonyl). 1) carboxylic acid group 2) "-amino group 3) side chain (a.k.a., R group) 4) ircle the "-carbon! amino group side chain N R carboxyl group 5) Is there a chiral (asymmetric) carbon atom? 3

B. Except for glycine (where R = ), the 20 common aa all have at least one chiral atom. Refer to models. 1. L- and D- designations are based on reference to glyceraldehyde. Biomolecules are linked through biosynthetic pathways. Biochemists usually go with this designation. 2. The R- & S- designations used in the modeling lab are geometrically based. 4

Most "-amino acids have a chiral atom. This means you can have L- and D- isomers. L-Alanine D-Alanine 5

. Amino acids (The 20 common. What does that mean?) can be grouped based on similarities in the side chains (R group) 1. Non-polar 2. Polar but uncharged at normal p 3. Negatively charged (Remember, we are referring to the side chain.) 4. Positively charged 6

Six of the 20 common amino acids Gly Ala Val 2 N 2 N 2 N ys Asp Lys 2 N 2 N 2 N ( 2 ) 4 S N 7

D. Why should we care about amino acid side chains? 1. The side chains play a major role in determining protein structure/function. 2. Example: Sickle-cell trait is caused by a valine being substituted for glutamic acid at only one position (out of ~146) in the $-chain of hemoglobin. 8

Importance of amino acid side chain structure in human health: Wild type human b has glutamic acid (Glu) at position 6 of its $-chain. Sickle-cell b has Val at position 6. The remaining 145 amino acid residues are identical! Glu Val N 6 N 6 2 3 2 3-9

III. Peptide Bond (links monomers to form a polymer) A. omment on building big molecules (a.k.a., macromolecules) 1. Essentially all biological macromolecules are polymers. Polymers are made by linking a large number of monomers together: See D. n A ö A-A-A-A-A-...-A n-2 -A n-1 -A n 2. This is like building a wall out of bricks (as opposed to from stucco). 10

3. In proteins, aa are the monomers. They are linked together by peptide bonds. Note -N-- -N---N--- repeating pattern (see below). Which is (are) the carbonyl-, which is the "-? Gly-Ala 3 - N + N Atoms shown in red are all in the same plane. omment re. nature of peptide bond. peptide bond 11

4. Nomenclature a) Two linked aa form a dipeptide (above = glycyl-alanine) b) Three form a tripeptide c) A moderate number (roughly < 30) form an oligopeptide d) A larger number form a polypeptide 12

A peptide containing 8 amino acid residues (an octomer) Full name: Valyl-istidyl-Leucyl-Threonyl-Prolyl-Glutamyl-Glutamyl-Lysine In 3 letter abbrev: Val-is-Leu-Thr-Pro-Glu-Glu-Lys In 1 letter abbrev: V--L-T-P-E-E-Y Atoms in the peptide backbone are shown in blue. + 3 N N N N N N N N - 3 2 2 2 2 2 3 3 3 2 2 2 N 3 2 N - - 2 an you locate each residue's side chain and determine whether it is non-polar, polar but not charged, acidic, or basic? N + an you make predictions about the solubility in water of each residue's side chain? 13

5. Peptides can be named by listing their aa sequence, starting from the amino terminal end. What is the amino terminal end? 6. The peptide bond exhibits resonance. What is it? (Darth Vader s voice.) a) Resonance occurs when there is more than one stable way to arrange the electrons in a molecule or ion. See next page. b) Structures with resonance often behave like something in between the different resonance forms. 14

c) Structures that exhibit resonance tend to be more stable than you would otherwise think. a a N N + a - a Peptide bond resonance: 1. All six atoms shown are in the same plane. 2. Therefore both the central and N atoms behave like they are trigonal planar, sp 2 hybridized. (right-hand structure). 3. Note that neither of the structures above provides a perfect model for all aspects of peptide bond structure/function. 15

IV. Primary (1 ) Structure of Proteins: the sequence of amino acids A. Specific proteins in your body have specific sequences. That is, every (? see below?) insulin A-chain starts with Gly the amino terminus, then Ile, etc. B. This sequence is called the primary structure of the protein. (Polymorphism? eterozygosity?) 16

V. Secondary (2 ) Structure of Proteins A. Secondary structure is regular, repetitive structure held in place by intrachain ydrogen Bonding and comes in two main forms: 1. "-helix 2. $-sheet (two forms of this): a) parallel [aligned Nö, Nö] b) anti-parallel [aligned Nö, ön] 17

B. Some generalizations: 1. Most proteins have obvious 2 structure. 2. Many proteins have more than 50% of their aa involved in 2 structure.. Specialized 2 structures exist. Example: ollagen triple helix. (proline hydroxylation and scurvy knaves.) 18

Part of the A "-helix from human b (beta chain) an you: 1) Trace the peptide backbone? 2) Find the amino terminal end? 3) Locate the ydrogen Bonds that maintain the "-helical structure? 4) Are these ydrogen Bonds perfectly aligned? Would the "-helical structure be maintained if the ydrogen Bonds were disrupted? 19

Drawing of a $-sheet R R N N N N N R R R R R R N N N N N R R an you: 1) Trace the peptide backbones? 2) Find the amino terminal ends of the backbones? 3) Is this a parallel or anti-parallel structure? 4) Are these ydrogen Bonds perfectly aligned? indicates ydrogen Bond 20

VI. Tertiary (3 ) Structure of Proteins A. Tertiary (3 ) describes the location of each of the protein s atoms in 3-D space. (Re. bends, twists, etc. in secondary structure) B. Usually, 100% of a given type of protein is in the same 3 structure (b, BSE & prions?); this is a very non-random, highly organized situation. If something is unfavorable in entropy terms ()S), there must be a significant amount of bonding ()) holding it in place. What forces maintain very non-random structures? 21

Remember: )G = )! T)S? 1. Peptide bonds (covalent) maintain 1 structure. 2. ydrogen bonds maintain 2 structure. 3. 3 structure is maintained by different amounts of a-e different proteins: a) covalent bonds (!S!S! are a common type) b) hydrogen bonds (??? re. bonds to solvent) c) ionic bonds (salt bridges) d) hydrophobic interactions (keep the inside on the inside) (actually, mostly a system )S term) omments re. ydrophobic ollapse & protein folding e) London Forces Essentially all proteins do b-e in various amounts. 22

VII. Quaternary (4 ) Structure of Proteins (requires multiple subunits) A. This describes how the subunits fit together. B. Examples of proteins with multiple subunits: 1. hemoglobin (" $ ) 2 2 2. insulin (A chain and B chain) 3. hg ($-subunit clinical importance? ) What does hg stand for? When do (& which?) humans make hg? 23

hg structure (pdb: 1hrp) "-subunit: blue; $-subunit: pale green. Red & bright green atoms are carbohydrate (sugar) molecules that are covalently attached to hg. Space-filling model Ribbon model (backbone) 2 structure is mostly $-sheet with a short "-helix in the alpha subunit. 24

VIII. Protein Structure re. to Function A. Protein structure has a massive effect on protein function. Usually alteration in structure radically alters (often destroys) protein function. B. The key to the function of most proteins is the creation of a unique environment (space) where catalysis, transport, or binding can occur. 25

IX. Myoglobin & emoglobin A. Myoglobin re. 2 storage and diffusion. 1. Myoglobin meaning: myo globin 2. Diving mammals (cetaceans) & myoglobin. See 1mbo Protein Data Bank structure. ur myoglobin is not used for 2 storage, but to increase the rate of 2 diffusion in our muscles. 26

B. emoglobin (b) and 2 & 2 transport. Maximize 2 binding & release efficiency!!! 1. b does have more than 1 stable conformation a) igh 2 affinity form: main form present in lungs (higher p). b) Low affinity form: present mostly in extremities (lower p). c) b shifts back & forth between these forms as it moves through your circulatory system. 27

This graph shows that b has different forms that have different affinity for 2. (From google images http://www.google.com/imgres?imgurl=http://3.bp.blogspot.com/_tepm5t-xssq/s5ufd4v6mni/aaaaaaaaa g/9a24hl_uta/s320/oxyhemoglobin%2bcurve.gif&imgrefurl=http://bronchialtimes.blogspot.com/2010/03/o xyhemoglobin-dissociation-curve.html&usg= li-yrxzq_9vwl97hpmwabwjg2a=&h=310&w=320&sz=45 &hl=en&start=135&zoom=1&tbnid=v8zgj_ie2edbm:&tbnh=142&tbnw=147&prev=/images%3fq%3doxyg en%2bhemoglobin%2bdissociation%2bcurve%26hl%3den%26biw%3d1280%26bih%3d839%26gbv%3d2%2 6tbs%3Disch:10%24423&itbs=1&iact=hc&vpx=1012&vpy=212&dur=8193&hovh=221&hovw=228&tx=143 &ty=93&ei=2z_ltjtjeyp98aaoj53ddq&oei=kd_ltlar4k8lqfx_y22w&esq=8&page=7&ndsp=23&ved= 1t:429,r:11,s:135&biw=1280&bih=839 8 8 tissues lungs Is all of the 2 is released as b( 2 ) 4 goes from lungs to tissues? 28

2. Logic: high affinity form binds 2 in lungs {b + 4 2 ö b( 2 ) 4 }, when b( 2 ) 4 reaches tissues, there is a shift to the low affinity form, and 2 is released {b( 2 ) 4 ö b + 4 2 }. 3. ther modifiers: bisphophoglycerate (BPG) and 2 favor formation of low affinity form. That is, they help b let go of its 2. 4. b also binds 2 (as 3! ) and transports it to the lungs for removal. 29

p Effects: from: http://www.neuroicu.info/respiratorycare.htm via gooogle images Left hand curve has a higher or lower fraction of the high-affinity b form than the right hand curve? Which part of your circulatory system would be a good match for the central curve? Which part for the right hand curve? 8 8 tissues lungs an you explain why one part of your circulatory system would be more acidic? 30

Altitude, etc. effects on 2 release from b are mediated by bisphosphoglycerate (BPG). The best figure I have found is at Univ Arizona Biochem class: http://www.google.com/imgres?imgurl=http://www.biochem.arizona.edu/classes/bioc462/462a/ntes/hemoglobin/altitude.gif&imgrefurl=http://ww w.biochem.arizona.edu/classes/bioc462/462a/ntes/hemoglobin/hemoglobin_function.htm&usg= XX4Sa3WZ2fGhQdvbNonAr4TY60=&h=348&w= 433&sz=6&hl=en&start=0&zoom=0&tbnid=Rf6x7RxmXhkM:&tbnh=101&tbnw=126&prev=/images%3Fq%3Dhemoglobin%2Bbpg%2Beffect%2Bdis sociation%2bcurve%26hl%3den%26sa%3dg%26biw%3d1280%26bih%3d839%26gbv%3d2%26tbs%3disch:1&itbs=1&iact=hc&vpx=1084&vpy=131 &dur=268&hovh=101&hovw=126&tx=93&ty=51&ei=ikfltku5b47lwejllm3w&oei=ikfltku5b47lwejllm3w&esq=1&page=1&ndsp=33&ved=1t: 429,r:6,s:0 Increasing [BPG] shifts b to which form, high-affinity for 2 or low-affinity? So BPG functions to help b. 31

uman hemoglobin Backbone: ribbons. ne heme associated w/ each subunit: cylinders. 32

. 2 transport and the fetal-maternal unit. 1. ne view: uman b is really good at binding 2, but not very good at releasing it. 2. What consequences does this have re. fetus? 3. ow do we deal with this problem? a) You didn t make much b $-chain when you were fetal. b) You made a variant of the $-chain called (. c) Therefore fetal b is " 2 ( 2. d) Fetal b has higher affinity for 2 than does adult b, in part because fetal b does not bind BPG. (So it stays in higher affinity form.) 33

Look at the myoglobin, normal hemoglobin, foetal (fetal) hemoglobin comparison figure at: http://www.s-cool.co.uk/alevel/biology/transport/blood.html 8 8 tissues lungs 34

D. Sickle ell Anemia. (bs = sickle cell hemoglobin) Thoughts from the group? 1. Small structure change = big function change 2. View structure of wild type (wt) human b. 3. ompare sequences (1 structure) of the wt (1a3n) & sickle-cell, bs, (2hbs) hemoglobin $-subunit. (Note: yellow-green and sea-foam colours represent the $-chains in the RasMol representation of 2hbs.pdb.) 35

See different pages titled: omparison of ba & bs Normal (wt) human $-hemoglobin subunit sequence: 1 6 10 Val-is-Leu-Thr-Pro-Glu-Glu-Lys-Ser-Ala-...-is 146 Sickle-cell human $-b subunit sequence: 1 6 10 Val-is-Leu-Thr-Pro-Val-Glu-Lys-Ser-Ala-...-is 146 nly one difference out of 146 aa residues!!! 36

4. ow does this change alter b and rbc function? a) Glu side chain is charged. 2 likes to be by it. b) Val side chain is non-polar. Does 2 like to be by it? Recall that ordered 2 cages are unfavorable ()S). c) During a Sickle ell crisis (favored by low P 2 ), separate bs molecules stick together to minimize Val 6 contact with water. This minimizes cage formation by 2, but bs forms insoluble polymers (all kinds of problems). bsa( 2 ) 4(aq) W bs (s) + 4 2(aq) What effect would decreasing [ 2 ] have on above equilibrium? (What percentage of b is normally in the deoxy form?) Should sickle-cell patients run wind sprints in the mountains? 37

5. Why has bs trait persisted in some populations? 6. ow different are human & chimpanzee b? 7. ow might this relate to human origins??? 38

X. Dietary Protein & Digestion (Atkins strikes again?) We can (no longer) make all of the necessary amino acids from scratch (from diet). These aa s are called (Should remind you of something?) A. They are: isoleucine leucine lysine methionine phenylalanine threonine tryptophan valine (In PKU patients?) 39

omment on high lysine corn. B. Example of an amino acid we can make: serine 3-phosphoglycerate ö 3-phosphohydroxypyruvate ö 3-phosphoserine ö serine Where in our metabolic processes is 3- phosphoglycerate produced? 40