Protein Structure Bioinformatics Introduction Basel, 27. September - PDF document

1 Swiss Institute of Bioinformatics Protein Structure Bioinformatics Introduction Basel, 27. September 2004 Biozentrum - Universität Basel Swiss Institute of Bioinformatics Torsten Schwede Klingelbergstr 50-70 CH - 4056 Basel, Switzerland Tel: +41-61 267 15 81 Torsten.Schwede@unibas.ch Introduction & Recapitulation Proteins Polypeptides Amino acids Physicochemical Properties 27.9.04 Introduction to Protein Structure Torsten Schwede

2 Introduction Three and one letter code: 27.9.04 Introduction to Protein Structure Torsten Schwede

3 Amino Acids with aliphatic Side-Chains H 3 C COO- CH 3 CH COO- CH CH + NH 3 H 3 C + NH 3 Ala (A) Val (V) H 3 C H 3 C CH 2 COO- COO- CH CH 2 CH CH CH H 3 C + H 3 C + NH 3 NH 3 Leu Ile (I) (L) Sidechains with hydroxyl (-OH) groups COO- HO CH 2 CH + NH 3 Ser (S) H 3 C pK=13 COO- CH CH HO + NH 3 Thr (T) pK=13 27.9.04 Introduction to Protein Structure Torsten Schwede

4 Sidechains containing sulphur COO- HS CH 2 CH + NH 3 Cys (C) pK=8.3 COO- H 3 C S CH 2 CH 2 CH + NH 3 Met (M) Acidic amino acids - COO- OOC CH 2 CH Asp (D) pK=3.9 + NH 3 - COO- OOC CH 2 CH 2 CH Glu (E) + pK=4.1 NH 3 27.9.04 Introduction to Protein Structure Torsten Schwede

5 Amides of acidic amino acids COO- H 2 N C CH 2 CH Asn (N) + O NH 3 COO- H 2 N C CH 2 CH 2 CH Gln (Q) + O NH 3 Basic Amino Acids COO- CH 2 CH 2 CH 2 CH HN Arg (R) + + C NH NH 3 pK=12.5 2 NH 2 COO- + NH 3 CH 2 CH 2 CH 2 CH 2 CH Lys (K) pK=10.8 + NH 3 COO- HC CH CH 2 CH His (H) + NH 3 HN N pK=6.0 C H 27.9.04 Introduction to Protein Structure Torsten Schwede

6 Side-chains with aromatic rings HC CH COO- HC C CH 2 CH Phe (F) + HC CH NH 3 HC CH COO- Tyr (Y) C CH 2 HO C CH pK=10.1 + HC CH NH 3 H C COO- C C CH 2 CH HC Trp (W) + HC C CH NH 3 C N H H Special cases … CH 2 COO- H 2 C CH Imino acid Pro (P) + H 2 C NH 2 COO- H CH Gly (G) + NH 3 27.9.04 Introduction to Protein Structure Torsten Schwede

7 Side Chain Structures Side Chain Properties Neutral Polar Glycine Serine Neutral Hydrophobic Threonine Alanine Tyrosine Valine Cysteine Leucine Asparagine Isoleucine Glutamine Proline Basic Tryptophane Lysin Phenylalanine Arginine Methionine (Histidine) Acidic Aspartic Acid Glutamic Acid 27.9.04 Introduction to Protein Structure Torsten Schwede

8 pH and pKa [ ] � pH + = − pH log H � Water ion product [ ][ ] = + − = − 14 K w H OH 10 [ ] [ ] + + − = − 14 log H log OH log 10 + = pH pOH 14 pH and pKa � Dissociation of weak acids ↔ + + − HA H A [ ][ ] [ ] + − [ ] H A HA + = = K H K [ ] [ ] a a − HA A [ ] [ ] HA + = + log H log K log [ ] a − A [ ] [ ] − A − + = − + log H log K log [ ] a HA 27.9.04 Introduction to Protein Structure Torsten Schwede

9 pH and pKa � Henderson - Hasselbach Equation [ ] − A = + pH pK log [ ] a HA pH and pKa Glycine 14 12 pK 2 10 8 pH 6 Isoelectric point 4 pK 1 2 zwitterion 0 0 0.5 1 1.5 2 +1 - added Equivalents of OH -1 NH 3 + NH 3 NH 2 + COOH COO - COO - 27.9.04 Introduction to Protein Structure Torsten Schwede

10 pH and pKa � Glu pH and pKa � Lys 27.9.04 Introduction to Protein Structure Torsten Schwede

11 pH and pKa � Enzymatic reactions often require proton transfer. � Q: Which amino-acid(s) are able to change their protonation state under physiological conditions? Why do proteins fold? MNIFEMLRID EGLRLKIYKD TEGYYTIGIG HLLTKSPSLN AAKSELDKAI GRNCNGVITK DEAEKLFNQD VDAAVRGILR NAKLKPVYDS LDAVRRCALI NMVFQMGETG VAGFTNSLRM LQQKRWDEAA VNLAKSRWYN QTPNRAKRVI TTFRTGTWDA YKNL 27.9.04 Introduction to Protein Structure Torsten Schwede

12 Anfinson’s paradigm � 1957, Nobel Prize 1972 Anfinson’s paradigm MNIFEMLRID EGLRLKIYKD TEGYYTIGIG HLLTKSPSLN AAKSELDKAI GRNCNGVITK DEAEKLFNQD VDAAVRGILR NAKLKPVYDS LDAVRRCALI NMVFQMGETG VAGFTNSLRM LQQKRWDEAA VNLAKSRWYN QTPNRAKRVI TTFRTGTWDA YKNL All the necessary information for the 3-dimensional structure of an enzyme is contained in the primary structure or sequence of the amino acids. 27.9.04 Introduction to Protein Structure Torsten Schwede

13 Levinthal's Paradox (1968) If a chain of a hundred amino acids is considered and it assumed each amino acid can exist in one of three conformations, extended, helical or loop, then there are 3 100 possible ways to arrange this chain. This is roughly 10 48 conformations. Bond rotation can be estimated to occur at a rate of roughly 10 14 s -1 . This means that search for the right conformation through random searching alone would take the order of 10 34 s or 10 26 years, several orders of magnitudes greater than the age of the universe! � [ J. Chim. Phys. , 1968 , 85 , 44] MNIFEMLRID EGLRLKIYKD TEGYYTIGIG HLLTKSPSLN AAKSELDKAI GRNCNGVITK DEAEKLFNQD VDAAVRGILR NAKLKPVYDS LDAVRRCALI NMVFQMGETG VAGFTNSLRM LQQKRWDEAA VNLAKSRWYN QTPNRAKRVI TTFRTGTWDA YKNL � Many proteins fold spontaneously to their native structure � Protein folding is relatively fast (nsec – sec) � Chaperones speed up folding, but do not alter the structure The protein sequence contains all information needed to create a correctly folded protein. 27.9.04 Introduction to Protein Structure Torsten Schwede

14 Why do proteins fold? - N - C α (HR 1 ) - CO - N - C α (HR 2 ) - CO - N - C α (HR 1 ) - CO - Side Chain Properties Neutral Polar Glycine Serine Neutral Hydrophobic Threonine Alanine Tyrosine Valine Cysteine Leucine Asparagine Isoleucine Glutamine Proline Basic Tryptophane Lysin Phenylalanine Arginine Methionine (Histidine) Acidic Aspartic Acid Glutamic Acid 27.9.04 Introduction to Protein Structure Torsten Schwede

15 Hydrophobic Effects � main driving force for protein folding Surface Definitions � Van der Waals Radius � Molecular Surface � Solvent Accessible Surface 27.9.04 Introduction to Protein Structure Torsten Schwede

16 Hydrogen Bonds � H-atoms bound to electronegative atoms (e.g. N, O) are polarized and can form H-bonds � H-bonding partners include: � main chain atoms N � side chain atoms H � water molecules � ligands, etc… O C N C Q: Do H-bonds stabilize a protein fold ? 27.9.04 Introduction to Protein Structure Torsten Schwede

17 Energetics of protein folding Energetics of protein folding H-bonds hydrophobic effects salt bridges SS - bonds ∆ G = ∆ H - T ∆ S loss of solvation entropy change dispersion / VdW contacts conformational energy � Difference of two very large energetic terms � Low overall stabilization energy Why do proteins fold? � Change of energy state from unfolded to folded � Folded state must have overall lower energy � Let’s assume the folded state is the lowest possible state for this polypeptide 27.9.04 Introduction to Protein Structure Torsten Schwede

18 Protein Sequence Space � How many different proteins are theoretically possible? � How many of these have been tested during evolution? Protein sequence space � Assuming a peptide of length 100 aa Possible combinations: n c = 20 100 ≈ 1.27 *10 130 Volume of one peptide: r atom ≈ 2Å v atom ≈ 35Å 3 packing ≈ 75% v peptide ≈ 1.3 * 10 5 Å 3 27.9.04 Introduction to Protein Structure Torsten Schwede

19 Protein sequence space � 1.27*10 130 combinations. For comparison … 3 16 Volume of the Earth: ≈ ≈ R 6.4 * 10 km 6.4 * 10 Å 4 3 51 3 = π ≈ V R 1 . 1 * 10 Å 3 51 1 . 1 * 10 Peptides/Earth: 45 ≈ ≈ n 7 . 7 * 10 p 5 1 . 3 * 10 Protein sequence space � 1.27*10 130 combinations. For comparison … Age of the Earth: 3 * 10 9 years ≈ 2.6 * 10 13 hours ≈ 9.5 * 10 16 sec ≈ 9.5 * 10 28 psec � If the whole planet consisted of peptides, and peptides were renewed every psec... ( ) ( ) 45 28 74 ≈ ≈ n 7 . 7 * 10 * 9 . 5 * 10 7 . 3 * 10 T 27.9.04 Introduction to Protein Structure Torsten Schwede

20 Protein sequence space � Assuming a peptide of length 100 aa Possible combinations: n c = 20 100 ≈ 1.27 *10 130 � If the whole planet consisted of peptides, and peptides were renewed every psec... ( ) ( ) 45 28 74 ≈ ≈ n 7 . 7 * 10 * 9 . 5 * 10 7 . 3 * 10 T ?!? 10 130 − 10 75 ≈ 10 130 Introduction & Recap Principles of Protein Structure � Primary Structure � Secondary Structure � Tertiary Structure � Quaternary Structure 27.9.04 Introduction to Protein Structure Torsten Schwede

21 Principles of protein structure Tertiary Primary Quaternary Secondary Geometry of a peptide bond H R H R 27.9.04 Introduction to Protein Structure Torsten Schwede

22 Dihedral angles Φ , Ψ , and ω Q: Which values would you you expect for ω ? ω Dihedral angles Φ and Ψ 27.9.04 Introduction to Protein Structure Torsten Schwede

23 Dihedral angles Φ and Ψ Φ = 0°, Ψ = 0° Ramachandran Plots Ψ (deg) Φ (deg) 27.9.04 Introduction to Protein Structure Torsten Schwede