Protein Structure Bioinformatics Introduction Basel, 27. September - - PDF document
1 Swiss Institute of Bioinformatics Protein Structure Bioinformatics Introduction Basel, 27. September 2004 Biozentrum - Universitt Basel Swiss Institute of Bioinformatics Torsten Schwede Klingelbergstr 50-70 CH - 4056 Basel, Switzerland
27.9.04 Introduction to Protein Structure Torsten Schwede 1
Swiss Institute of Bioinformatics
Protein Structure Bioinformatics Introduction
Basel, 27. September 2004
Biozentrum - Universität Basel Swiss Institute of Bioinformatics Klingelbergstr 50-70 CH - 4056 Basel, Switzerland Tel: +41-61 267 15 81 Torsten.Schwede@unibas.ch
Torsten Schwede
Introduction & Recapitulation Proteins Polypeptides Amino acids Physicochemical Properties
27.9.04 Introduction to Protein Structure Torsten Schwede 2
Introduction Three and one letter code:
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NH3
+
COO- CH CH H3C H3C CH2
Ala (A) Val (V) Leu (L) Ile (I)
NH3
+
COO- CH CH3 NH3
+
COO- CH CH H3C H3C NH3
+
COO- CH CH H3C H3C CH2
Amino Acids with aliphatic Side-Chains
Ser (S) pK=13 Thr (T) pK=13 NH3
+
COO- CH CH2 HO H3C NH3
+
COO- CH HO CH
Sidechains with hydroxyl (-OH) groups
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Cys (C) pK=8.3 Met (M) NH3
+
COO- CH CH2 HS H3C NH3
+
COO- CH CH2 CH2 S
Sidechains containing sulphur
Asp (D) pK=3.9 Glu (E) pK=4.1 NH3
+
COO- CH CH2 CH2 OOC
+
COO- CH CH2 OOC
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Asn (N) Gln (Q) NH3
+
COO- CH CH2 H2N C O NH3
+
COO- CH CH2 CH2 H2N C O
Amides of acidic amino acids
Arg (R) pK=12.5 Lys (K) pK=10.8 His (H) pK=6.0 CH2 CH2 CH2 NH3
+
COO- CH CH2 NH3
+
CH2 NH3
+
COO- CH HN CH HC N C H HN NH3
+
COO- CH CH2 CH2 CH2 C NH NH
2 2 +
Basic Amino Acids
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Phe (F) Tyr (Y) pK=10.1 Trp (W) NH3
+
COO- CH CH2 CH HC CH HC C HC NH3
+
COO- CH CH2 CH HC CH HC C C HO C H C H N H HC HC C C CH C NH3
+
COO- CH CH2
Side-chains with aromatic rings
Imino acid Pro (P) NH2
+
COO- CH CH2 H2C H2C Gly (G) NH3
+
COO- CH H
Special cases …
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Side Chain Structures
Neutral Hydrophobic Alanine Valine Leucine Isoleucine Proline Tryptophane Phenylalanine Methionine Neutral Polar Glycine Serine Threonine Tyrosine Cysteine Asparagine Glutamine Acidic Aspartic Acid Glutamic Acid Basic Lysin Arginine (Histidine)
Side Chain Properties
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pH and pKa pH Water ion product
[ ]
+
− = H pH log
[ ][ ] [ ] [ ]
14 10 log log log 10
14 14
= + = + = =
− − + − − +
pOH pH OH H OH H Kw
[ ][ ]
[ ]
[ ]
[ ]
[ ] [ ]
[ ]
[ ] [ ] [ ]
[ ]
HA A K H A HA K H A HA K H HA A H K A H HA
a a a a − + − + − + − + − +
+ − = − + = = = + ↔ log log log log log log
pH and pKa Dissociation of weak acids
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HA A log pK pH
a −
+ =
pH and pKa Henderson - Hasselbach Equation
2 4 6 8 10 12 14 0.5 1 1.5 2
Equivalents of OH
pH pK1 pK2 Isoelectric point
Glycine NH3
+
COOH NH3
+
COO- NH2 COO- zwitterion +1
pH and pKa
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pH and pKa Glu pH and pKa Lys
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pH and pKa Enzymatic reactions often require proton transfer.
Q: Which amino-acid(s) are able to change their protonation state under physiological conditions?
MNIFEMLRID EGLRLKIYKD TEGYYTIGIG HLLTKSPSLN AAKSELDKAI GRNCNGVITK DEAEKLFNQD VDAAVRGILR NAKLKPVYDS LDAVRRCALI NMVFQMGETG VAGFTNSLRM LQQKRWDEAA VNLAKSRWYN QTPNRAKRVI TTFRTGTWDA YKNL
Why do proteins fold?
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Anfinson’s paradigm
1957, Nobel Prize 1972 All the necessary information for the 3-dimensional structure of an enzyme is contained in the primary structure or sequence of the amino acids.
MNIFEMLRID EGLRLKIYKD TEGYYTIGIG HLLTKSPSLN AAKSELDKAI GRNCNGVITK DEAEKLFNQD VDAAVRGILR NAKLKPVYDS LDAVRRCALI NMVFQMGETG VAGFTNSLRM LQQKRWDEAA VNLAKSRWYN QTPNRAKRVI TTFRTGTWDA YKNL
Anfinson’s paradigm
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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 3100 possible ways to arrange this chain. This is roughly 1048 conformations. Bond rotation can be estimated to
conformation through random searching alone would take the order of 1034s or 1026 years, several orders of magnitudes greater than the age
Levinthal's Paradox (1968)
The protein sequence contains all information needed to create a correctly folded protein.
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
MNIFEMLRID EGLRLKIYKD TEGYYTIGIG HLLTKSPSLN AAKSELDKAI GRNCNGVITK DEAEKLFNQD VDAAVRGILR NAKLKPVYDS LDAVRRCALI NMVFQMGETG VAGFTNSLRM LQQKRWDEAA VNLAKSRWYN QTPNRAKRVI TTFRTGTWDA YKNL
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Why do proteins fold?
Neutral Hydrophobic Alanine Valine Leucine Isoleucine Proline Tryptophane Phenylalanine Methionine Neutral Polar Glycine Serine Threonine Tyrosine Cysteine Asparagine Glutamine Acidic Aspartic Acid Glutamic Acid Basic Lysin Arginine (Histidine)
Side Chain Properties
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Hydrophobic Effects
main driving force for protein folding
Surface Definitions Van der Waals Radius Molecular Surface Solvent Accessible Surface
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H-atoms bound to electronegative atoms (e.g. N, O) are polarized and can form H-bonds H-bonding partners include: main chain atoms side chain atoms water molecules ligands, etc…
Hydrogen Bonds
N O C C N H Q: Do H-bonds stabilize a protein fold ?
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Energetics of protein folding H-bonds hydrophobic effects salt bridges SS - bonds loss of solvation entropy change dispersion / VdW contacts conformational energy
∆G = ∆H - T∆S
Energetics of protein folding
Difference of two very large energetic terms Low overall stabilization energy 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
Why do proteins fold?
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Protein Sequence Space How many different proteins are theoretically possible? How many of these have been tested during evolution?
Possible combinations: nc = 20100 ≈ 1.27 *10130
Protein sequence space
Assuming a peptide of length 100 aa
Volume of one peptide: ratom ≈ 2Å
vatom ≈ 35Å3 packing ≈ 75% vpeptide ≈ 1.3 * 105 Å3
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Peptides/Earth:
45 5 51 p
10 * 7 . 7 10 * 3 . 1 10 * 1 . 1 n ≈ ≈
Protein sequence space
1.27*10130 combinations. For comparison … Volume of the Earth:
3 51 3 3 4 16 3
Å 10 * 1 . 1 R V Å 10 * 6.4 km 10 * 6.4 R ≈ π = ≈ ≈
( ) ( )
74 28 45 T
10 * 3 . 7 10 * 5 . 9 * 10 * 7 . 7 n ≈ ≈
Protein sequence space
1.27*10130 combinations. For comparison … If the whole planet consisted of peptides, and peptides were renewed every psec... Age of the Earth: 3 * 109 years ≈ 2.6 * 1013hours
≈ 9.5 * 1016 sec ≈ 9.5 * 1028 psec
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Protein sequence space
Assuming a peptide of length 100 aa
If the whole planet consisted of peptides, and peptides were renewed every psec...
10130 − 1075 ≈ 10130 ( ) ( )
74 28 45 T
10 * 3 . 7 10 * 5 . 9 * 10 * 7 . 7 n ≈ ≈
Possible combinations: nc = 20100 ≈ 1.27 *10130
Introduction & Recap Principles of Protein Structure Primary Structure Secondary Structure Tertiary Structure Quaternary Structure
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Principles of protein structure
Primary Secondary Tertiary Quaternary
H R R H
Geometry of a peptide bond
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Dihedral angles
ω
Q: Which values would you you expect for ω?
Φ, Ψ, and ω
Dihedral angles Φ and Ψ
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Dihedral angles Φ and Ψ
Φ = 0°, Ψ = 0°
Ramachandran Plots
Φ (deg) Ψ (deg)
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Ramachandran Plots
Φ (deg) Ψ (deg)
Amino acid preferences Alanine and Arginine
ALA ARG
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Amino acid preferences
Amino acid with special preferences:
GLY PRO
Alpha helices
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Beta strands / beta sheets Anti-parallel beta sheet
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Parallel and anti-parallel beta sheets
Left-handed twist in beta-sheets
Bovine pancreatic trypsin inhibitor
0° - 30° per aa
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Turns and loops
Schematic diagram showing the interresidue backbone hydrogen bonds that stabilize the reversal of the chain direction. Side chains are depicted as large light purple spheres. Due to the tight geometry of the turn, some residues are found more commonly in turns than
Turns and loops Hairpin loops
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Conformational Preferences
Biochimica et Biophysica Acta 916: 200-204 (1987).
RT
Protein Structure / Fold Databases
PDB: http://www.pdb.org EBI-MSD http://www.ebi.ac.uk/msd
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PDB Holdings PDB Holdings
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PDB Growth
Pair wise protein structure comparison
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Pair wise protein structure comparison
Root mean square deviation
Comparing two structures A and B Ri,A = Position of atom i in structure A n = Number of equivalent atoms
n R R d s m r
n i B i A i
=
− =
2 , ,
) ( . . . .
RMSD Comparing two structures
n R R d s m r
n i B i A i
∑
=
− =
2 , ,
) ( . . . .
Min:
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RMSD Comparing two structures References
Garland Publishing. P.E.Bourne, H. Weissig. Structural Bioinformatics, Wiley- Liss and Sons. G.A. Petsko, D. Ringe. Protein Structure and Function, New Science Press.