Biomolecules: lecture 10

Transcription

1 Biomolecules: lecture 10 - understanding in detail how protein 3D structures form - realize that protein molecules are not static wire models but instead dynamic, where in principle every atom moves (yet maintaining the overall structure of the protein) - realize that even very small changes of atom or atom group positions in a protein molecule may cause a big difference to the function of the protein (and thus be biologically relevant)

2 Parameters for regular polypeptide conformations Ramachandran! Secondary structure f y residues/turn residue advance Pitch Right handed a helix (n+4) Å 5.4Å 3 10 helix (n+3) Å 6.0Å p-helix (n+5) Å 5.06Å Parallel b-sheet Å 6.4Å Antiparallel b-sheet Å 6.8Å random conformation regular conformation

3 Right handed α-helices nitrogen of aa 5 carbonyl oxygen of aa 1 N 1

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5 a motif (motiivi) - a supersecondary structure (a higher-order local structure formed by secondary structure elements)

6 Hydrogen bonds in anti-parallel β-sheets are stronger than those in parallel β-sheets, although the latter ones are shorter. How come? (NOTE: compare to covalent bonds, e.g. single bond vs. double bond) Reproduced from: Biochemistry by T.A. Brown, ISBN: Scion Publishing Ltd, 2017

7 Reproduced from: Biochemistry by T.A. Brown, ISBN: Scion Publishing Ltd, 2017 parallel β-sheet anti-parallel β-sheet

8 Fibroin silk, structure (Gly Ala Gly Ala Gly Ser) n has mainly antiparallel β-sheet with β-strands stacking together with close packing of side chains

9 β-sheet twists β-sheets often twist : β-strands do not line up in a strictly planar way

10 β-turns nitrogen of aa 4 carbonyl oxygen of aa 1 Allow complete reversal of polypeptide chain direction in only 4 residues

11 Adapting to a certain secondary structure depends on Amino acids differ in their ability to fulfil f, y angle combinations Side chain-side chain interactions Side chain entropy (entropy diminishes when residues are bound in a secondary structure) Steric effects (small vs. bulky side chains) Tertiary packing

12 Observations from protein structure data 1. Tightly packed hydrophobic core 2. Torsion angles adopt low energy states (Ramachandran) 3. Hydrogen bonding must be satisfied - always between amino group (donor) and carboxy group (acceptor) of the main chain Problem: - why is it so that the hydrogen bonds that keep a secondary structure together form between main chain atom groups?

13 Observations from protein structure data 4. More than 60% of residues are in regular secondary structure 5. Side chain packing patterns a) charged (orientation specific, e.g. salt bridges) b) nonpolar (random) 6. Water molecules "fill" gaps

14 Deviations usually imply a functional role Buried charged residues or non-hydrogen bonded buried polar residues are often involved in catalytic mechanisms Non-polar (hydrophobic) surface groups are often involved in protein-protein interactions > Problem: please explain! Distorted peptide bond of trypsin inhibitor cannot be cleaved by trypsin

15 Collagen, structure (Gly-X-Y)n where X and Y are usually Pro or Hyp forms a left handed supercoil. Chains are staggered so that Gly, X and Y from differing chains are level. This is a regular structure. All of the amino acids are in secondary structure. This is NOT a regular secondary structure as Gly, X and Y have different phi/psi angles. The smallest regular unit is the tripeptide.

16 Protein structures are often non-static: Protein conformation is dynamic and is dependent on environment - two structures of the same enzyme compared (one of them has a mutation which alters its dynamics) - almost identical, except one residue (W310)

17 - proteins (polypeptide chains) fold into a 3D-structure post- or co-translationally - this may be assisted by chaperones, which are proteins or other molecules - disulphide bridges may also form and be cleaved during the folding process - some proteins have large unfolded regions, but most proteins are very compact Reproduced from: Biochemistry by T.A. Brown, ISBN: Scion Publishing Ltd, 2017

18 - proteins may contain chemical groups other than the amino acids forming the polypeptide chain - these groups are mostly needed for activity prosthetic groups (non-covalently bound) ligands (covalently or non-covalently bound) coenzymes (covalently or non-covalently bound) examples: a metal ion a heme (next pages)

19 A case study: hemoglobin - contains a heme group - a prosthetic group (prosteettinen ryhmä) - heme binds the oxygen or carbon dioxide - a porphyrin ring (porfyriini) - formed from 4 pyrrole rings (pyrroli) - an iron atom as the central atom in the heme

20 deoxy Hb (blue) vs. oxy Hb (red) Problem: - using this figure and the figure on the next page, please explain what happens upon oxygen binding

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22 - hemoglobin is a tetrameric protein = forms a non-covalent complex of four individual hemoglobin molecules - 2 α-chains and 2 β-chains >> α2β2 - the conformational change upon oxygen binding by the first Hb molecule affects the conformation of the other three molecules such that they bind oxygen easier; this is called allostery (allosteria)

23 Another important property of proteins, which is made possible via conformational change: when an enzyme binds its substrate The specificity of interactions between a protein and another molecule, e.g. an enzyme and a substrate, depends on the precisely defined arrangement of atoms. For tight interactions attractive forces must be maximized and repulsive forces minimized

24 Often substrate binding is accompanied by a conformational change in the protein. This is called induced-fit binding

25 Lectures continue later with carbohydrates and lipids. Now its time to give feedback! > palaute.oulu.fi You can give feedback anytime, multiple times. - give feedback also to lab course teachers (the feedback system may not recognize individual teachers so please give feedback to them by mentioning their name on the open questions section)