Τάσος Οικονόµου ιαλεξη 8 Kινηση, λειτουργια, ελεγχος http://ecoserver.imbb.forth.gr/bio321.htm
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Cell
The peptide bond
Polypeptides are stabilized by: 1. Covalent bonds= amide bond 2. Noncovalent, weakly polar interactions 3. Covalent bonds= disulfide bridges
In the absence of water, C=O and N-H bond between them and stabilize regular structures=secondary structure
Secondary structure elements = F and Y torsion angles of the backbone repeat in regular patterns
Surface water is important for 3D structure
Integral membrane proteins in a lipid bilayer membrane (plasma)
Folded protein as thermodynamic comrpomise Free energy difference between protein folded and unfolded states is: 20-40 kj/mol
Proteins can be easily unfolded 1. Temperature 2. Mutations (ts) 3. Chaotropes 4. Detergents
Noncovalent, weakly polar interactions form and break. This allows polypeptides to be flexible, to breath and water to enter the structure
Covalent bonds add stability to polypeptide structures
Post-translational modifications can alter structure/stability
Domain= autonomous structure
Domains can be discontinuous Alanine racemase
Multi-Domain proteins derive form gene duplications-fusions-insertions Thioesterase Thioester dehydrase 2 identical domains/1 gene homodimer/1 gene
In evolution domains maintain their secondary structure framework but allow changes of their connecting loops
Proteins are flexible molecules
Conformational fluctuations - Transitions form one folding pattern to another are rare - Ligand bind can stabilize disordered structures - Ligand binding rarely destabilizes ordered structures - Polypeptide subunts may associate/ dissociate upon ligand binding
Motions of internal/external protein atoms External >1A Internal <1A flexible rigid
Protein motions involve bonded and nonbonded groups
Proteins may have distinct alternate states T4 lysozyme
Optimal balance of rigidity/flexibility is essential for catalysis GAPDH yeast Thermotoga
Ligand-triggered conformational changes Aspartate aminotransferase
Lid-like movement over ligand site Text Mobile Lid Triosephosphate isomerase
Ligands can drive large-scale conformational changes AMP AMP AMP-PNP Adenyate kinase
Protein surface properties and binding sites
Proteins work by binding other molecules
Binding occurs because of steric and charge complementarity
Protein-ligand complementarity Anthrax toxin MAPKK-2 aminoterminal peptide
Protein binding site nomenclature: 1. Ligand-binding sites (molecular recongition only) 2. Active sites (molecular recongition and catalysis)
Proteins adapt to their ligands Protein kinase A+peptide analogue
Protein flexibility/adaptability explains efficiency of some drugs HIV protease haloperidol crixivan Natural peptide
Proteins can bind ligands with a wide range of affinities Low K D = 10-3 M High K D = 10-12 M
Binding sites for macromolecules can be multiple
Binding sites for macromolecules: protruding helix fits into DNA grooves
Binding sites for macromolecules: 1. Large contiguous surface (>100 A2) 2. Multiple surfaces 3. Protruding loops or cavities or flat surfaces
Binding sites for small molecules: Clefts, pockets, cavities
Catalytic sites often occur at domain and subunit interfaces 3 isopropylmalate dehydrogenase NADPH
Binding sites frequently have exposed hydrophobic surfaces Cytochrome c6 Haeme binding pocket
Interaction domains control protein flow
Ligand binding controls protein function competitive
Ligand binding controls protein function cooperative
Ligand binding controls protein function cooperative
Ligand binding can cause conformational changes at distant sites
Allosteric effectors Allosteric inhibitors
Transcarbamoylase An allosteric enzyme Carbamoyl phosphate aspartate
Protein nucleotide switches control signalling and motions
G-proteinSwitching mechanism
G-protein Switching mechanism is controlled by other proteins
G-proteins
DNA polymerase replication factory
Cell division: the FtsZ ring
Helicases