Principles of Protein Structure PDF

Principles of Protein Structure Helena Kühn [email protected] Matrikelnummer: 22886106 Agenda 01 Peptide Bond 07 Protein Domains 02 Stabilization of folded proteins 08 Protein Motifs 03 Secondary Structure 09 Classes of Domain Folds 04 Tertiary Struct...

Principles of Protein Structure Helena Kühn [email protected] Matrikelnummer: 22886106 Agenda 01 Peptide Bond 07 Protein Domains 02 Stabilization of folded proteins 08 Protein Motifs 03 Secondary Structure 09 Classes of Domain Folds 04 Tertiary Structure 10 Quaternary Structure 05 Membrane Protein Structure 11 Protein flexibility 06 Protein Stability Medizinische Fakultät 03 November 2024 2 Peptide Bond Peptide bond: covalent bond between carboxylic acid and amino group Properties of peptide bond influence stability and flexibility of the chain in water Resonance: polarity and partial double-bond character of the peptide bond Coplanar rigid bonds (rotation limited) Rotable N-Cα and Cα-C bonds Φ (Phi) torsion angle Ψ (Psi) torsion angle Petsko (2004), p. 9. Medizinische Fakultät 03 November 2024 3 Peptide Bond Torsion angles and Ramachandran plot Steric constraints due to the physical size of atoms Combinations of possible phi and psi torsion angles limited Visualized with Ramachandran plot Figure: Ramachandran plot. Changdev (2015). Medizinische Fakultät 03 November 2024 4 Stabilization of folded proteins Noncovalent interactions Covalent bonds Van der Waals interaction Peptide bonds Hydrogen bond Disulfide bridges: -Cys-S-S-Cys- Salt bridge Main stabilization comes from these interactions Medizinische Fakultät 03 November 2024 5 Secondary Structure Common structural elements Beta sheets Helices Beta turns Petsko (2004), p. 17. Heinrich (2022), p. 87. Medizinische Fakultät 03 November 2024 6 Secondary Structure Alpha helix Carbonyl oxygen atom of each residue hydrogen-bonds with amide nitrogen four residues further away in the sequence Side chains on the outside  interactions with other parts of the protein or other proteins Predominantly right-handed Distance between residues: 1,5 Å Helix dipole Kadereit (2021), p. 285. Medizinische Fakultät 03 November 2024 7 Secondary Structure Alpha helix 3.6 residues per turn Hydrophobic face rotation of 100° per residue Arrangement of residues can form hydrophobic or hydrophilic faces  amphipathic alpha helix Hydrophilic face Petsko (2004), p. 15. Medizinische Fakultät 03 November 2024 8 Secondary Structure Beta sheet Parallel, antiparallel or mixed beta sheet Distance between residues: 3,3 Å Antiparallel Usually right-handed twist beta sheet Amphipathic beta sheets found on surfaces of proteins Parallel beta sheet Kadereit (2021), p. 285. Medizinische Fakultät 03 November 2024 9 Secondary Structure Amino acid tendencies Table: Examples of amino acids which are preferably found in specific structural elements. Alpha helix Beta sheet Beta turn Leucine, methionine, Valine, isoleucine, favoured glutamine and glutamic Proline, glycine phenylalanine acids disfavoured Proline, glycine Only tendencies and unreliable predictions Medizinische Fakultät 03 November 2024 10 Tertiary Structure Folding of soluble proteins Polar and charged side chains and polar peptide groups can hydrogen-bond with water  often positioned on the surface of the folded protein where they bind water Hydrophobic effect of nonpolar side chains  hydrophobic core of protein Arrangement of secondary structural elements Often long stretches of amino acids in between secondary structural elements  sites for protein recognition, ligand binding and membrane interaction Packing motifs, e.g. „ridges and grooves“ arrangement due to interdigitation of helices Figure: Interdigitation of helices. Petsko (2004), p. 23. Medizinische Fakultät 03 November 2024 11 Membrane Protein Structure Hydrophobic interior of membranes (about 30 Å) Usually with hydrophobic side chains Polar backbone carbonyl and amide groups would interact with nonpolar lipid tails  to avoid these interactions, groups hydrogen-bond each other Polar head-group layers on each side (5-10 Å) Polar side chains: on surface outside the membrane or in the core of the membrane protein Only all-helical or all-beta-barrel membrane proteins Figure: all-helical (left) and all-beta-barrel membrane proteins. Petsko (2004), p. 24-25. Medizinische Fakultät 03 November 2024 12 Protein Stability Proteins are only marginally stable  Essential for flexibility and function Table: Most common Post-Translational Modifications Reversible Irreversible Disruption of protein structure through Disulfide bridge Cofactor binding Thermal denaturation Cofactor binding proteolysis Chemical denaturation glycosylation ubiquitination phosphorylation Peptide tagging Post-Translational Modifications acylation Lysine hydroxylation ADP-ribosylation methylation  Covalent bonds  influencing stability carbamylation N-acetylation Medizinische Fakultät 03 November 2024 13 Protein Domains Globular proteins can be composed of two or more structural domains often with continuous amino acid sequence In aqueous solutions, independently expressed domains often fold stably by its own and retain parts of the biochemical function of the protein Number of protein folds limited: different sequences, but similar folding Insertion and deletion of amino acids into a surface loop  often no changes in folding Figure: Structure of alanine racemase. Petsko (2004), p. 30. Medizinische Fakultät 03 November 2024 14 Protein Motifs Two different definitions of the term motif 1. Sequence motif 2. Structural motif Particular amino acid sequence with a characteristic group of contiguous secondary structure elements or biochemical function whole domain or protein form a domain E.g. zinc finger motif in DNA-binding proteins E.g. four-helix bundle Additional distinction: Petsko (2004), p. 35. Petsko (2004), p. 34. Functional motifs: sequence or structural motif associated with a particular biochemical function Medizinische Fakultät 03 November 2024 15 Classes of Domain Folds Alpha domains Beta domains Alpha/beta domains Alpha+beta domains Cross-linked domains Medizinische Fakultät 03 November 2024 16 Classes of Domain Folds Alpha Domains Consisting entirely of alpha helices Two common motifs: Four-helix bundle Globin fold Hydrophobic pocket Myohemerythrin Myoglobin Petsko (2004), p. 36. Medizinische Fakultät 03 November 2024 17 Classes of Domain Folds Beta Domains Consisting entirely of antiparallel beta sheets with tight turns and irregular loop structures Two types of antiparallel sheet connectivity: Up-and-down structural motif Greek-key motif Neuraminidase beta- Subunit of pre-albumin Light chain of Immunoglobin propeller domain (beta barrel) (beta sandwich) Arrangements of these two types: Beta barrel Beta sandwiches: two separate beta sheets binding together Figures: Petsko (2004), p. 36-37. Medizinische Fakultät 03 November 2024 18 Classes of Domain Folds Alpha/Beta Domains Beta strands with connecting helical segments: Beta-alpha-beta-alpha motif Parallel or mixed strands Two major motifs: Alpha/beta barrel Alpha/beta twist TIM barrel (triosephosphate Asparate semi-aldehyde isomerase) dehydrogenase Petsko (2004), p. 38. Medizinische Fakultät 03 November 2024 19 Classes of Domain Folds Alpha+beta Domains Separate beta sheet and alpha helix motifs No special organizing principles Beta sheets often antiparallel or mixed Figure: TATA Box. Petsko (2004), p. 39. Medizinische Fakultät 03 November 2024 20 Classes of Domain Folds Cross-Linked Domains Little or none secondary structure Stabilization through disulfide bridges (extracellular) or metal ion (intracellular) Disulfide-linked protein (scorpion toxin) Metal ion cross-linked domain (zinc finger) Petsko (2004), p. 39. Medizinische Fakultät 03 November 2024 21 Quaternary Structure Proteins with multiple polypeptide chains (monomers)  dimers, trimers, tetramers, … Hetero-oligomers or homo-oligomers Symmetry of proteins with identical subunits Complementarity necessary for intermolecular interactions Stabilization of intermolecular interfaces: hydrophobic interactions hydrogen bonds salt bridges Sometimes cross-linking interactions Petsko (2004), p. 45. Medizinische Fakultät 03 November 2024 22 Protein Flexibility Types of protein motions: 1. Fluctuations, e.g. atomic vibrations 2. Collective motions of bonded and non-bonded neighbouring groups of atoms, e.g. Flipping of an aromatic ring Domain movement 3. Ligand-induced conformational changes Figure: Triosephosphate isomerase: ligand binding to active site causes movement of loop (red: open) which lays over the active side (blue: closed). Petsko (2004), p. 46. Medizinische Fakultät 03 November 2024 23 References Petsko G, Ringe D (2004). Protein Structure and Function. New Science Press, p. 8-47. Berg JM, Tymoczko JL, Stryer L (2013). Stryer Biochemie. Berlin. Heidelberg: Springer. Figures: Petsko G, Ringe D (2004). Protein Structure and Function. New Science Press, p. 8-47. Changdev G. Gadhe, Anand Balupuri & Seung Joo Cho (2015): In silico characterization of binding mode of CCR8 inhibitor: homology modeling, docking and membrane based MD simulation study, Journal of Biomolecular Structure and Dynamics, DOI: 10.1080/07391102.2014.1002006 Kadereit JW, Körner C, Nick P, Sonnewald U (2021). Strasburger – Lehrbuch der Pflanzenwissenschaften. Springer Berlin Heidelberg, p. 285. Heinrich P, Ed. (2022). Löffler/Petrides Biochemie und Pathobiochemie. Springer Berlin, Heidelberg, p. 87. Medizinische Fakultät 03 November 2024 24 Take-home messages 1. Stability and flexibility of peptide chains are influenced by resonance, coplanar rigid bonds and rotable N-Cα and Cα-C bonds. 2. Mainly noncovalent interactions (especially van der Waals interactions, hydrogen bonds, salt bridges), but also covalent bonds (especially peptide bonds, disulfide bridges) stabilize folded proteins. 3. While polar and charged side chains are often found on the protein surface where they can bind water, nonpolar side chains build the hydrophobic core of the protein. 4. Loops of amino acids in between the secondary structural elements often serve as sites for protein recognition, ligand binding and membrane interaction. 5. Proteins are only marginally stable (essential for flexibility and function). 6. The five classes of domain folds are alpha domains, beta domains, alpha/beta domains (Beta-alpha-beta-alpha motif), alpha+beta domains (separate beta sheet and alpha helix motifs) and cross-linked domains (with disulfide bridges or metal ion). 7. Protein motions like fluctuations, collective motions of bonded and non-bonded neighbouring groups of atoms and ligand-induced conformational changes influence the flexibility of proteins Medizinische Fakultät 03 November 2024 25 Take-home messages Representative protein structure Structure of triosephosphate isomerase (TIM): Example of an alpha/beta domain composed of eight beta strands (blue) with eight connecting helical segments (red) forming a closed barrel. Petsko (2004), p. 38. Medizinische Fakultät 03 November 2024 26 Thank you for your attention!