Structure-Function Analysis 11 Jan DNA/Protein structure-function analysis and prediction Basics of Protein Structure: –Short Introduction to Molecular Structures –“Introduction to Protein Structure” Chapters 1 to 5 Carl Branden & John Tooze ISBN: (recommended)‏

Structure-Function Analysis 11 Jan DNA/Protein structure-function analysis and prediction Basics of Protein Structure: –The building blocks (Ch. 1)‏ –Motifs of protein structure (Ch. 2)‏ –Alpha domain structures (Ch. 3)‏ –Alpha/Beta structures (Ch. 4)‏ –Beta structures (Ch. 5)‏

Structure-Function Analysis 11 Jan Prelude: molecular structures John Dalton (1810) A new system of chemistry Elements, but no structures yet Mendeljev (1869)‏

Structure-Function Analysis 11 Jan Johannes van ’t Hoff Chimie dans l’Espace “Proposal for the development of three-dimensional chemical structural formulae” (1875)‏ Tetraedrical carbon atom

Structure-Function Analysis 11 Jan Linus Pauling (1951)‏ Atomic Coordinates and Structure Factors for Two Helical Configurations of Polypeptide Chains Alpha-helix

Structure-Function Analysis 11 Jan James Watson & Francis Crick (1953)‏ Molecular structure of nucleic acids

Structure-Function Analysis 11 Jan James Watson & Francis Crick (1953)‏ Molecular structure of nucleic acids

Structure-Function Analysis 11 Jan DNA/Protein structure-function analysis and prediction Basics of Protein Structure: –The building blocks (Ch. 1)‏ –Motifs of protein structure (Ch. 2)‏ –Alpha domain structures (Ch. 3)‏ –Alpha/Beta structures (Ch. 4)‏ –Beta structures (Ch. 5)‏ Chains of aminoacids Three-dimensional Structures Four levels of protein architecture Aminoacids: classes Disulphide bridges Histidine Proline Ramachandran plot

Structure-Function Analysis 11 Jan The Building Blocks (proteins) Proteins consist of chains of aminoacids Bound together through the peptide bond Special folding of the chain yields structure Structure determines the function

Structure-Function Analysis 11 Jan Chains of aminoacids

Structure-Function Analysis 11 Jan Three-dimensional Structures Four levels of protein architecture

Structure-Function Analysis 11 Jan Aminoacids: klassen Hydrophobic aminoacids AlanineAlaAValineValV PhenylalaninePheFIsoleucineIleI LeucineLeuLProlineProP MethionineMetM Charged aminoacids Aspartate (-)AspDGlutamate (-)GluE Lysine (+)LysKArginine (+)ArgR Polar aminoacids SerineSerSThreonineThrT TyrosineTyrYCysteineCysC AsparagineAsnNGlutamineGlnQ HistidineHisHTryptophaneTrpW Glycine (sidechain is only a hydrogen)‏ GlycineGlyG

Structure-Function Analysis 11 Jan Disulphide bridges Two cysteines can form disulphide bridges Anchoring of secundary structure elements

Structure-Function Analysis 11 Jan Histidine Histidine has a pK value ~6.5 Also different forms possible Important for formation of H-bond networks

Structure-Function Analysis 11 Jan Proline Restricts flexibility of the backbone “Misses” the backbone hydrogen (N-H): –Structure-breaker

Structure-Function Analysis 11 Jan Ramachandran plot Only certain combinations of values of phi (  and psi (  angles are observed phi psi omega

Structure-Function Analysis 11 Jan DNA/Protein structure-function analysis and prediction Basics of Protein Structure: –The building blocks (Ch. 1)‏ –Motifs of protein structure (Ch. 2)‏ –Alpha domain structures (Ch. 3)‏ –Alpha/Beta structures (Ch. 4)‏ –Beta structures (Ch. 5)‏ Secundary structure elements Renderings of proteins Alpha helix Beta-strands & sheets Turns and motifs Domains formed by motifs

Structure-Function Analysis 11 Jan Motifs of protein structure Global structural characteristics: –Outside hydrophylic, inside hydrophobic (unless…)‏ –Often globular form (unless…)‏ Artymiuk et al, Structure of Hen Egg White Lysozyme (1981)‏

Structure-Function Analysis 11 Jan Secundary structure elements Alpha-helix Beta-strand

Structure-Function Analysis 11 Jan Renderings of proteins Irving Geis:

Structure-Function Analysis 11 Jan Renderings of proteins Jane Richardson:

Structure-Function Analysis 11 Jan Alpha helix Hydrogen bond: from N-H at position n, to C=O at position n-4 (‘n-n+4’)‏

Structure-Function Analysis 11 Jan Other helices Alternative helices are also possible –3 10 -helix: hydrogen bond from N-H at position n, to C=O at position n-3 Bigger chance of bad contacts –  -helix: hydrogen bond from N-H at position n, to C=O at position n-4 –  -helix: hydrogen bond from N-H at position n, to C=O at position n-5 structure more open: no contacts Hollow in the middle too small for e.g. water At the edge of the Ramachandran plot

Structure-Function Analysis 11 Jan Helices Backbone hydrogenbridges form the structure –Directed through hydrophobic center of protein Sidechains point outwards –Possibly: one side hydrophobic, one side hydrophylic

Structure-Function Analysis 11 Jan Beta-strands: beta-sheets Beta-strands next to each other form hydrogen bridges

Structure-Function Analysis 11 Jan Parallel or Antiparallel sheets Anti-parallel Parallel Usually only parallel or anti-parallel Occasionally mixed Sidechains alternating

Structure-Function Analysis 11 Jan Turns and motifs Between the secundary structure elements are loops Very short loops between twee  -strands: turn Different secundary structure elementen often appear together: motifs –Helix-turn-helix –Calcium binding motif –Hairpin –Greek key motif –  -motif

Structure-Function Analysis 11 Jan Helix-turn-helix motif Helix-turn-helix important for DNA recognition by proteins EF-hand: calcium binding motif

Structure-Function Analysis 11 Jan Hairpin / Greek key motif Different possible hairpins : type I/II Greek key: anti-parallel beta-sheets

Structure-Function Analysis 11 Jan  motif Most common way to obtain parallel  -sheets Usually the motif is ‘right- handed’

Structure-Function Analysis 11 Jan Domains formed by motifs Within protein different domains can be identified –For example: ligand binding domain DNA binding domain Catalytic domain Domains are built from motifs of secondary structure elements

Structure-Function Analysis 11 Jan Summary Aminoacids form polypeptide chains Chains fold into three-dimensional structure Specific backbone angles are permitted or not: Ramachandran plot Secundary structure elements:  -helix,  -sheet Common structural motifs: Helix-turn-helix, Calcium binding motif, Hairpin, Greek key motif,  -motif Combination of elements and motifs: tertiary structure Many protein structures available: PDB

Structure-Function Analysis 11 Jan Pauze

Structure-Function Analysis 11 Jan DNA/Protein structure-function analysis and prediction Basics of Protein Structure: –The building blocks (Ch. 1)‏ –Motifs of protein structure (Ch. 2)‏ –Alpha domain structures (Ch. 3)‏ –Alpha/Beta structures (Ch. 4)‏ –Beta structures (Ch. 5)‏ Coiled coil Four helix bundle Globin fold

Structure-Function Analysis 11 Jan  -domains Common  -domains Coiled coil Four helix bundleGlobin fold

Structure-Function Analysis 11 Jan Coiled coil Two helices twisted around each other –residues per turn 3.6  3.5 –heptad repeat a-b-c-d-e-f-g –hydrophobic center lined with ionic interactions

Structure-Function Analysis 11 Jan Coiled coil: knobs in holes backbone of two helices parallel put ‘d’ residues side by side residues ‘a’ and ‘d’ of helix 1 fit into hollows in helix 2 results in ~18 degree angle(calculate!)‏

Structure-Function Analysis 11 Jan Four helix bundle hydrophobic residues packed close together sequential helices against each other sometimes two coiled coils: knobs-in-holes

Structure-Function Analysis 11 Jan Four helix bundle: ridges in grooves Group aminoacids and recognize lines Fit these lines onto each other results in 60 or 20 degree angle (calculate)‏ –Depends strongly on helical parameters n,n+4n,n+3

Structure-Function Analysis 11 Jan Globin fold Common theme 8 helices (ABCDEFGH), short loops Still much variation (16 – 99 % similarity)‏ –Helix length –Exact position –Shift through the ridges

Structure-Function Analysis 11 Jan DNA/Protein structure-function analysis and prediction Basics of Protein Structure: –The building blocks (Ch. 1)‏ –Motifs of protein structure (Ch. 2)‏ –Alpha domain structures (Ch. 3)‏ –Alpha/Beta structures (Ch. 4)‏ –Beta structures (Ch. 5)‏ Different  -  -  groups Alpha/beta barrels Horseshoe fold Twisted open-sheet structures Predicting location of active site

Structure-Function Analysis 11 Jan Alpha/beta structures BarrelOpen twisted sheet Horseshoe fold

Structure-Function Analysis 11 Jan Different  groups barrels / horseshoeopen twisted sheet

Structure-Function Analysis 11 Jan Alpha/beta barrels TIM barrel after triosephosphate isomerase Usually 8  -strands, at least 200 aminoacids Often hydrophobic interior –alternating aminoacids in the strands

Structure-Function Analysis 11 Jan Alpha/beta barrels Active site formed by (variable) loop regions at top of the barrel Exception: in the core of methylmalonyl-coenzyme A mutase

Structure-Function Analysis 11 Jan Horseshoe fold Repetetive sequenties (20 aminoacids)‏ Leucine-containing Found in about 60 proteins

Structure-Function Analysis 11 Jan Twisted open-sheet structures Helices at both sides of the sheet Active site is usually found at junction of the sheet Much variation in structures

Structure-Function Analysis 11 Jan Predicting location of active site When sequence of the strands is broken, usually a crevice, which often contains the active site

Structure-Function Analysis 11 Jan DNA/Protein structure-function analysis and prediction Basics of Protein Structure: –The building blocks (Ch. 1)‏ –Motifs of protein structure (Ch. 2)‏ –Alpha domain structures (Ch. 3)‏ –Alpha/Beta structures (Ch. 4)‏ –Beta structures (Ch. 5)‏ Up-and-down barrels Greek key barrels Jelly-roll barrels Propeller structures Beta-helices Compare parallel sheets

Structure-Function Analysis 11 Jan Beta structures barrels –up-and-down barrels –greek key barrels –jelly roll barrels propeller like structure beta helix

Structure-Function Analysis 11 Jan Up-and-down barrels Relatively simple structure Aminoacids alternating hydrophobic / hydrophilic –inside – outside Example retinol binding protein But also OmpX P2 family: 10 strands

Structure-Function Analysis 11 Jan Greek key barrels Greek key motif occurs also in barrels –two greek keys (  crystallin)‏ –combination greek key / up-and-down

Structure-Function Analysis 11 Jan Jelly-roll barrels Kind of mega-greek key motif well vaak distorted structures als twee sheets

Structure-Function Analysis 11 Jan Propeller structures Different sheets together form a ‘propellor’ Active site in the middle top (or bottom) of the propellor

Structure-Function Analysis 11 Jan Beta-helices Yet another way of obtaining parallel beta-sheets

Structure-Function Analysis 11 Jan Compare parallel sheets beta-loop-alpha-loop-beta becomes beta-loop-beta-loop-beta In  /  -barrel helices at 20 degrees (ridges & grooves)‏ –sheets also at 20 graden In beta-helix strands really parallel

Structure-Function Analysis 11 Jan Summary Alpha domains –coiled coil (knobs-in-holes)‏ –four helix bundle –globin fold(ridges & grooves)‏ Alpha/beta structures –  /  barrel –twisted open sheet –horseshoe fold Beta structures –  -barrels: up-and-down, greek key, jelly roll –propeller like structures –beta-helix

Structure-Function Analysis 11 Jan Overview Aminoacids – Chains – Structure – Motifs – Domains Specific backbone angles are permitted or not: Ramachandran plot Secundary structure elements:  -helix,  -sheet Common structural motifs: Helix-turn-helix, Calcium binding,  -hairpin, Greek key,  Combination of elements and motifs: tertiary structure Alpha domains coiled coil, four helix bundle, globin fold Alpha/beta structures  /  barrel, twisted open sheet, horseshoe fold Beta structures  -barrels, propeller-like structures, beta-helix

Structure-Function Analysis 11 Jan