3 … i i+1 i+2 C±C± C±C± C±C± The ï¢...
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The (extended) conformationGeneral shape
Ctop viewside viewNThe (extended) conformationHydrogen bonds
The conformationSome facts and statistics:~30% of globular proteinsStrands lie side by side to form a sheetUp to about10 residues per strand3 rise per residueSidechains project upwards and downwardsMain-chain amides and carbonyls of different strands H-bond to reduce polarity
The sheet has a ~30 right twistThe sheet can be parallel, anti-parallel (-meander) or mixed (only 20% of sheets)Backbone amide-carbonyl H-bonds occur between strands
The (extended) conformationStructural motifs-- motifTwisted -sheet (thioredoxin)
The (extended) conformationStructural motifs-barrel
Why are helices and sheets so common?The energy change (in kcal/mol) of transferring a charged sphere from water into a hydrophobic environment:E = El Ew = 166 (q2/r) (1/l - 1/w)
cWhy are helices and sheets so common?
Why build helices and sheets?By pairing polar main-chain amide and carbonyl groups in H-bonds, helices/sheets electrostatically mask them from the hydrophobic core of the proteinDisruption of one H-bond in the protein core: +5.3 kcal/mol (Ben-Tal et al, 1996)
Disruption of 20 H-bonds (average helix): +106 kcal/molSince the proteins are only marginally stable (5-20 kcal/mol), this means the disruption of protein structure!
Reverse turns and loops-turns locations-turn structureLoops
LoopsConnect secondary structure elements that create the hydrophobic core of the proteinUsually hydrophilic and face the outside of the proteinHydrophilic nature results from polar residues and fewer satisfied main-chain H-bondsOften create binding/active sites of receptors and enzymes
Secondary elements are more ordered than loops
FibrousGlobularTwo types of proteins
UnfoldedFoldedFolded globular proteins have nonpolar core and overall polar surface
Globular proteins play different roles in numerous and diverse cellular activities (enzymes, transporters, immune, and regulatory proteins)This requires some properties that can only be conferred by the globular shape
The globular shape allows secondary structures to go in different directions This allows the protein to achieve:Compactness (an advantage in the extremely dense cytoplasm)Keeping hydrophilic residues outside (confers water solubility) while maximizing the burial of hydrophobic partsEasy for creating binding sites (cavities)Allows the joining of functional residues that are separated by sequence
Creation of binding site from residues separated by sequence
Some basic characteristics of tertiary structureInteractions that stabilize 3D structure:Covalent interactions (disulfide) less frequent because they limit protein dynamicsNon-covalent vdW, electrostatic (ionic, H-bond), non-polar (hydrophobic)[reversible, confer specificity and allow dynamics]
The Ca2+-binding EF-hand motif (Lewit-Bentely and Rety (2000))Ca2+ is involved in many signaling pathways in the cell, as well as in muscle contractionCa2+ works by binding to signaling proteins (e.g. calmodulin) and inducing conformational changes that allow further binding to other signaling proteinsHelical motifs: helix-turn-helix
abHelical motifs: helix-turn-helixEF-hand (Ca2+ binding)
The Ca2+ binding motifs in proteins are of limited configurationsThe most common motif is the EF hand, adopted also by bacteriaThis motif was first discovered in the muscle protein Parvalbumin (Krestinger)1.1 Helix-loop-helix (HLH) motifsThe motif is formed by the 5th and 6th helices (termed E, F) in parvalbumin, hence the nameBased on this structure and the sequence constraints emerging from it, Krestinger predicted EF hand motifs in troponin C and calmodulin, which were later confirmed
The hand analogy describes both the fold (helix-loop-helix) and the motion induced by Ca2+ binding (a)The Ca2+-binding loop usually includes 12 residues with the pattern XYZGYXZ, where X, Y, Z, X, Y and Z are the ligands that participate in metal coordination (b) and marks any amino acidIn Parvalbumin, Ca2+is coordinated by the carboxylate sidechains of 5 residues (Asp/Glu), by main-chain carbonyl groups and by H2O The 6th residue of the loop is Gly, preventing disturbance to the structureX, Y: ~ D/NZ: ~ D/N/S-Y:~peptide carbonyl-X:~ water-Z:~E/D
Some EF-hand motifs cannot bind Ca2+ (e.g. p11). In these, the EF-hand conformation is maintained in the open (analogous to Ca2+-loaded) form by a network of H-bonds (c)The motif is detected in small proteins (e.g. calmodulin), or within the domains of larger proteins (e.g. myosin or calpain)EF-hand motifs usually occur in pairs (two, or four in a dimer), with cooperative binding
cdCa2+FreeBoundmyosin light chainHelical motifs: helix-turn-helixThe EF-hand motif in calmodulin (CaM)
efHelical motifs: helix-turn-helixThe EF-hand motif in CaM
DNA-binding proteins (e.g. transcription factors) are able to recognize nucleotide sequences both specifically and non-specifically (the difference results from affinity)Helical motifs: helix-turn-helix
DNA TF Helical motifs: helix-turn-helixHelix-turn-helix (DNA binding)
Direct read-out of the DNA usually requires the protein to penetrate into the major and/or the minor grooves of the DNAOne way to achieve this type of penetration is by using HTH motifs (the connection here is a short -turn)The -turn and first helix position the second helix in an orientation that allows it to fit inside the major groove of the DNA DNA-binding HTH motifs
DNA-binding HTH proteins are used by both bacteria and eukaryotesIn eukaryotes, they serve in developmental regulation of gene expressionSuch are the homeodomain proteins, which contain an extended HTH motifDNA-binding HTH motifs
motifs hairpin meander Greek key
-sheet-sheet motifsThe sandwich motif
VLCLVHCH1CH2CH3heavy chainslight chainsantigen binding siteThe immunoglobulin motif motifs
Other motifs propeller helix
*Figure 2-16. The conformation. (a) A three-residue protein segment in conformation. The typical zigzag (extended) shape of the backbone is shown, with the carbonyl and amide groups pointing upwards and downwards, and with the side-chains (not shown) pointing to and away from the viewer. The distance between sequential C atoms is denoted. *(b) Structure and hydrogen bond pattern (dashed lines) of anti-parallel -sheets. The strands are often depicted in the literature as wide arrows (top right). The side-chains of residues in -sheets face either up or down the sheet's plane (bottom, for clarity, only the C and C atoms are shown) *(c) A parallel two-stranded -sheet in a form of a structural motif called -- (PDB entry 1tph). (d) A twisted -sheet, taken from the structure of thioredoxin (PDB entry 2trx)*(e) The -barrel structure of porins, presented from the side (left) and top (right) (PDB entry 1a0s). *Figure 2-17. The Born model for the transfer of a charged sphere between two media of different polarity. (a) The cation is represented as a sphere of charge q, radius r and dielectric 2. (b) The cation is transferred from an aqueous solution of dielectric constant () of 80 (blue box) to a nonpolar medium of dielectric 2 (yellow box). *(c) A schematic description of the arrangement of water molecules around the cation, illustrating the concept of electrostatic masking.
*Figure 2-18. Reverse turns and loops. (a) The location of -turns in -sheets. The turns are marked by red circles (b) The structure of the -turn. The numbers denote the four principle amino acids positions within the -turn structure. The second position is often cis-proline and the forth position glycine. (c) A loop, marked by the red circle. *Figure 1. The dependence of RMSD on secondary structure. 12 NMR structures of myoglobin (PDB entry: 1myf). The figure clearly shows that the secondary structures are much more ordered than the loops. *Figure 2-20. Globular vs. fibrous proteins. The former is represented in the figure by the enzyme carbonic anhydrase (PDB entry 1ray), and the latter is represented by the structural protein collagen (PDB entry 1bkv). *Figure 2-21. Solvent exposure of various protein regions in the folded vs. unfolded states. In both cases, polar and nonpolar residues are colored in magenta and green, respectively. The solvent (water) molecules surrounding the protein are represented as spheres. In the folded state nonpolar residues reside in the protein core away from the solvent, whereas in the unfolded state both polar and nonpolar residues are exposed to the solvent. Water molecules were added to the protein computationally by the PDB_hydro server, at the Delarue group, Institut Pasteur. ******Figure 2-22. The helix-turn-helix (HTH) motif. (a) The isolated motif. (b) The HTH motif as part of the EF-hand structure. The figure on the left demonstrates the 'hand' analogy of the motif, whereas the figure on the right shows the calcium binding residues. ****(c) Calmodulin (CaM) in its free state (PDB entry 1osa). The molecule contains 4 HTH motifs, each binding one Ca2+ ion (blue sphere). (d) CaM bound to the myosin light chain (PDB entry 2bbm). *(e+f) Free and bound states of CaM, with polar and nonpolar residues colored in red and green, respectively. The myosin chain in (f) is colored in blue. The figure shows how CaM folds in a way, which surrounds the bound peptide with nonpolar residues. **(g) Human transcription factor (TF) Max in complex with DNA (PDB entry 1hlo). Max contains an HTH motif, which positions the second hel