SupersecondarySupersecondary StructuresStructures (structural(structural motifs)motifs) VariousVarious SourcesSources Lecture 2 Biochemistry 4000 Slide 1 Supersecondary Structures (Motifs) Supersecondary Structures (Motifs): Combinations of secondary structures in specific geometric arrangements ● Simple supersecondary structures consisting of 3 or fewer secondary structures considered here ● Large supersecondary structures (ie. Greek Key and Jelly-Roll) consisting of more than 3 secondary structures will be considered along with tertiary structures and folds ● Why? Large supersecondary structures can be domains. Simple supersecondary structures are typically composed of two secondary structures (ie. strands or helices) and a turn (or loop) Helix-turn-helix DNA binding motif Lecture 2 Biochemistry 4000 Slide 2 Supersecondary Structures (Motifs) Supersecondary Structures Hierarchy of Protein Structure (Motifs): Combinations of α β secondary structures in specific geometric arrangements Simple supersecondary structures are the 'building blocks' of …. αα βαβ ββ a) Complex Supersecondary Structures b) Tertiary Structure / Domain folds ββββ Simple supersecondary structures αααα are relatively stable components of Greek 4 helix βαβαβ βββ the 'Molten Globule' protein folding Key bundle β intermediate Rossman β-meander fold Lecture 2 Biochemistry 4000 Slide 3 β-hairpin Simple and Common supersecondary structure β-hairpin: two antiparallel β-strands joined by a turn or loop ● Very small supersecondary structure (typically less than 10 residues) β-hairpin Turn: Short loop segment joining two antiparallel β-strands ● Hairpin turns are a special case of Reverse turns ● Favor type I' and II' turns in contrast to reverse turns which favor type I and II β-hairpin supersecondary structures are further subdivided based upon the size of the β-hairpin turn. Lecture 2 Biochemistry 4000 Slide 4 2 Residue β-hairpins β-hairpin turns (2 residues) are almost always a Type I' or Type II' (right) Type I' X-Gly ● Residue 1 (left-handed helix) favors Gly, Asp or Asn (High turn propensity) ● Residue 2 is almost always Gly (disallowed region of Ramachandran for non-Gly) Type II' Gly-X ● Residue 1 is almost always Gly ● Residue 2 favors small polar (Ser, Thr) Bioinformatics Presence of Gly between predicted β-strands (ie. suggests a possible β-hairpin turn) increases 'confidence' of prediction Lecture 2 Biochemistry 4000 Slide 5 3 Residue β-hairpins Residues at ends of β-sheets often make only a single H-bonds (typically has two H-bonds) Intervening 3 residues have distinct conformational preferences ● Residue 1 right-handed helical conformation ● Residue 2 bridge region between helix and sheet ● Residue 3 left-handed helical conformation (favors Gly, Asn, Asp) Bioinformatics Presence of Gly, Asn or Asp between predicted β-strands (ie. suggests a possible β-hairpin turn) increases 'confidence' of prediction Lecture 2 Biochemistry 4000 Slide 6 4 Residue β-hairpins Last common β-hairpin Intervening 4 residues have preferred conformations ● Residue 1 right-handed helical conformation ● Residue 2 right-handed helical conformation ● Residue 3 bridge region between helix and sheet ● Residue 4 left-handed helical conformation (favors Gly, Asn, Asp) Bioinformatics Presence of Gly, Asn or Asp between predicted β-strands (ie. suggests a possible β-hairpin turn) increases 'confidence' of prediction Lecture 2 Biochemistry 4000 Slide 7 Long Loop ΩΩ β-hairpins looploop Wide-range of conformations with no particular sequence preferences Long loop β-hairpins are special case of Ω loops Loop looks similar to the Greek Letter Often referred to as a 'random coil' Ω conformation ● Consecutive antiparallel β-strands joined by long loop β-hairpin turns are referred to as the β-meander supersecondary structure Lecture 2 Biochemistry 4000 Slide 8 β-Corner (revisted) β-corner – two residue disruption of β-sheet hydrogen bonding β-corners can also be thought of as a supersecondary structure consisting of a β-hairpin with a two residue β-bulge 90° change in direction of β-strand Gly typically opposite the β-bulge Antiparallel sheet with β-corner Lecture 2 Biochemistry 4000 Slide 9 Helix (or αα) hairpins αα-hairpin – two antiparallel α-helices connected by a loop Long loops have many possible conformations (and sequences) Shortest loops (2 and 3 residues) have only a single allowed conformation αα-hairpin Parallel and antiparallel helices generally interact via hydrophobic interactions Requires one hydrophobic residue per turn of helix of each helix ● αα-hairpins typically involve amphipathic helices Lecture 2 Biochemistry 4000 Slide 10 Helix (or αα) hairpins 2 residue αα-hairpin (right) X-Gly Loop is ~ perpendicular to helix axes ● Residue 1 has a bridging conformation (between α and β) ● Residue 2 must by Gly 3 residue αα-hairpin (not shown) X-Gly ● Residue 1 has a bridging conformation Residue 1 of the αα-hairpin turn (between α and β) caps the first helix ● Residue 2 has left-handed helical conformation Residue 2 of the 2 residue αα-hairpin turn caps the terminii ● Residue 3 has a β-strand conformation of both helices Lecture 2 Biochemistry 4000 Slide 11 4 residue Helix (or αα) hairpins αα-hairpin – two antiparallel α-helices connected by a loop Only two possible conformations for 4 residue αα-hairpin turns Conformation 1) Similar to 3 residue αα-hairpin turn (4th residue is in β-strand conformer ● Residue 1 Bridging ● Residue 2 left-handed helix ● Residues 3 & 4 β-strand Conformation 2) ● β Residues 1 & 3 -strand αα-hairpin ● Residues 2 & 4 Bridging Lecture 2 Biochemistry 4000 Slide 12 Helix (or αα) corners αα-corner – two roughly perpendicular α-helices connected by a short loop Shortest loop is 3 residues long and adopts a single allowed conformation ● Residue 1 Small (Gly or Ala) to avoid steric conflicts ● Residue 2 Hydrophobic residue inserted between α-helices ● Residue 3 Small polar residue (Ser or Asp) Residue 1 & 3 cap the first and second helices, respectively N Virtually all αα-corners are right-handed due to steric conflicts in left-handed corners αα-corner (right handed) Left Handed Right Handed C Lecture 2 Biochemistry 4000 Slide 13 Functional Motifs eg. Helix-turn-Helix (a.k.a. EF-Hand) Loop regions connecting helices - can have important biological functions - resulting supersecondary structures are both structural and functional Note: EF-Hands always Functional supersecondary structure (ubiquitous) occur in pairs that pack involved in Ca2+ binding against one another ● 12 residue loop between helices ● Invariant Gly at position 6 ● Asp and Glu required at 4 positions (direct Ca2+ interaction) Troponin C Lecture 2 Biochemistry 4000 Slide 14 Helix 1 Functional Motifs eg. Helix-loop-Helix Loop regions connecting helices - can have important biological functions - resulting supersecondary Helix 2 structures are both structural and functional Cro repressor (phage λ) Functional supersecondary structure (procaryotes Note: Helix-turn-Helix primarily) involved in DNA binding supersecondary structures always occur in pairs as they recognize ● Helix 2 lies within major groove of B-DNA palindromic sequences ● Helix 1 and loop position Helix 2 within major groove ● Sequence differences in Helix 2 give rise to specificity for different DNA sequence Lecture 2 Biochemistry 4000 Slide 15 βαβ-motif Parallel β-sheets are connected by longer segments of polypeptide chain (in comparison with antiparallel) Frequently (most examples), the connections between parallel β-sheets contain helices forming the βαβ structural motif Helix is parallel to the β-sheet and the connections are variable in length Virtually all βαβ have a right-handed twist ● Viewed along the sheet edge ● Clockwise rotation from front to back Lecture 2 Biochemistry 4000 Slide 16.