SupersecondarySupersecondary StructuresStructures (structural(structural motifs)motifs)

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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 β-hairpins ΩΩ 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 structures are both structural Helix 2 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