Secondary Structure Motifs of Proteins

1
Secondary StructureMotifs of Proteins

• Chapter 2

2
Their Diverse Functions Require Proteins to Have
Irregular Structures

• Kendrew's model of the low-resolution structure
  of myoglobin shown in three different views. The
  sausage-shaped regions represent ? helices, which
  are arranged in a seemingly irregular manner to
  form a compact globular molecule. (Courtesy of
  J.C. Kendrew.)

3
Types of Secondary Structure

• There are three common secondary structures in
  proteins, namely alpha helices, beta sheets, and
  turns.
• That which cannot be classified as one of the
  standard three classes is usually grouped into a
  category called "other" or "random coil". This
  designation is unfortunate as no portion of a
  proteins three dimensional structure is truly
  random and it is usually not a coil.
• A common element of most secondary structures is
  the presence of characteristic hydrogen bonds
  e.g., CO of residue i to HN of residue i4 (i,
  i4). They are formed when a number of
  consecutive residues have the same phi and psi
  angles.

4
Helix

• In a helical conformation, the relationship of
  one peptide unit to the next is the same for all
  alpha-carbons. This means that the dihedral angle
  pairs phi and psi (phii, psii) are the same for
  each residue in the helical conformation.
• Helices are classified as repetitive secondary
  structure since their backbone phi and psi angles
  repeat
• Two parameters describe the helix about this
  axis
• n - the number of residues per helical turn
• r - the rise per helical residue
• By convention, a positive value of n denotes a
  right-handed helix. (Curling the fingers of your
  right hand along the helical path, your thumb
  will point in the direction of your fingertips if
  the helix is right-handed.)

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Three Regular Polypeptide Helices
?-helix
a-helix
310 helix
phi psi a-helix -57.8 -47.0 310-helix
-74.0 -4.0 p-helix -57.1 -69.7 Idealized
model of the conformations of polyalanine are
displayed.
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The Alpha (a) Helix

• Main-chain N and O atoms are hydrogen-bonded to
  each other ? helices. There are 3.6 residues per
  turn in an ? helix, which corresponds to 5.4 Å
  (1.5 Å per residue).

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The Alpha (a) Helix
The Side chains project out from the alpha helix .
8
The Alpha Helix has a Dipole Moment
Negatively charged groups such as phosphate ions
frequently bind to the amino ends of a helices.
The dipole moment of an a helix as well as the
possibility of hydrogen-bonding to free NH groups
at the end of the helix favors such binding.

• (a) The dipole of a peptide unit. Values in boxes
  give the approximate fractional charges of the
  atoms of the peptide unit. (b) The dipoles of
  peptide units are aligned along the a-helical
  axis, which creates an overall dipole moment in
  the a helix, positive at the amino end and
  negative at the carboxyl end.

9
The Helical Wheels

• The helical wheel or spiral. Amino acid residues
  are plotted every (360/3.6) 100 around the
  spiral.
• Green is an amino acid with a hydrophobic side
  chain, blue is a polar side chain, and red is a
  charged side chain.

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Helix Wheels
11
Some Amino Acids are Preferred in a Helix

• Eight Most Common Residues as Helix Formers
• Glu, Met, Ala, Leu, Lys, Phe, Gln, Trp
• Eight Least Common Residues as Helix Formers
• Gly, Pro, Asn, Tyr, Cys, Ser, Thr, Arg

12
310 Helix

• Only 3.4 of the residues are involved in 310
  helices in the Kabsch and Sander database (1983),
  and nearly all those in helical segments
  containing 1 - 3 hydrogen bonds (96 4
  residues).
• The average of the backbone dihedral angles were
  found to differ slightly from the ideal 310 helix
  (-74.0, -4.0) with values of -71.0 and -18.0
  degrees, for phi and for psi, respectively. It
  has a larger radius (2.0 versus 1.9 Å) and a
  larger number of residues per helical turn (3.2
  versus 3.0).
• The end result being a slightly better staggering
  of sidechains along the helical axis.
• Hydrogen bonds within a 310-helix also display a
  repeating pattern in which the backbone CO of
  residue i hydrogen bonds to the backbone HN of
  residue i3.

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?-helix

• Hydrogen bonds within a p-helix display a
  repeating pattern, in which the backbone CO of
  residue i hydrogen bonds to the backbone HN of
  residue i5.
• The p-helix is an extremely rare secondary
  structural element in proteins.
• The infrequency of this particular form of
  secondary structure stems from the following
  properties
• 1. the phi and psi angles lie at the very edge
  of an allowed, minimum energy region of the
  Ramachandran (phi, psi) map.
• 2. the p-helix requires that the angle tau
  (N-CA-C') be larger (114.9) than the standard
  tetrahedral angle of 109.5 degrees.
• 3. the large radius of the p-helix forms an
  axial hole too small for solvent water to fill.
• 4. side chains are more staggered than the
  ideal 310 helix but not as well as the ?-helix.

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b-sheet

• Beta sheets are another major structural element
  in globular proteins containing 20 28 of all
  residues (Kabsch Sander, 1983 Creighton,
  1993).
• The basic unit of a beta sheet is a beta strand
  with approximate backbone dihedral angles phi
  -120 and psi 120 producing a translation of
  3.2 to 3.4 Å/residue for residues in
  anti-parallel and parallel strands, respectively.
• Due to the extended nature of the chain, there
  are no significant intra-segment hydrogen bonds
  and van der Waals interactions between atoms of
  neighboring residues. This extended conformation
  is only stable as part of a beta sheet where
  contributions from hydrogen bonds and van der
  Waals interactions between aligned strands exert
  a stabilizing influence.
• The beta sheet is sometimes called the beta
  "pleated" sheet since sequentially neighboring Ca
  atoms are alternately above and below the plane
  of the sheet.

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Anti-parallel b sheet

• Main-chain NH and O atoms within a b sheet are
  hydrogen bonded to each other. The amino acids in
  successive strands have alternating directions
  (anti-parallel).

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Anti-parallel b sheet
A residue in an antiparallel beta strand has
values of -139 and 135 degrees for the backbone
dihedral angles phi and psi,respectively.
Antiparallel beta sheets are thought to be
intrinsically more stable than parallel sheets
due to the more optimal orientation of the
interstrand hydrogen bonds and that peptide bond
dipoles of nearest neighbors within a strand
cancel whereas in the parallel sheet, components
of the dipoles parallel to the strands align and
may interact unfavorably.
17
Parallel b sheet

• The amino acids in the aligned strands run in the
  same direction.

18
Twisted ? Sheets in Thioredoxin
19
Twist of b Sheet

• The classical beta sheets originally proposed are
  planar but most sheets observed in globular
  proteins are twisted (0 to 30 º/ residue).
• Antiparallel beta sheets are more often twisted
  than parallel sheets. This twist is always of the
  same handedness, but unfortunately, it has been
  described using two conflicting conventions in
  the literature. If defined in terms of the
  progressive twist of the hydrogen-bonding
  direction, the twist is right-handed.
• Two-stranded beta strands show the largest
  twists.

20
b-Bulge

• Another irregularity found in antiparallel beta
  sheets is the hydrogen-bonding of two residues
  from one strand with one residue from the other
  called a beta bulge.
• Bulges are most often found in antiparallel
  sheets with 5 of bulges occurring in parallel
  strands (Richardson, 1981). Bulges, like "Turns"
  effect the directionality of the polypeptide
  chain.

21
Turns

• Turns are the third of the three "classical"
  secondary structures. Approximately one-third of
  all residues in globular proteins are contained
  in turns that serve to reverse the direction of
  the polypeptide chain.
• This is perhaps not so surprising since the
  diameter of the average globular protein domain
  is roughly 25 Å (an extended polypeptide
  conformation would require 7 residues to
  traverse the domain before having to change
  directions).
• Turns are located primarily on the protein
  surface and accordingly contain polar and charged
  residues. Antibody recognition, phosphorylation,
  glycosylation, hydroxylation, and intron/exon
  splicing are found frequently at or adjacent to
  turns.

22
Gamma Turn

• The hydrogen bond between CO of residue i and NH
  of residue i2.
• The dihedral angles of residue i1 are (70, -60)
  and (-70, 60) for phi and psi of the classical
  and inverse gamma turns.

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Type I Turn.

• The hydrogen bond between CO of residue i and NH
  of residue i3.
• The backbone dihedral angles are (-60, -30) and
  (-90, 0) of residues i1 and i2, respectively,
  for the type I turn.

• Proline is often found in position i1 in type I
  turns as its phi angle is restricted to -60 and
  its imide nitrogen does not require a hydrogen
  bond. Glycine is favored in this position in the
  type II' as it requires a positive (left-handed)
  phi value.

24
Type II Turn.

• The hydrogen bond between CO of residue i and NH
  of residue i3.
• The backbone dihedral angles are (-60, 120) and
  (80, 0) of residues i1 and i2, respectively,
  for the type II turn.
• Glycine is favored in this position in the type
  II' as it requires a positive (left-handed) phi
  value.

25
Type III Turn.

• The hydrogen bond between CO of residue i and NH
  of residue i3.
• This is a single turn of right-handed (III) and
  left-handed (III') 310 helix. The backbone
  dihedral angles are (-60, -30) and (-60, -30) of
  residues i1 and i2, respectively, for the
  classical type III turn.

26
Preferred Residues for b Sheet and Turns

• Eight most common residues for beta-sheet
• Val, Ile, Tyr, Trp,
• Phe, Leu, Cys, Thr
• Eight least common residues for beta-sheet
• Glu, Asp, Pro, Ser,
• Lys, Gly, Ala, Asn

• Eight most common residues for turns
• Gly, Asn, Pro, Asp,
• Ser, Cys, Tyr, Lys
• Eight least common residues for turns
• Ile, Val, Met, Leu, Phe, Ala, Glu, Trp

27
Loops

• In Leszczynski Rose (1986), out of 67 proteins
  surveyed, they tabulated 26 helix, 19 sheet,
  26 turns and 21 in loops.
• These loop structures contain between 6 and 16
  residues and are compact and globular in
  structure. Like turns, they generally contain
  polar residues and hence are predominantly at the
  protein surface.

28
b-hairpin Loop

• Adjacent antiparallel b strands are joined by
  hairpin loops. Such loops are frequently short
  and do not have regular secondary structure.
  Nevertheless, many loop regions in different
  proteins have similar structures.

29
Schematic Structural Diagrams of Myoglobin
30
Richardson Diagrams
Myoglobin
Triosephosphate isomerase
Cylinder for a helices arrows for b strands,
which gives the direction of the strand from N
to C and the ribbons for the remaining part.
31
Beta Sheet Topology Diagrams
plastocyanin
transcarbamoylase
flavodoxin

• Beta sheets are usually represented simply by
  arrows in topology diagrams that show both the
  direction of each ? strand and the way the
  strands are connected to each other along the
  polypeptide chain.

32
Super Secondary Structures (Motifs)

• Simple combinations of a few secondary structure
  elements with a specific geometric arrangement
  are called super secondary structures or motifs.
• They may have functional and structural
  significance.
• Common motifs
• Helix-turn-helix
• b-hairpin, b-meander
• b-barrel, Geek key
• bab

33
Helix-Turn-Helix Motif

• Two ? helices that are connected by a short loop
  region in a specific geometric arrangement
  constitute a helix-turn-helix motif. (a) the
  DNA-binding motif and (b) the calcium-binding
  motif, which are present in many proteins whose
  function is regulated by calcium.

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EF-hand Calcium-binding Motif

• The calcium atom is bound to one of the motifs in
  the muscle protein troponin-C through six oxygen
  atoms one each from the side chains of Asp (D)
  9, Asn (N) 11, and Asp (D) 13 one from the main
  chain of residue 15 and two from the side chain
  of Glu (E) 20. In addition, a water molecule (W)
  is bound to the calcium atom.

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Amino Acid Sequences of EF-hand Motifs
1 3 5 7 9 12

The side chains of hydrophobic residues on the
flanking helices form a hydrophobic core between
the a helices
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The b Hairpin Motif
Snake Venom Erabutoxin
Bovine Trypsin Inhibitor

• The hairpin motif is very frequent in b sheets
  and is built up from two adjacent b strands that
  are joined by a loop region.

37
Greek Key Motif

• The Greek key motif is found in antiparallel b
  sheets when four adjacent b strands are arranged
  in the pattern shown as a topology diagram in
  (a). The three dimensional structure of the
  enzyme Staphylococcus Nuclease shown in (b) in
  blue and red is also a Greek key motif.

38
Forming Greek Key Motif

• Suggested folding pathway from a hairpin-like
  structure to the Greek key motif.
• Beta strands 2 and 3 fold over such that strand
  2 is aligned adjacent and antiparallel to strand
  1.

39
b-a-b Motif

• Two adjacent parallel b strands are usually
  connected by an a helix from the C-terminus of
  strand 1 to the N-terminus of strand 2.
• Most protein structures that contain parallel b
  sheets are built up from combinations of such
  b-a-b motifs.

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b-a-b Handedness

• The b-a-b motif can in principle have two
  "hands."
• (a) This connection with the helix above the
  sheet is found in almost all proteins and is
  called right-handed because it has the same hand
  as a right-handed a helix.
• (b) The left-handed connection with the helix
  below the sheet.

41
Domain Organization

• Small protein molecules like the epidermal growth
  factor, EGF, are comprised of only one domain.
  Others, like the serine proteinase chymotrypsin,
  are arranged in two domains that are required to
  form a functional unit. Many of the proteins that
  are involved in blood coagulation and
  fibrinolysis have long polypeptide chains that
  comprise different combinations of domains.

42
Domains

• "Within a single subunit polypeptide chain,
  contiguous portions of the polypeptide chain
  frequently fold into compact, local
  semi-independent units called domains." -
  Richardson, 1981
• Domains may be considered to be connected units,
  which are to varying extents independent in terms
  of their structure, function and folding
  behavior.
• Each domain can be described by its fold. While
  some proteins consist of a single domain, others
  consist of several or many. A number of globular
  protein chains consist of two or three domains
  appearing as 'lobes'.
• In other cases, the domains may be of a very
  different nature. For example, some proteins
  located in cell membranes have a globular
  intracellular or extracellular domain distinct
  from that which spans the membrane.

43
Adjacent Motifs

• Motifs that are adjacent in the amino acid
  sequence are also usually adjacent in the
  three-dimensional structure.
• Triose-phosphate isomerase is built up from four
  b-a-b-a motifs that are consecutive both in the
  amino acid sequence (a) and in the three
  dimensional structure (b).

44
Mosaic Proteins

• Mosaic proteins are those which consist of many
  repeated copies of one or a few domains, all
  within one polypeptide chain.
• Many extracellular proteins are of this nature.
  The domains in question are termed modules and
  are sometimes relatively small. Note that this
  term is often applied to sequences whose
  structures may not be known for certain.