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Introduction to Protein Structure


Gives you an visual image of how proteins look like. ... which makes them difficult to see in either x-ray or NMR studies of proteins ... – PowerPoint PPT presentation

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Title: Introduction to Protein Structure

Introduction to Protein Structure
Q ?Whats that?
A Something, you get Noble prize for...
John Kendrew Max Perutz 1962 Structures of
myoglobin hemoglobin
Subjects, covered in this lecture
  • Amino acids and their properties
  • Peptide geometry
  • Secondary structure
  • Motifs
  • Domains
  • Quaternary structure

Why bother about protein structure?
  • Gives you an visual image of how proteins look
  • Study of protein structures allows to gain an
    insight into how protein really accomplish their
  • Nobel prizes...

Amino Acids
  • 20 different ones, sharing a common backbone but
    varying side chain.
  • Classed according to their chemical properties
  • L-form

nonpolar amino acids
  • R group consists of carbon chains

leucine and isoleucine are structural isomers
nonpolar amino acids
- R group consists of carbon chains
Phenylalanine and tryptophan have aromatic rings
which are flat due to the double bond
network Tryptophan is often classified as being
polar because of the NH group. In practice,
however it has more of hydrophobic properties
Proline has its R group bound to the amino
nitrogen to form a ring network
Methionine has a sulphur atom in its
sidechain sulphur has the same valence as oxygen
polar amino acids
- R group consists of carbon, oxygen and nitrogen
atoms together they make the sidechain more
Ser and thr are a mix of carbon chains and
hydroxyl functional groups (-OH). Cysteine has a
thiol group (-SH) which is otherwise structurally
similar to serine but not chemically similar
Asn and gln have an amide functional group
charged amino acids
- R group has a charge at physiological pH (7.4).
pK of the charged groups vary
carboxyl group
carboxyl group
amino group
guanidinio group
imidazole group, sometimes charged Most often
classified as a polar amino acid
Cysteine and disulphides
  • The almost exclusively only way to covalently
    link two non-sequential residues is by forming a
    disulphide bridge
  • Formation of disulphide requires an oxidative
    environment, threfore disulphides are very rare
    in intracellular proteins but quite abundant in
    secretory proteins

Peptide units
  • A peptide is a set of covalently bonded amino
  • The covalent bond is usually referred as peptide

Biochemists peptide unit from N to C all main
chain atoms within the unit lie in the same
  • Angles phi (f) N-Ca
  • Angle psi (y) Ca-CO
  • Angle omega (w) C-N

The w angle, cis- and trans- peptides
  • Because of the partly double nature of peptide
    bond, w is always close to 180o for trans-
    peptides or 0o for cis- peptides (30o in exterme
  • Cis- peptides are energetically extremely
    unfavourable (1000 fold) because of steric
    clashes between the neighbouring Ca atoms

  • The only exception is peptide bond before
    proline, where cis- peptide is just 4 times less
    favourable than trans- peptide, because there are
    some steric clashes in both cis- and trans- forms
  • Proline cis-trans isomerization is an important
    factor in protein folding, which is why there are
    special enzymes prolylpeptydyl isomerases to
    catalyze the transition from one form to another

  • According to statistics, 0.03 of non-proline
    peptides and 5.2 of X-Pro peptides are in cis-
    conformation, resulting in a total of 0.3
  • In most cases cis- peptides, especially
    non-proline, occur for a good reason, for example
    to maintain some particular conformation in the
    active site of enzyme

Main chain conformations (I)
  • Only certain combinations of y and f are allowed,
    due to steric clashes of backbone atoms and Cb
    atom. Plot of these combinations yields the
    Ramachandran plot.
  • All amino acids clusters in specific regions
    (called allowed regions) except Gly (explains why
    Glycine is an important amino acid).

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  • In good quality structures only about 2 of amino
    acid residues are found in the disallowed regions
    of Ramachandran plot
  • Of course, residues with disallowed conformations
    often have some important function in proteins

Side chain conformations
  • Side chains can have in principle different
    conformations (rotation of Ca-Cb...)
  • The observed conformations in protein structures
    are the ones which are more energetically
    favourable (rotamers).

Name three amino acids which are very different
from others!
  • Proline
  • No free amino group
  • Very rigid
  • Introduces breaks in a helices and b strands
  • Glycine
  • Lacks a side chain
  • Can be found anywhere in Ramachandran plot
  • In proteins often found in flexible regions with
    unusual backbone conformations
  • Cysteine
  • Disulphides

Primary, secondary, tertiary and quaternary
The hydrophobic core
  • The hydrophobic sidechains of protein has a
    tendency to cluster together in order to avoid
    unfavourable contacts with polar water molecules
  • As a result, in general, hydrophobic sidechains
    are located in the interior of protein, forming
    the hydrophobic core
  • Polar and charged amino acids usually are located
    on the surface of the protein
  • Polar and charged residues also can make
    hydrophobic contacts with their aliphatic carbon
  • Polar and charged residues are seldom completely
    buried within the core and even when they are,
    the polar groups are almost invariably involved
    in hydrogen bond formation

The reasons of secondary structure formation
  • Since sidechains of hydrophobic residues are
    located in the hydrophobic core, the mainchain
    atoms of the same residues in most cases are also
    within the hydrophobic core
  • Since the presence of polar groups in hydrophobic
    environment is very unfavourable, the main chain
    N- and O- atoms have to be neutralised by
    formation of hydrogen bonds
  • The two most efficient ways of hydrogen bond
    formation is to build an alpha helix or a beta

The alpha helix
  • 3.6 residues per turn
  • the hydrogen bonds are made between residues n
    and n4

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Variants of alpha helix
  • In regular a helix, residue n makes a H-bond with
    residue n4
  • In 310 helix, residue n makes a H-bond with
    residue n3. There are 3 residues per turn,
    connected by 10 atoms, hence the name 310
  • In p helix, residue n makes a H-bond with residue
  • In p helix there is a hole left in the middle of
    helix and in 310 helix the main chain atoms are
    packed very tightly. None of above is
    energetically favourable
  • 310 and especially p helices occur rarely and
    usually only at the ends of regular a helix or as
    a separate single-turn helix

Handedness of alpha helix
  • The a helices as well as 310 and p helices ale
    almost exclusively right-handed
  • In very rare occasions, left handed a and 310
    helixes can occur. They are always very short (4-
    6 residues) and normally involved in some
    important function of protein like in active site
    or ligand binding
  • There are about 30 reported cases of left-handed
    helices. In contrast, the number of known right
    handed helices is of order of hundreds of

The dipole moment of a helix
Good and bad helix formers
  • Different side chains have been found to have
    weak but definite preferences for helix forming
  • Ala, Glu, Leu and Met are good helix formers
  • Pro, Gly, Tyr and Ser are very poor helix formers
  • The above preferences are not strong enough to be
    used in accurate secondary structure predictions

Periodic patterns in a helices
  • The most common location of an a helice is along
    the outside of protein, with one side of the
    helix facing the hydrophobic core and other side
    facing the solvent
  • Such a location results in a periodic pattern of
    alterating hydrophobic and polar residues
  • On itself, however, the pattern is not reliable
    enough for structure prediction, since small
    hydrophobic residues can face the solvent and
    some helices are completely buried or completely

Beta sheets
A mixed b sheet
A mixed b sheet is far less common than
antiparallel or parallel
Twist in b sheets
  • Almost all b sheets in the known protein
    structures are twisted
  • The twist is always right-handed

  • Loops connect secondary structure elements
  • Loops are located on the surface of protein
  • In general, main chain nitrogen and carbonyl
    oxygen atoms do not make H-bonds each to other in
  • Loops are rich in polar and charged residues
  • The lenght of loops can vary from 2 to more than
    20 residues
  • Loops are very flexible, which makes them
    difficult to see in either x-ray or NMR studies
    of proteins
  • Loops frequently participate in forming of ligand
    binding sites and enzyme active sites
  • In homologous protein families loop regions are
    far less conserved than secondary stucture
  • Insertions and deletions in homologous protein
    families occur almost exclusively in loop regions

Hairpin loops and reverse turns
  • Loops, which connect two adjacent antiparallel
    beta strands are called hairpin loops
  • 2 residues long hairpin loops are often called
    reverse turns, beta turns or simply turns

Type I turn Type II turn
Hairpin loop
  • Simple combinations of a few secondary structure
    elements occur frequently in protein structures
  • These units are called supersecondary structure
    or motifs
  • Some motifs can be associated with a specific
    biological function (e.g. DNA binding)
  • Other motifs have no specific biological function
    alone, but are part of larger structural and
    functional assemblies

Helix-loop-helix motifs
Calcium binding motif
DNA binding motif
The hairpin b motif
  • Two adjacent anti-parallel b strands, joined by a
  • The hairpin motif can occur both as an isolated
    unit or as a part of bigger b sheet

Snake venom- erabutoxin
Bovine trypsin inhibitor
24 different ways to connect two b hairpins
  • Only the first 8 arrangements exist in known

The Greek key motif
  • The most common way to connect 4 adjacent
    antiparallel b strands

The Greek key motif in Staphilococcus nuclease
The b-a-b motif
  • A convinient way to connect two paralel beta
  • b-a-b motif is a part of almost all proteins,
    containing a paralel beta sheet

The handedness of b-a-b motif
  • Theoretically, two distinct hands can exist in
    b-a-b motif, with a helice above or below the
    plane of beta sheet
  • In almost all cases the right handed motif exists

  • Domain ia a polypeptide chain or a part of a
    polypeptide chain that can fold indepedently in a
    stable tertiary structure with its own
    hydrophobic core
  • Domains can be formed from several simple motifs
    and additional secondary structure elements
  • Proteins can have anything from one to several
    tens of domains
  • In proteins with sevaral domains, most often each
    domain is associated with a distinct biological

2xb hairpin b strand
2x Greek key
  • Domains are most often, but not always continuous
    pieces of primary structure

Example of proteins with several domains - lac
Helix-turn-helix domain (binds to DNA)
hinge helix
Core domain, containing two subdomains, which in
turn contain several b-a-b motifs (binds ligand)
  • C-terminal helix (tetramerization)

Intact IgG contains 12 immunoglobulin-like domains
Each domain is made of two beta sheets with a
topology similar to two Greek key motifs
The quaternary structure
  • Some proteins are biologically active as
    monomers. For those proteins quaternary structure
    does not exist
  • Other proteins, however, are active as homo- or
    hetero- polymers
  • The simplest case and by far the most common form
    of quaternary structure is a homodimer
  • The monomers in homopolymers are often arranged
    in a symmetric fashion with one or several
    symmetry axes going through the molecule or some
    sort of helical arrangement
  • Some biologically active units have a very
    complicated quaternary structure like ribosomes
    or viral capsids

2-fold symmetry in Glutahione-S-transferase
9-fold symmetry in light-harvesting complex II
from Rhodopseudomonas acidophila.
222 symmetry in prealbumin
A simple icosahedral virus 180 chemically
identical subunits
Small subunit of ribosome a lot of different
proteins, no symmetry