HP Dr. Drake
L. Van Warren
1. Secondary Structure
- The properties of a protein are largely determined
by its three-dimensional structure.
- A polymer's secondary structure (2' structure)
is defined as the local conformation of its backbone.
A. Peptide Bond
- The peptide group has a rigid, planar structure
which is a consequence of resonance interactions that give the peptide bond
a ~40% double-bond character.
- Peptide groups, with few exceptions, assume the
trans conformation. Successive Ca atoms are on opposite sides of the peptide
bond joining them.
- Polypeptide Backbone Conformations May Be Described
by Their Torsion Angles
- Allowed Conformations of Polypeptides are Indicated
by the Ramachandran Diagram
- Only three small regions of the conformational
map are physically accessible to a polypeptide chain.
B. Helical Structures
- Only one helical polypeptide conformation has
simultaneously allowed conformation angles and a favorable hydrogen bonding
pattern: the alpha helix.
- The alpha helix is a rigid arrangement of the
- It was discovered via model building by Pauling
- There are other polypeptide helices.
- The 2.27
ribbon and The 310 helix
- The nm notation
is such that n is the number of residues per turn and m is the number of atoms
including hydrogen in the ring that is closed by the hydrogen bond.
- With this notation the alpha helix is 3.613
- the pi helix is a 4.416
and is rarely observed
C. Beta Structures
- There is also the beta pleated sheet whose peptide
angles fall within
the allowed regions on the Ramachandran diagram.
- There are two beta pleated sheets.
The most common is the antiparallel sheet in which polypeptide chains run
in opposite directions. So opposite is most common.
- The parallel beta pleated sheets are less common.
D. Nonrepetitive Structures
- Regular secondary structures - helices and beta
sheets - comprise around half of the average globular protein.
2. Fibrous Proteins
- Fibrous proteins are highly elongated molecules
whose secondary structures are their dominant structural motifs. They occur
in skin, tendon, bone and connective tissue.
A. alpha Keratin - A Helix of Helices
- Keratin is a mechanically durable and chemically
unreactive protein occurring in all higher vertebrates.
- Mammalian keratin is called alpha keratin, which
comes in 30 variants.
- Birds and reptiles have beta keratin.
- alpha keratin polypeptides form closely associated
pairs of alpha helices in which each pair is composed of a Type I and a Type
II keratin chain twisted in parallel into a left handed coil.
- The conformation of alpha keratin's coiled coil
is a consequence of its primary structure.
- Keratin Defects Result in a Loss of Skin Integrity.
B. Silk Fibroin - A beta Pleated Sheet
- Insects and Spiders produce silk for cocoons,
nests and webs.
- The polypeptide chains of silk form antiparallel
beta sheets that run along the fiber axis.
- The sequence of silk are (-Gly-Ser-Gly-Ala-Gly-Ala-)
- Silk fibers are strong but only slightly extensible
since stretching would require breaking The covalent bonds of its nearly fully
extended polypeptide chains.
C. Collagen - A Triple Helical Cable
- Collagen occurs in all multicellular animals
and is The most abundant protein of vertebrates.
- There are at least 30 genetically distinct polypeptide
- There are 16 collagen variants that occur in
different tissues of The same person.
- Collagen has a distinctive amino acid composition:
Nearly 1/3 of its residues are Glycine,
Another 15 to 30% of its residues are Proline and 4-hydroxyproline (Hyp).
- 3Hyp and 4Hyp occur but in smaller amounts.
- The hydroxylation is posttranslationally modified.
- Hyp stabilizes collagen.
- Pro is converted to Hyp via Prolyl hydrolase
- It takes Vitamin C to make Prolyl hydrolase.
- Scurvy is a lack of Prolyl hydrolase
- The amino acid sequence of bovine collage, which
is similar to that of other collagens, consists of monotonously repeated triplets
of sequence Gly-X-Y over a 1000 residue stretch.
- Collagen's three polypeptide chains, which individually
resemble polyproline II helices, are parallel and wind around each other With
a gentle, right-handed, ropelike twist to form a triple-helical structure.
Every third reside passes through The center of The triple helix so that only
a Gly side chain can fit there. That is why Gly is a must.
- Collagen's well-packed, rigid, triple helical
structure is responsible for its characteristic tensile strength.
- Collagen is organized into Fibrils.
- Collagen Fibrils are Covalently Cross-Linked
Via Lysyl Oxidase
- Collagen Defects Are Responsible for a Variety
of Human Disease
D. Elastin - A Nonrepetitive Coil
- Elastin is a protein With rubberlike elastic
properties whose fibers can stretch to several times their normal length.
- Elastin is 30% Glycine, over 1/3 Ala + Val and
is rich in Pro.
- Elastin has no regular secondary structure, but
is a 3 dimensional network.
3. Globular Proteins
- Globular proteins are highly diverse group of
substances that in their native state, exist as compact spheroidal molecules.
- Enzymes are globular proteins.
- Transport proteins are globular.
- Receptor proteins are globular.
A. Interpretation of Protein X-Ray and
- X-Ray crystallography is a technique that directly
- An X-Ray structure is an electron density map
taken from multiple angles.
- Protein Crystal Structures Exhibit Less Than
- Most Crystalline Proteins Maintain Their Native
- Crystalline proteins usually assume The same
structures they have in solution.
- Protein Structure is Also Determined by 2D-NMR
- Protein Molecular Structures Are Most Effectively
Illustrated in Simplified Form
B. Tertiary Structure
- The tertiary structure (3' structure) of a protein
is its three dimensional arrangement, that is, The folding of its 2' structural
elements, together With The spatial deposition of its side chains.
- Globular Proteins May Contain Both alpha Helices
and beta Sheets
- Side Chain Location Varies With Polarity
- Nonpolar resides belong INSIDE The protein: Val
Leu, Ile, Met and Phe
- Charged Polar resides belong ON The protein surface:
Arg, His, Lys, Asp, and Glu
- Uncharged polar groups can be both IN and ON:
Ser, Thr, Asn, Gln, Tyr and Trp
Nearly all buried Hydrogen bond donors form H bonds With buried acceptor groups.
- Globular Protein Cores are Efficiently Arranged
With Their Side Chains in Relaxed Conformations.
- The interior of a protein is more like a crystal
than like an oil drop, it is efficiently packed!
- Large Polypeptides Form Domains
- Domains are structurally independent units that
each have The characteristics of a small globular protein.
- Supersecondary Structures Have Structural and
Certain groupings of secondary structural elements named supersecondary structures
or motifs, occur in many unrelated globular proteins.
motif: most common
- b hairpin motif
- aa motif:
parallel coils pack against each other.
- b barrels
4. Protein Stability
- Native proteins are only marginally stable entities
under physiological conditions.
A. Electrostatic Forces
- Ionic Interactions Are Strong but Do Not Greatly
Ion pairs therefore contribute little stability
towards a protein's native structure.
- Dipole-Dipole Interactions Are Weak but Significantly
Stabilize Protein Structures
van der Waals forces.
- In The low dielectric constant core of a protein,
dipole-dipole interactions significantly influence protein folding.
- The great numbers of interatomic contacts in
proteins makes London forces a major influence in determining their conformations.
B. Hydrogen Bonding Forces
- Internal hydrogen bonding cannot significantly
stabilize, and, indeed, may even slightly destabilize, The structure of a
native protein relative to its unfolded state.
- The internal hydrogen bonds of a protein provide
a structural basis for its native folding pattern.
C. Hydrophobic Forces
- The hydrophobic effect is the name given to those
influences that cause nonpolar substances to minimize their contacts With
water, and amphipathic molecules, such as soaps and detergents, to form micelles
in aqueous solutions.
- Hydrophobic interactions must be an important
determinant of protein structures.
- It is enthalpically more favorable for nonpolar
molecules to dissolve in water than in nonpolar media
- The transfer of a hydrocarbon from an aqueous
medium to a nonpolar medium is entropically driven. The same is true of The
transfer of a nonpolar protein group from an aqueous environment to The protein's
- These entropy changes arise from some sort of
ordering of The water structure.
- Clathrates are hydrogen bonded cages that form
around nonpolar groups.
- The nonpolar substance is excluded from The aqueous
- Hydrophobic forces ARE A MAJOR INFLUENCE in causing
proteins to fold into their native conformations.
- Hydropathies have been cataloged for AA side
- The effects of hydrophobic forces are called
D. Disulfide Bonds
- Since disulfide bonds form as a protein folds
they stabilize The three dimensional structure.
E. Protein Denaturation
- When a protein is heated its conformationally
sensitive properties change abruptly over a narrow temperature range. This
is usually < 100' C except for thermophiles.
- Such a nearly discontinuous change indicates
that The native protein structure unfolds in a cooperative manner: Any partial
unfolding of The structure destabilizes The remaining structure, which must
simultaneously collapse to The random coil.
- The midpoint of this is known as The proteins
- Some salts stabilize proteins in heated conditions,
- (NH4)2SO4 and KH2PO4 stabilize
- KCl and NaCl are neutral
- KSCN and LiBr destabilize
- The various ions are ordered in The Hofmeister
- Destabilizing ions are called chaotropic, they
also increase solubility of nonpolar substances in water.
5. Quaternary Structure
- Quaternary structure is known as its 4' structure.
A. Subunit Interactions
- hemoglobin is alpha2beta2
- proteins With identical subunits are called oligomers,
"gomers", get it?
- The identical units are called protomers.
- Hemoglobin is a dimer of two alphabeta protomers
- The contact regions between subunits resemble
The interior of a single subunit protein.
B. Symmetry in Proteins
- In the vast majority of oligomeric proteins,
the protomers are symmetrically arranged.
- Proteins can only have rotational symmetry.
- Mirror image or Inversion symmetries are not
allowed since that would require left handed residues to have right handed
- Cyclic symmetry is the simplest kind of rotational
- Dihedral symmetry is slightly more complex.
- Other symmetries include solids such as tetrahedral,
cubic, octahedral and icosahedral
- Helical symmetry can be a macro building block
as in muscle fibers.
C. Determination of Subunit Composition
- Hybridization Yields Quaternary Structural Information
- Succinylation Yields Quaternary Structural Information
- Cross-Linking Agents Stabilize Oligomers That