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 polypeptide chain.
• It was discovered via model building by Pauling in 1951.
• 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 chains .
• 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 NMR Structures

• X-Ray crystallography is a technique that directly images molecules.
• An X-Ray structure is an electron density map taken from multiple angles.
• Protein Crystal Structures Exhibit Less Than Atomic Resolution
• Most Crystalline Proteins Maintain Their Native Conformation
• 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 Functional Roles
  Certain groupings of secondary structural elements named supersecondary structures or motifs, occur in many unrelated globular proteins.
• bab 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 Stabilize Proteins
  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 nonpolar interior.
• 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 phase.
• Hydrophobic forces ARE A MAJOR INFLUENCE in causing proteins to fold into their native conformations.
• Hydropathies have been cataloged for AA side chains.
• The effects of hydrophobic forces are called hydrophobic bonding.

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 melting temperature.
• Some salts stabilize proteins in heated conditions, some destabilize.
• (NH4)2SO4 and KH2PO4 stabilize
• KCl and NaCl are neutral
• KSCN and LiBr destabilize
• The various ions are ordered in The Hofmeister series.
• 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 duals.
• Cyclic symmetry is the simplest kind of rotational symmetry.
• 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 Decompose Easily