CHEM 437 Chp 6

What is true of similar structures in proteins?

They usually have a similar function. However, sometimes tertiary structures are exceptionally similar, even though their functions differ greatly.

What are the basic principles of protein structure and function?

• Function depends on the structure.

• The structure depends on the sequence and weak, noncovalent forces.

• The number of protein folding patterns is significant, but is not infinite.

• Structures of globular proteins are marginally stable.

• Marginal stability facilitates motion.

• Motion enables function.

What holds together the primary structure of a protein?

Covalent bonds

What are the weak forces that stabilize higher-level protein structures?

Hydrogen Bonding:

• Both between atoms in the peptide backbone and between side chains.

• Usually on the surface of proteins, but can also exist in the interior of proteins.

Ionic Interactions:

• Generally located on the surface of proteins.

Hydrophobic Interactions:

• Primarily found in the interior of proteins (drives protein folding).

Van der Waals Interactions:

• Van der Waals interactions are ubiquitous.

What are the four levels of protein structure? Describe them.

Primary Structure:

• The amino acid sequence.

Secondary Structure:

• Organization of amino acids into structures through hydrogen bonds.

Tertiary Structure:

• 3-dimensional organization of the secondary structures.

Quaternary Structure:

• Organization of several proteins, subunits.

Explain the plane characteristics of the peptide bond.

• The peptide bond is planar.

  • Rotation is allowed around two bonds.

    • The bond linking the a-carbon with its carbonyl carbon (its angle denoted with phi) and the bond linking the a-carbon with its amide nitrogen (its angle denoted with psi).

What are some unfavorable combinations of phi and psi?

• Phi= 0, psi= 180

• Phi= 180, psi= 0

• Phi= 0, psi= 0

Describe the secondary structures in proteins.

• Describe local conformations of the polypeptide chain that are stabilized by hydrogen bonds between adjacent amino acid residues.

• Involve the amide H of one peptide group and the carbonyl O of another.

• Allows the proteins to form regular structures.

• These structures can be helices or pleated segments.

What are the two principal secondary structures found in proteins?

• a-helices

• B-sheets

What is the a-helix?

• Ubiquitous component of proteins.

• Stabilized by H-bonds that are in the same direction.

• Right-handed helix

• Phi= -60, psi= -45

• Residue n forms a hydrogen bond with the n+4 residue.

  • 3.6 residues per turn

• Each amino acid extend 1.5 A along the helix axis, this is the rise per residue.

What is the substantial net dipole moment in a-helix?

• Each peptide bond possess a dipole moment that arises from the polarities of the N-H and C=O groups.

• Because these groups are aligned the helix axis, the a-helix has a significant dipole moment.

  • Partial +ve at the N-terminus.

  • Partial -ve at the C-terminus.

• The first four amide hydrogens and the last four carbonyl oxygens cannot participate in helix hydrogen bonds.

Which amino acids are helix formers?

Ala, Gly, Phe, His, Ile, Leu, Met, Gln, Arg, Trp, and Tyr

Which amino acids are variable?

Cys, Asp, Lys, Thr, Val

Which amino acid is a helix breaker?

Pro

What amino acid is indifferent?

Gly

What amino acids are random coil?

Asn and Ser

What are B-strands and B-sheets? S

• β-strands form when a stretch of amino acids adopts ɸ and ψ angles of -120 and 120, respectively.

• β-strands do not exist standalone because there is nothing to stabilize the structure.

• To stabilize, another stretch of amino acids should form a β strand, with which the first strand can interact, which forms a β sheet.

• Side chains, or R groups, of consecutive amino acids are on opposite sides of the sheet.

How are B-strands represented?

With arrows with the arrowhead indicating the direction from N-terminus to C-terminus.

Describe the parallel/antiparallel nature of B-sheets.

• At least 5 strands in parallel are needed for 𝛽-sheets to be stable, whereas

antiparallel sheets are stable with 2.

• 3.25 A for the rise/residue of parallel strands.

• 3.47 A for the rise/residue of antiparallel strands.

What are loops?

• Connect 𝛼-helices and β-strands.

• Divided into structured and unstructured loops.

What are B-turns?

• Most proteins are globular structures, so the polypeptide chain must be able

to bend to achieve the final structure.

• This occurs through a fascinating process called β-turn formation. In this

case, the peptide chain forms a loop, with the carbonyl oxygen of one amino

acid forming a hydrogen bond with the amide hydrogen of the residue three

residues down the chain.

• Four residues are required to form a β-turn

Describe the tertiary structure of proteins.

• The arrangement of all atoms of a single polypeptide chain in 3-dimensional space, how the polypeptide folds upon itself.

• Proteins fold to form the most stable structure possible. The stability of most proteins arises from the following:

  • The formation of many intramolecular hydrogen bonds.

  • The reduction in the surface area accessible to the solvent that occurs upon folding.

• Proteins are typically a mixture of hydrophilic and hydrophobic amino acids.

• The hydrophobic groups tend to cluster together in the folded interior of the protein.

• Stabilized by van der Waals interactions, hydrophobic interactions, hydrogen bonding, electrostatic interactions, and disulfide covalent bonds.

What are the three main classes of biological proteins and some of their basic characteristics?

• Fibrous

  • Simple, linear structure

  • Insoluble in water

• Globular

  • Roughly spherical

  • Soluble in water

• Membrane

  • Hydrophobic exterior

  • Insoluble in water

What are fibrous proteins?

• Consist of polypeptide chains organized along a single axis, producing long fibers.

• Tend to be mechanically strong and play a structural role in nature.

• Usually insoluble

• Ex: 𝛼-keratin, fibroin, collagen

What is a-keratin?

• a-keratins are the predominant constituents of claws, fingernails, hair,
  etc., in mammals.

• 𝛼-helical segments dominate their structure.

• The sequence consists of 311-314-residue-long 𝛼-helical rod segments
  capped with non-helical N- and C-termini.

• The primary structure of helical rods consists of 7-residue repeats: (a-

b-c-d-e-f-g)n, where a and d are nonpolar.

• This structure promotes helix association to form coiled coils.

What is fibroin?

• Found in silk fibers and bird feathers.

• Fibroin proteins form extensive β-sheets with an alternating sequence: Gly-Ala/Ser-Gly-Ala/Ser...

What is collagen?

• The principal constituent of connective tissues.

• Very high proline content.

• 1 out of 3 residues is glycine, forming long stretches of the polypeptide chain consisting of Gly-Pro-Pro repeats.

• Not suitable for 𝛼-helices or β-sheets.

• Suited for the collagen triple helix: three intertwined helical strands.

What are globular proteins?

• Globular proteins exist in an enormous variety of 3D structures.

• Nearly all globular proteins contain large amounts of 𝛼-helices and β-sheets folded into a compact structure.

• Both polar and nonpolar interactions stabilize the tertiary structure of globular proteins.

• Helices and sheets make up the core of most globular proteins.

• Most polar residues face the outside of the protein and interact with solvent.

• Most hydrophobic residues face the interior of the protein and interact with each other.

• Globular proteins include enzymes and the proteins involved in signaling and immune responses.

Give an example of a globular protein and describe.

• Bovine ribonuclease A

• The space between the helices and sheets in the interior of the protein is tightly filled with residues that have mostly hydrophobic side chains.

• Most polar side chains face the outside of the structure and interact with water.

How does water play a critical role in globular protein structure?

• The surface structure of a globular protein also includes water molecules.

• There are often several water molecules per amino acid residue.

• The polar backbone and side chain groups on the protein surface make H-bonds with solvent water.

• Relatively few water molecules are found inside the protein.

What is a-helix wheel representation?

• A helical wheel presentation can reveal the amphiphilic nature of an α-helix.

• One face of this 𝛼-helix has four hydrophobic residues (inner), while the other face (outer) contains predominantly hydrophilic residues.

• Less commonly, an 𝛼-helix can be buried in the interior of a protein.

• This 𝛼-helix is highly hydrophobic and contains only two polar residues.

• Less commonly, an 𝛼-helix can be completely exposed to solvent.

• This 𝛼-helix consists of ten charged residues, two polar residues, and only two nonpolar residues.

What are the four classes of protein groups based on secondary structure arrangements?

• All α proteins, in which α helices predominate.

• All β proteins, in which β sheets predominate.

• α/β proteins, in which helices and sheets are intermingled.

• (α + β) proteins, which contain separate α-helical and β-sheet domains.

Describe the quaternary structure of proteins.

• Quaternary structure is used in cases where proteins are composed of two or more polypeptide chains (also called subunits).

• How the polypeptide chains/subunits interact with each other.

• Stabilized by hydrophobic interactions, hydrogen bonding, electrostatic interactions, disulfide bonds, Van der Waals interactions, and sometimes, interactions with metal ions.

What has all of the information required for protein folding?

• All the information needed to fold a polypeptide into its native structure is contained within the amino acid sequence.

• This was confirmed in the 1950s with a study examining the denaturation and renaturation of proteins.

  • Solutions of ribonuclease were treated with a combination of:

    • Urea: Unfolded the protein.

    • BME: Reduced the disulfide bridges.

What is Levinthal’s Paradox?

A typical protein can adopt so many conformations that it does not have enough time to reach its most stable state by sampling all possible configurations.

What dictate function?

• Stability is important for function, but proteins are often only marginally stable. So, flexibility and motion are important for proteins to function, and proteins are best viewed as dynamic structures.

• Most globular proteins oscillate and fluctuate continuously about their average structures.

• This flexibility is essential for a variety of protein functions, including:

  • Ligand binding

  • Enzyme catalysis

  • Enzyme regulation

What are the folding tendencies and patterns in globular proteins?

• Globular proteins adopt the most stable tertiary structure possible by:

  • Satisfying the constraints inherent in their own structure.

  • Folding to bury the hydrophobic side chains.

    • This leads to the formation of “layers” of structure in the protein.

• Polypeptide chains tend to twist slightly in a right-handed direction.

• This tendency is manifested in the formation of right-handed twists in β-sheets and right-handed crossovers in parallel β-sheets.

What is the form of natural proteins?

• Many proteins are multimeric, and they are symmetric arrangements of asymmetric objects.

• Proteins with two or four subunits predominate in nature.

• The typical KD for two subunits: 10−8 to 10−16 M, which correspond to energies of 50 to 100 kJ/mol at 37° C.

  • Entropy loss due to association is unfavorable, and entropy gain due to burying of hydrophobic groups is favorable.

What are intrinsically unstructured proteins (IUPs)?

• Many proteins exist and function normally in a partially unfolded state.

• Characterized by an almost complete lack of folded structure and high flexibility.

• Adopt well-defined structures in complexes with their target proteins.

• Characterized by an abundance of polar residues and a lack of hydrophobic residues.

What is an example of an IUP?

• p53 is a tumor suppressor protein consisting of an N-terminal disordered domain of 93 residues, a central DNA-binding domain of 200 residues, a C-terminal disordered domain of 100 residues.

• N-terminal domain of p53 binds to over 40 different proteins, and C-terminal domain of p53 binds to over 50 different proteins.

• This large number of interactions is consistent with the involvement of p53 in multiple signaling and regulatory pathways.

What is the denaturation of proteins?

• Weak, noncovalent forces maintain the secondary, tertiary, and quaternary levels of protein structures.

• A variety of external stresses can disrupt these weak forces (e.g., pH and heat).

  • Heat will unfold the structure, losing the function.

  • Chemicals will disrupt the weak forces, covalent bonds are not affected.

• Denaturation is the loss of protein structure and function.