Lecture 5 - Protein Structure and Function - part 1: Sequences Determines Structure

What drives protein folding

• why do proteins want to fold - to produce what kind of structure

• folding by covalent and non-covalent interactions

• Proteins will fold to find the most stable structure

Three common themes in a 3D protein structure

• flexible enough to function with other proteins

• Stable enough that it will not change to another conformation

• Exposed amino acids are compatible to the environment where proteins will function

Levels of protein structure

• primary: linear sequence of AA Encoded by the DNA

• Secondary: periodic, regular structures (folding of a -helix and B-beta strands)

• Tertiary: Secondary structures folding into motifs and domains through non-covalent interactions

• Quaternary: assembly of multiple polypeptides to form multiple subunit structures

Primary structure chains of amino acids

• directionality

• Which atom does the backbone of the peptide chain begin with?

• Amino (N) terminal end is the beginning of the chain

• Backbone consists of the peptide bonds and the a-carbons of each amino acidss

Peptide bond

• characteristics

• Polar, uncharged bonds

• experiences resonance, and the characteristics of a double-bond

• Rigid and planar - e.g. very little rotation

𝜙 and Ѱ angles

• how does it rotate (which atoms)

• How much can it twist?

• rotation allowed around the bond linking of amide 𝜙 and carbony Ѱ from the

• can twist range of -180 to +180, but depending on the structure, not all angles are premitted

• Steric clashes need to be minimized to reduce hydrophobic strains, therefore should not twist with side chains are trans to one another

Levels of proteins structure: types of bonding

• primary: peptide bonds

• secondary: hydrogen bonds

• tertiary and quaternary: disulfide bonds, electrostatic interactions hydrogen bonds, hydrophobic interactions

Secondary structure - H bonding

• types of bonding

• a-helix

• B-strands and b-sheet: includes B-turns

a-helices: where in the strand does this folding occur in

• intra-strand h-bonds forming between peptide backbone

• Carboxyl bonds with an amino group 4 residues away

• 3.6 residues per 360 turn, 1.5 A high each

Proline: Helix breaker

• what is special about proline

• proline is an amino acid not typically present in a a-helix

• This is because it is called a helix breaker

  • its side chains will covalently bind to the amino group in the peptide bond

  • Doesn’t allow for the proper 𝜙 and carbony Ѱ angle to form the coil we typically see in a helix

A-helices: projecting side-chains

• shape of the helix + side chain facing what direction

• right handed helix with side chains pointing out from the coil

B strands and B sheets

• how does H-bonding work

• H bond links to nearby or distant portions of the polypeptide to form b-sheets

  • R groups alternating to prevent steric strain

• Strand either runs parallel, antiparallel, or mixed of both

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B-pleated sheet

• difference compared to a-helices

• dimensions more extended when compared to the a-helices (spaced out)

• Strands come together results in the sheet to get twisted

B-turns

• a 4 residue segment allowing for turn of peptide 180 degrees

• found on the surface of a globular proteins, connecting secondary structure

• H bonds form between the carbonyl o2 and the amine hydrogen of the peptide backbone at position 1 and four

• Proline amino acid common at position 2

• Gly, Adn, and Ser is freq seen in turns \

Side chains and secondary structures

• the allowable angles for the two bonds depend on the side chains

Tertiary structure

• Electrostatic (ionic) Interactions

• Hydrogen bonds

• Hydrophobic Interactions

• Disulphide bonds

• Electrostatic (ionic) Interactions: interactions between charged groups on different amino acids

• Hydrogen bonds: interactions between amino acids mediated by the partial positive charger on hydrogen and partial negative charges on other atoms

• Hydrophobic interactions: grouping of non-polar amino acids (non-specific associations between closely packed atoms a.k.a Wan der Waals)

• Disulphide bonds: a covalent bond only forms by two cyctseines to form a cystine

Tertiary structure

• What are non-covalent bonds responsible for

• What are ligands responsible for

• What are post-translational modifications responsible for

• non-covalent interactions and disulphide bonds helps form the 3D shape of the protein structure through brining distant regions of the polypeptide together

• Ligands: Stabilizes or prevent specific interactions between the r groups

• Post-translational modification: alter the functional group and therefore the structure of the protein

Protein Folding

• what interaction is the main driving force to protein folding

• What do chaperones help with

• Meaning of random coils

• Why do proteins like being in their native structure

• hydrophobic effect: main driving force in protein folding

• Chaperones: prevent aggregation of the newly synthesizes and unfolded protein by binding to exposed hydrophobic regions

• Random coils: no random - may be very stable

• Native protein structure = best energetically stable conformation

Tertiary structure protein folding

• what are motifs + functions

• What are domains

• motifs: common combinations of secondary structures

  • Common motifs = common functions

• Domains: independently folding regions within a polypeptide , connected by a short, flexible linker segment

  • Common domains = common functions - analysis of a protein sequence can help predict the functional domains

Post-translational modifications (PTMs)

• what are ptm’s

• What structure do they change

• what opportunities do they provide

• PTMs modify an amino acid within a protein

• Altering interactions btw/ amino acids and change the teritary and quaternary structure

• provides new sites for protein-protein interactions

Quaternary structure

• the arrangwment of multiple subunits of polypeptide chains

• may consist of non-identical or identical polypeptides

• different subunits due to the multiple genes of the post-translational cleavage of precursors

Protein Denaturation

• protein structure held together by numerous weak forces

• Denaturation: the disruption of the weak forces by external stresses like heat, ph or chemical treatments

• the result is the loss of structure and function

Human genome and the globin protein

• the globin protein have 9 isoforms

• Depending on the context, have similar functions