Lecture 4

Protein 3-Dimensional Structure and Function

• Conformation – spatial arrangement of atoms in a protein • Native conformation – conformation of functional protein

Protein Classification
• Simple – composed only of amino acid residues • Conjugated – contain prosthetic groups (metal ions, co-factors, lipids, carbohydrates) Example: Hemoglobin – Heme

Protein Classification
• One polypeptide chain - monomeric protein • More than one - multimeric protein • Homomultimer - one kind of chain • Heteromultimer - two or more different chains (e.g. Hemoglobin is a heterotetramer. It has two alpha chains and two beta chains.)

Protein Classification
Fibrous –
2) 3) 4) 5) polypeptides arranged in long strands or sheets water insoluble (lots of hydrophobic AA’s) strong but flexible Structural (keratin, collagen)

Globular –
8) 9) 10) 11) polypeptide chains folded into spherical or globular form water soluble contain several types of secondary structure diverse functions (enzymes, regulatory proteins)




4 Levels of Protein Structure
linear sequence of amino acids regular patterns formed by primary structure folding

completely folded polypeptide with one or more domains

association of multiple polypeptides; not found in all proteins

Non-covalent forces important in determining protein structure
• • • • van der Waals hydrogen bonds ionic bonds hydrophobic interactions

1o Structure Determines 2o, 3o, 4o Structure Sickle Cell Anemia – single amino acid change in hemoglobin related to disease (6th A.A. (glutamic acid)  valine).

2o Structure Related to Peptide Backbone
•Double bond nature of peptide bond cause planar geometry •Free rotation at N - aC and aC- carbonyl C bonds •Angle about the C(alpha)-N bond is denoted phi (f) •Angle about the C(alpha)-C bond is denoted psi (y) •The entire path of the peptide backbone is known if all phi and psi angles are specified

Not all φ/ψ angles are possible

Ramachandran Plots
• Describes acceptable ψ/Ф angles for individual AA’s in a polypeptide chain. • Helps determine what types of 2o structure are present

Based on calculations

Based on observations in known protein structurs

solid line (permissible of Ф and ψ, for most residue dashed line (permissible Ф and ψ, for an alanine residue. blank area (non permissible Ф and ψ)

Enclosed inner region = found inhigh frequency Enclosed outer region = found in less frequency + α-helix; + β-strand; + other

Classes of 2o Structure
• Alpha helix • B-sheet • Loops and turns

• First proposed by Linus Pauling and Robert Corey in 1951 and by Max perutz. • Identified in keratin. • Most common component of proteins • Stabilized by H-bonds

Right handed helix •Residues per turn: 3.6 •Rise per residue: 1.5 Angstroms •Rise per turn (pitch): 3.6 x 1.5A = 5.4 Angstroms •amino hydrogen Hbonds with carbonyl oxygen located 4 AA’s away forms 13 atom loop

Alpha-Helix dipole
All H-bonds in the alpha-helix are oriented in the same direction giving the helix a dipole with the N-terminus being positive and the Cterminus being negative

•Side chain groups point outwards from the helix •Ala most common A.A. •AA’s with bulky side chains (Tyr, Asn) less common in alpha-helix •Gly and pro destabilizes alpha-helix

Amphipathic Alpha-Helices

One side of the helix (dark) has mostly hydrophobic AA’s Two amphipathic helices can associate through hydrophobic interactions

Beta-Strands and Beta-Sheets
• • • • • Also first postulated by Pauling and Corey, 1951. β-strands almost fully extended α-helix. Sheet is multiple β-strands in sheets or layer Strands may be parallel or antiparallel Rise per residue: – 3.47 Angstroms for antiparallel strands – 3.25 Angstroms for parallel strands – 1.5 Angstroms for α-helix

• Beta-sheets formed from multiple sideby-side beta-strands. • Can be in parallel or anti-parallel configuration • Anti-parallel betasheets (H-bond perpendicular) more stable

• Side chains point alternately above and below the plane of the beta-sheet • 2- to 15 beta-strands/beta-sheet • Each strand made of ~ 6 amino acids

Loops and turns
• Non repetitive 3-D structure. • Cause directional change in the polypeptide backbone. • Bond angles are constrained, so that only certain directional changes are permitted. Loops • Loops usually contain hydrophillic residues. • Found on surfaces of proteins • Connect alpha-helices and beta-sheets Turns • Loops with < 5 AA’s are called turns • Beta-turns are common

• allows the peptide chain to reverse direction • carbonyl C of 1rst residue is H-bonded to the amide proton of a4rth residue (n+3). • proline and glycine are prevalent in beta turns