Protein Architecture & Biological Function (Chapter 4)

™The functional activity of a protein under cellular conditions depends on

its folding into a distinct, 3D structure called the native conformation.
4.1 General Principles of Protein Design
-the amino acid sequence (1° structure) strongly influences a protein’s 3D
structure & function
-noncovalent interactions contribute to structural stability of a protein
4.2 Elements of Secondary Structure
-localized regions of a protein that fold into regular repeating structures such
as the α-helix, β-sheet, bends & loops
4.3 Protein Tertiary Structure
-describes the position of all atoms in a polypeptide including side chains
-a protein with a unique 1° structure will fold spontaneously into its distinct,
biologically active 3° structure (molecular chaperones may assist)
4.4 Protein Quaternary Structure
-4° structure defines the arrangement of subunits in a multisubunit protein
4.5 Protein Structure & Biological Function
-hemoglobin transports O2 through bloodstream; binding of O2 at heme Fe2+
induces conformational changes within that subunit & in its adjacent
subunits (allosteric interactions & positive cooperativity)
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4.1 General Principles of Protein Design

Learning Objectives: know the structural factors that contribute to the 3D arrangement of
proteins; strong influence of 1° structure on 3° structure & noncovalent interactions are
important in the structural stability of proteins
™Extended polypeptide chain folds into “native” biologically active 3D
shape (conformation)
™Folded structure depends on noncovalent interactions, solvent
interactions, pH, ionic strength & sequence of amino acids in the protein

™EXAMPLE: What specific covalent and/or noncovalent interactions stabilize

each of the four levels of protein structure?
1º Structure –

2º Structure –

3º & 4º Structure –
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Examples of the Stabilizing Forces in Proteins

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Structure of the Peptide Bond

™Four Structural Characteristics of the Peptide Bond
1) Trans Geometry

2) Partial Double Bond Character

3) Coplanar (Amide Plane)

4) Polar
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4.2 Elements of Secondary Structure

Learning Objectives: be able to describe the important structural features that make up
the secondary structure of proteins (α-helix, β-sheet, β-bend & loop regions)

The α-Helix

™EXAMPLE: What specific noncovalent

interaction stabilizes the α-helix?

™EXAMPLE: What is the length of an

α-helix containing 20 amino acids?

™EXAMPLE: What amino acids destabilize the α-helix?

™EXAMPLE: What amino acids stabilize the α-helix?

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Secondary Structure
The β-Sheet

™EXAMPLE: What specific noncovalent

interaction stabilizes the β-sheet?

™EXAMPLE: Is the β-sheet at right (a)

considered parallel or antiparallel?

™EXAMPLE: Is the β-sheet at right (b)

considered parallel or antiparallel?
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Secondary Structure
Bends (Reverse Turns)

™EXAMPLE: What amino acids are prevalent in

bends & turns?

Loop Regions

™EXAMPLE: Give one example of a

supersecondary structure or structural motif.
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4.3 Protein Tertiary Structure

Learning Objectives: have a general understanding of how proteins fold into their native
conformation

™The 3° structure of a protein describes the positions of all atoms in the

protein including side chains
™Hydrophobic interactions (formation of a hydrophobic core) drive the
process of protein folding
™EXAMPLE: What are disulfide bonds & what is their role in the protein folding
process?
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Protein Folding
™Protein Folding in Three Steps
1) rapid 2° structure formation/hydrophobic collapse (<5 µs)
2) continued growth of 2° structure, protein motifs combine to form protein
domains (5 – 1000 ms)
3) packing into a single compact structure, formation of disulfide bonds (>1 s)
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Molecular Chaperones
™Although many small proteins fold spontaneously after synthesis at the
ribosome, some are assisted in the protein folding process by molecular
chaperones
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Protein Unfolding
™Denaturation of a protein is the loss of 2°
& 3° structure AND the loss of biological
function. Sometimes is reversible.
™EXAMPLE: When a protein denatures, are
the covalent peptides bonds (1° structure)
broken?

™EXAMPLE: List common agents

used to denature protein.

™EXAMPLE: What effect would

disulfide bonds have on the
process of denaturation?
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4.4 Protein Quaternary Structure

Learning Objectives: understand how some protein subunits associate together to form a
quaternary structure
™The association of separate folded monomeric protein subunits into
oliogomeric protein is the 4° structure (subunit organization)
™Advantages of 4º Structure
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Architecture of Protein Molecules

™Three Classes of Proteins:
-Fibrous Proteins

-Globular Proteins

-Membrane Proteins
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4.5 Protein Structure & Biological Function

Learning Objectives: have a general understanding of the relationship between the
structure of a protein & its biological function, specifically hemoglobin
™Myoglobin & hemoglobin serve as a paradigm for understanding 1º, 2º, 3º
& 4º structure in proteins
™Myoglobin (Mb)

™Hemoglobin (Hb)
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Oxygen Binding to Myoglobin and Hemoglobin

™Myoglobin has a hyperbolic O2 binding curve (follows traditional
Michaelis-Menten enzyme kintics)
™Hemoglobin has a sigmoidal O2 binding curve (exhibits positive
cooperativity & allosteric control among subunits)
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Conformational Change in Hemoglobin Upon O2 Binding

™Deoxy Hb & Oxy Hb have significant structural differences at the heme
active site & in subunit interactions
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O2 Binding Affinity of Hemoglobin Affected by pH & BPG

™The Bohr effect is the decrease in O2 binding affinity as the pH decreases
™2,3-Bisphosphoglycerate (BPG) also decreases O2 binding affinity