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Chapter 3
• Protein Structure
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The SH2 domain
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SEQUENCE DETERMINES STRUCTURE
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Levels of protein structure
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PRIMARY STRUCTURE
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A peptide bond
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The requirement that no two atoms overlap limits greatly the possible bond angles in a polypeptide chain
Each amino acid contributes three bonds (red) to thebackbone of the chain. The peptide bond is planar(gray shading) and does not permit rotation. Rotationcan occur about the C-C bond, whose angle of rotationis called psi (), and about the N-C bond, whose angleof rotation is called phi ()
The conformation of the main-chain atoms in a proteinis determined by one pair of and angles for eachacid. Because of steric collisions between atoms withineach amino acid, most pairs of and angles do notoccur. Each dot, in the Ramachandran plot shown here, represents an observed pair of angles in a protein. In-helices, the backbone dihedral angles, and have repeating values of -60°and -40° respectively.
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some proteins containing proline.
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SECONDARY STRUCTURE
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The helix is one of the major elements of secondary structure in proteins.
Main-chain N and O atoms are hydrogen-bonded to each other within helices. (a) Idealized diagram of the path of the main chain in an helix. Alpha helices are frequently illustrated in this way. There are 3.6 residues per turn in an helix, which corresponds to 5.4 angstrom (1.5 angstrom per residue). (b) The same as (a) but with approximate positions for
main-chain atoms and hydrogen bonds included. The arrow denotes the direction from the N-terminus to the C-terminus. (c) Schematic diagram of an helix. Oxygen atoms are red, and N atoms are blue. Hydrogen bonds between O and N are
red and striated. The side chains are represented as purple circles.
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The α-helix. The NH of every peptide bond is hydrogen-bonded to the CO ofa neighboring peptide bond located four peptide bonds away in the same
chain
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The b-sheet. The individual peptide chains (strands) in a b-sheet are heldtogether by hydrogen-bonding between peptide bonds in different strands
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The structure of a coiled-coil
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TERTIARY STRUCTURE
Proteins fold into a conformation of lowest energy
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Three types of noncovalent bonds that help proteins fold
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A protein folds into a compact conformation
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Hydrogen bonds in a protein molecule
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A protein domain is a fundamental unit of organization
domains - structural units that fold more or less independently of each other
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The Src protein
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The Src protein
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Ribbon models of three different protein domains
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PROTEIN FOLDING
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How does a protein chain achieves its native conformation?
As an example, E. coli cells can make a complete, biologically activeprotein containing 100 amino acids in about 5 sec at 37°C.
If we assume that each of the amino acid residues could take up 10 different conformations on average, there will be 10100 differentconformations for this polypeptide.
If the protein folds spontaneously by a random process in which ittries all possible conformations before reaching its native state, andeach conformation is sampled in the shortest possible time (~10-13 sec),it would take about 1077 years to sample all possible conformations.
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There are two possible models to explain protein folding:
In the first model, the folding process is viewed as hierarchical, in whichsecondary structures form first, followed by longer-range interactions toform stable supersecondary structures. The process continues untilcomplete folding is achieved.
In the second model, folding is initiated by a spontaneous collapse of thepolypeptide into a compact state, mediated by hydrophobic interactionsamong non-polar residues. The collapsed state is often referred to as the‘molten globule’ and it may have a high content of secondary structures.
Most proteins fold by a process that incorporates features of both models.
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Takada, Shoji (1999) Proc. Natl. Acad. Sci. USA 96, 11698-11700
Thermodynamically, protein folding can be viewed as a free-energy funnel
- the unfolded states are characterized by a high degree of conformational entropy and relatively high free energy- as folding proceeds, narrowing of the funnel represents a decrease in the number of conformational species present (decrease in entropy) and decreased free energy
Schematic pictures of a statistical ensemble of proteins embedded in a folding funnel for a monomeric -repressor domain. At the top, the protein is in its denatured state and thus fluctuating wildly, where both energy and entropy are the largest. In the middle, the transition state forms a minicore made of helices 4 and 5 and a central region of helix 1 drawn in the right half, whereas the rest of protein is still denatured. At the bottom is the native structure with the lowest energy and entropy.
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A schematic energy landscape for protein foldingNature 426:885
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Steps in the creation of a functional protein
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The co-translational folding of a protein
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The structure of a molten globule – a molten globule form of cytochrome b562
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Molecular chaperones help guide the folding of many proteins
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A current view of protein folding
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A unified view of some of the structures that can be formed by polypeptide chains
Nature 426: 888
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The hsp70 family of molecular chaperones. These proteins act early,recognizing a small stretch of hydrophobic amino acids on a protein’s
surface.
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The hsp60-like proteins form a large barrel-shaped structure that actslater in a protein’s life, after it has been fully synthesized
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Nature 379:420-426 (1996)
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Cellular mechanisms monitor protein quality after protein synthesis
Exposed hydrophobic regions provide critical signals for protein quality control
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The ubiquitin-proteasome pathwayNature 426: 897
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The proteasome
Processive cleavage of proteins
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Figure 6-90 Molecular Biology of the Cell (© Garland Science 2008)
Processive protein digestion by the proteasome
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Figure 6-91a Molecular Biology of the Cell (© Garland Science 2008)
The 19S cap – a hexameric protein unfoldase
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Figure 6-91b Molecular Biology of the Cell (© Garland Science 2008)
Model for the ATP-dependent unfoldase activity of AAA proteins
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Ubiquitin – a relatively small protein (76 amino acids)
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Abnormally folded proteins can aggregate to cause destructive human diseases
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(C) Cross-beta filament, a common type of protease-resistant protein aggregate
(D) A model for the conversion of PrP to PrP*, showing the likely change of two α-helices into four β-strands
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Regulation of protein folding in the ER
Nature 426: 886
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A schematic representation of the general mechanism of aggregation to form amyloid fibrils.
Nature 426: 887
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Proteins can be classified into many families – each family memberhaving an amino acid sequence and a three-dimensional structure
that resemble those of the other family members
The conformation of two serine proteases
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A comparison of DNA-binding domains (homeodomains) of the yeast α2 protein (green) and the Drosophila engrailed protein (red)
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Sequence homology searches can identify close relatives
The first 50 amino acids of the SH2 domain of 100 amino acids compared for the human and Drosophila Src protein
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Multiple domains and domain shuffling in proteins
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Domain shuffling
An extensive shuffling of blocks of protein sequence (protein domains)has occurred during protein evolution
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A subset of protein domains, so-called protein modules, are generallysomewhat smaller (40-200 amino acids) than an average domain
(40-350 amino acids)
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Each module has a stable core structure formed from strands of β sheet and they can be integrated with ease into other proteins
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Fibronectin with four fibronectin type 3 modules
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Figure 3-18 Molecular Biology of the Cell (© Garland Science 2008)
Relative frequencies of three protein domains
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Figure 3-19 Molecular Biology of the Cell (© Garland Science 2008)
Domain structure of a group of evolutionarily related proteins that have a similar function – additional domains in
more complex organisms
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Quaternary structure
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Lambda cro repressor showing “head-to-head” arrangement of identical subunits
Larger protein molecules often contain more than one polypeptide chain
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DNA-binding site for the Cro dimer
ATCGCGATTAGCGCTA
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The “head-to-tail” arrangement of four identical subunits that form a closed ring in neuraminidase
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HEMOGLOBIN
A symmetric assembly of two different subunits
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A collection of protein molecules, shown at the same scale
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Protein Assemblies
Some proteins form long helical filaments
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Helical arrangement of actin molecules in an actin filament
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Helices occur commonly in biological structures
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A protein molecule can have an elongated, fibrous shape
Collagen
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Elastin polypeptide chains are cross-linked together to form rubberlike, elastic fibers
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Disulfide bonds
Extracellular proteins are often stabilized by covalent cross-linkages
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Proteolytic cleavage in insulin assembly