Protein Structure And Folding Flashcards
Secondary Structure components
• α-‐helices • β-‐strands and β-‐sheets • Other (loops)
Four levels of Protein Structure
Primary structure – amino acid sequence •
Secondary structure –local conforma=on of pep=de backbone • Ter2ary structure – interac=on of different secondary structures in the same polypep=de •
Quaternary structure – interac=on between different polypep=des in a protein containing two or more polypep=des
The Alpha (α) Helix
The alpha (α) helix is a regularly repea=ng structure of amino acids with 3.6 residues per turn and 5.4 Angstroms (Å) per turn. •
It was the first secondary structure proposed. •
The carbonyl (C=O) and amide (N-‐H) groups of the pep=de bonds are hydrogen bonded. •
Hydrogen bonding occurs between the i and i+4 residues in the helix. • The α-‐helix is a right-‐handed helix. •
All of the amino acid side chains are on the outside of the helix.
The Beta Sheet
• Each unit of the β-‐sheet is called a β-‐strand. •
Proteins o_en contain β-‐sheet or β-‐barrel structures. •
The β-‐strands may interact in parallel or an=parallel orienta=ons. •
The C=O group of an amino acid in one β-‐strand forms a hydrogen bond with the N-‐H group of an amino acid in the adjacent strand. • Side chains point in opposite direc=ons along the length of the strand. • β-‐sheets are o_en twisted.
Anti-Parallel β-Sheet
In an=-‐parallel β-‐sheets, the polypep=de chains of neighboring β-‐strands have opposite orienta=ons.
Parallel Beta Sheet
In parallel β-‐sheets, the polypep=de chains of neighboring β-‐strands have the same orienta=on.
Mixed β-‐Sheets
Contain both parallel and anti parallel
Loops in Protein Structures
Loops are irregular structures that connect to secondary structures in proteins (shown in red)
Beta sheets can twist to such an extent that they close in themselves and form a beta barrel
Loops between α- helices or β-sheets often are very important functional domains of proteins •
Loops do not adopt regular secondary structure with defined geometry as do α- helices and β-strands.
Ter=ary Structure of Proteins
Ter=ary structure describes how the secondary structure elements (e.g., α-‐ helices and β-‐strands) are oriented rela=ve to each other in space. • The structure of globular proteins can be composed of α-‐helices, β-‐strands, or a combina=on of the two types of secondary structures.
Myoglobin
Composed of α-‐helices.
Fatty Acid-‐binding Protein:
Composed mostly of β-‐strands.
Some alpha helical elements
Domain Structure of Proteins
A domain is a discrete region of the polypep=de chain that folds into an independent unit. •
A protein can consist of one or more domains. Larger proteins (≥300 amino acids in length) o_en consist of mul=ple domains, such as shown below for the protein CD4
• The conforma=on of the domain is mostly independent of other domains in the protein. •
The domains are usually globular and consist of 100 to 400 amino acids that fold independently. •
Domains can be composed of either α-‐helices, β-‐sheets, or a mixture of the two types of secondary structures.
Quaternary Structure
Proteins composed of two or more polypep=de chains possess quaternary structure. •
Quaternary structure refers to the orienta=on and interac=ons of the polypep=de chains in the protein.
Example:
Cro Protein: a dimer composed of two polypep=des (colored red and yellow)
Hemoglobin: a tetramer of 2 α subunits (red) and 2 β subunits (yellow)
Protein Folding
A newly synthesized protein is produced in an unfolded state and can adopt many different conforma=ons referred to as an unfolded ensemble. •
Folded proteins generally adopt a single uniform conforma=on. •
The process by which proteins fold is powered by the hydrophobic effect. •
Many weak interac=ons, such as electrosta=c interac=ons, hydrogen bonds and van der Waals interac=ons, stabilize the three-‐dimensional structure of a folded protein.
Protein Folding and the Hydrophobic Effect
The folding of protein from a polypep=de chain is driven by the hydrophobic effect. •
Hydrophobic amino acids in the polypep=de are buried in the interior of the protein, shielding them from water. •
Hydrophilic and charged amino acids are generally found on the surface of the protein where they can form hydrogen bonds with water.
Thermodynamics of Protein Folding Can Be Represented by a Funnel
The free energy difference between the unfolded (denatured) and folded states of a typical 100 residue protein is 42 kcal/mol. •
The top of the funnel represents all possible conforma=ons of the denatured protein. •
The molten globule states represent intermediates in the folding pathway between the denatured state and the na=ve structure. •
At the bojom of the funnel is the folded (na=ve) structure of the protein, represen=ng the lowest energy state.
Unfolded proteins have hydrophobic side chains which water forms cage structures around, which is unfavorable for water because they want to diffuse freely. Water molecules released as hydrophobic side chains pack within interior of protein
Ribonuclease A – Example of a Protein with Disulfide Bonds
Ribonuclease A is an enzyme that degrades RNA
Ribonuclease A has four pairs of disulfide bonds (color-‐coded in the figures above). •
Ribonuclease A cannot be readily denatured (unfolded) because the disulfide bonds stabilize the protein’s ter=ary structure. •
To denature Ribonuclease A, the disulfide bonds must first be reduced by β-‐ mercaptoethanol or another reducing reagent.
β-‐mercaptoethanol
Reagent that Reduces Disulfide Bonds
β-‐mercaptoethanol (βME) reduces disulfide bonds in proteins, genera=ng the reduced sullydryl groups in cysteine. •
In the process of reducing the protein’s disulfide bonds, 2 molecules of β-‐ mercaptoethanol form a disulfide bond.
Ribonuclease A – Effect of β-Mercaptoethanol During Denaturation
Ribonuclease A is resistant to denatura=on because the 4 disulfide bonds stabilize its ter=ary structure. •
β-‐mercaptoethanol can be used to reduce the 4 disulfide bonds in Ribonuclease A. •
After the disulfide bonds are reduced, Ribonuclease A can be unfolded using denaturing reagents, such as urea or guanidinium chloride.
Certain Neurological Diseases Result from Protein Misfolding
Bovine Spongiform Encephali=s (BSE, mad cow disease) and Creutzfeldt-‐Jacob (CJD) disease result from prion protein (PrP) aggrega=on in neural =ssue, which is associated with the death of the neurons. •
Forma=on of amyloid fibers and plaques from neuronal proteins are also believed to contribute to neurodegenera=ve disorders, such as Alzheimer and Parkinson Diseases, by killing neurons. NOT BY PRIONS
