Structure of Proteins
-adopt a specific three-dimensional conformation
-able to fulfill a specific biological function
-called the native fold
-native fold has a large number of favorable interactions within the protein
-There is a cost in conformational entropy of folding the
Favorable Interactions in Proteins
Hydrophobic effect
Hydrogen bonds
London dispersion
Electrostatic interactions
Hydrophobic effect
Release of water molecules from the structured solvation layer around the molecule as protein folds increases the net entropy
Hydrogen bonds
Interaction of N-H and C=O of the peptide bond leads to local regular structures such as alpha-helices and beta-sheets
London dispersion
Medium-range weak attraction between all atoms contributes significantly to the stability in the interior of the protein.
Electrostatic interactions
Long-range strong interactions between permanently charged groups
Salt-bridges, esp. buried in the hydrophobic environment strongly stabilize the protein
4 levels of protein structure
PRIMARY- aa sequence
SECONDARY- A regular repeating aa sequence that have close interactions.
TERTIARY- longer range (more than 10 AAs apart) and has two types which are fibrous and globulus proteins
QUATERNARY-multiple subunits come together in non coval
Structure of the peptide bond
The resonance causes these bonds:
-to be less reactive compared to esters, for example
-to be quite rigid and nearly planar
-to exhibit a large dipole moment in the favored trans configuration
Each peptide bond has some double-bond character due to resona
Rotation around bonds connected to the______________ is permitted?
alpha carbon
What are phi and psi?
are rotational angles around the alpha carbon
(phi): angle around the alpha-carbon and alpha-amine
(psi): angle around the alpha-carbon and alpha carboxyl
In a fully extended polypeptide, both y and f are 180�
The ___________ is made up of a series of planes linked at ? carbons
The rigid peptide backbone limits the range of conformation possible for this chain
polypeptide
what is the angle at the intersection of two planes?
dihedral
Distribution of phi and psi Dihedral Angles
Some phi and psi combinations are very unfavorable because of steric crowding of backbone atoms with other atoms in the backbone or side chains
Some combinations are more favorable because of chance to form favorable H-bonding interactions along the backb
Ramachandran plot
-shows the distribution of phi and psi dihedral angle rotations that are found in a protein
-shows the common secondary structure elements
-reveals regions with unusual backbone structure
Secondary Structures
-refers to a local spatial arrangement of the polypeptide backbone
-The alpha helix and beta sheet
-Irregular arrangement of the polypeptide chain is called the random coil
Alpha helix
-stabilized by hydrogen bonds between nearby residues
-Helical backbone is held together by hydrogen bonds between the backbone amides of an n and n+4 amino acids
-Right-handed helix with 3.6 residues (5.4 �) per turn
-Peptide bonds are aligned roughly pa
Beta sheets
-stabilized by hydrogen bonds between adjacent segments that may not be nearby.
-Backbone nearly fully extended (not coiled)
The planarity of the peptide bond & tetrahedral geometry of the alpha-carbon create a pleated sheet-like structure
-Sheet-like arr
The inner diameter of the helix (no side chains) is about _______ �
Too small for anything to fit "inside"
The outer diameter of the helix (with side chains) is ____- �
Happens to fit well into the major groove of dsDNA
Residues 1 and 8 align nicely on to
4-5, 10-12
The twist of the helix ensures that critical interactions occur between AA side chains and the side chains _______ residues away
three
? acts as a helix breaker because the tiny R-group supports other conformations
Gly
? acts as a helix breaker because the rotation around the N-Ca bond is impossible
Pro
In regards to helix stability, Attractive or repulsive interactions between side chains 3-4 amino acids apart will affect what?
formation
Recall that the peptide bond has a strong _____ moment
Carbonyl O negative
Amide H positive
All peptide bonds in the helix have a similar orientation
The helix has a large macroscopic "" moment
Negatively charged residues often occur near the positive e
dipole
In _________ b sheets the H-bonded strands run in the same direction
Resulting in bent H-bonds (weaker) .
6.5 Angstroms apart
parallel
In ____________ b sheets the H-bonded strands run in opposite directions
Resulting in linear H-bonds (stronger)
7 Angstroms apart
antiparallel
Beta Turns
-occur frequently whenever strands in b sheets change the direction
-The 180� action is accomplished over four amino acids
-The action is stabilized by a hydrogen bond from a carbonyl oxygen to amide proton three residues down the sequence
-Proline in pos
Loops
-No regular, recognizable or periodic structures
Longer "excursions" of backbone than simple reverse turns
-Usually at surface of protein
-Often mediate interactions with other molecules
Proline Isomers
Most peptide bonds not involving proline are in the trans configuration (>99.95%)
For peptide bonds involving proline, about 6% are in the cis configuration. Most of this 6% involve ?-turns
Proline isomerization is catalyzed by proline isomerases
Circular Dichroism (CD) Analysis
measures the molar absorption difference of left- & right-circularly polarized light
Chromophores in the chiral environment produce characteristic signals
Signals are obtained when a peptide bond is in a folded environment
CD signals from peptide bonds de
Tertiary structure
refers to the overall spatial arrangement of atoms in a protein
Stabilized by numerous weak interactions between amino acid side chains.
Largely hydrophobic and polar interactions
Can be stabilized by disulfide bonds
Interacting amino acids are not necess
Fibrous proteins
with polypeptide chains arranged in long stands or sheets
simple repeating element of secondary structure
and their tertiary structure is relatively simple
Structures are usually associated with providing support, shape, and external protection
All insolu
Globular proteins
with chains folded into a spherical or globular shape
often contain several type of secondary structure
Are enzymes and regulatory proteins
alpha keratin
alpha helix crossed linked by disulfide bonds
a type of fibrous protein
characteristics: tough, insoluble protective structures of varying hardness and flexibility.
Found only in mammals; in hair, wool, nails, claws, quills, horns, hoovers, and outer laye
silk fibroin
a type of fibrous protein
the main protein in silk from moths and spiders
Antiparallel b sheet structure
Small side chains (Ala and Gly) allow the close packing of sheets
Structure is stabilized by
hydrogen bonding within sheets
London dispersion interact
collagen
is an important constituent of connective tissue: tendons, cartilage, bones, cornea
a type of fibrous protein
Each collagen chain is a long Gly- and Pro-rich left-handed helix
Coiled-coil structure; three collagen chains intertwine into a right-handed sup
Spider Silk
Used for webs, egg sacks, and wrapping the prey
Extremely strong material
stronger than steel
can stretch a lot before breaking
A composite material
crystalline parts (fibroin-rich)
rubber-like stretchy parts
Water-Soluble Globular Proteins
-generate a more compact shape
-The folding provides the structural diversity necessary for proteins to carry out a wide array of biological functions:
Enzymes
Transport proteins
Motor proteins
Regulatory proteins
Structures of Myoglobin
1st crystal structure solved
Oxygen binding protein in muscle cells
Single polypeptide chain and a single heme group
Protein data bank (PDB): myoglobin; 1MBO
Globin fold eg myoglobin - 8 helices in two layers
Motifs
-otherwise known as folds
-Specific arrangement of several secondary structure elements:
All alpha-helix
All beta-sheet
Both
-can be found as reoccurring structures in numerous proteins
-Proteins are made of different"" folded together
-may or may not be
Simple motif
Alpha helix connects two beta-structures. Ex: Beta-alpha-Beta loop
More elaborate motif
beta-structures twist and coils to form closed structure. Ex: beta barrel
Domains
Domain is a part of a polypeptide chain that is independently stable or could undergo movements as a single entity with respect to the entire protein. PDB ID 4TNC?
Quaternary structure
-is formed by the assembly of individual polypeptides into a larger functional cluster.
-4 subunits such as 2 betas and 2 alphas.
-Oligomers and Protomers
-Eg hemoglobin is a oligomer of two protomers or a dimer of ?? protomers.
Oligomers and protomers
quaternary structures where proteins have identical subunits
Protein-Protein Interface
-Hydrophobic interactions between those of protein interiors and exteriors.
~77% of inter subunit H-bonds are between side chains vs ~68% H-bonds within subunits between backbone atoms.
-Around 56% protein-protein interfaces contain salt bridges.
Quaternary Structure: Symmetry
Main types:
Cyclical
Dihedral
Others also include: tetrahedral, octahedral & icosahedral
Helical (eg actin & tubulin)
Protein Structure Methods: X-Ray Crystallography
-Steps needed:
Purify the protein
Crystallize the protein
Collect diffraction data
Calculate electron density
Fit residues into density
-Pros
No size limits
Well-established
-Cons
Difficult for membrane proteins
only get a single crystal structure
Structure Methods: Biomolecular NMR
get a more dynamic solution structure of a protein.
-Steps needed:
Purify the protein
Dissolve the protein
Collect NMR data
Assign NMR signals
Calculate the structure
-Pros
No need to crystallize the protein
Can see many hydrogens
-Cons
Difficult for inso
Intrinsically Disordered Proteins
Contain protein segments that lack definable structure
Composed of amino acids whose higher concentration forces less-defined structure
Lys, Arg, Glu, and Pro
Disordered regions can conform to many different proteins, facilitating interaction with numerou
Proteostasis
how proteins are made and degraded in the cell. Proteins try to not aggregate and folds into correct structure..
Process in 3 steps: First, proteins are synthesized on a ribosome. Second, multiple pathways contribute to protein folding, many of which invo
denaturation
-definition: Loss of structural integrity with accompanying loss of activity
-what causes this on proteins:
heat or cold (causes abrupt changes in many of its conformationally sensitive properties over a narrow temperature range)
pH extremes (alter ioniza
_______ perturb hydrophobic interactions.
detergents
Ion pair or salt bridge
association of two ionic protein groups of opposite charge ex: Asp and Lys (mostly on protein surface)-little contribution to stability.
___________has the greatest influence on protein stability.
Hydrophobic effect
____________- not an essential stabilizing force. Cytoplasm is a reducing environment. Mainly found in proteins secreted from the cell.
Disulfide bonds
In regards to protein stability,
-Metal ions can stabilize some small domains eg Zn2+ ions stabilize a motifs called _________________.
-25-60 residues arranged around 1-2 Zn2+ ions that are tetrahedrally coordinated by the side chains of Cys, His, and oc
Zinc fingers and small
In regards to protein denaturation, we can use the Tm to figure out how stable a protein is. (Lower Tm require less energy.) What is Tm?
melting point
Protein Folding
Process in which a polypeptide chain goes from a linear chain of amino acids with vast number of more or less random conformations in solution to the native, folded tertiary (and for multi-chain proteins, quaternary) structure. Ordered process
Thermodynam
?Gfolding (change in free energy) between unfolded structure and folded structure is SMALL.
Under physiological conditions, what is the ?Go' of folding and unfolding?
- ?Gunfolding > 0 under "native" conditions
- ?Gfolding < 0 under "native" conditions
Enthalpy changes from ?Gfolding
-electrostatic effects (hydrogen bonds, salt bridges)
-solvation/desolvation of charged residues
-van der Waals interactions
-steric factors
Entropychanges from ?Gfolding
entropy (hydrophobic effect)
conformational entropy (degrees of freedom, flexibility)
?Gfolding results from a near balance of opposing large forces.
Small differences in energy are important -- loss of 1 or 2 hydrogen bonds might shift ____________ from folded state to unfolded form of protein.
equilibrium
Renaturation
Can add something to cause a protein to "" into its native conformation from its denatured state.
All info for folding is contained in the primary structure.
How can proteins fold so fast?
-It is mathematically impossible for protein folding to occur by randomly trying every conformation until the lowest-energy one is found (Levinthal's paradox)
-Search for the minimum is not random because the direction toward the native structure is therm
Protein folding process
First - 2 degree structures form (very fast, ms) (close by)
Then - motifs and domains
Then - hydrophobic collapse (yields state known as molten globule).
Hydrophobic collapse - buries hydrophobic regions in interior of protein.
Molten globule - most of 2
Protein folding is ___________ - small local elements lead to larger elements.
Folding is a ___________ process(small transition btwn when a protein is unfolded to folded.)
Protein goes from high energy, _______ entropy to low energy, ______ entropy state
hierarchal, cooperative, high, low
Protein Disulfide Isomerase
Breaks disulfide bonds that may have formed incorrectly.
Most peptide bonds _________ proline are in the trans configuration (>99.95%)
For peptide bonds __________ proline, about 6% are in the cis configuration. Most of this 6% involve ?-turns
not involving and involving
When some proteins don't fold into their correct conformation and that's where the molecular ___________ come in and unfolds it give it a 2nd chance to fold correctly into its native conformation.
chaperones
what are the several classes of chaperone?
-Hsp70 (heat shock proteins found a lot in bacteria)
-Chaperonins
-Hsp90
-Trigger factor
-they are ATPases
Molecular chaperones: DNA --> RNA?
transcription
Molecular chaperones: RNA-->polypeptide?
translation
Molecular chaperones: polypeptide --> functional protein?
folding
When proteins misfold they will ___________.
aggregate
chaperones do what?
chaperonins do what?
prevent misfolding and facilitate folding in a barrel in an exclusive environment.
What disease represents fails to fold incorrectly?
cystic fibrosis
What disease represents insoluble fibrous aggreagates?
Amyloids
What disease represents: Forms insoluble aggregates that deposit toxically
neurodegenerative disease: Alzheimers' Parkinsons, type 2 diabetes, Huntington disease (misfolded proteins)
set of diseases eg Alzheimer's, Huntington's, and Parkinson's disease and Prion disease: mad cow disease, sheep, and human.?
Characterized by deposition of normally soluble proteins in the form of amyloids in certain tissues.
Amyloidoses
Unlike most correctly folded proteins, both soluble and insoluble aggregates can not be toxic to cells through unknown mechanisms.
True or false?
false, both can be toxic
Alzheimer's Disease
-Characterized by amyloid plaques (deposits) surrounded by dead and dying neurons in brain tissue.
-Plaques consist mainly of fibrils of 40-42 residue protein called amyloid-?-protein (A?)
-A? is a fragment of a 770-residue membrane protein, the A? precur
____________ are rich in ?-structures, with individual strands oriented perpendicular to fiber axis.
Amyloid fibrils
All of the following are considered "weak" interactions in proteins, except:
A) hydrogen bonds.
B) hydrophobic interactions.
C) ionic bonds.
D) peptide bonds.
E) van der Waals forces.
d
The most important contribution to the stability of a protein's conformation appears to be the:
A) entropy increase from the decrease in ordered water molecules forming a solvent shell around it.
B) maximum entropy increase from ionic interactions between
a
In an aqueous solution, protein conformation is determined by two major factors. One is the formation of the maximum number of hydrogen bonds. The other is the:
A) formation of the maximum number of hydrophilic interactions.
B) maximization of ionic inter
d
Pauling and Corey's studies of the peptide bond showed that:
A) at pH 7, many different peptide bond conformations are equally probable.
B) peptide bonds are essentially planar, with no rotation about the C�N axis.
C) peptide bonds in proteins are unusual
b
In the diagram below, the plane drawn behind the peptide bond indicates the:
A) absence of rotation around the C�N bond because of its partial double-bond character.
B) plane of rotation around the C?�N bond.
C) region of steric hindrance determined by th
a
Which of the following best represents the backbone arrangement of two peptide bonds?
A) C?�N�C?�C�C?�N�C?�C
B) C?�N�C�C�N�C?
C) C�N�C?�C?�C�N
D) C?�C�N�C?�C�N
E) C?�C?�C�N�C?�C?�C
d
Which of the following pairs of bonds within a peptide backbone show free rotation around both bonds?
A) C?�C and N�C?
B) C=O and N�C
C) C=O and N�C?
D) N�C and C?�C
E) N�C? and N�C
a
Roughly how many amino acids are there in one turn of an ? helix?
A) 1
B) 2.8
C) 3.6
D) 4.2
E) 10
c
In the ? helix the hydrogen bonds:
F) are roughly parallel to the axis of the helix.
G) are roughly perpendicular to the axis of the helix.
H) occur mainly between electronegative atoms of the R groups.
I) occur only between some of the amino acids of the
a
In an ? helix, the R groups on the amino acid residues:
A) alternate between the outside and the inside of the helix.
B) are found on the outside of the helix spiral.
C) cause only right-handed helices to form.
D) generate the hydrogen bonds that form the
b
Thr and/or Leu residues tend to disrupt an ? helix when they occur next to each other in a protein because:
A) an amino acids like Thr is highly hydrophobic.
B) covalent interactions may occur between the Thr side chains.
C) electrostatic repulsion occurs
d
A D-amino acid would interrupt an ? helix made of L-amino acids. Another naturally occurring hindrance to the formation of an ? helix is the presence of:
A) a negatively charged Arg residue.
B) a nonpolar residue near the carboxyl terminus.
C) a positivel
d
An ? helix would be destabilized most by:
A) an electric dipole spanning several peptide bonds throughout the ? helix.
B) interactions between neighboring Asp and Arg residues.
C) interactions between two adjacent hydrophobic Val residues.
D) the presence
e
The major reason that antiparallel ?-stranded protein structures are more stable than parallel ?-stranded structures is that the latter:
A) are in a slightly less extended configuration than antiparallel strands.
B) do not have as many disulfide crosslink
e
Amino acid residues commonly found in the middle of ? turn are:
A) Ala and Gly.
B) hydrophobic.
C) Pro and Gly.
D) those with ionized R-groups.
E) two Cys.
c
A sequence of amino acids in a certain protein is found to be -Ser-Gly-Pro-Gly-. The sequence is most probably part of a(n):
A) antiparallel ? sheet.
B) parallel ? sheet.
C) ? helix.
D) ? sheet.
E) ? turn.
e
The three-dimensional conformation of a protein may be strongly influenced by amino acid residues that are very far apart in sequence. This relationship is in contrast to secondary structure, where the amino acid residues are:
A) always side by side.
B) g
b
The ?-keratin chains indicated by the diagram below have undergone one chemical step. To alter the shape of the ?-keratin chains�as in hair waving�what subsequent steps are required?
A) Chemical oxidation and then shape remodeling
B) Chemical reduction an
d
Which of the following statements is false?
A) Collagen is a protein in which the polypeptides are mainly in the ?-helix conformation.
B) Disulfide linkages are important for keratin structure.
C) Gly residues are particularly abundant in collagen.
D) Sil
a
Kendrew's studies of the globular myoglobin structure demonstrated that:
A) "corners" between ?-helical regions invariably lacked proline residue.
B) highly polar or charged amino acid residues tended to be located interiorally.
C) myoglobin was completel
d
Determining the precise arrangement of atoms within a large protein is possible only through the use of:
A) electron microscopy.
B) light microscopy.
C) molecular model building.
D) Ramachandran plots.
E) x-ray diffraction.
e
Analysis of x-ray diffraction data yields a(n) ; analysis of 2D NMR data yields a(n) .
A) electron density map; count of hydrogen atoms in the molecule
B) shadow of protein's outline; estimate of protein's molecular volume
C) table of interatomic distance
d
Proteins often have regions that show specific, coherent patterns of folding or function. These regions are called:
A) domains.
B) oligomers.
C) peptides.
D) sites.
E) subunits.
a
Which of the following statements concerning protein domains is true?
A) They are a form of secondary structure.
B) They are examples of structural motifs.
C) They consist of separate polypeptide chains (subunits).
D) They have been found only in prokaryo
e
The structural classification of proteins (based on motifs) is based primarily on their:
A) amino acid sequence.
B) evolutionary relationships.
C) function.
D) secondary structure content and arrangement.
E) subunit content and arrangement.
d
Proteins are classified within families or superfamilies based on similarities in:
A) evolutionary origin.
B) physico-chemical properties.
C) structure and/or function.
D) subcellular location.
E) subunit structure.
c
Which of the following statements about oligomeric proteins is false?
A) A subunit may be similar to other proteins.
B) All subunits must be identical.
C) Many have regulatory roles.
D) Some oligomeric proteins can further associate into large fibers.
E)
b
A repeating structural unit in a multimeric protein is known as a(n):
A) domain.
B) motif.
C) oligomer.
D) protomer.
E) subunit.
d
Which of the following statements concerning rotational symmetry in proteins is false?
A) It involves rotation of proteins inside the cell.
B) It is frequently seen in the subunits of oligomeric proteins.
C) It is frequently seen in viruses.
D) It may inv
a
An average protein will not be denatured by:
A) a detergent such as sodium dodecyl sulfate.
B) heating to 90�C.
C) iodoacetic acid.
D) pH 10.
E) urea.
c
Which of the following is least likely to result in protein denaturation?
A) Altering net charge by changing pH
B) Changing the salt concentration
C) Disruption of weak interactions by boiling
D) Exposure to detergents
E) Mixing with organic solvents such
b
Experiments on denaturation and renaturation after the reduction and reoxidation of the �S�S� bonds in the enzyme ribonuclease (RNase) have shown that:
A) folding of denatured RNase into the native, active conformation, requires the input of energy in the
e
Which of the following statements concerning the process of spontaneous folding of proteins is false?
A) It may be an essentially random process.
B) It may be defective in some human diseases.
C) It may involve a gradually decreasing range of conformation
a
Protein S will fold into its native conformation only when protein Q is also present in the solution. However, protein Q can fold into its native conformation without protein S. Protein Q, therefore, may function as a ____________ for protein S.
A) ligand
b
Which of the following is not known to be involved in the process of assisted folding of proteins?
A) Chaperonins
B) Disulfide interchange
C) Heat shock proteins
D) Peptide bond hydrolysis
E) Peptide bond isomerization
d
Any given protein is characterized by a unique amino acid sequence (primary structure) and three-dimensional (tertiary) structure. How are these related?
The three-dimensional structure is determined by the amino acid sequence. This means that the amino acid sequence contains all of the information that is required for the polypeptide chain to fold up into a discrete three-dimensional shape.
Name four factors (bonds or other forces) that contribute to stabilizing the native structure of a protein, and describe one condition or reagent that interferes with each type of stabilizing force.
Among forces that stabilize native protein structures are (a) disulfide bonds, (b) hydrogen bonds, (c) hydrophobic interactions, and (d) ionic interactions. Agents that interfere with these forces are (a) mercaptoethanol or dithiothreitol, (b) pH extremes
When a polypeptide is in its native conformation, there are weak interactions between its R groups. However, when it is denatured there are similar interactions between the protein groups and water. What then accounts for the greater stability of the nati
In the unfolded polypeptide, there are ordered solvation shells of water around the protein groups. The number of water molecules involved in such ordered shells is reduced when the protein folds, resulting in higher entropy. Hence, the lower free energy
Draw the resonance structure of a peptide bond, and explain why there is no rotation around the
C�N bond.
The intermediate resonance structure imparts a partial double bond characteristic to the C�N bond, thereby prohibiting rotation.
Pauling and Corey showed that in small peptides, six atoms associated with the peptide bond all lie in a plane. Draw a dipeptide of two amino acids in trans linkage (side-chains can be shown as �R), and indicate which six atoms are part of the planar stru
The N and H of the amino and the C and O of the carbonyl are all in the same plane with the two C? atoms, which are diagonally opposite relative to the C�N bond.
Draw the hydrogen bonding typically found between two residues in an ? helix
Hydrogen bonds occur between every carbonyl oxygen in the polypeptide backbone and the peptide �NH of the fourth amino acid residue toward the amino terminus of the chain
Describe three of the important features of the ?-helical polypeptide structure predicted by Pauling and Corey. Provide one or two sentences for each feature.
The ?-helical structure of a polypeptide is tightly wound around a long central axis; each turn of the right-handed helix contains 3.6 residues and stretches 5.4 � along the axis. The peptide NH is hydrogen-bonded to the carbonyl oxygen of the fourth amin
Describe three of the important features of a ? sheet polypeptide structure. Provide one or two sentences for each feature.
In the ? sheet structure, several extended polypeptides, or two regions of the same polypeptide, lie side by side and are stabilized by hydrogen bonding between adjacent chains. Adjacent chains may be either parallel (with a repeat distance of about 6.5 �
Why are glycine and proline often found within a ? turn?
A ? turn results in a tight 180� reversal in the direction of the polypeptide chain. Glycine is the smallest and thus most flexible amino acid, and proline can readily assume the cis configuration, which facilitates a tight turn.
Explain how circular dichroism spectroscopy could be used to measure the denaturation of a protein.
Circular dichroism spectroscopy measures the amount of ?-helix in a given protein. As the protein denatures, the amount of ?-helix should decrease as the protein chain becomes disordered; this change would be detectable using CD spectrography.
In superhelical proteins, such as collagen, several polypeptide helices are intertwined. What is the function of this superhelical twisting?
The superhelical twisting of multiple polypeptide helices makes the overall structure more compact and increases its overall strength.
Why is silk fibroin so strong, but at the same time so soft and flexible?
Unlike collagen and keratin, silk fibroin has no covalent crosslinks between adjacent strands, or between its stacked sheets, making it very flexible. Fibroin's unusual tensile strength derives from the fact that the peptide backbone of antiparallel ?-str
What is typically found in the interior of a water-soluble globular protein?
Hydrophobic amino acid residues cluster away from the surface in globular proteins, so much of the protein's interior is a tightly packed combination of hydrocarbon and aromatic ring R groups with very few water molecules.
How does one determine the three-dimensional structure of a protein? Your answer should be more than the name of a technique.
The protein is crystallized, and the crystal structure is determined by x-ray diffraction. The pattern of diffracted x-rays yields, by Fourier transformation, the three-dimensional distribution of electron density. By matching electron density with the kn
Describe a reservation about the use of x-ray crystallography in determining the three-dimensional structures of biological molecules.
To obtain an x-ray picture of a biomolecule, the molecule must be purified and crystallized under laboratory conditions far different from those encountered by the native molecule. Biomolecules in the cell also have more flexibility and freedom of motion
Explain what is meant by motifs in protein structure.
Motifs are particularly stable arrangements of elements of secondary structure (e.g., ? helix and ? conformation), including the connections between them, which are found in a variety of proteins.
Draw a ??? loop, and describe what is found in the interior of the loop.
Hydrophobic amino acid residues are usually found in the interior of the loop; these help stabilize the arrangement through hydrophobic interactions.
Describe the quaternary structure of hemoglobin.
Each protein molecule is composed of two copies each of two different subunits ? and ?. The two ?? protomers are arranged with C2 symmetry.
Describe briefly the two major types of symmetry found in oligomeric proteins and give an example of each.
1) Rotational: In rotational symmetry, subunits are superimposable after rotation about one or more of the axes. Some examples are hemoglobin and thepoliovirus capsid. 2) Helical: In helical symmetry, subunits are superimposable after a helical rotation.
What is the rationale for many large proteins containing multiple copies of a polypeptide subunit?
Each different polypeptide requires a separate gene that must be replicated and transcribed. It is therefore more efficient to have fewer genes, encoding shorter polypeptides that can be used to construct many large proteins.
Explain (succinctly) the theoretical and/or experimental arguments in support of this statement: "The primary sequence of a protein determines its three-dimensional shape and thus its function.
Anfinsen showed that a completely denatured enzyme (ribonuclease) could fold spontaneously into its native, enzymatically active form with only the primary sequence to guide it.
Each of the following reagents or conditions will denature a protein. For each, describe in one or two sentences what the reagent/condition does to destroy native protein structure.
(a) urea
(b) high temperature
(c) detergent
(d) low pH
(a) Urea acts primarily by disrupting hydrophobic interactions. (b) High temperature provides thermal energy greater than the strength of the weak interactions (hydrogen bonds, electrostatic interactions, hydrophobic interactions, and van der Waals forces
How can changes in pH alter the conformation of a protein?
Changes in pH can influence the extent to which certain amino acid side chains (or the amino and carboxyl termini) are protonated. The result is a change in net charge on the protein, which can lead to electrostatic attractions or repulsions between diffe
Once a protein has been denatured, how can it be renatured? If renaturation does not occur, what might be the explanation?
Because a protein may be denatured through the disruption of hydrogen bonds and hydrophobic interactions by salts or organic solvents, removal of those conditions will reestablish the original aqueous environment, often permitting the protein to fold once
What are two mechanisms by which "chaperone" proteins assist in the correct folding of polypeptides?
Chaperones protect unfolded polypeptides from aggregation by binding to hydrophobic regions. They can also provide a microenvironment that promotes correct folding.
Structure of Proteins
#NAME?
Favorable Interactions in Proteins
Hydrophobic effect
Hydrogen bonds
London dispersion
Electrostatic interactions
Hydrophobic effect
Release of water molecules from the structured solvation layer around the molecule as protein folds increases the net entropy
Hydrogen bonds
Interaction of N-H and C=O of the peptide bond leads to local regular structures such as alpha-helices and beta-sheets
London dispersion
Medium-range weak attraction between all atoms contributes significantly to the stability in the interior of the protein.
Electrostatic interactions
Long-range strong interactions between permanently charged groups
Salt-bridges, esp. buried in the hydrophobic environment strongly stabilize the protein
4 levels of protein structure
PRIMARY- aa sequence
SECONDARY- A regular repeating aa sequence that have close interactions.
TERTIARY- longer range (more than 10 AAs apart) and has two types which are fibrous and globulus proteins
QUATERNARY-multiple subunits come together in non coval
Structure of the peptide bond
The resonance causes these bonds:
-to be less reactive compared to esters, for example
-to be quite rigid and nearly planar
-to exhibit a large dipole moment in the favored trans configuration
Each peptide bond has some double-bond character due to resona
Rotation around bonds connected to the______________ is permitted?
alpha carbon
What are phi and psi?
are rotational angles around the alpha carbon
(phi): angle around the alpha-carbon and alpha-amine
(psi): angle around the alpha-carbon and alpha carboxyl
In a fully extended polypeptide, both y and f are 180�
The ___________ is made up of a series of planes linked at ? carbons
The rigid peptide backbone limits the range of conformation possible for this chain
polypeptide
what is the angle at the intersection of two planes?
dihedral
Distribution of phi and psi Dihedral Angles
Some phi and psi combinations are very unfavorable because of steric crowding of backbone atoms with other atoms in the backbone or side chains
Some combinations are more favorable because of chance to form favorable H-bonding interactions along the backb
Ramachandran plot
#NAME?
Secondary Structures
#NAME?
Alpha helix
-stabilized by hydrogen bonds between nearby residues
-Helical backbone is held together by hydrogen bonds between the backbone amides of an n and n+4 amino acids
-Right-handed helix with 3.6 residues (5.4 �) per turn
-Peptide bonds are aligned roughly pa
Beta sheets
#NAME?
The inner diameter of the helix (no side chains) is about _______ �
Too small for anything to fit "inside"
The outer diameter of the helix (with side chains) is ____- �
Happens to fit well into the major groove of dsDNA
Residues 1 and 8 align nicely on to
4-5, 10-12
The twist of the helix ensures that critical interactions occur between AA side chains and the side chains _______ residues away
three
? acts as a helix breaker because the tiny R-group supports other conformations
Gly
? acts as a helix breaker because the rotation around the N-Ca bond is impossible
Pro
In regards to helix stability, Attractive or repulsive interactions between side chains 3-4 amino acids apart will affect what?
formation
Recall that the peptide bond has a strong _____ moment
Carbonyl O negative
Amide H positive
All peptide bonds in the helix have a similar orientation
The helix has a large macroscopic "" moment
Negatively charged residues often occur near the positive e
dipole
In _________ b sheets the H-bonded strands run in the same direction
Resulting in bent H-bonds (weaker) .
6.5 Angstroms apart
parallel
In ____________ b sheets the H-bonded strands run in opposite directions
Resulting in linear H-bonds (stronger)
7 Angstroms apart
antiparallel
Beta Turns
-occur frequently whenever strands in b sheets change the direction
-The 180� action is accomplished over four amino acids
-The action is stabilized by a hydrogen bond from a carbonyl oxygen to amide proton three residues down the sequence
-Proline in pos
Loops
-No regular, recognizable or periodic structures
Longer "excursions" of backbone than simple reverse turns
-Usually at surface of protein
-Often mediate interactions with other molecules
Proline Isomers
Most peptide bonds not involving proline are in the trans configuration (>99.95%)
For peptide bonds involving proline, about 6% are in the cis configuration. Most of this 6% involve ?-turns
Proline isomerization is catalyzed by proline isomerases
Circular Dichroism (CD) Analysis
measures the molar absorption difference of left- & right-circularly polarized light
Chromophores in the chiral environment produce characteristic signals
Signals are obtained when a peptide bond is in a folded environment
CD signals from peptide bonds de
Tertiary structure
refers to the overall spatial arrangement of atoms in a protein
Stabilized by numerous weak interactions between amino acid side chains.
Largely hydrophobic and polar interactions
Can be stabilized by disulfide bonds
Interacting amino acids are not necess
Fibrous proteins
with polypeptide chains arranged in long stands or sheets
simple repeating element of secondary structure
and their tertiary structure is relatively simple
Structures are usually associated with providing support, shape, and external protection
All insolu
Globular proteins
with chains folded into a spherical or globular shape
often contain several type of secondary structure
Are enzymes and regulatory proteins
alpha keratin
alpha helix crossed linked by disulfide bonds
a type of fibrous protein
characteristics: tough, insoluble protective structures of varying hardness and flexibility.
Found only in mammals; in hair, wool, nails, claws, quills, horns, hoovers, and outer laye
silk fibroin
a type of fibrous protein
the main protein in silk from moths and spiders
Antiparallel b sheet structure
Small side chains (Ala and Gly) allow the close packing of sheets
Structure is stabilized by
hydrogen bonding within sheets
London dispersion interact
collagen
is an important constituent of connective tissue: tendons, cartilage, bones, cornea
a type of fibrous protein
Each collagen chain is a long Gly- and Pro-rich left-handed helix
Coiled-coil structure; three collagen chains intertwine into a right-handed sup
Spider Silk
Used for webs, egg sacks, and wrapping the prey
Extremely strong material
stronger than steel
can stretch a lot before breaking
A composite material
crystalline parts (fibroin-rich)
rubber-like stretchy parts
Water-Soluble Globular Proteins
#NAME?
Structures of Myoglobin
1st crystal structure solved
Oxygen binding protein in muscle cells
Single polypeptide chain and a single heme group
Protein data bank (PDB): myoglobin; 1MBO
Globin fold eg myoglobin - 8 helices in two layers
Motifs
-otherwise known as folds
-Specific arrangement of several secondary structure elements:
All alpha-helix
All beta-sheet
Both
-can be found as reoccurring structures in numerous proteins
-Proteins are made of different"" folded together
-may or may not be
Simple motif
Alpha helix connects two beta-structures. Ex: Beta-alpha-Beta loop
More elaborate motif
beta-structures twist and coils to form closed structure. Ex: beta barrel
Domains
Domain is a part of a polypeptide chain that is independently stable or could undergo movements as a single entity with respect to the entire protein. PDB ID 4TNC?
Quaternary structure
-is formed by the assembly of individual polypeptides into a larger functional cluster.
-4 subunits such as 2 betas and 2 alphas.
-Oligomers and Protomers
-Eg hemoglobin is a oligomer of two protomers or a dimer of ?? protomers.
Oligomers and protomers
quaternary structures where proteins have identical subunits
Protein-Protein Interface
-Hydrophobic interactions between those of protein interiors and exteriors.
~77% of inter subunit H-bonds are between side chains vs ~68% H-bonds within subunits between backbone atoms.
-Around 56% protein-protein interfaces contain salt bridges.
Quaternary Structure: Symmetry
Main types:
Cyclical
Dihedral
Others also include: tetrahedral, octahedral & icosahedral
Helical (eg actin & tubulin)
Protein Structure Methods: X-Ray Crystallography
#NAME?
Structure Methods: Biomolecular NMR
get a more dynamic solution structure of a protein.
-Steps needed:
Purify the protein
Dissolve the protein
Collect NMR data
Assign NMR signals
Calculate the structure
-Pros
No need to crystallize the protein
Can see many hydrogens
-Cons
Difficult for inso
Intrinsically Disordered Proteins
Contain protein segments that lack definable structure
Composed of amino acids whose higher concentration forces less-defined structure
Lys, Arg, Glu, and Pro
Disordered regions can conform to many different proteins, facilitating interaction with numerou
Proteostasis
how proteins are made and degraded in the cell. Proteins try to not aggregate and folds into correct structure..
Process in 3 steps: First, proteins are synthesized on a ribosome. Second, multiple pathways contribute to protein folding, many of which invo
denaturation
-definition: Loss of structural integrity with accompanying loss of activity
-what causes this on proteins:
heat or cold (causes abrupt changes in many of its conformationally sensitive properties over a narrow temperature range)
pH extremes (alter ioniza
_______ perturb hydrophobic interactions.
detergents
Ion pair or salt bridge
association of two ionic protein groups of opposite charge ex: Asp and Lys (mostly on protein surface)-little contribution to stability.
___________has the greatest influence on protein stability.
Hydrophobic effect
____________- not an essential stabilizing force. Cytoplasm is a reducing environment. Mainly found in proteins secreted from the cell.
Disulfide bonds
In regards to protein stability,
-Metal ions can stabilize some small domains eg Zn2+ ions stabilize a motifs called _________________.
-25-60 residues arranged around 1-2 Zn2+ ions that are tetrahedrally coordinated by the side chains of Cys, His, and oc
Zinc fingers and small
In regards to protein denaturation, we can use the Tm to figure out how stable a protein is. (Lower Tm require less energy.) What is Tm?
melting point
Protein Folding
Process in which a polypeptide chain goes from a linear chain of amino acids with vast number of more or less random conformations in solution to the native, folded tertiary (and for multi-chain proteins, quaternary) structure. Ordered process
Thermodynam
?Gfolding (change in free energy) between unfolded structure and folded structure is SMALL.
Under physiological conditions, what is the ?Go' of folding and unfolding?
- ?Gunfolding > 0 under "native" conditions
- ?Gfolding < 0 under "native" conditions
Enthalpy changes from ?Gfolding
#NAME?
Entropychanges from ?Gfolding
entropy (hydrophobic effect)
conformational entropy (degrees of freedom, flexibility)
?Gfolding results from a near balance of opposing large forces.
Small differences in energy are important -- loss of 1 or 2 hydrogen bonds might shift ____________ from folded state to unfolded form of protein.
equilibrium
Renaturation
Can add something to cause a protein to "" into its native conformation from its denatured state.
All info for folding is contained in the primary structure.
How can proteins fold so fast?
-It is mathematically impossible for protein folding to occur by randomly trying every conformation until the lowest-energy one is found (Levinthal's paradox)
-Search for the minimum is not random because the direction toward the native structure is therm
Protein folding process
First - 2 degree structures form (very fast, ms) (close by)
Then - motifs and domains
Then - hydrophobic collapse (yields state known as molten globule).
Hydrophobic collapse - buries hydrophobic regions in interior of protein.
Molten globule - most of 2
Protein folding is ___________ - small local elements lead to larger elements.
Folding is a ___________ process(small transition btwn when a protein is unfolded to folded.)
Protein goes from high energy, _______ entropy to low energy, ______ entropy state
hierarchal, cooperative, high, low
Protein Disulfide Isomerase
Breaks disulfide bonds that may have formed incorrectly.
Most peptide bonds _________ proline are in the trans configuration (>99.95%)
For peptide bonds __________ proline, about 6% are in the cis configuration. Most of this 6% involve ?-turns
not involving and involving
When some proteins don't fold into their correct conformation and that's where the molecular ___________ come in and unfolds it give it a 2nd chance to fold correctly into its native conformation.
chaperones
what are the several classes of chaperone?
#REF!
Molecular chaperones: DNA --> RNA?
transcription
Molecular chaperones: RNA-->polypeptide?
translation
Molecular chaperones: polypeptide --> functional protein?
folding
When proteins misfold they will ___________.
aggregate
chaperones do what?
chaperonins do what?
prevent misfolding and facilitate folding in a barrel in an exclusive environment.
What disease represents fails to fold incorrectly?
cystic fibrosis
What disease represents insoluble fibrous aggreagates?
Amyloids
What disease represents: Forms insoluble aggregates that deposit toxically
neurodegenerative disease: Alzheimers' Parkinsons, type 2 diabetes, Huntington disease (misfolded proteins)
set of diseases eg Alzheimer's, Huntington's, and Parkinson's disease and Prion disease: mad cow disease, sheep, and human.?
Characterized by deposition of normally soluble proteins in the form of amyloids in certain tissues.
Amyloidoses
Unlike most correctly folded proteins, both soluble and insoluble aggregates can not be toxic to cells through unknown mechanisms.
True or false?
false, both can be toxic
Alzheimer's Disease
-Characterized by amyloid plaques (deposits) surrounded by dead and dying neurons in brain tissue.
-Plaques consist mainly of fibrils of 40-42 residue protein called amyloid-?-protein (A?)
-A? is a fragment of a 770-residue membrane protein, the A? precur
____________ are rich in ?-structures, with individual strands oriented perpendicular to fiber axis.
Amyloid fibrils
All of the following are considered "weak" interactions in proteins, except:
A) hydrogen bonds.
B) hydrophobic interactions.
C) ionic bonds.
D) peptide bonds.
E) van der Waals forces.
d
The most important contribution to the stability of a protein's conformation appears to be the:
A) entropy increase from the decrease in ordered water molecules forming a solvent shell around it.
B) maximum entropy increase from ionic interactions between
a
In an aqueous solution, protein conformation is determined by two major factors. One is the formation of the maximum number of hydrogen bonds. The other is the:
A) formation of the maximum number of hydrophilic interactions.
B) maximization of ionic inter
d
Pauling and Corey's studies of the peptide bond showed that:
A) at pH 7, many different peptide bond conformations are equally probable.
B) peptide bonds are essentially planar, with no rotation about the C�N axis.
C) peptide bonds in proteins are unusual
b
In the diagram below, the plane drawn behind the peptide bond indicates the:
A) absence of rotation around the C�N bond because of its partial double-bond character.
B) plane of rotation around the C?�N bond.
C) region of steric hindrance determined by th
a
Which of the following best represents the backbone arrangement of two peptide bonds?
A) C?�N�C?�C�C?�N�C?�C
B) C?�N�C�C�N�C?
C) C�N�C?�C?�C�N
D) C?�C�N�C?�C�N
E) C?�C?�C�N�C?�C?�C
d
Which of the following pairs of bonds within a peptide backbone show free rotation around both bonds?
A) C?�C and N�C?
B) C=O and N�C
C) C=O and N�C?
D) N�C and C?�C
E) N�C? and N�C
a
Roughly how many amino acids are there in one turn of an ? helix?
A) 1
B) 2.8
C) 3.6
D) 4.2
E) 10
c
In the ? helix the hydrogen bonds:
F) are roughly parallel to the axis of the helix.
G) are roughly perpendicular to the axis of the helix.
H) occur mainly between electronegative atoms of the R groups.
I) occur only between some of the amino acids of the
a
In an ? helix, the R groups on the amino acid residues:
A) alternate between the outside and the inside of the helix.
B) are found on the outside of the helix spiral.
C) cause only right-handed helices to form.
D) generate the hydrogen bonds that form the
b
Thr and/or Leu residues tend to disrupt an ? helix when they occur next to each other in a protein because:
A) an amino acids like Thr is highly hydrophobic.
B) covalent interactions may occur between the Thr side chains.
C) electrostatic repulsion occurs
d
A D-amino acid would interrupt an ? helix made of L-amino acids. Another naturally occurring hindrance to the formation of an ? helix is the presence of:
A) a negatively charged Arg residue.
B) a nonpolar residue near the carboxyl terminus.
C) a positivel
d
An ? helix would be destabilized most by:
A) an electric dipole spanning several peptide bonds throughout the ? helix.
B) interactions between neighboring Asp and Arg residues.
C) interactions between two adjacent hydrophobic Val residues.
D) the presence
e
The major reason that antiparallel ?-stranded protein structures are more stable than parallel ?-stranded structures is that the latter:
A) are in a slightly less extended configuration than antiparallel strands.
B) do not have as many disulfide crosslink
e
Amino acid residues commonly found in the middle of ? turn are:
A) Ala and Gly.
B) hydrophobic.
C) Pro and Gly.
D) those with ionized R-groups.
E) two Cys.
c
A sequence of amino acids in a certain protein is found to be -Ser-Gly-Pro-Gly-. The sequence is most probably part of a(n):
A) antiparallel ? sheet.
B) parallel ? sheet.
C) ? helix.
D) ? sheet.
E) ? turn.
e
The three-dimensional conformation of a protein may be strongly influenced by amino acid residues that are very far apart in sequence. This relationship is in contrast to secondary structure, where the amino acid residues are:
A) always side by side.
B) g
b
The ?-keratin chains indicated by the diagram below have undergone one chemical step. To alter the shape of the ?-keratin chains�as in hair waving�what subsequent steps are required?
A) Chemical oxidation and then shape remodeling
B) Chemical reduction an
d
Which of the following statements is false?
A) Collagen is a protein in which the polypeptides are mainly in the ?-helix conformation.
B) Disulfide linkages are important for keratin structure.
C) Gly residues are particularly abundant in collagen.
D) Sil
a
Kendrew's studies of the globular myoglobin structure demonstrated that:
A) "corners" between ?-helical regions invariably lacked proline residue.
B) highly polar or charged amino acid residues tended to be located interiorally.
C) myoglobin was completel
d
Determining the precise arrangement of atoms within a large protein is possible only through the use of:
A) electron microscopy.
B) light microscopy.
C) molecular model building.
D) Ramachandran plots.
E) x-ray diffraction.
e
Analysis of x-ray diffraction data yields a(n) ; analysis of 2D NMR data yields a(n) .
A) electron density map; count of hydrogen atoms in the molecule
B) shadow of protein's outline; estimate of protein's molecular volume
C) table of interatomic distance
d
Proteins often have regions that show specific, coherent patterns of folding or function. These regions are called:
A) domains.
B) oligomers.
C) peptides.
D) sites.
E) subunits.
a
Which of the following statements concerning protein domains is true?
A) They are a form of secondary structure.
B) They are examples of structural motifs.
C) They consist of separate polypeptide chains (subunits).
D) They have been found only in prokaryo
e
The structural classification of proteins (based on motifs) is based primarily on their:
A) amino acid sequence.
B) evolutionary relationships.
C) function.
D) secondary structure content and arrangement.
E) subunit content and arrangement.
d
Proteins are classified within families or superfamilies based on similarities in:
A) evolutionary origin.
B) physico-chemical properties.
C) structure and/or function.
D) subcellular location.
E) subunit structure.
c
Which of the following statements about oligomeric proteins is false?
A) A subunit may be similar to other proteins.
B) All subunits must be identical.
C) Many have regulatory roles.
D) Some oligomeric proteins can further associate into large fibers.
E)
b
A repeating structural unit in a multimeric protein is known as a(n):
A) domain.
B) motif.
C) oligomer.
D) protomer.
E) subunit.
d
Which of the following statements concerning rotational symmetry in proteins is false?
A) It involves rotation of proteins inside the cell.
B) It is frequently seen in the subunits of oligomeric proteins.
C) It is frequently seen in viruses.
D) It may inv
a
An average protein will not be denatured by:
A) a detergent such as sodium dodecyl sulfate.
B) heating to 90�C.
C) iodoacetic acid.
D) pH 10.
E) urea.
c
Which of the following is least likely to result in protein denaturation?
A) Altering net charge by changing pH
B) Changing the salt concentration
C) Disruption of weak interactions by boiling
D) Exposure to detergents
E) Mixing with organic solvents such
b
Experiments on denaturation and renaturation after the reduction and reoxidation of the �S�S� bonds in the enzyme ribonuclease (RNase) have shown that:
A) folding of denatured RNase into the native, active conformation, requires the input of energy in the
e
Which of the following statements concerning the process of spontaneous folding of proteins is false?
A) It may be an essentially random process.
B) It may be defective in some human diseases.
C) It may involve a gradually decreasing range of conformation
a
Protein S will fold into its native conformation only when protein Q is also present in the solution. However, protein Q can fold into its native conformation without protein S. Protein Q, therefore, may function as a ____________ for protein S.
A) ligand
b
Which of the following is not known to be involved in the process of assisted folding of proteins?
A) Chaperonins
B) Disulfide interchange
C) Heat shock proteins
D) Peptide bond hydrolysis
E) Peptide bond isomerization
d
Any given protein is characterized by a unique amino acid sequence (primary structure) and three-dimensional (tertiary) structure. How are these related?
The three-dimensional structure is determined by the amino acid sequence. This means that the amino acid sequence contains all of the information that is required for the polypeptide chain to fold up into a discrete three-dimensional shape.
Name four factors (bonds or other forces) that contribute to stabilizing the native structure of a protein, and describe one condition or reagent that interferes with each type of stabilizing force.
Among forces that stabilize native protein structures are (a) disulfide bonds, (b) hydrogen bonds, (c) hydrophobic interactions, and (d) ionic interactions. Agents that interfere with these forces are (a) mercaptoethanol or dithiothreitol, (b) pH extremes
When a polypeptide is in its native conformation, there are weak interactions between its R groups. However, when it is denatured there are similar interactions between the protein groups and water. What then accounts for the greater stability of the nati
In the unfolded polypeptide, there are ordered solvation shells of water around the protein groups. The number of water molecules involved in such ordered shells is reduced when the protein folds, resulting in higher entropy. Hence, the lower free energy
Draw the resonance structure of a peptide bond, and explain why there is no rotation around the
C�N bond.
The intermediate resonance structure imparts a partial double bond characteristic to the C�N bond, thereby prohibiting rotation.
Pauling and Corey showed that in small peptides, six atoms associated with the peptide bond all lie in a plane. Draw a dipeptide of two amino acids in trans linkage (side-chains can be shown as �R), and indicate which six atoms are part of the planar stru
The N and H of the amino and the C and O of the carbonyl are all in the same plane with the two C? atoms, which are diagonally opposite relative to the C�N bond.
Draw the hydrogen bonding typically found between two residues in an ? helix
Hydrogen bonds occur between every carbonyl oxygen in the polypeptide backbone and the peptide �NH of the fourth amino acid residue toward the amino terminus of the chain
Describe three of the important features of the ?-helical polypeptide structure predicted by Pauling and Corey. Provide one or two sentences for each feature.
The ?-helical structure of a polypeptide is tightly wound around a long central axis; each turn of the right-handed helix contains 3.6 residues and stretches 5.4 � along the axis. The peptide NH is hydrogen-bonded to the carbonyl oxygen of the fourth amin
Describe three of the important features of a ? sheet polypeptide structure. Provide one or two sentences for each feature.
In the ? sheet structure, several extended polypeptides, or two regions of the same polypeptide, lie side by side and are stabilized by hydrogen bonding between adjacent chains. Adjacent chains may be either parallel (with a repeat distance of about 6.5 �
Why are glycine and proline often found within a ? turn?
A ? turn results in a tight 180� reversal in the direction of the polypeptide chain. Glycine is the smallest and thus most flexible amino acid, and proline can readily assume the cis configuration, which facilitates a tight turn.
Explain how circular dichroism spectroscopy could be used to measure the denaturation of a protein.
Circular dichroism spectroscopy measures the amount of ?-helix in a given protein. As the protein denatures, the amount of ?-helix should decrease as the protein chain becomes disordered; this change would be detectable using CD spectrography.
In superhelical proteins, such as collagen, several polypeptide helices are intertwined. What is the function of this superhelical twisting?
The superhelical twisting of multiple polypeptide helices makes the overall structure more compact and increases its overall strength.
Why is silk fibroin so strong, but at the same time so soft and flexible?
Unlike collagen and keratin, silk fibroin has no covalent crosslinks between adjacent strands, or between its stacked sheets, making it very flexible. Fibroin's unusual tensile strength derives from the fact that the peptide backbone of antiparallel ?-str
What is typically found in the interior of a water-soluble globular protein?
Hydrophobic amino acid residues cluster away from the surface in globular proteins, so much of the protein's interior is a tightly packed combination of hydrocarbon and aromatic ring R groups with very few water molecules.
How does one determine the three-dimensional structure of a protein? Your answer should be more than the name of a technique.
The protein is crystallized, and the crystal structure is determined by x-ray diffraction. The pattern of diffracted x-rays yields, by Fourier transformation, the three-dimensional distribution of electron density. By matching electron density with the kn
Describe a reservation about the use of x-ray crystallography in determining the three-dimensional structures of biological molecules.
To obtain an x-ray picture of a biomolecule, the molecule must be purified and crystallized under laboratory conditions far different from those encountered by the native molecule. Biomolecules in the cell also have more flexibility and freedom of motion
Explain what is meant by motifs in protein structure.
Motifs are particularly stable arrangements of elements of secondary structure (e.g., ? helix and ? conformation), including the connections between them, which are found in a variety of proteins.
Draw a ??? loop, and describe what is found in the interior of the loop.
Hydrophobic amino acid residues are usually found in the interior of the loop; these help stabilize the arrangement through hydrophobic interactions.
Describe the quaternary structure of hemoglobin.
Each protein molecule is composed of two copies each of two different subunits ? and ?. The two ?? protomers are arranged with C2 symmetry.
Describe briefly the two major types of symmetry found in oligomeric proteins and give an example of each.
1) Rotational: In rotational symmetry, subunits are superimposable after rotation about one or more of the axes. Some examples are hemoglobin and thepoliovirus capsid. 2) Helical: In helical symmetry, subunits are superimposable after a helical rotation.
What is the rationale for many large proteins containing multiple copies of a polypeptide subunit?
Each different polypeptide requires a separate gene that must be replicated and transcribed. It is therefore more efficient to have fewer genes, encoding shorter polypeptides that can be used to construct many large proteins.
Explain (succinctly) the theoretical and/or experimental arguments in support of this statement: "The primary sequence of a protein determines its three-dimensional shape and thus its function.
Anfinsen showed that a completely denatured enzyme (ribonuclease) could fold spontaneously into its native, enzymatically active form with only the primary sequence to guide it.
Each of the following reagents or conditions will denature a protein. For each, describe in one or two sentences what the reagent/condition does to destroy native protein structure.
(a) urea
(b) high temperature
(c) detergent
(d) low pH
(a) Urea acts primarily by disrupting hydrophobic interactions. (b) High temperature provides thermal energy greater than the strength of the weak interactions (hydrogen bonds, electrostatic interactions, hydrophobic interactions, and van der Waals forces
How can changes in pH alter the conformation of a protein?
Changes in pH can influence the extent to which certain amino acid side chains (or the amino and carboxyl termini) are protonated. The result is a change in net charge on the protein, which can lead to electrostatic attractions or repulsions between diffe
Once a protein has been denatured, how can it be renatured? If renaturation does not occur, what might be the explanation?
Because a protein may be denatured through the disruption of hydrogen bonds and hydrophobic interactions by salts or organic solvents, removal of those conditions will reestablish the original aqueous environment, often permitting the protein to fold once
What are two mechanisms by which "chaperone" proteins assist in the correct folding of polypeptides?
Chaperones protect unfolded polypeptides from aggregation by binding to hydrophobic regions. They can also provide a microenvironment that promotes correct folding.