Protein structures (primary, secondary, tertiary, etc.) Flashcards
Why would a protein want to have a quaternary structure (subunits)?
1) Error frequency in translation
2) Ease of folding of small vs. large polypeptide chains
3) Signalling/communication (“division of labor”, regulatory functions…)
4) Use of same subunit in different multi‐subunit proteins/complexes
Do all proteins have quaternary structures?
no, only proteins that have more than one polypeptide chain (subunits) have quaternary structure
also most proteins with a MW greater than 100kD is most likely comprised of subunits
subunits in quarternary structures are held together by what types of bonds/
non covalent interactions, salt bridges, van der waal’s, hydrogen bonds, and hydrophobic interactions
What are oligomers?
proteins with more than one subunits, if identical they are called protomers
if you have two identical subunits you call them?
dimers (2 protomers)
What happens if there are two non identical subunits?
the efficiency of the enzyme is detrimentally affected b/c the reaction would depend on the diffusion of the intermediate to the second subunit and there might be other enzymes in the cell that would compete for the intermediate
How is cn rotational symmetry classiified?
by a single rotational axis
What is the meaning of quasi equivalent?
subunits that are not strictly equivalent in environment
What is tertiary structure of proteins?
3D arrangement of secondary structures and side chains
What two methods can be used to determine tertiary structure?
x-ray crystallography or NMR spectroscopy
Which amino acids are hydrophobic and what does it mean when it comes to interactoins?
F, I, L, M, V, W
hydrophobic interactions usually drive these into the interior
Which amino acids are uncharged polar? where are they located in a peptide
H, N, Q, S, T Y
located either in or exterior but when interior they are usually bonded with a Hydrogen
Which amino acids are charged polar? where are they located?
D, E, K R
located mostly on the exterior but if interior will either be in a salt bridge or involve in a specific function such as catalysis, metal ligation etc.
These are very unstable internally if they don’t interact w/another species
If uncharged residues are found interior what type of bond will they have?
predominantly be H bonded
Are hydrogen bonds stronger in a non-polar environment or an aqueous solution?
stronger in non-polar
what is. domain?
a region of polypeptide or protein that fold independently of each other and are functioning units that are connected by polypeptide segments
How can we classify domains?
using the CATH classification
C-class overall secondary-structure of the domain
A- architecture - high structural similarity but no evidence of homology
T-topology/fold - large-scale grouping of topologies which share particular structural features
Homologous superfamily: demonstrable evolutionary relationship
What is the dominant secondary structure seen in fibrous proteins?
coiled coil structure and it is the basic building block of fibrous proteins
What gives keratin its fibrous nature?
the alpha helix.
the fundamental building block of keratin is the two chain coiled coil, where two alpha helices twist around each other.
What are protofilaments?
part of the keratin structure - two chain coiled coil comes together w/another two chain coiled coil in a staggered arrangement and form protofilaments
a bunch of protofilaments for what?
protofibril
Keratin is a component of what?
hair, nails, horn, feathers, porcupine quills etc.
What is the differences between type I and type II alpha helices in keratin? What do they do together?
Type I: acidic, right handed structure
Type II: basic, right handed structure
Type I and Type II twist around each other to form the coiled coil structure. and become a combined left handed structure
What motif do you look for in any protein primary structure to see if it has a twisted coil-coil structure associate w/it?
-look for a 7 amino acid sequence (a, b, c, d, e, f, g) that repeats one after another. this heptad repeat can extend over hundred residues
in position a (1) and position d (4) are usually hydrophobic amino acids ( Leu, Ile, Val, etc) the residues in the e and g positions are generally charged
What is a pseudorepeat?
when some keratin repeats do not have hydrophobic residues at site a or site d
Why are residues in a and d in the keratin pseudo-repeat usually hydrophobic?
residues a and d ffrom the two strands in the coil-coil interact with each other due to helix alignment and are buried at the helix helix interface due to hydrophobic effect
e and g are charged and can form ion ion interactions or salt bridges
Alpha keratin is rich in what type of residues?
cys residues = disulfide bridges
why is one form of keratin as in hair flexible and springy while the other form as in the horn, hard and inflexible?
due to its chemical composition of different forms
Springy characteristic: low concentration of Cys and more hydrogen bonds
Stiffness:
cysteine forms disulfide bonds and more cystine and more disulfide bonds decrease springiness and increase hardness
How do amyloid fibrils form?
from globular soluble proteins
What are amyloid fibrils?
important fibrous protein involved in bovine spongiform encephalopathy (BSE = mad cow disease) and other prion diseases
-alzheimer’s disease and transthyretin amyloidosis
How do amyloid fibrils contribute to diseases like mad cow and other prion disease?
normally globular soluble proteins become deposited as stable insoluble plaques in the extracellular space of the brain or eye
in prions, the alpha helix globular protein becomes beta sheet fibril
in transthyretin beta sheet globular protein becomes beta sheet fibril
What is the role of transthyretin (amyloid fibrils)?
thransthyretin is a transpor protein
in the serum and cerebrospinal fluid that carries hormone thyroxine and retinol-binding protein in bloodstream
What mutation causes transthyretin to cause amyloidosis?
single point mutation from Valine to Methionine and unfolding of c and d strands leads to fibril development
What is the structure of amyloid fibrils of transthyretin? How does it differ from keratin?
twisted beta sheets, each around 10 amino acids long. Has a repeat unit of 24 beta strand and each repeat unit is 4 transthyretin molecules. Unlike keratin, there are no consensus sequences
collagen is comprised of how many polypetide chains?
3 polypeptide chains termed alpha chains that form LEFT HANDED HELICES
-the 3 LEFT HANDED helices in turn form a coiled-coil RIGHT HANDED structure (tropocollagen)
How are the triple helical tropocollagen elements in collagen cross linked?
via lysine side chains
collagen is found where?
bone cartilage teeth skin blood vessels
provides strong stress bearing material
What is the amino acid composition of collagen?
33% glycine and 15-30% 4-hydroxyproline
it typically has a sequence repeat that is glycine-proline-4-hydroxyproline
sometimes 5 hydroxylysine - but only needed to add sugars groups
What is 4-hydroxyproline?
found in collagen, it is a post-translational modification of proline
How is vitamin C related to collagen?
primates can not synthesize collagen - leads to vitamin c deficiency aka scurvy - gum disease
vitamin c is a reducing agent (antiscorbutic factor) and donates 2 electrons in propyl 4-hydroxylase reaction
vitamin c is also required to keep the iron atoms in the ferrous or +2 state
How are the cross link between tropocollagen molecules formed?
oxidation and aldol condensation of lysine side groups as catalyzed by the enzyme lysyl oxidase
What are the three criteria that must be met for ordered tertiary structures?
1) nearly all residues must be in low energy conformation to be thermodynamically stable
2) fulfill hydrogen bonding requirements of buried polar groups
3) form compact packed structures so van der waals can have a strong effect
If there are polar groups buried in the interior of a peptide, what must happen?
polar groups must be hydrogen bonded or form ionic interactions to a suitable partner since water is not an available partner
Rotation occurs about which atom?
alpha carbon ins the common point of rotation between consecutive planes ( phi and psi bonds)
What is trans and cis configuration and which is the most common? What is an exception?
Trans - the two alpha carbons are on opposie sides of the peptide bond - most common
cis - the two alpha carbons are on the same side of hte peptide bond - rare
Proline can adopt the cis configuration and trans since both have steric hindrance
Rotation is allowed between which carbon bonds on a peptide? what is the name of these rotational angles?
rotational angles: phi and psi
Phi: alpha carbon and N bond
Psi: alpha carbon and carboxyl bond
carboxyl and amide do not rotate
When do ramachandran plots of amino acids look similar? what is the exception
Plots look similar w/amino acids that have a larger R group having a smaller allowed area.
Glycine is exception - has the smallest R group and can adopt widest range of conformations
Which amino acid is the most constrained?
Proline due to the cyclic side chain and it limits its phi (alpha carbon - N) range from -60 to +/- 25
What are the four basic types of ramachandran plots? q
1) generic (18 amino acids no G or P)
2) Glycine
3) proline
4) pre-proline (refers to residues that precede
What are the most common and stable regular secondary structures? What role do they play?
alpha helix and beta sheet conformations
play a role in protein stability
beta turns and w loops also play a role but not as common
What is the main driving folding force when there is a water soluble globular protein?
the need to pack the hydrophobic side chains into the interior or core of the protein.
Is the polypeptide backbone chain polar or non polar?
it is polar and hydrophilic with one hydrogen bond donor N-H and one H bond acceptor C00- in each peptide unit
In an alpha helix how are the hydrogen bonds between amino acids?
the H bond are between one amino acid and another acid that is 4 residues awy
H bonds occur between the amino N and the O atom of the carbonyl. AKA every main chain c=o and N-H group is hydrogen bonded.
For L amino acids, which alpha helix is preferred the right-handed or left handed? Why?
Right handed is preferred and energetically favored due to less steric clash between side chains and back bones. AKA essentially all alpha helices are RIGHT HANDED
Can all amino acids form an alpha helix? What determines if they do?
Which amino acid has the greatest probability of being found in an alpha helix? which has the least?
Each of the 20 amino acids has an inherent propensity to form an alpha helix. this propensity is determined by the properties of its R group in how it affects the ability of the main chain atoms to take on the characteristics of phi and psi?
Alanine has the greatest as its free energy change is closer to negative and proline has the least probability as its value is high
What are the helix breakers?
amino acids least likely to for an alpha helix; proline and glycine
which residues prefer beta sheets?
Valine Isoleucine Tyrosine Cysteine Tryptophan Phenylalanine Threonine
What is antiparallel beta sheets? what makes it antiparallel?
the beta strands are opposite to one another and R groups alternate above and below the plane.
how many strands are needed to form an antiparallel beta sheet?
a minimum of 2 strands for a sheet; 15 strands is the max and overall average is 6 strands
How does H bonding occur in antiparallel beta sheets?
antiparallel beta sheets are almost fully extended and when strands align with each other the C=O can hydrogen bond with the N-H of the neighboring strand and vice versa. The H-binding patter is narrowly spaced H bond pairs that alternate with wider spaces between them.
The H bonds connect each amino acid of one strand to a single amino acid of the adjacent strands all possible H bonds are formed except for the two flanking strands of the beta sheet
AKA the hydrogen bonds are linear and stronger than the bent H bonds in parallel sheets
What is the minimum required beta strands for parallel beta sheets?
minimum of 5 strands
How do hydrogen bonds form in parallel beta sheets?
Hydrogen bonding is not linear and this makes the H bonds of the parallel sheet weaker.
the H bond density per residue is also lower than antiparallel b/c the H bonds connect each amino acid of one strand w/two different amino acids of the adjacent. H bond are also evenly spaced
Why is the parallel beta sheet not as stable as antiparallel?
H-bonds of parallel are weaker since they are not linear and the hydrogen bond density is lower in parallel
Can a protein have both parallel and antiparallel beta sheets?
yes, you can have a mix
are beta sheets left or right handed? why?
they are right handed twist ; thought to be a consequence of non-bonded interactions between the L-amino acid residues in the extended polypeptide chain
In beta and alpha sheets are R groups extended in or out?
extend out!
What is the 3-10-helix
A type of helix that rarely occurs but when it does it is mostly as a single turn transition between one end of the helix and the adjoining portion of the peptide chain.
It is thinner and longer than the alpha helix due to its pitch and residues per turn . its R groups can encounter steric hindrance
What are loops and turns?
part of secondary protein structures that connect alpha helices and/or beta sheets . they can be of various lengths and irregular shapes
What occurs to residues in loops and why?
Residues in loops make good sites for hypervariable substitution, insertions and deletions. and when homologous amino acid sequences from different species are aligned, insertions and deletions occur almost exclusively in the loop regions
Where do loops and turns lie on proteins?
the surface of proteins and for this reason are involved in interactions with other proteins and other molecules
Due to their flexibility turns and loops are good for what?
to cap off protein active sites and provide catalytic residues as substrates bind and products are released.
A helix-turn-helix motif is known for?
DNA binding
A helix-loop-helix is known for?
Calcium binding proteins, parvalbumin and calmodulin
What are disordered regions?
usually involved in recognition and/or binding
How are peptide bonds formed?
formed via dehydration between alpha carboxyl acid and alpha amino groups of the two acids aka you’re losing water
Are amino acid condensation reactions are favored when in the forward or reverse reaction?
favored in the reverse reaction. The forward reaction takes place even though it is not thermodynamically favorable b/c during protein synthesis at the ribosome, the carboxyl group of one of the amino acids is modified or activated making it thermodynamically more favorable
-even during chemical synthesis of polypeptides in the lab the carboxyl group has to be modified so that the forward reaction is favored
Why do primary structures or sequence of amino acids/residues dictate the way the protein fold in 3D space when exposed to an aqueous environment?
B/c peptide folds is dependent on the R groups of the residues that form that chain. R groups are hydrophobic and hydrophilic
How do we determine primary sequences of proteins?
1) Edman degradation - chemical sequencing of proteins
2) Proteomics - mass spec or crystallography
3) Bioinformatics and genomics (DNA sequencing) - can lead to errors b/c it cannot account for protein processing or post-translational modifiction
How do you determine if a residue is important in a mechanism of actin like binding, catalysis etc?
use site directed mutagenesis to probe structure function
Walker motif in proteins means what about your protein? What is the motif?
Motif: G-X-X-X-XG-K-T/S
-means protein likely binds to ATP
What is the p-loop sequence?
protein has an Ala or Gly in the first position then any four amino acids followed by glycine in the 5th position, lysine in 6th and either Thr or serine in 7th. P look also bind to ATP or similar compound
What do motifs tell us about a protein?
motifs are certain patterns that we can recognize in the primary sequence and associated it to a function
can we know the function of a protein just by knowing its primary sequence and not its 3D?
yes, by looking at motifs or mutagenesis
When changes in residues occur what is it due to?
-chemical mutations of DNA changes in codon sequence
it is not due to DNA rep or RNA translation errors
What are the three types of sequence change that may occur in proteins?
1) Neutral drift
2) deleterious mutations
3) Deletion and insertions
What is a neutral drift?
if sequence undergoes neutral drift then the primary structure has changed from the original form but the protein still has the same function and 3D structure as before
What happens in deleterious mutation?
the protein encoded will not fold and/or function properly and the organism will be at a competitive disadvantage. Natural selection works against these mutations being fixed in a population aka lethal effect
What do insertion and deletions do to a protein?
affect protein structure by either deleting an amino acid or inserting amino acids into sequence
What are invariant residues?
residues that don’t change over long evolutionary periods. Changes in these residues lead to deleterious mutations and are important for chemical structural properties that are critical for proteins structure/function
What is conservative residues/substitution? give an example of this type of substitution
occur frequently in proteins as they evolve as long as they are not deleterious.
this type of change leads to substitutions of similar amino acids but the side chain chemistry has not changed much
Example: aspartic acid could be mutated to glutamic acid or lysine to arginine or one hydrophobic amino acid for another
What are hypervariable residues?
residues where a position may tolerate several different amino acids indicating that that particular position is non-specific
What can sequence alignment tell us?
how closely related organisms or species are
what are homologous proteins?
proteins derived from a common ancestor that share similarities in both sequence and overall 3D structure
What is homology scoring?
align sequences (accounting for gaps) and calculate the % identity. Works best for proteins over 100a.a
% identity tells us how many residues have not changed between the two proteins
