Protein Folding Review Flashcards
interactions that govern protein folding stability
non-covalent
hydrophobic
non-covalent interactions
Van der Waals interactions (short range repulsion)
hydrogen bonds
electrostatic forces (e.g. ion pairs and salt bridges)
hydrophobic interactions
nonpolar groups do not interact favorably with water
their favorable interactions are primarily the results of their exclusion from water
the hydrophobic interaction is a major factor in the folding and stability
determinants of folding
secondary structure (for an efficient packing)
hierarchical folding
hydrophobic effect
context dependent
alpha helix is stabilized by intrachain hydrogen bonds between the _____ and ______ groups
NH
C=O
hydrogen bonds in alpha helix form _____ amino acid residues ahead in the sequence
4
alpha helices can be right (clockwise) and left handed, alpha helices found in proteins are _____ - handed because they are energetically more favorable
right
beta sheets are stabilized by hydrogen bonding between _______ strands
polypeptide
a beta sheet is formed by linking
2 or more beta strands via hydrogen bonds
beta sheets can run in
parallel or antiparallel direction
reversal directions in polypeptide chain provides
compact and globular shapes for polypeptide chain; they’re called reverse turn, beta turn, and hairpin turn
in many reverse turns, C=O and N-H groups form
hydrogen bonds for stability
loops do not have regular periodic structure, they are often ______ ; positioned ______ ; and participate in ______ and ______
well defined and rigid
on the surface of the protein
protein-protein interactions and interactions with other molecules
heptad repeat
a type of random repeat sequence in which a group of 7 amino acids occurs many times in a protein sequence
often found in superhelix
folding funnel steps
- rapid formation of secondary structures
- formation of domains through cooperative aggregation (concept of folding nuclei)
- formation of assembled domains (concept of molten globule)
- adjustment of conformation
- more rigid structure
molten globule state charactersitics
- the presence of a native-like content of secondary structure
- the absence of a specific tertiary structure produced by the tight packing of amino acid side chains
- compactness in the overall shape of the protein molecule, with a radius 10-30 percent larger than that of the native state
- the presence of a loosely packed hydrophobic core that increases the hydrophobic surface area accessible to solvent
- it is not specific and occurs in early stage of protein folding
tertiary structure
spatial arrangement of amino acid residues that are far apart in the sequence and to the pattern of disulfide (S-S) bonds
protein disulfide isomerase (PDI)
rearranges the polypeptide’s non-native S-S bonds
fixes incorrect disulfide bonds
protein folding is a highly ______ process
cooperative
proteins can be denatured by several treatments to disrupt
the tertiary structure
protein folding and unfolding in a ______ process
all or none
molten globule stage is ______ and ______
intermediate
very short
partially loss of folding destabilizes the
remainder of the structure
quaternary structure
spatial arrangement of subunitS and nature of their interaction
PPI (peptidyl prolyl cis-trans isomerase)
assists with cis-trans transition
mitochondria contain their own _____ and _____ molecules that are distinct from those that function in the cytosol
Hsp60
Hsp70
functions of molecular chaperons Hsp70/40
ATP-driven
reverses misfolds; assists with newly synthesized proteins; unfold/refold of trafficked proteins
chaperonins are a subtype type
chapernons
molecular chaperon functions
- essential proteins that bind to unfolded and partially folded polypeptide chains
- they prevent the improper association of exposed hydrophobic segment
- non-native folding, polypeptide aggregation, and precipitation will not occur
- they allow misfolded proteins to refold into their native conformation
native protein –> soluble –> _______ tries to refold, if not it ubiquinates and _____ assists with proteasoe
Hsp40
Hsp70
native protein –> insoluble –> ______ and ______ ubiquinate and send to proteasome
Hsp40
Hsp70
ubiquitinated proteins are processed to ______ ; which are further processed to yield ______ ; these can can used for
peptide fragments
free amino acids
biosynthetic rxns
what structures or processes are involved in cellular quality control system
proteasomes
autophagy
ERAD (ER-Associated Degradation)
how does protein-folding cause diseases?
improper degradation
overactive cellular degradation systems (ERAD, autophagy) can contribute to the accumulation of mutant, misfolded, incomplete degraded proteins
this improper degradation of proteins can contribute to the development of more severe diseases
e.g. cystic fibrosis
how does protein-folding cause diseases?
improper localization
for proper trafficking to target organelles, proteins must fold correctly
incorrectly folded proteins lead to improper subcellular localization (resulting in loss-of-function: protein isn’t transported correctly to target organ so target organ cannot function properly or gain-of-function: protein isn’t able to be transported out of original organ and causes dysfunction in organ where it was synthesized)
e.g. AAT
how does protein-folding cause diseases?
dominant negative mutation
a mutant protein antagonizes the function of the wild-type protein leading to: loss of protein activity; and mutant protein presence interferes with function of the WT protein at cellular and structural levels
e.g. p53
how does protein-folding cause diseases?
gain-of-toxic function
protein conformational changes can cause dominant phenotypes
e.g. ApoE in Alzheimer’s disease; Src kinases in cancer
how does protein-folding cause diseases?
amyloid accumulation
e.g. cataracts and alzhiemer’s disease
amyloid fibers
insoluble protein aggregates
amyloidogenic proteins have ______ sequence
VQIVY
lower order oligomers cause
toxic effect
amyloid deposits could be a
protective mechanisms
several amyloidogenic proteins from pore-like structures that
disrupts the cell membrane integrity
misfolded forms of the protein are frequently observed in
the elderly as part of the natural aging process
individuals with mutations in the protein early in life
how do amyloid fibers progress to amyloid plaques
seeding (nucleation) –> fibril formation –> deposit
keystones for environmental stress
to detect
to respond
to adopt
intrinsic induction of stress defense programs and resulting adaptation can
increase life expectancy
proteostasis
maintenance of protein homeostasis
cellular and organismal functionality requires
protein production
folding
degradation
complex pathways to ensure proteostasis in different compartments include
cytosol (Heat Shock Response)
ER (UPRer)
Mitochondria (UPRmt)
cellular proteins are folded
by chaperons
membrane and secreted proteins fold and mature where
in the ER
what is the last line of defense in regards to maintaining proteostasis
apoptotic pathway
heat shock response (HSR) manages denatured proteins in
the cytosol
unfolded protein response ER (UPRer)
unfolded or misfolded proteins accumulate in ER causing ER stress
ER stress initiates a single pathway called unfolded protein response (UPR)
this pathway is intended to save the cell
functions of UPRer
increase protein chaperones
increase rate of ERAD
decrease protein production
last resort is apoptosis
steps of autophagy
isolation membrane formation
identification and collection of cellular components for degradation
completion of autophagosome
fusion of autophagosomoe with lysosome
formation of autolysosome and degradation of contents
steps of ERAD
translocation into ER
degradation of misfolded proteins through translocation out of ER and into proteasome
which UPR pathway is most recently discovered
UPRmt
mitochondrial proteome is composed of how many proteins
1500
mitochondria proteins are encoded by
nuclear and mitochondrial genome
13 essential proteins of ______ are encoded by mtDNA
ETC
what are the 2 major mitochondrial chaperon systems
mtHSP70
multimeric HSP60-HSP10 machinery in the matrix
UPRmt protein quality control (PQC) proteases:
are specific for each mitochondrial compartment
recognize and degrade the proteins that don’t fold and that aren’t properly assembled
if the UPRmt senses the overload of the QC (quality control) system, it
activates the transcription of nuclear encoded protective genes by retrograde signaling
re-establishes the mitochondrial homeostasis
