L6: Protein Folding I Flashcards
determinants of protein folding
- 2ndary structure
- hierarchical folding
- hydrophobic effect
- context dependent
secondary structures
a-helix
or
B-sheets
interactions that govern protein folding stability
noncovalent interactions
—-H bonding determines stability
hydrophobic interactions
non-covalent interactions that govern protein folding stability
van der waals forces
H bonds
electrostatic forces
van der waals forces
short range repulsion
examples of electrostatic forces
ion pairs
salt bridges
hydrophobic interactions that govern protein folding stability
- nonpolar does not want to interact w/ water
- their favorable interactions are results of their exclusion from water
- hydrophobic interaction is major factor in protein folding
relate short range repulsion and interatomic distance
too close = repulsion
too far = no attraction
optimal distance = attraction
elements that possibly make H bonds
NOF only
hydrogen bonds are much ______ than covalent bonds because ?
weaker
longer bond length but more flexible
energy of H bonds
1 - 5 kcal/mol
relate charges to electrostatic forces of proteins
aq conditions
charges must be on outside of proteins
the hydrophobic effect
2 nonpolar molecules joining together
the hydrophobic effect
2 nonpolar molecules joining together
a-helix stabilization
by H bonds between NH and C=O groups
this H bonds form 4 aa residues ahead in the sequence
aa residues in a-helix formations
each aa residue is related to the next one by:
- -a rise of 1.5A helix axis
- -100 degree rotation
- -3.6 aa residue per turn
direction of a-helices
right-handed = clockwise
left-handed = counter
a-helices found in proteins are ______-handed, which is ?
right (almost always)
energetically more favorable
B-sheets are stabilized by ?
H bonding between polypeptide strands
B-sheets are composed of ?
2 or more polypeptide chains = B strands
–fully extended
distance between adjacent amino acids in B-strands
~3.5A
a B-sheet is formed by linking ?
2 or more B-strands via H bonds
B-sheet directions
parallel direction
or
antiparallel
reversal directions provide ?
compact and globular shapes for polypeptide chains
example of names of reversal directions
reverse turn
B-turn
hairpin turn
in many reverse turns ___ and _____ groups form H bonds for stability
C=O and N-H
reverse loop locations
- -do not have regular periodic structure
- -well defined and rigid
- -on surface of protein
- -participate in interactions
superhelix, a-helical coiled coil structural role
keratin
collagen cell cytoskeleton
muscle proteins
superhelix, a-helical coiled coil biological functions
regulation of gene expression
oncoproteins
the 2 helices in a-keratin are characterized by a central region of ?
300 amino acids w/ heptad repeats
how the 2 helices interact w/ each other
intracellular proteins usually lack ____ bonds
S-S bonds
calmodulin
a Ca sensor
contains 4 similar units in a single polypeptide chain
each unit binds a Ca ion
concept of context-dependent
the same sequence of amino acids can adopt different conformations in dif proteins
define molten globule state
an intermediate conformational state between naïve and fully unfolded forms
the molten globule state has the absence of specific _____ structure produced by ?
tertiary
tight packing of aa side chains
compactness in the overall shape of the protein molten globule state has a radius ?
10 to 30% larger than that of the native state
hydrophobic core of molten globule state
is loosely packed
thus increasing the hydrophobic surface area accessible to solvent
the molten globule state is not _____ and occurs ?
specific
occurs in early stage of protein folding
the molten globule is a compact globule w/ a molten _______ structure that is primarily stabilized by ?
side-chain
by nonspecific hydrophobic interactions
protein folding obeys the laws of ________ and prefers _____ state
thermodynamics
lower nrg states
