3-3D structure, tertiary Flashcards
what determines tertiary structure
amino acid sequence + environment where protein is
how do soluble proteins fold best
when in an aqueous environment
how do membrane proteins fold best
only fold properly in presence of membrane (or suitable replacements, like detergents)
what are the critical forces in determining tertiary structures
hydrophobic effect!!!
van der waals interactions
H-bonds
ionic interactions
why are van der waals important in determining 3ary structure even if they are weak
weak but many so they are significant
what is delta G for folding
-100kJ/mol
what energy state is the native conformation
low energy (folded)
can there be more than 1 native conformation
yes
why can there be more than one stable functional state (what are the other things that can make more)
- ligand binding (allostery)
- flexible portions of proteins (like a.a. that are not super useful/needed in that polypeptide)
- “breathing”-kinetic motions of atoms in proteins
what are some methods to determine protein structure
circular dichroism
Xray crystallography
Protein NMR
what kind of techniques can be used to yield general characteristics of secondary structure
circular dichrois,
what kind of techniques can be used to yield detailed atomic information
X-ray crystallography
protein NMR
how does circular dichroism work
depends on differential absorption of left and right circularly polarized light
what is circular dichroism sensitive to (like what does it detect)
secondary structure
when is circular dichroism most useful in (what kind of experiments)
denaturation/ renaturation
transition from folded to unfolded
what kind of structures have characteristics circular dichroism spectra
alpha helices
beta sheets
random coil/irregular structures
how do you make the crystals in X-ray crystallography
protein preparations are used to grow crystals-must be very pure samples
what wavelength is exposed to the crystals
X-rays which are 1A
what kind of info does X-ray crystals give us - directly and indirectly
(aka what info is gotten from the experiment and how is it used)
makes a diffraction pattern which can be used to make an electron density map
is 6A or 1A better resolution
1A (smaller distance means easier to distinct between 2 points)
what do regions of high electron density mean in X-Ray diffraction
location of atomic nuclei
what are 3 pros for Xray
highly detailed
rapid solutions (sometimes, like drug companies wanna see quick before and after with drug)
useful for large proteins
what are 4 cons for Xray
requires crystal growth (difficult)
crystals must deffract (not all do)
structures are static (cant have dynamic action)
cannot see hydrogens!!! (usually-you see things with lots of electrons, so not H)
what are off diagonal peaks in 2D NMR
signals generated by close range interactions of protons
what can you do with a combination of off diagonal peaks
helps provide info on the 3D structure of protein
what does magnetic coupling provide information about
distances between atoms
what kind of information is protein NMR combined with
ideal geometry information (dont worry just one line)
does NMR give a single solution
gives a range of solution which reflects both dynamics/motions and error
what do the multiple lines on an NMR represent
a family of structures consistent with the distance constraints of NMR
what does it mean when there are areas that are less defined in protein NMR
they may be in motion or only have a few distances determined (not sure what is the exact conformation)
what are 2 pros of protein NMR
dynamic info (real time) proteins are in solution (doesnt need to be a crystal which can be hard to deal with)
what are 2 cons of protein NMR
difficult for large macromolecules
synthesis of peptides containing isotopes (13C and 15N) can be expensive and time consuming
what amino acids are often found in alpha keratin
and why
alanine (alpha helix) and cysteine (crosslinks)
what reinforces the alpha keratin structure
disulphides
what does more disulphides in keratin cause
it becomes “harder”
what does less disulphides in keratin cause
it becomes “softer”
what direction is the individual alpha helix in alpha keratin
right handed
how many chains are in alpha helix
2 (dimer)
what happens to the 2 alpha helices in alpha keratin +RH or LH
they are twisted in a left handed superhelix
what % of protein mass in mammals is made from collagen
25-35%
what are the main forms of collagen in humans
extracellular matrix proteins like skin bones teeth
what kind of structure is collagen
regular, helical
how many residues per turn in collagen
3
what direction are the individual chains in collagen
left handed
how many chains are in collagen
3
what direction do the 3 chains coil into in collagen
right handed (superhelix)
where are the H bonds in collagen
interchain
what characterizes the primary structure of collagen (which aa)
glycine proline hydroxyproline
which 4 aa is collagen rich in
glycine
proline
4-hydroxyproline
5-hydroxylysine
where do H bonds happen in the collagen helix
between strands, NOT WITHIN (like between the 3 chains, not within)
what is 4-hydroxyproline
a post translational carbon with a hydroxyl group on carbon 4
what is the point of 4-hydroxyproline
to ensure appropriate conformation in collagen helix
when does hydroxylation happen of proline in collagen
after protein synthesis
what does 4-hydroxyproline require to occur properly
vitamine c / ascorbic acid
where does 5-hydroxylysine occur
at intervals in collagen polypeptides
what is required in 5-hydroxylysine creation
modified lysine residues - requires vit C
what causes cross-linking of peptides in collagen
lysine, hydroxylysine (and histidine) residues
what are 4 similarities amongst soluble globular proteins
- mix of 2ary structures( irregular + regular required)
- hydrophobic core hydrophilic exterior
- closely packed interiors
- maximized H bonds in interior
what are 3 differences between soluble globular proteins
secondary structure composition
prosthetic groups
presence of disulfides
where are disulfides present/ allowed
extracellular proteins
what are 3 rules for soluble globular proteins (3ary)
hydrophobic interactions are critical
extensive H-bonding occurs within 2ary structure (NOT between)
knots do not form
what is required to form hydrophobic interactions
2 layers of secondary structure must come together (interior and exterior)
where are non polar vs polar amino acids in globular proteins
non polar buried inside
polar aa on surface
where do H bonds occur in globular proteins
within 2ary structure
are elements closer in 1ary usually close in 3ary
yes
are elements closer in 3ary usually close in 1ary
no not necessarily
what directionality are connections between sequential beta strands in parallel beta sheets
usually Right handed
is structure or sequence typically conserved better
structure
what are 3 different classifications for tertiary structure
SCOP
CATH
Pfam
what do SCOP CATH and Pfam do
attempt to describe the structure of a protein (in search of common features and relationships) - usually describe overall strucutre like alpha, beta, alpha/beta
what are motifs/folds
recognizable combinations of 2ary structure that appear in a number of different proteins (can be a large or small part of the structure)
what are domains
discrete, independently-folded compact units within a polypeptide (may be composed of or include motifs)
can domains function if another part of the protein isnt working
likely yes, they can fold and function without other parts (if they have different functions)
are there more intradomain interactions or interdomain interactions
more intradomain (more within that between)
