chapter 4 3D structures of proteins

what are the secondary structures of proteins

alpha helix and beta sheets

what is the primary structure of a protein

amino acid

what is the tertiary structure of a protein

polypeptide chain

what is the quaternary structure of a protein

assembled subunits

do proteins always fold the same way

yes

what is the name of the structure that a protein assume every time

native fold

what is significant abt the native fold

has a large number of favorable interaction within the protein

what is the cost of the protein folding in a specific native fold

entropy cost

conformations

thermodynamically the most stable (lowest Gibbs free energy)

native

proteins in any functional, folded confirmations

stability

tendency of a protein to maintain a native confirmation

unfolded proteins have what?

high conformational entropy

how do chemical interactions stabilize native conformations?

1. strong disulfide bonds are uncommon

2. weak (noncovalent) interactions and numerous forces are numerous

3. H bonds

4. hydrophobic effect

5. ionic interactions

how are natural protein structures constrained

by peptide bonds

C-N bonds are…

shorter and planar

peptide bond details

• resonance hybrid

• favors trans dipole

• resonance around double bond

resonance in the peptide bond causes what?

• to be less reactive

• to be rigid and nearly planar

• exhibit large dipole moment inn favored trans configuration

why is rotation around the peptide bond not permitted

rigid resonance structure

what rotation around the bond is permitted?

rotation around the alpha carbon

• the phi and psi

phi angle around the alpha carbon

amide nitrogen bond

psi angle around the alpha carbon

carbonyl carbon bond

in a fully extended polypeptide-both phi and psi are what

180 degrees

what determines the secondary structures

• organization around peptide bond

• identity of R group

why are some phi and psi combos unfavorable

steric crowding in backbones or side chains

why are some phi and psi combos favorable

form favorable H bonding interactions along the backbone

what does a Ramachandran plot show

the distribution of phi and psi dihedral angles that are found in a protein

• common secondary structure elements

• reveals regions w unusual backbone structure

where are the allowed conformations found on a Ramachandran plot

in blue

where are the unallowed confirmations found on a Ramachandran plot

in white

what does secondary arrangement refer to?

local spatial arrangement of the polypeptide backbone

alpha helix

stabilized by H bonds between nearby residues

beta sheets

stabilized by H bonds between adjacent segments (not nearby)

random coil

irregular arrangement of polypeptide chain (not a type of structure)

helical backbone

• held together by H bonds between amides and residue (n) of amino acids

right hand helix has how many residues

3.6 residues, 5.4 A per turn

how are peptide bonds aligned w helical axis

parallel

how are side chains aligned with helical axis

perpendicular

alpha helix only have what type of helix

right handed (R group protrude away from backbone, more stable)

top view of the alpha helix

• inside diameter is 4-5 A (too small for things to fit inside it)

• outside diameter is 10-12 A (fits well into dsDNA)

what is dsDNA

double stranded DNA

what are some strong helix formers

ala and leu

Pro. sequence

• helix breaker

• rotation of N-ca is impossible is impossible

Gly. sequence

• helix breaker

• tiny R groups supports other conformations

attractive/repulsive forces between side chains 3 to 4 does what

affects formation

does the peptide bond have a strong dipole moment?

yes

what is the charge on C-O

negative

what is the charge on N-H

positive

where do negatively charged residues often occur

near the positive end of the helix dipole

what are multi beta interactions called

sheets

how are sheets held together

• H bonding on amide

• carbonyl groups of the peptide bond from opposite strands para

parallel beta sheets

• H bonded strands run in same direction

• H bonds strands are bent (weak)

antiparallel beta sheets

• H bonded run in opposite directions

• H strands are linear (stronger)

when do beta sheet occur frequently?

when the strands in the beta sheets change directions

what is the beta sheet turn angle and where does it occur

• 180 degrees

• over 4 amino acids

how is the beta sheet turn stabilized

H bond from the carbonyl O to the amide proton three residues down

what amino acids kink often are are often found in B sheets?

• proline (position 2)

• glycine (postion 3)

what are the turn allowed angles for antiparallel

120-180 phi

what arrest the turn allowed angles for parallel

60-120 phi

circular dichroism (CD) spectroscopy

measures differences in the molar absorption of the left handed vs right handed circularly polarized light

CD spec details -

• cannot obtain a high resolution 3D structure

• focuses on what happens with the secondary elements

chromophore

absorbs light, peptide bond

tertiary structure def

• described the well-defined, 3D fold adopted by a protein

• spatial arrangement of a protein

quaternary structure def

interactions between components of a multi subunit assembly

how is a tertiary structure stabilized

numerous weak interactions between amino acid side chains (hydrophobic and polar interactions, stabilized by disulfide bonds)

fibrous proteins

• adopted for structural function

• give strength/ flexibility

• water insoluble bc high concentration of hydrophobic residues

alpha helix (cross linked by disulfide bonds)

• tough, insoluble protective structures

• ex. alpha keratin of hair, feathers and nails

beta confirmation

• soft, flexible filaments

• ex. silk fibron

collagen triple helix

• high tensile strength, without stretch

• ex. collagen of tendons, bone matrix

structure of alpha keratin in hair

• right handed alpha helix

• 2 strands of alpha keratin in parallel orientation wrap around each other to form super twisted coil

super-twisted helical path is what

left handed

cross links in alpha keratin are stabilized by what

disulfide bonds

alpha keratin is rich in what

Ala, Val, Leu, Ile, Met, Phe

what is a protofilament

multiple 2-chain coiled coil, 20-30 A

what is a protofibril

multiple protofilaments

how does a perm work

1. reducing agent added to break down disulfide bonds

2. curlers put in place of new shape

3. oxidizing agent added to reform disulfide bonds

what is collagen

important constituent of connective tissue

what are examples of collagen

tendons, cartilage, bones, cornea of eye

details abt collagen

• Gly and Pro rich

• left handed helix

superhelical triple helix

• three collagen chains intertwined

• higher tensile strength than steel wire

• strong biological material

triple helices

assemble bingo collagen fibril

is collagen an alpha helix

no, because it is left handed

4-hydroxyproline in collagen

• forces proline into favorable pucker

• offers more H bonds between 3 strands of collagen

posttranlational processing catalyzed by what

prolylhyroxylase and require alpha-ketoglutarate, molecular oxygen and ascorbate (vitamin C)

how are collagen superstructures formed

crosslinking of collagen triple helices to form collagen fibrils

what are cross links

covalent bonds between Lys or HyLys ro His amino acid residues

silk fibroin

main protein in silk from spiders and moths

details of silk fibroin

• antiparallel B sheet structure

• small side chains allow close packing of sheets (Gly, Ala)

what is silk fibroin structure stabilized by?

• H bonding in sheets

• LDS interactions between sheets

what makes silk fibroin unique?

• strong but very stretchy

• composite material (made of lots of things)

• strongest biological material

• rubber like stretchy parts

• crystalline parts (fibroin rich)

Globular protiens

• more compact

• fold back on each other

• enzymes, transport proteins, motor proteins, regulatory proteins, immunoglobulins

how does myoglobin store oxygen

hydrophobic areas keep protein folded, has a pocket to bind oxygen

how compact is globular protein

100 × 60 A

what does myoglobin do

stores oxygen

protein data bank (PDB)

archive of experimentally determined 3D structures

motif (fold)

recognizable folding pattern involving 2+ elements of secondary structures and then connections

where can motifs be found

reoccurring structures in numerous proteins

how are globular proteins composed

different motifs folded together

domain

part of polypeptide chain that is independently stable or could undergo movements as a sable entity

domain details

• may be distinct or hard to find

• small proteins only have one domain