Chapter 4 - 3D Structures of Proteins

conformation

3D shape and arrangement of atoms that depends on the rotation of bond(s)

native conformation

each protein folds into a single stable shape

• biological function of proteins are dependent on

proteomics

study of large sets of proteins like the entire complement of proteins produced by a cell

globular proteins

usually water soluble, compact, roughly spherical, tightly folded

• hydrophobic interior, hydrophilic surface

• ex: enzymes, carriers and regulatory proteins

fibrous proteins

provide mechanical support

• components of large subcellular or extracellular structures

  • ribosomes, cilia

• assembles into large cables or threads

• ex: alpha keratins (hair and nails), collagen (tendon, skin, bones, teeth)

primary structure

structure of polypeptide or protein resulting from amino acid linear sequence in polypeptide chain

secondary structure

structure of polypeptide or protein resulting from H-bond interactions between peptide groups relatively close to each other

• can be on same or different polypeptide chain

• major structures: alpha helices & beta strands (and sheets)

tertiary structure

structure of fully folded polypeptide chain into closely packed 3D structures

• aka supersecondary structures

• includes all AA residues (side chains)

• stabilized by noncovalent interactions between side chains

motids in supersecondary structures

reoccurring protein structures

• helix-loop-helix

• coiled-coil

• helix bundle

• βαβ unit

• hairpin

• β meander

• greek key

• β sandwich

helix-loop-helix

two helices connected by a turn

coiled-coil

two amphipathic α helices interact in parallel through hydrophobic edges

helix bundle

several α helices that associate in antiparallel manner to form bundle

βαβ unit

two parallel β strands linked to intervening α helix by two loops

hairpin

two adjacent antiparallel β strands connected by β turn

β meander

antiparallel sheet composed of sequential β strands connected by loops or turns

greek key

4 antiparallel strands

• strands 1, 2 in middle

• strands 3, 4 on outer edge

β sandwich

stacked β strands or sheets

quaternary structure

arrangement of 2+ polypeptide chains into a multiunit molecules

• subunits have defined stoichiometry and arrangement that are held together by many weak noncovalent interactions

X-ray crystallography

used to determine 3D conformation of proteins

• beam of x-rays are aimed at crystal protein molecule

• catalytic activity of enzymes in crystalline state shows proteins crystallize in their vivo native conformation

• extra: Dorothy Crowfoot Hodgkin received Nobel prize in 1964 for determining structure of VitB12 using this technique

nuclear magnetic resonance (NMR)

used to determined structure of larger macromolecules like carbs, nucleic acids, and small-average proteins in solutions

• shows conformational changes, protein folding, disulfide bridges, and interactions with other molecules

conformation of peptide groups

• consist of 6 atoms

• some have double bonds that restrict their conformation to trans or cis

  • cis is less favorable due to steric interference of alpha carbon side chains

  • trans is more favorable because two alpha carbons are on opposite sides and corners of the planar peptide group

• has repeating N-C_α-C backbone

  • rotation about N-C_α (ϕ, phi) and C_α-C (ψ, psi) is possible

properties of α-helix

• C=O forms H-bond with amide H of residue n+4

• all C=O point to C-terminus (helix has dipole with (+) N, (-) C-termini)

• stabilized by many H-bonds (parallel to long axis of helix)

• Pitch = 0.54 nm

• Rise = 0.15 nm along long axis

• 3.6 AA per turn

• most are right-handed (from C-terminus, going down, helix turns clockwise)

• extra: Linus Pauling & Robert Corey won Nobel prize in 1954)

β strands

polypeptide chains that are almost fully extended

• stabilized by H-bonds between C=O and -NH on adjacent strands

β sheets

multiple β strands arranged side-by-side

parallel β sheets

strands that run in the same N- to C-terminal direction

• distorted H-bonds

antiparallel β sheets

strands run in opposite N- to C-terminal directions

• H-bonds are nearly perpendicular to chains

• more stable than parallel chains

interactions of β sheets

• project alternately above and below plan of β strands

• one surface may consist of hydrophobic side chains that interact with hydrophobic residues

  • hydrophobic faces of β sheets can interact with hydrophobic side chains of amphipathic a-helices

how are helices and strands connected

loops and turns allow peptide chain to fold back on itself to make compact structure

loops

often contain hydrophilic residues

• found on protein surfaces

turns

loops containing 5 or less residues

beta turns (reverse turns)

connect different antiparallel beta strands

domains

independently folded, compact units in proteins

• size: ~25 - ~300 AA residues

• connected by loops, bound by weak interactions between side chains

• image contains 3 domains

all α domain

domain that consists of only α helices and loops

all β domain

domain only consists of β sheets and non-repetitive structures that link β strands

mixed α / β domain

domain containing supersecondary structures like αβα motif, regions of α helix and β strands alternate

α + β domain

domain consists of local clusters of α helices and β sheets in separate, continuous regions of polypeptide chain

domain function

• binding small molecules

• catalyzing single reactions

domain structure

interfaces provide crevices, grooves, and pockets on surface of protein for binding or catalytic sites

denaturation

disruption of native conformation of a protein

• loss of biological activity

• minimal energy required

• caused by heat or chemicals (chaotropic agents and detergents)

  • some can be refolded/renatured

how do chemicals denature proteins

high conc. of chaotropic agents (urea, guanidinium salts, SDS) allow water to solvate nonpolar groups inside proteins

• 2-mercaptoethanol reduce disulfide bonds

folds

combo of secondary structures that form core of domain

• folded proteins occupy low energy well = more stable

• proteins fold spontaneously and rapidly (<1 sec)

hydrophobic effect

nonpolar side chains associate with each other causing polypeptide chain to collapse to molten globule

• driving force is large increase in entropy from water released

• hydrophobic collapse occurs at same time as formation of secondary structures

molecular chaperones

increase rate of correct folding

• prevents incorrect formation of folded intermediates

• can bind to unassembled protein subunits

• most are heat shock proteins (synthesized as temp increases)

• hydrolysis of ATP is needed

collagen

• major protein in connective tissue (25-35% of total protein in mammals)

  • tendons (ropelike fibers) and skin (loosely woven fibers)

• consists of 3 left-handed helical chains coiled around each other in right-handed supercoil

• 3 AA per turn

• rise: 0.31nm per residue

• more extended than α helix

globin

protein component of Mb and Hb

• His-93 is complexed to iron atom

• His-64 forms H-bond with oxygen

myoglobin (Mb)

monomeric protein that facilitates the diffusion of oxygen

• composed of 8 α helices

• interior all hydrophobic AA

• extra: John Kendrew determined the structure of myoglobin

hemoglobin (Hb)

tetrameric protein that carries oxygen in the blood

• α₂β₂ tetramer (2 α globin, 2 β globin subunits)

  • each globin similar in structure to myoglobin and has heme group

• extra: Max Perutz determined the structure of hemoglobin

heme

consists of a tetrapyrrole ring called protoporphyrin IX complexed with iron

• heme of Mb and Hb binds oxygen for transport

• occupies hydrophobic cleft formed by 3 α helices and 2 loops

oxymyoglobin

oxygen bearing myoglobin

• 6 ligands are coordinated to ferrous ions in octahedral symmetry

• oxygen is coordinated between iron and imidazole side-chain of His-64

deoxymyoglobin

oxygen-free myoglobin

allosteric interactions

ex: regulates oxygen binding and releasing from Hb

allosteric effectors (modulators)

bind to protein at site separate from functional binding site

• regulated activity of allosteric protein