REVIEW Biochemistry Protein structure

3D structures

chemical or structural functions relate to unique ___

conformations

thermodynamically the most stable, lowest Gibbs free energy 3D structures

native

protein in any functional, folded conformations

stability

tendency of a protein to maintain a native conformation

• unfolded proteins have low ___ and high entropy

• __ provided by multiple weak, noncovalent interactions

hydrophobic effect

predominating weak interaction stabilizing protein by forming solvation layer

solvation layer

highly structured shell of H2O around a hydrophobic molecule

• decreases nonpolar groups cluster

hydrogen bonding

repeating secondary structures (beta sheets and alpha helices) optimize ___

salt bridges

polar groups interacting with others of opposite charges form ion pairs and thus ___

van der Waals

___ interactions apply only on short distance and only contribute to protein stability in high numbers

dipole

peptide bond is rigid and planar and has a small ___

• 3 covalent bonds separate alpha carbons of adjacent amino acids

• resonance between carbonyl oxygen and amide nitrogen create partial + and - charges thus creating a small electric ___

peptide bond

___ links the C-terminal of one amino acid to the N-terminal of another, thus linking 6 atoms in a single plane, meaning that the ___ CANNOT ROTATE FREELY.

dihedral angles

angles defining peptide conformation

• phi (usually between -180 and +180 degrees)

• psi (usually between -180 and +180 degrees)

• omega

many phi and psi conformations cannot happen due to steric interferences (cannot both be 0 degrees for example)

secondary structure

describes the spatial arrangement of the main-chain atoms in a segment of polypeptide chain

• alpha helix

• beta sheets

• beta turn

• coils

alpha helix

simplest arrangement with the maximum number of hydrogen bonds

• each helical turn is ~3.6 residues

• R groups protrude from imaginary longitudinal backbone

• most of them are right-handed

• H bond between nitrogen atom of residue n and carbonyl oxygen atom of residue n+4 (both atoms end up stacked on top of each other)

3 to 4

interactions between R chains spaced ___ residues apart significantly affect helix stability

• ion pair and hydrophobic effect stabilize

• charge, size, and shape can destabilize

proline, glycine

__ & __ occur infrequently in alpha helices

• ___ causes destabilizing kinks due to rigid ring

• __ causes high conformational flexibility and creates coiled structure

positively, negatively

in alpha helices, ___ charged amino acid found near COO- terminus & ___ charged amino acids found near NH3+ terminus

• balance everything out

Beta strand

single protein segment whose backbone extends into zigzogs

beta sheets

several strands in beta conformation side by side forming zigzag pattern

• H bonds form between backbone atoms of adjacent segments

antiparallel

opposite orientation of beta strands

• occurs more frequently

parallel

beta stands have the same orientation

beta turn

connect ends of 2 adjacent segments of an antiparallel beta sheet

• 180 degrees turn involving 4 residues

• H bond forms between 1st and 4th residue

• Glycine and proline often occur in ___

Ramachandran plots

visualize all phi and psi angles and test quality of 3D protein structures

• beta sheets in upper left quadrant

• right-handed helices lower left quadrant

• left-handed helices upper right quadrant

• glycine often falls outside of predicted range

circular dichroism

also called CD spectroscopy, it measures the difference in molar absorption of left-handed vs. right-handed circularly polarized light

• chromophore = peptide bond

tertiary structure

overall 3D arrangement of all the atoms in a protein

• weak interactions and covalent bonds hold interacting segments in position

quaternary structure

arrangement of 2+ separate polypeptide chains in 3D complexes

fibrous protein

arranged in long stands or sheets

• give strength and/or flexibility

• simple repeating element of secondary structure

• H2O insoluble due to high concentration of hydrophobic residue

• alpha-keratin, collagen, fibroin

globular proteins

folded into a spherical shape

• fold back on each other

• more compact than fibrous proteins

• includes enzymes, transport proteins, motor proteins, regulatory proteins, immunoglobins

• each ___ protein had a distinct structure adapted for its biological function

membrane proteins

embedded in hydrophobic lipid layers

intrinsically disordered proteins

proteins lacking stable tertiary structure

• lack definable structure

• often lack hydrophobic core

• high densities of charged residues (K, R, E) and P

• facilitate interactions with multiple binding partners

• same segment can have different structure in different disordered proteins

alpha keratin

• fibrous protein

• right-handed alpha helix

• 2 strands with parallel orientation wrapping around each other

• supertwisted coil

  • supertwisted pattern is left handed

• rich in hydrophobic residues (A, V, L, I, M, F)

• cross-linked stabilized by disuldfide bonds

collagen

• fibrous protein

• found in connective tissues

• left-handed secondary structure

  • repeated tripeptide (Gly-X-Y, often Gly-Pro-4-Hyp)

• right-handed tertiary and quaternary structure

  • right-handed twisting o 3 polypeptides

• covalent crosslinks (Lys, 5-hydroxylysine, or HIs)

• vitamin C required for hydroxylation of proline and lysine in ___

fibroin

• fibrous protein

• main protein in silk

• predominantly beta conformation

• rich in A and G

• stabilized by H bonds and Van der Waals interactions

domain

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

• small proteins usually only have 1 ___

motif

aka fold

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

• B-alpha-B loop

• B barrel

beta-alpha-beta loop

2 beta strands joined by an alpha helix connecting through loops

• often found in parallel beta sheet patterns

beta barrel

beta sheet composed of tandem repeats that twist and coil to form a toroidal structure aka take the shape of a barrel

protein folding rules

• burial of hydrophobic R groups requires 2+ layers of secondary structure

• alpha helices and beta sheets are found in different layers

• adjacent amino acid segments are usually stacked adjacent

• the beta conformation is more stable with right-handed connections

alpha-beta barrel

series of β-α-β loops arranged such that the β strands form a barrel

protein family

proteins with significant similarity in primary structure and/or tertiary structure and function are in the same ___

• indicate strong evolutionary relationship

superfamilies

2+ families that have little sequence similarity, but the same major structural motif and have functional similarities

• evolutionary relationship probable

oligomer

aka multimer

multisubunit protein

protomer

repeating protein structural unit

proteostasis

continual maintenance of the active set of cellular proteins required under a given set of conditions

denaturation

loss of 3D structure sufficient to cause loss of function

• heat, extreme pH, miscible organic solvents, detergents

• often leads to protein precipitation

renaturation

process by which certain denatured globular proteins regain their native structure and biological activity

• amino acid sequence contains all info needed to fold the chain (Anfinsen experiment)

folding stepwise process

• local secondary structures fold first (ionic interactions)

• longer range interactions like hydrophobic effect follow

• etc. until polypeptide is folded

Levinthal’s paradox

mathematically impossible for a protein folding to occur by randomly trying every conformation until the lowest energy one is found

chaperone proteins

facilitate correct folding pathways or ideal microenvironments

• Hsp70 binds to hydrophobic regions

• chaperonins required for the folding of proteins that do not fold spontaneously

amyloid fiber

protein secreted in misfolded state and converted to an insoluble extracellular fiber

amyloidose diseases

• type 2 diabetes

• Alzheimer’s disease

• Huntington disease

• Parkinson’s disease

native

high degree of beta-sheet structure

aggregation

misfolded proteins, especially beta amyloid, promote ___

Alzheimer’s disease

extracellular amyloid deposition by neurons

• amyloid-B-peptide

Parkinson disease

misfolded form of alpha-synuclein which aggregates into spherical filamentous masses called Lewy bodies

Huntington disease

involves the intracellular aggregation of huntingtin (protein with long polyglutamine repeat)

prion

PrP

misfolded brain protein

X-ray crystallography

pattern of diffracted X-rays collected directly and image is reconstructed by mathematical techniques basically giving you an electron density map

• limited to crystallized molecules

• info depends on degree of structural order of protein

• Fourier transform (electron density map)

• little info on molecular movement of protein due to difference in environment compared to living biological system

nuclear magnetic resonance

NMR

• molecules in solutions

• captures dynamics of protein structure (conformational changes, folding, interactions with other molecules)

cryo-electron microscopy

cryo-EM

sample of structure of interest is quick frozen in vitreous/non-crystalline ice and kept frozen while being observed in 2D with the EM

• reduce damages to specimen

• useful for large, dynamic, macromolecular complexes and integral membrane proteins