Ch6: 3-D Structure of Proteins

Flowchart nodes

• 3-D

• 6.1

• 6.2-Fibrous protein structure

• 6.3-Globular proteins

• 6.4-Factors 

• 6.5-Dynamics

• 6.6-Predictions

• 6.7. 4 structure

• Linus Pauling:Rules for 2 str

• 2ndary structures

• Ramachandran plot

• 1Noncovalent bonds (particularlyhydrogen bonds) stabilize 3-Dstructure

• α helix

• β sheet

• 310 helixThe polypeptide II helix

• -3.6 a.a/turn=n+4           -amphiphilic

• -Parallel-Antiparallel

• 1.Pauling's.~Not often found in Proteins~(n+3)2.Polyplorine(1/3Pro), Not Pauling's:~Left-handed a-helix~not stabilized by H-bonds

• shows sterically allowedϕ and ψ anglesThe allowed regions would be smaller for amino acids with larger R groups.

• α-keratin

• Silk fibroin

• Collagen

• 1.α-helix2.Coil-coiled(l)3.Intermediate filaments4.DiSulfinde B5.1/4 Hydrophobic res.2.Coil-coiled(l)3.Intermediate filaments4.DiSulfinde B5.1/4 Hydrophobic res.

• 1.B-sheet(anti)2.~1/2 Gly 3.Max.stretched 4.Flexible,because bonding between sheets involves only weak van der Waals

• Tropocollagen1.Triple α-helixG-X-YX=ProY=Pro,Hyp2.Gly-decreases steric interactions3.Hyp-stabilizes fiber by H-bonds4.Lysine-Tough collagenVitamin C*

• ~NMR and X-ray Diffraction~Domain(TIM)~Motiffs (α/b/α)  pH=7

• 3Thermodynamic 1.Favorable  H2.Favorable S3."Hydrophobic effect"

• 1.Charge-charge2.H-bonds3.Disulfide bonds4.van der Waals5.Ionic

•  Virtually all proteins, under appropriate conditions, can be reversibly unfolded and refolded into their native structure under in vitro conditions. This is known as spontaneous folding. Anfinsen (1973)

• 1.PPIase-catalysis cis-trans isomerization 2.PDI-catalysis of -S-S- 3.Caperons-aggregation (Gro-EL/ES) ATP is required.

• α helix:Ala,Leu,Met,Gluβ sheet:Ile,Val,Pheβ-turn:Gly

•  1.helical symmetry(tabaco)2.point-group symmetry (Cn)

• 6A.6.B1.Absorption SPectroscopya.Infrared Spectroscopyb.Ultraviolet Spectroscopy2.Fluoroscene3.Circular Dicroism4.Nuclear Magnetic Resonance Spectroscopy(NMR)5.SDS-PAGE GEL Electrophoresis