Chapter 7 Protein Function
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Transcript of Chapter 7 Protein Function
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Chapter 7 Protein Function
Ligand --- a molecule bound reversibly by a protein
Binding site --- the site on protein to which a ligand binds
Induced fit --- the structure adaptation that occurs between protein and ligand
Substrate --- the molecule acted upon by enzymes
Catalytic/active site --- the substrate/ligand binding site
Ch 7 --- Noncatalytic functions of proteins
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Fig. 7-1,2Heme
Reversible binding of a protein to a ligand: Oxygen-binding proteins
protoporphyrin
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Fig. 7-3 The structure of myoglobulin
*a single binding site for O2
*78% helices (8)
*His93 or HisF8 (the 8th residue in helix F) binds to heme
*Bends between helices
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Protein-ligand interactions can be described quantitatively
P + L PL Ka = [PL]/[P][L] Kd = [P][L]/[PL]
= (binding sites occupied)/(total binding sites) = [PL]/[PL] + [P] = [L]/([L] +1/Ka)
Fig. 7-4 Graphical representation of ligand binding
= 0.5 [L] = 1/Ka, or Kd
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Dissociation constant, Kd = [P][L]/[PL]
P + L PL Ka = [PL]/[P][L]
= (binding sites occupied)/(total binding sites) = [PL]/[PL] + [P] = [L]/([L] +1/Ka) = [L]/([L] +Kd)
When [L] = Kd = 0.5 (half saturation) [L] = 9 Kd = 0.9Kd: the molar concentration of ligand at which half of the available ligand-binding sites are occupied
Kd , affinity ( ? )
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When O2 binds to Mb
P50 = 0.26 kPa
= [L]/([L] +Kd)
= [O2]/([O2] + Kd) = [O2]/([O2] + [O2]0.5)
The concentration of a volatile substance in solution is always proportional to its partial pressure in the gas phase above the solution
= pO2/(pO2 + P50)
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Protein structure affects how ligands bind
1. Steric effects2. Molecular motions/breathing in the structure
1: 20,000 1: 200
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Oxygen is transported in blood by hemoglobin (Hb)
In arterial blood, Hb ~96% saturatedIn venous blood, Hb ~64% saturated
P50 = 0.26 kPa
Mb
Mb has only one subunit,as an oxygen-storage protein
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Fig. 7-6 Comparison between Mb and Hb
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Fig. 7-7 Comparison of aa between whale Mb and Hb,
A-H helices
Only 27 aa identical
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Fig. 7-8 Dominant interactions between Hb subunits
>30 aa
19 aa (hydrophobic, H-bonds,affected strongly upon O2 binding)
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Hb undergoes a structural change on binding oxygen
Fig. 7-10 The T(tense) R(relaxed) transition
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Fig. 7-9 Some ion pairs that stabilize the T state of deoxyHb
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Fig. 7-11 Changes in conformation near heme on O2 binding
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Hb binds oxygen cooperatively
Fig. 7-12 A sigmoid (cooperative) binding curve
4 vs. 13.3 kPa
Mb – a singlesubunit protein
Hb – 4 subunits,an allosteric protein
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Allosteric protein – a protein in which the binding of a ligand to one site affects the binding properties of another site on the same protein
allos --- otherstereos --- solid or shape
Homotropic interaction --- liagnd = modulator
Heterotropic interaction --- ligand = modulator
O2 --- as both a normal ligand and an activating homotropic modulator for Hb
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Cooperative ligand binding can be described quantitatively
Dissociation constant, Kd = [P][L] n/[PLn]
P + nL PLn Ka = [PLn]/[P][L]n
= (binding sites occupied)/(total binding sites) = [L]n/([L]n +Kd)
= [L]n/Kd
Log{ = n log [L] – log Kd (Hill equation, 1910)
Log{ = n log pO2 – log P50
nH – the Hill coefficient (slope of Hill plot)<, =, > 1
Fig. 7-13
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Two models suggest mechanisms for cooperative binding
Concerted (all-or-none), 1965 Sequential, 1966
Fig. 7-14
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O2 binding to Hb is regulated by 2,3-bisphosphoglycerate (BPG)
HbBPG + O2 HbO2 +BPG4 1
[BPG] during hypoxia
Fig. 7-16
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Fig. 7-17Binding of BPG to deoxyHb
T state
T
R
O2
++
BPG is negatively charged
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Sickle-cell anemia is a molecular disease of Hb
Val6 mutates to Glu6 in two chains
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Complementary interactions between proteins and ligands: The immune system and immunoglobulins
MHC (major histocompatibility complex)
all vertebrate cells macrophages, B cells
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Structure of a human class I MHC protein
Recognized by T-cell receptor
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Over view of the immune response to a viral infection
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The structure of immunoglobulin G (IgG)
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Binding of IgG to an antigen
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Induced fit in the binding of an antigen to IgG
Heavy chain
Light chain Kd~10-10M
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The Ab-Ag interaction is the basis fro a variety of important analytical procedures
Ployclonal vs. monoclonal Ab
ELISA (enzyme-linked immunosorbent assay)
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Immunoblot assay (Western Blot)
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Protein interactions modulated by chemical energy Actin, myosin, and molecular motors
Fig. 7-29 Myosin
S1
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The major components of muscle
Fig. 7-29
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Structure of skeletal muscle
relaxed
contracted
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Muscle contraction
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Molecular mechanism of muscle contraction
3~4 pN of forces, 5~10 nm movement/cycle