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Structure of the α-Helix
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Structure of the β−Sheet
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Protein Dynamics
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Basics of Quenching HDX
Hydrogen exchange of amide protons is catalyzed by H2O, OH-
, and H3O+, but it’s most dominated by base catalyzed reactions.
Ka 6.95E-01 Kb 1.87E+08 Kw 5.27E-04
Place of Quenched Reaction
Half Life of Back Exchange
My hand 1 minute
In a Theoretical Lab 4 minutes
In a UAB Lab 7 minutes
On Ice (0C) 1 hour
In the -20C Fridge 14 hours
In the -80C Fridge 7 Years
In Liquid Nitrogen When Hell Freezes Over
In addition to lowering the pH, chemical kinetics are considerable slowed with decreasing temperature.
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Kinetics of HDX For exchange to occur: 1. The site needs to be at least transiently exposed to the bulk solvent. 2. The site must be available to form new hydrogen bonds. If it is either exposed with an unavailable site for hydrogen bonding or buried (most always hydrogen bonded in this case), it is described as protected.
In HDX experiments, the degree of protection (Pf) is empirically determined by the extent the rate of exchange (kex) is slowed from the predicted chemical rate (kch) . 0
0.2
0.4
0.6
0.8
1
1.2
0 0.2 0.4 0.6
Deut
eriu
m U
ptak
e
Time (s)
Kch Kex
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Kinetic Range of Protection
0
0.2
0.4
0.6
0.8
1
1.2
0 0.25 0.5 0.75 1
Unprotectedlog Pf 0.5
log Pf 1
log Pf 2
log Pf 3
log Pf 4
0
0.2
0.4
0.6
0.8
1
1.2
0 20 40 60Deu
teriu
m U
ptak
e
Unprotectedlog Pf 0.5
log Pf 1
log Pf 2
log Pf 3
log Pf 4
0
0.2
0.4
0.6
0.8
1
1.2
0 200 400 600Time (s)
Unprotectedlog Pf 0.5
log Pf 1
log Pf 2
log Pf 3
log Pf 4
A wide span of different kinetics can be observed for the range of protection that can occur within a single protein.
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Kinetic Range of Protection
0
0.2
0.4
0.6
0.8
1
1.2
0.001 0.1 10 1000
Deu
teriu
m U
ptak
e
Time (s)
Unprotectedlog Pf 0.5
log Pf 1
log Pf 2
log Pf 3
log Pf 4
Log Pf 6
A wide span of different kinetics can be observed for the range of protection that can occur within a single protein.
Because of this, the data is more reasonably visualized on the log scale.
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0°C
-1°C
-1°C Sample Loop
Waste
Quaternary Pump
0°C
Pepsin Column
Binary Pump
Trap
Waste
C18
QTOF
Sample Injection *
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0°C
-1°C
-1°C Sample Loop
Waste
Quaternary Pump
0°C
Pepsin Column
Binary Pump
Trap
Waste
C18
QTOF
Sample Injection *
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0°C
-1°C
-1°C Sample Loop
Waste
Quaternary Pump
0°C
Pepsin Column
Binary Pump
Trap
Waste
C18
QTOF
Online Pepsin Digestion
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0°C
-1°C
-1°C Sample Loop
Waste
Quaternary Pump
0°C
Pepsin Column
Binary Pump
Trap
Waste
C18
QTOF
Online Pepsin Digestion
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0°C
-1°C
-1°C Sample Loop
Waste
Quaternary Pump
0°C
Pepsin Column
Binary Pump
Trap
Waste
C18
QTOF
Online Pepsin Digestion
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0°C
-1°C
-1°C Sample Loop
Waste
Quaternary Pump
0°C
Pepsin Column
Binary Pump
Trap
Waste
C18
QTOF
Online Pepsin Digestion
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0°C
-
1°C
-1°C
Sample Loop
Waste
Quaternary Pump
0°C
Pepsin Colum
n Binary Pump
Trap
Waste
C18
QTOF
Online Pepsin Digestion
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0°C
-
1°C
-1°C
Sample Loop
Waste
Quaternary Pump
0°C
Pepsin Colum
n Binary Pump
Trap
Waste
C18
QTOF
Online Pepsin Digestion
*
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0°C
-
1°C
-1°C
Sample Loop
Waste
Quaternary Pump
0°C
Pepsin Colum
n Binary Pump
Trap
Waste
C18
QTOF
Peptide Separation
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0°C
-
1°C
-1°C
Sample Loop
Waste
Quaternary Pump
0°C
Pepsin Colum
n Binary Pump
Trap
Waste
C18
QTOF
Peptide Separation
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0°C
-
1°C
-1°C
Sample Loop
Waste
Quaternary Pump
0°C
Pepsin Colum
n Binary Pump
Trap
Waste
C18
QTOF
Peptide Separation and Analysis
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0°C
-
1°C
-1°C
Sample Loop
Waste
Quaternary Pump
0°C
Pepsin Colum
n Binary Pump
Trap
Waste
C18
QTOF
Peptide Separation and Analysis
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0°C
-
1°C
-1°C
Sample Loop
Waste
Quaternary Pump
0°C
Pepsin Colum
n Binary Pump
Trap
Waste
C18
QTOF
Peptide Separation and Analysis
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0°C
-
1°C
-1°C
Sample Loop
Waste
Quaternary Pump
0°C
Pepsin Colum
n Binary Pump
Trap
Waste
C18
QTOF
Peptide Separation and Analysis
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0°C
-1°C
-1°C Sample Loop
Waste
Quaternary Pump
0°C
Pepsin Column
Binary Pump
Trap
Waste
C18
QTOF
Peptide Separation and Analysis *
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Reproducibility and Peptide Diversity
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HuTrim5a Coverage Map
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FRACTION BURIED
0-0.2
0.2-0.4
0.4-0.6
Aspergillus Protease Complements Pepsin
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• Calculate isotope distribution using known chemical composition
• Calculate theoretical spectra for peptide +1, +2, +3 …. Deutrons
• Fit experimental spectra with Gaussian distributed sum of calculated spectra
• Assess quality of fit, calculate percent exchange
Data Analysis using HDExaminer
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0.50s
1s
3s
10s
12s
30s
90s
5m
15m
45m
2h
8h
0.50s
1s
3s
10s
12s
30s
90s
5m
15m
45m
2h
8h
0.50s
1s
3s
10s
12s
30s
90s
5m
15m
45m
2h
8h
121
181
Q S L R E L I S D L E H R L Q G S V M E L L Q G V D G V I K R T E N V T L K K P E T F P K N Q R R V F R A P D L K G M L
E V F R E L T D V R R Y W V D V T V A P N N I S C A V I S E D K R Q V S S P K P Q I I Y G A R G T R Y Q T F V N F N Y C
T G I L G S Q S I T S G K H Y W E V D V S K K T A W I L G V C A G F Q P D A M C N I E K N E N Y Q P K Y G Y W V I G L E 241
125 130 135 140 145 150 155 160 165 170 175 180
185 190 195 200 205 210 215 220 225 230 235 240
245 250 255 260 265 270 275 280 285 290 295 300
Heat Map Showing Exchange Kinetics
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Effect of pH on Tail Needle
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TM
Immature Mature
SU
Gag
MA
CA
RNA
NC
MA CA p2 NC p1 p6
Gag
HIV Assembly & Maturation
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Immature and Mature Virions are Pleomorphic
Immature Mature
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CA is Comprised of Distinct N- and C-Terminal Structural Domains
N-domain
C-domain
H1
Cyclophilin loop
H1
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CA Cylinders are Based on a Hexamer Lattice
From Li et al, Nature 407:409 (2000)
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+NaCl
CA does not Form Hexamers without the C-Domain (dimer) Interaction
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Mass spectrometry
CA Dimers and Tubes
Pepsin digestion
•Exchange with D20 •Quench with low pH over time
•Fragment size 10-20 residues
•Assignment of peptides •Quantifying exchange
H/D Exchange Experimental Protocol
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Changes in Exchange Rates due to CA Assembly
H4
H9
H1
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Crosslinking of Intact Tubes will Allow Identification of Intersubunit Interfaces
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Lysine 70 was Cross-Linked to Lysine 182
31 to 131 = 10 948.9 171 to 199 = 3 375.9 +DST = 114.0 Expected mass = 14 438.8 Observed mass = 14 439
Lys70 cross-linked to 182 Lys 70
Lys 182
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1 2
B
3 A
A’
B’
A Model for An N-domain to C-domain Interaction in CA Assembly
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Immature viral-like particles
Mature viral-like particles
Hydrogen Deuterium Exchange Studies on Virus-Like Particles
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CAfast is Partially Protected at Early Times
30 sec
5 min
45 min
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CA in Mature Virus-Like Particles is 50% Free and 50% Core-Incorporated
+ CAslow CAfast
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The N:C Interface is Bimodal in Mature Virions
m/z752750748746
746 748 750 752
m/z
0 sec
20 sec
4 min
16 min
1 h
4 h
16 h Mature virus- like particles
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Immature virus- like particles
The N:C Interface is Not Formed in Immature Virions
m/z 0 sec
20 sec
4 min
16 min
1 h
4 h
16 h
m/z752750748746746 748 750 752
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1 2 B 3
A
A’
B’
1 B
A 3 A’
B’
+
The N-domain:C-domain Interaction is Crucial for Viral Maturation
3
A
A’
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C:C
N:C
N:N
Three Sites of Interaction During Assembly and Maturation
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5
5 5
6
dsDNA Containing Phage Morphology
12
5
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Scaffold Coat
Portal Minor Procapsid
Closure proteins Mature Virus
tailspike
The dsDNA Phage Assembly Pathway
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Phi29 Scaffold Has a Helix-Loop-Helix Motif and a Disordered Tail
Marc C Morais et al., Nature Structural Biology 2003
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Both Free and Bound Scaffold Exchange Bimodally
1 min
40 sec
0 sec
10 sec
10 min
3 min
857 858 859 860 861 862 863 864m/z0
100
%
0
100
%
0
100
%
0
100
%
0
100
%
0
100
%
Free scaffold 13+
m/z
Partially exchanged species
Fully exchanged species
857 858 859 860 861 862 863 864m/z0
100
%
0
100
%
0
100
%
0
100
%
0
100
%
0
100
%
Prohead scaffold
m/z
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What does Bimodality Indicate? A group of residues open cooperatively & completely exchange before close again.
857 858 859 860 861 862 863 864m/z
1
4
2
3 slower components opened cooperatively
closed
exchanged
surface residues exchanged
1 2
4 4
3
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The Bimodality Maps to N-terminal Helix-Loop-Helix
1.2min
40 sec
0 sec
20 sec
45 min
3.2min
R 20-31
m/z 687 688 689 690 691 692 693 694
691.92691.41
690.92690.40
692.42
692.92
691.91691.41
690.90690.41689.91
692.42
692.92 693.43
689.90689.41
688.906.40
688.42
690.41691.41 691.92
692.42
692.92 693.39
689.41
688.90
688.40
689.91
690.41691.42 691.91
692.42692.93 693.45
689.40688.90
688.39687.90
689.92
690.41 690.91691.41
687.39
687.89
687 688 689 690 691 692 693 694
m/z
1.2min
40 sec
20 sec
45 min
3.2min
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Peptides Derived from H-L-H Region Have Similar Opening Kinetics
0 20 40 60 80 100 120 140 160 180 580 600
0
20
40
60
80
100
% c
ompl
etel
y ex
chan
ged
spec
ies
exchange time ( sec )
R 1-19 R 20-31 R 32-38 Whole protein
R 1-19
R 20-31
R 32-38
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686 687 688 689 690 691 692 693
686 687 688 689 690 691 692 693
20 sec
3 min
5 min
30 hr
7 min
20 sec
3 min
1.5 hr
9 hr
30 hr
4.5 hr
m/z m/z
The Cooperative Motions can Be “Frozen” by Lowering the Temperature
20 °C 10 °C
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Does Bimodality Originate from Opening of the Interface between Helices 1 & 2 ?
L3C & N35C
2.58 Å
Tethered Form
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686 687 688 689 690 691 692 693 694
686 687 688 689 690 691 692 693 694
Reduced form
Oxidized Form ( Tethered )
The Tethered Form Cannot Open Cooperatively
5 min
2 min
10 sec
1 min
10 min
1 min
10 sec
20 sec
10 min
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• Does Binding Alter the Exchange Kinetics?
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686 687 688 689 690 691 692 693
686 687 688 689 690 691 692 693
0 50 100 150 200 250 2500 3000
0.0
0.2
0.4
0.6
0.8
1.0
% c
ompl
etel
y ex
chan
ged
sec
Free Prohead
Free Scaffold Prohead Scaffold
20 sec
40 sec
80 sec
45 min
200 sec
Prohead Bound Scaffold has Faster Kinetics
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Model : The Interactions Stabilizing H-L-H are Weakened when Contact with Capsid
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