Hydration of Small Peptides - UC Santa Barbara
Transcript of Hydration of Small Peptides - UC Santa Barbara
Hydration of Small Peptides
Thomas Wyttenbach, Dengfeng Liu,and Michael T. Bowers
http://bowers.chem.ucsb.edu/
Why study hydration?Is a certain property of a molecule
(e.g. conformation)inherent to the molecule
or a consequence of solute–solvent interaction?
water(theory)3
apolar solvent(NMR)1
water:2
• no NMR structure• no α-helix• no β-sheet• hydrophobic core
1 Crescenzi et al Eur J Biochem 269, 5642 (2002)
2 Zhang et alJ Struct Biology 130, 130 (2000)
3 Baumketner, SheaUCSB, unpublished
Alzheimer amyloid β-peptide
gasphase
(theory)3
Why study hydration?
Bridge gas phase and solution phase
Study effect of individual water molecules on solute molecules
• energetics (water binding energy)
• structureconformations, foldingzwitterion formationhydration sites
Myoglobin
NMR structure
3
6
90
m/z
Mass SpectraNeurotensin
2 torr H2O286 K
(M+2H)2+
(M+3H)3+
(M+H)+
1 H2O(ELYENKPRRPYIL)
1
2
ESI IonSource
ESI IonSource
IonFunnel
IonFunnel
DriftCell
DriftCell MSMS DetectorDetector
Instrumentation
M+ M+•(H2O)n
H2O
~1 torr H2O
Liquid N2 cooling
Electricalheaters
3
6
90
m/z
Mass SpectraNeurotensin
2 torr H2O286 K
(M+2H)2+
(M+3H)3+
(M+H)+
1 H2O(ELYENKPRRPYIL)
1
2
M+ M+•(H2O)n
H2O
~1 torr H2Om/z
1800 µs
900 µs
2700 µs
drift time
Neurotensin (M+2H)2+
290 K, 1.8 torr H2O
Equilibrium?YES
3
6
90
m/z
Mass SpectraNeurotensin
2 torr H2O286 K
(M+2H)2+
(M+3H)3+
(M+H)+
1 H2O(ELYENKPRRPYIL)
1
2
M+ M+•(H2O)n
H2O
~1 torr H2O
Equilibrium?
ratio ofpeak intensities
equilibriumconstant
van’t Hoff
∆H° and ∆S°
Data Analysis
∆H° ∆S°+
YES
⊕ ⊕
• Amine
• Guanidine
• Imidazole
• Carboxylate
lysN-terminus
arg
his
aspgluC-terminus
In peptides and proteins they are:
Charged groups are important.
Ionic Groups The Ammonium GroupThe Guanidinium GroupThe Carboxylate Group
Several Ionic GroupsMultiply Charged IonsSalt Bridges
Challenges AheadChange of ConformationZwitterion Formation
Entropy
HY
DR
AT
ION
OF
PE
PT
IDE
SH
YD
RA
TIO
N O
F P
EP
TID
ES
HY
DR
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OF
PE
PT
IDE
S
CH3NH3+
B3LYP/6-311++G**
2
13
4
secondsolvation
shell
1 2 3 4 56
8
10
12
14
16
18 Experiment MM DFT
Number of water molecules
Wat
er b
indi
ng e
nerg
y (k
cal/m
ol)
n-decylamine
Experiment
second solvation shell
MolecularMechanicsAMBER, TIP3P
first solvation shell
Ionic hydrogen bond:
δ+
δ–
electrostatic interaction important
⊕
⊕⊕
δ+
δ+
17kcal/molexperiment1
& DFT2
15 kcal/molexperiment2
1 Meot-NerJACS 1984, 106, 1265
2 Liu, Wyttenbach, Barran, Bowers,JACS 2003, 125, 8458
⊕
δ+
δ+
M+•(H2O)n
103122151
∆H°kcal/mol
n
0.100.903
0.080.922
0.050.951
—0.35 0.65
1.000
(H2O)nCH3—NH3+n
NBO charges onCH3NH3
+•(H2O)n
B3LYP/6-311++G**
1 2 3 4 5
Experiment MM DFT
Number of water molecules
Exp Ele
Elec
tros
tatic
ene
rgy
Eel
n-decylamine
Electrostaticinteraction
∑∑=ij
jiel r
qqE
qi qjΣΣ=CH3NH3
+
(H2O)n–1
nth
H2O
n–1
qi
qj
etc.
etc.
n–1
qi
qj
etc.
etc.
2 kcal/mol
1 2 3 4 5
Experiment MM DFT
Number of water molecules
Exp Ele
n-decylamine
Electrostaticinteraction
∑∑=ij
jiel r
qqE
qi qjΣΣ=CH3NH3
+
(H2O)n–1
nth
H2O
vsExperimental
water binding energy(C10H21NH3
+)
2 kcal/mol
1 2 3 4 56
8
10
12
14
16
18 Experiment MM DFT
Number of water molecules
Wat
er b
indi
ng e
nerg
y (k
cal/m
ol) DFT
methylamine
Experimentn-decylamine
AMBERn-decylamine
NH CH C
CH2
NH
O
CH2
CH2
CH2
NH3
C
O
CH C NH
O
R
Peptides
self-solvationH3C C NH2
O
δ+
δ–3.7 D
H3C C OH
O 1.7 D
δ+
δ–
lysine
Nα-acetyl-L-lysineAMBER
AMBER
δ+⊕
OH
Experimental binding energies(–∆H° in kcal/mol)
of nth water molecule
9.638.412.12
10.614.81
Nα-acetyl-L-lysine
n-decyl-amine
n
NH CH C
CH3
NH
O
CH C
CH3
NH
O
CH C
CH2
NH
O
CH2
CH2
CH2
NH2
CH C
CH3
NH
O
CH C
CH3
OH
O
CH3C
O
Ac-AAKAA
AMBER
NH CH C
CH3
NH
O
CH C
CH3
NH
O
CH3C
O
CH C
CH3
NH
O
CH C
CH3
NH
O
CH C
CH2
OH
O
CH2
CH2
CH2
NH2
Ac-AAAAK
chargeremote
AMBER
Ac-AAKAA vs Ac-AAAAK
AMBER
8.5kcal/mol
experimentalwater binding
enthalpy6.9
kcal/mol
Ac-AxK
(c)
NH3+NH3+⊕δ–
δ+
α-helix
AMBER AMBERx = 8x = 20 Jarrold JACS (1998) 120, 12974
x = 4
Experimental water binding energies (kcal/mol)
n/an/an/a
7
8
Ac-A20K
Ac-A8K
Ac-AAAAK
Ac-AAKAA
n-decylamine 101215
≤4n/an/an/a5n/an/an/a7n/an/an/a79n/an/a
n/a
321
First solvation shell Secondsolvation
shellChargeremote
10 8 8acetyllysine
a
a Estimated based on: Jarrold JACS (2002) 124, 11148
Ammonium Group
Ionic Groups The Ammonium GroupThe Guanidinium GroupThe Carboxylate Group
Several Ionic GroupsMultiply Charged IonsSalt Bridges
Challenges AheadChange of ConformationZwitterion Formation
Entropy
HY
DR
AT
ION
OF
PE
PT
IDE
SH
YD
RA
TIO
N O
F P
EP
TID
ES
HY
DR
AT
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OF
PE
PT
IDE
S
HO
HN
NH3
O
O
CH3
CH3
NH2
NH2
NHHO
O
NH2
(Arg–OMe + H)+ 9.2C10H21NH3+ 14.8
(Arg + H)+ 9.0(Ala-Ala + H)+ 14.8–∆H° (kcal/mol)–∆H° (kcal/mol)
GuanidineAmine
Experimental water binding energies
N
CN N
H
H
H
H
H
R = arginine
Ac-AAAAK vs Ac-AAAAR
ArgLys
⊕⊕
AMBER
9.49.5
10.29.3
9.0
–∆H°kcal/mol
(Ac-AAAAK + H)+
(Ac-AAKAA + H)+
(AAAAA + H)+
C10H21NH3+
(AARAA-OMe + H)+
(Ac-AARAA + H)+6.9(AARAA + H)+8.5(RAAAA + H)+10.5
(Arg + H)+Exposed14.8
–∆H°kcal/mol
Self-solvated
Amines Guanidinespe
ntap
eptid
esExperimental water binding energies
Guanidines –∆H° kcal/mol
9.49.5
10.29.3
1st H2O
8.48.18.47.8
2nd H2O
7.6
7.1
3rd H2O
(AARAA-OMe + H)+
(Ac-AARAA + H)+
(AARAA + H)+
(RAAAA + H)+
Experimental water binding energies
Ionic Groups The Ammonium GroupThe Guanidinium GroupThe Carboxylate Group
Several Ionic GroupsMultiply Charged IonsSalt Bridges
Challenges AheadChange of ConformationZwitterion Formation
Entropy
HY
DR
AT
ION
OF
PE
PT
IDE
SH
YD
RA
TIO
N O
F P
EP
TID
ES
HY
DR
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ION
OF
PE
PT
IDE
S
Carboxylate(Ala-Ala – H)–
Ammonium(Ala-Ala + H)+
H2N CH C
CH3
NH
O
CH COO
CH3
H3N CH C
CH3
NH
O
CH COOH
CH3
Ala-Ala
14.8
–∆H°kcal/mol
1st H2O 11.61st H2O
–∆H°kcal/mol
8.53rd H2O8.93rd H2O
9.42nd H2O10.52nd H2O
1
24
N CH C
CH3 O
OH
+ 4 H2O
3AMBER
firstsolvationshell
(Ala-Ala – H)–
AMBER11.9
13.1
15.6
B3LYP/6-31G*
Calculated (B3LYP/6-31G*)water binding energy (kcal/mol)
CH C
CH3
N
O
CH C
(CH2)x
N
O
CO O
CH C
CH3
O
H H
Peptide self-solvation
x=1 aspartic acidx=2 glutamic acid
(Ala-Ala) • (Ala-Ala – H)–
AMBER
4
3
[(AA)2-H]-
0 2 4 6 8
(AA–H)–•(AA)•(H2O)m
Dimer
(AA–H)–•(H2O)n
Monomer
n
319
8
3
160 180 200 220 240 260 280 300
320 340 360 380 400 420 440 460 480
m/z
1.3 Torr H2O, 260 K
⟨n⟩ – ⟨m⟩ ≅ 4
(AA–H)–•(H2O)5.2
Average: ⟨n⟩ = 5.2
(AA–H)–•(AA)•(H2O)1.3
Average: ⟨m⟩ = 1.3
AMBER
(AA–H)–
AMBER
(AA–H)–•(AA)
AMBER
(AA–H)–•(H2O)4
AMBER
Overlap of (AA–H)–
conformation in(AA–H)–
(AA–H)–•(H2O)4(AA–H)–•(AA)
Ionic Groups The Ammonium GroupThe Guanidinium GroupThe Carboxylate Group
Several Ionic GroupsMultiply Charged IonsSalt Bridges
Challenges AheadChange of ConformationZwitterion Formation
Entropy
HY
DR
AT
ION
OF
PE
PT
IDE
SH
YD
RA
TIO
N O
F P
EP
TID
ES
HY
DR
AT
ION
OF
PE
PT
IDE
S
Experimental binding energiesof nth water molecule
13.64
13.4312.12
15.72
15.7114.81
–∆H°kcal/mol
n–∆H°kcal/mol
n
H3N H3N
NH3
CH3(CH2)9NH3+ H3N(CH2)12NH3
2+Blades, Klassen, KebarleJACS 118, 12437 (1996)
Na+ Ca2+n1 ~5524
(radius 0.97 Å) (radius 0.99 Å)
Na+ Ca2+n1 ~5524
(radius 0.97 Å) (radius 0.99 Å)
m/z
Hydration Mass SpectraNeurotensin
1.3 Torr H2O260 K
(ELYENKPRRPYIL)
96
3
820 840 860 880 900 920 940 960
12
12
H2O
560 580 600 620 640 660 680 700
15
189
1660 1700 1740 1780 1820
3
(M+2H)2+
(M+3H)3+
(M+H)+6
0
0
0
n −∆H°n (kcal/mol)
+1 +2 +3 1 9.2 10.3 (15) 2 9.8 8.9 (12) 3 (9) 9.6 9.5 4 (9) 9.4 9.3 5 8.5 9.4 6 (8) 9.8 7 (9) 8.8 8 (10) 9 (9) 10 (9)
Experimental ∆H°-values for binding nth water molecule to neurotensin (ELYENKPRRPYIL) in charge states +1, +2, and +3
± 0.3 kcal/mol± 1 kcal/mol for values in parenthesis
910 1210
10
10
9
8
9
n −∆H°n (kcal/mol)
+1 +2 +3 1 9.2 10.3 (15) 2 9.8 8.9 (12) 3 (9) 9.6 9.5 4 (9) 9.4 9.3 5 8.5 9.4 6 (8) 9.8 7 (9) 8.8 8 (10) 9 (9) 10 (9)
Experimental ∆H°-values for binding nth water molecule to neurotensin (ELYENKPRRPYIL) in charge states +1, +2, and +3
± 0.3 kcal/mol± 1 kcal/mol for values in parenthesis
13.64
13.4312.12
15.72
15.7114.81
–∆H°kcal/mol
n–∆H°kcal/mol
n
13.64
13.4312.12
15.72
15.7114.81
–∆H°kcal/mol
n–∆H°kcal/mol
n
CH3(CH2)9NH3+ H3N(CH2)12NH3
2+Blades, Klassen, KebarleJACS 118, 12437 (1996)
H3N
NH3
H3N
NH3Degree of charge exposureNature of charged groups
n −∆H°n (kcal/mol)
+1 +2 +3 1 9.2 10.3 (15) 2 9.8 8.9 (12) 3 (9) 9.6 9.5 4 (9) 9.4 9.3 5 8.5 9.4 6 (8) 9.8 7 (9) 8.8 8 (10) 9 (9) 10 (9)
Experimental ∆H°-values for binding nth water molecule to neurotensin (ELYENKPRRPYIL) in charge states +1, +2, and +3
± 0.3 kcal/mol± 1 kcal/mol for values in parenthesis
⊕
⊕⊕
⊕
⊕⊕
Degree of charge exposureNature of charged groups
n −∆H°n (kcal/mol)
+1 +2 +3 1 9.2 10.3 (15) 2 9.8 8.9 (12) 3 (9) 9.6 9.5 4 (9) 9.4 9.3 5 8.5 9.4 6 (8) 9.8 7 (9) 8.8 8 (10) 9 (9) 10 (9)
± 0.3 kcal/mol± 1 kcal/mol for values in parenthesis
Experimental ∆H°-values for binding nth water molecule to neurotensin (ELYENKPRRPYIL) in charge states +1, +2, and +3Experimental ∆H°-values for binding nth water molecule to neurotensin (ELYENKPRRPYIL) in charge states +1, +2, and +3
+1 +2
Experimental ∆H°-values for binding nth water molecule to neurotensin (ELYENK
+3
Degree of charge exposureNature of charged groups
⊕
⊕⊕
⊕
⊕⊕
Expect 15 kcal/mol for exposed ammonium
independent of the presence of other charges
(A) number of preferred hydration sites ∝ z(B) water binding energy ≠ f(z)
Multiply Charged Ions
(A) H3N
NH3
(B)
Ionic Groups The Ammonium GroupThe Guanidinium GroupThe Carboxylate Group
Several Ionic GroupsMultiply Charged IonsSalt Bridges
Challenges AheadChange of ConformationZwitterion Formation
Entropy
HY
DR
AT
ION
OF
PE
PT
IDE
SH
YD
RA
TIO
N O
F P
EP
TID
ES
HY
DR
AT
ION
OF
PE
PT
IDE
S
⊕
⊕
Same sign vs opposite sign charges
Coulomb repulsion Coulomb attraction⊕
Salt Bridge
⊕
Salt Bridge
N
CN N
H
H
H
H
H
O OC
N
CN N
H
H
H
H
H
O OC
N
CN N
H
H
H
H
H
O
O
C
N
CN N
H
H
H
H
H
O
O
C
N
H
H
O
O
C
H
N
H
H
O
O
C
H
⊕
⊕δ+δ–
δ+δ–
Bradykinin
AMBER Barran, Liu, Wyttenbach, Bowers; unpublished
⊕
⊕δ+δ–
δ+δ–
⊕
⊕δ+δ–
δ+δ–
AMBER
Experimental ∆H° and ∆S° values for bindingnth water molecule to bradykinin (M+H)+
2710.24
2610.13
2510.12
2610.71
–∆S°kcal/mol
–∆H°kcal/moln
±0.3 ±1
Bradykinin
Understand first steps of hydration:• Water binding sites• Energetics
for given peptide/protein structure.
However, peptide/protein structurechanges as hydration proceeds.
• Conformation• Zwitterion formation
Hydration Sites & Energies
Ionic Groups The Ammonium GroupThe Guanidinium GroupThe Carboxylate Group
Several Ionic GroupsMultiply Charged IonsSalt Bridges
Challenges AheadChange of ConformationZwitterion Formation
Entropy
HY
DR
AT
ION
OF
PE
PT
IDE
SH
YD
RA
TIO
N O
F P
EP
TID
ES
HY
DR
AT
ION
OF
PE
PT
IDE
S
Change of Conformation
H2O
aqAlzheimer amyloid β-peptide
ESI IonSource
ESI IonSource MSMS Drift Cell
(helium)Drift Cell(helium) MSMS DetectorDetector
form M±z•(H2O)n in the source
Measure collision cross sections of hydrated ions in helium
Williams, J. Am. Soc. Mass Spectrom. 1997, 8, 565Beauchamp, J. Am. Chem. Soc. 1998, 120, 11758.
measure cross sections in heliumWyttenbach, Bowers, Top. Curr. Chem. 2003, 225, 207.
Ionic Groups The Ammonium GroupThe Guanidinium GroupThe Carboxylate Group
Several Ionic GroupsMultiply Charged IonsSalt Bridges
Challenges AheadChange of ConformationZwitterion Formation
Entropy
HY
DR
AT
ION
OF
PE
PT
IDE
SH
YD
RA
TIO
N O
F P
EP
TID
ES
HY
DR
AT
ION
OF
PE
PT
IDE
S
H2O
aq
H3N CH2 C
O
O
H2N CH2 C
OH
O
Glycine
neutral
Gly zwitter-ion
TheoryJensen and Gordon JACS, 117, 8159 (1995)Gly•(H2O)2
12 kcal/mol
zwitter-ion
Photoelectron spectroscopyXu, Nilles, BowenJ.Chem.Phys., 119, 10696 (2003)
zwitter-ion
Gly•(H2O)5
Glycine
kcal/moldrop per H2O
2NNH
NH NHO
O
O
O
O
OH
D vs Lresidue
NHNH
NHNH
O
O
O
O
NH
H2N NH2+
H3N+
O
O–
Peptides
H3N CH2 C
O
O
HO
NH
H2N NH2+
HO
NH
H2N NH2+
AARAA
AARAAdifferent
2NO
RNHOR’
2NNH
NH NHO
O
O O
residue
NHNH
NHNH
O
O
O
O
NH
H2N NH2+
O
500 502 504
MH
458 460 462 464 466 468 4700
25
50
75
100
AARAA
MH
m/z72 474 476 4
AARAR = AcR’= H
gas-phaseH/D exchange
with D2O
R = HR’= H
R = H R’= CH3
zwitterion
+all1Hall1H
Wyttenbach, Paizs, Barran, Breci, Liu, Suhai, Wysocki, Bowers
JACS 125, 13768 (2003)
AARAAdifferent
+1.80.0
(AARAA)H+·H2O
+4.80.0
(AARAA)H+
Energy (kcal/mol)AMBER & B3LYP/6-31+G(d,p)
zwitterion
neutral termini
different
2NO
H2NOH
2NNH
NH NHO
O
O O
residue
NHNH
NHNH
O
O
O
O
NH
H2N NH2+
O
Wyttenbach, Paizs, Barran, Breci, Liu, Suhai, Wysocki, Bowers
JACS 125, 13768 (2003)kcal/mol
drop per H2OCAUTIONwith interpretation of
gas-phase H/D exchange
data
binding energy (kcal/mol)
AARAA
10.2 ± 0.3Experiment
8.9Theory
B3LYP/6-31+G(d,p)BSSE & ZPE correction
(AARAA)H+···H2O
Wyttenbach, Paizs, Barran, Breci, Liu, Suhai, Wysocki, Bowers
JACS 125, 13768 (2003)
C-terminus
N-terminus
Wyttenbach, Paizs, Barran, Breci, Liu, Suhai, Wysocki, Bowers
JACS 125, 13768 (2003)
B3LYP/6-31+G(d,p)
set up forH/D exchange
relay mechanism
(AARAA)H+•H2ONeutral termini
(AARAA)H+•H2OZwitterion
C-terminus
N-terminus
Wyttenbach, Paizs, Barran, Breci, Liu, Suhai, Wysocki, Bowers
JACS 125, 13768 (2003)
B3LYP/6-31+G(d,p)
(AARAA)H+•H2OTransition state
C-terminus
N-terminus
Wyttenbach, Paizs, Barran, Breci, Liu, Suhai, Wysocki, Bowers
JACS 125, 13768 (2003)
B3LYP/6-31+G(d,p)
Ionic Groups The Ammonium GroupThe Guanidinium GroupThe Carboxylate Group
Several Ionic GroupsMultiply Charged IonsSalt Bridges
Challenges AheadChange of ConformationZwitterion Formation
Entropy
HY
DR
AT
ION
OF
PE
PT
IDE
SH
YD
RA
TIO
N O
F P
EP
TID
ES
HY
DR
AT
ION
OF
PE
PT
IDE
S
–∆S°cal/mol/K
–∆H° kcal/mol
all other data:• all molecules• all charge states• all hydrates 1st–nth H2O
1st H2Oon small
molecules
2nd H2Oon small
molecules
1st H2Oon small
molecules
∆S° < 0loss of 3 translational
and 3 rotational degrees of freedom(gain of 6 vibrationaldegrees of freedom)
all datapositive andnegative ions
floppy
tightly bound H2O• large binding energy• large loss of entropy
strong entropy–enthalpy correlation (red data)
exceptions are:
• Addition of 1st H2O to small molecules (blue data) yields smaller than average loss of entropy→ floppy hydrates
• Addition of 2nd H2O to small molecules (yellow data) yields data between blue and red
Understand first steps of hydration:• Water binding sites• Water binding energies• Loss of entropy
Future challenges include:• Hydration beyond the first steps• Change of protein conformation• Zwitterion formationH
YD
RA
TIO
N O
F P
EP
TID
ES
HY
DR
AT
ION
OF
PE
PT
IDE
SH
YD
RA
TIO
N O
F P
EP
TID
ES
?