Hydration of Small Peptides (8.29 MB pdf) - The Bowers Group

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

Alzheimer amyloid β-peptide
apolar solvent
(NMR) 1
water
(theory) 3
gas
phase
(theory) 3
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 al
J Struct Biology 130,
130 (2000)
3
Baumketner, Shea
UCSB, unpublished

Why study hydration
Bridge gas phase and solution phase
Study effect of individual water molecules
on solute molecules
• energetics (water binding energy)
• structure
• conformations, folding
• zwitterion formation
• hydration sites

Myoglobin
NMR structure

(M+H) +
1 H 2 O
1
Mass Spectra
Neurotensin
(ELYENKPRRPYIL)
2 torr H 2 O
286 K
3
(M+2H) 2+
2
6
(M+3H) 3+
0
9
m/z

Instrumentation
ESI Ion
Source
Ion
Funnel
Drift
Cell
MS
Detector
H 2 O
Liquid N 2 cooling
M +
~1 torr H 2 O
M + •(H 2 O) n
Electrical
heaters

drift time
900 µs
(M+H) +
1 H 2 O
Mass Spectra
Neurotensin
(ELYENKPRRPYIL)
1800 µs
H 2 O
2700 µs
(M+2H) 2+
(M+3H) 3+
0
1
2
6
2 torr H 2 O
286 K
Equilibrium
3
YES
9
m/z
M +
m/z
~1 torr H 2 O
M + •(H 2 O) n
Neurotensin (M+2H) 2+
290 K, 1.8 torr H 2
O

Data Analysis
ratio of
peak intensities
equilibrium
constant
van’t Hoff
∆H° and ∆S°
⊕
H 2 O
M +
+
(M+H) +
(M+2H) 2+
(M+3H) 3+
~1 torr H 2 O
0
1 H 2 O
1
∆H° ∆S°
2
M + •(H 2 O) n
Mass Spectra
Neurotensin
(ELYENKPRRPYIL)
6
2 torr H 2 O
286 K
Equilibrium
3
YES
⊕
9
m/z

Charged groups are important.
In peptides and
proteins they are:
• Amine
• lys
• N-terminus
• Guanidine
• arg
• Imidazole
• his
• Carboxylate
• asp
• glu
• C-terminus

HYDRATION OF PEPTIDES
Ionic Groups
The Ammonium Group
The Guanidinium Group
The Carboxylate Group
Several Ionic Groups
Multiply Charged Ions
Salt Bridges
Challenges Ahead
Change of Conformation
Zwitterion Formation
Entropy

CH 3 NH 3
+
2
1
3
second
solvation
shell
4
B3LYP/6-311++G**

Water binding energy (kcal/mol)
18
16
14
12
10
8
6
first solvation shell
Experiment
MM
DFT
1 2 3 4 5
Number of water molecules
n-decylamine
second solvation shell
Molecular
Mechanics
AMBER, TIP3P
Experiment

δ+
δ–
⊕
Ionic hydrogen bond:
electrostatic interaction important

17kcal/mol
experiment 1
& DFT 2
15 kcal/mol
experiment 2
δ+
⊕
⊕
1
Meot-Ner
JACS 1984, 106, 1265
2
Liu, Wyttenbach,
Barran, Bowers,
JACS 2003, 125, 8458
δ+

δ+
⊕
δ+

M + •(H 2 O) n
n
1
2
3
∆H°
kcal/mol
15
12
10

NBO charges on
CH 3 NH 3
+ • (H 2 O) n
B3LYP/6-311++G**
n
0
1
2
3
CH 3 —NH 3
+
0.35 0.65
1.00
0.95
0.92
0.90
(H 2 O) n
—
0.05
0.08
0.10

Electrostatic energy E el
2 kcal/mol
q j
n–1
etc.
etc.
q i
E
el
=
Exp
Ele
Σ∑
∑Σ
Experiment
=
MM n-decylamine n th
H 2 O
DFT
CH 3 NH
+
3
(H 2 O) n–1
Electrostatic
interaction
q q
q i qj
j
r
ij
1 2 3 4 5
Number of water molecules

Experimental
water binding energy
(C 10 H 21 NH 3 + )
vs
E
el
=
Exp
Ele
Σ∑
∑Σ
Experiment
=
MM n-decylamine n th
H 2 O
DFT
CH 3 NH
+
3
(H 2 O) n–1
Electrostatic
interaction
q q
q i qj
j
r
ij
2 kcal/mol
1 2 3 4 5
Number of water molecules

Water binding energy (kcal/mol)
18
16
14
12
10
8
6
DFT
methylamine
Experiment
n-decylamine
Experiment
MM
DFT
1 2 3 4 5
Number of water molecules
AMBER
n-decylamine

lysine
NH 3
CH 2
CH 2
CH 2
Peptides
self-solvation
δ–
O
3.7 D
H 3 C C NH 2
δ+
O
C
CH 2
O
NH CH C
NH
O
CH C NH
R
δ–
O
H 3 C C OH
1.7 D
δ+

Nα-acetyl-L-lysine
AMBER

δ+
⊕
Experimental binding energies
(–∆H° in kcal/mol)
of n th water molecule
n
1
2
3
n-decylamine
14.8
12.1
9.6
OH
Nα-acetyl-
L-lysine
10.6
8.4
AMBER

Ac-AAKAA
O
O
O
O
O
O
H 3 C
C
NH CH C
NH
CH C
NH
CH C
NH
CH C
NH
CH C
OH
CH 3
CH 3
CH 2
CH 3
CH 3
CH 2
CH 2
CH 2
NH 2
AMBER

Ac-AAAAK
O
O
O
O
O
O
H 3 C
C
NH CH C
NH
CH C
NH
CH C
NH
CH C
NH
CH C
OH
CH 3
CH 3
CH 3
CH 3
CH 2
CH 2
CH 2
CH 2
charge
remote
NH 2
AMBER

Ac-AAKAA vs Ac-AAAAK
8.5
kcal/mol
experimental
water binding
enthalpy
6.9
kcal/mol
AMBER

Ac-A x K
AMBER
x = 8
x = 20 Jarrold JACS (1998) 120, 12974
AMBER
x = 4
⊕
NH δ–
+
3
c)
α-helix
δ+

Ammonium Group
Experimental water binding energies (kcal/mol)
First solvation shell Second
solvation
1 2 3 shell
Charge
remote
n-decylamine 15 12 10 8
acetyllysine n/a 10 8 8
Ac-AAKAA
Ac-AAAAK
Ac-A 8 K
Ac-A 20 K
n/a
n/a
n/a
n/a
n/a
n/a
n/a
n/a
9
n/a
n/a
n/a
7
n/a
n/a
n/a
7
7
5
≤4
a Estimated based on: Jarrold JACS (2002) 124, 11148
a

HYDRATION OF PEPTIDES
Ionic Groups
The Ammonium Group
The Guanidinium Group
The Carboxylate Group
Several Ionic Groups
Multiply Charged Ions
Salt Bridges
Challenges Ahead
Change of Conformation
Zwitterion Formation
Entropy

Experimental water binding energies
Amine
Guanidine
O
O
NH 2
HO
CH 3
H
N
NH 3
HO
NH
NH 2
CH 3
O
NH 2
–∆H° (kcal/mol)
(Ala-Ala + H) + 14.8
C 10 H 21 NH 3
+
14.8
–∆H° (kcal/mol)
(Arg + H) + 9.0
(Arg–OMe + H) + 9.2

H
H
H
N
C
N
H
N
H
R = arginine

Ac-AAAAK vs Ac-AAAAR
Lys
⊕
⊕
Arg
AMBER

Experimental water binding energies
Amines
Guanidines
–∆H°
kcal/mol
–∆H°
kcal/mol
C 10 H 21 NH 3
+
14.8
Exposed
(Arg + H) +
9.0
pentapeptides
(AAAAA + H) +
(Ac-AAKAA + H) +
(Ac-AAAAK + H) +
10.5
8.5
6.9
Selfsolvated
(RAAAA + H) +
(AARAA + H) +
(Ac-AARAA + H) +
(AARAA-OMe + H) +
9.3
10.2
9.5
9.4

Experimental water binding energies
Guanidines –∆H° kcal/mol
1 st H 2 O
2 nd H 2 O
3 rd H 2 O
(RAAAA + H) +
9.3
7.8
7.1
(AARAA + H) +
10.2
8.4
(Ac-AARAA + H) +
9.5
8.1
(AARAA-OMe + H) +
9.4
8.4
7.6

HYDRATION OF PEPTIDES
Ionic Groups
The Ammonium Group
The Guanidinium Group
The Carboxylate Group
Several Ionic Groups
Multiply Charged Ions
Salt Bridges
Challenges Ahead
Change of Conformation
Zwitterion Formation
Entropy

Ammonium
(Ala-Ala + H) +
O
O
H 3 N CH C
H 2 N CH C
CH 3
N
H
Ala-Ala
CH COOH
CH 3
–∆H°
kcal/mol
Carboxylate
(Ala-Ala – H) –
CH 3
N
H
CH COO
CH 3
–∆H°
kcal/mol
1 st H 2 O 14.8
1 st H 2 O 11.6
2 nd H 2 O
10.5
2 nd H 2 O
9.4
3 rd H 2 O
8.9
3 rd H 2 O
8.5

CH 3
O
N
CH C
+ 4 H 2 O
H
O
1
4
2
first
solvation
shell
AMBER
3

(Ala-Ala – H) –
Calculated (B3LYP/6-31G*)
water binding energy (kcal/mol)
15.6
13.1
AMBER
B3LYP/6-31G*
11.9

Peptide self-solvation
CH C
CH 3
O
N
H
O
CH C
(CH 2 ) x
N
H
O
CH C
CH 3
O
C
O
x=1 aspartic acid
x=2 glutamic acid

AMBER
(Ala-Ala) • (Ala-Ala – H) –

0 2 4 6 8
n
1.3 Torr H 2 O, 260 K
(AA–H) – •(H 2 O) 5.2
Average: 〈n〉 = 5.2
3
319
8
(AA–H) – •(H 2 O) n
Monomer
160 180 200 220 240 260 280 300
[(AA) 2
-H] -
(AA–H) – •(AA)•(H 2 O) 1.3
Average: 〈m〉 = 1.3
3
4
(AA–H) – •(AA)•(H 2 O) m
Dimer
320 340 360 380 400 420 440 460 480
m/z
〈n〉 – 〈m〉 ≅ 4

AMBER
(AA–H) –

AMBER
(AA–H) – •(AA)

AMBER
(AA–H) – •(H 2 O) 4

Overlap of (AA–H) –
conformation in
• (AA–H) –
• (AA–H) – •(H 2 O) 4
• (AA–H) – •(AA)
AMBER

HYDRATION OF PEPTIDES
Ionic Groups
The Ammonium Group
The Guanidinium Group
The Carboxylate Group
Several Ionic Groups
Multiply Charged Ions
Salt Bridges
Challenges Ahead
Change of Conformation
Zwitterion Formation
Entropy

H 3 N
Experimental binding energies
of n th water molecule
CH 3 (CH 2 ) 9 NH 3
+
H 3 N(CH 2 ) 12 NH 3
2+
Blades, Klassen, Kebarle
JACS 118, 12437 (1996)
H 3 N
n
–∆H°
n
–∆H°
kcal/mol
kcal/mol
1
14.8
1
15.7
2
15.7
2
12.1
3
13.4
n
Na + Ca 2+
4
13.6
NH 3
1 24
~55
(radius 0.97 Å) (radius 0.99 Å)

(M+H) + 6
(M+2H) 2+
(M+3H) 3+
0
1660 1700 1740 1780 1820
0
3
6
820 840 860 880 900 920 940 960
0
3
9
9
Hydration Mass Spectra
Neurotensin
12
12
m/z
(ELYENKPRRPYIL)
15
1.3 Torr H 2 O
260 K
18
H 2 O
560 580 600 620 640 660 680 700

Experimental ∆H°-values for binding n th water molecule to
neurotensin (ELYENKPRRPYIL) in charge states +1, +2, and +3
n −∆H° n (kcal/mol)
+1 +2 +3
1 9.2 9 10.3 (15)
2 9.8 10
10
8.9 (12)
3 (9) 9 9.6 9.5
10
4 (9) 9.4 9.3
5 8.5 9.4
8
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
12
10
9

Experimental ∆H°-values for binding n th water molecule to
neurotensin (ELYENKPRRPYIL) in charge states +1, +2, and +3
n −∆H° n (kcal/mol)
H 3 N
+1 +2 +3
1 9.2 10.3 (15)
2 9.8 8.9 (12)
CH
3 (9) 3 (CH 2 ) 9 NH
+ 3 H 3 N(CH
9.6 2 ) 12 NH
2+ 3
Blades, Klassen, Kebarle 9.5
JACS 118, 12437 (1996)
4 (9) 9.4 9.3
5 n
–∆H° 8.5 n
–∆H° 9.4
kcal/mol
kcal/mol
6 (8) 9.8
1
7 14.8
1
(9) 15.7 8.8
2
8 15.7 (10)
9 Degree 2
of charge exposure
12.1
3
13.4 (9)
10 NH 3
Nature of charged groups
4
(9)
13.6
± 0.3 kcal/mol
± 1 kcal/mol for values in parenthesis
H 3 N
NH 3

Experimental ∆H°-values for binding n th water molecule to
neurotensin (ELYENKPRRPYIL) in charge states +1, +2, and +3
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 Degree of charge exposure (9)
10
Nature of charged groups
(9)
± 0.3 kcal/mol
± 1 kcal/mol for values in parenthesis
⊕

Experimental ∆H°-values for binding n th water molecule to
neurotensin (ELYENKPRRPYIL) in charge states +1, +2, and +3
n −∆H° n (kcal/mol)
+1 +2
+3
1 9.2 10.3 (15)
2 9.8 8.9 (12)
exposed 3 (9) ammonium
⊕
9.6 9.5
⊕
4 (9) 9.4 9.3
5 ⊕of other charges 8.5 9.4
6 ⊕ (8) ⊕9.8
7 (9) 8.8
8 (10)
9 Degree of charge exposure (9)
10
Nature of charged groups
(9)
± 0.3 kcal/mol
± 1 kcal/mol for values in parenthesis
Expect 15 kcal/mol for
independent of the presence
⊕

Multiply Charged Ions
(A)
(B)
number of preferred hydration sites ∝ z
water binding energy ≠ f(z)
(A)
(B)
H 3 N
NH 3

HYDRATION OF PEPTIDES
Ionic Groups
The Ammonium Group
The Guanidinium Group
The Carboxylate Group
Several Ionic Groups
Multiply Charged Ions
Salt Bridges
Challenges Ahead
Change of Conformation
Zwitterion Formation
Entropy

Same sign vs opposite sign charges
⊕
Coulomb repulsion
⊕
Coulomb attraction
⊕

Salt Bridge
⊕
Salt Bridge
N
C
N
N
H
H
H
H
H
O
O
C
N
C
N
N
H
H
H
H
H
O
O
C
N
C
N
N
H
H
H
H
H
O
O
C
N
C
N
N
H
H
H
H
H
O
O
C
N
H
H
O
O
C
H
N
H
H
O
O
C
H

Bradykinin
⊕
δ–
δ+
δ–
δ+
⊕
AMBER
Barran, Liu, Wyttenbach, Bowers; unpublished

⊕
δ–
δ+
δ–
δ+
⊕
AMBER

Bradykinin
Experimental ∆H° and ∆S° values for binding
n th water molecule to bradykinin (M+H) +
n
–∆H°
kcal/mol
–∆S°
kcal/mol
1
2
3
4
10.7
10.1
10.1
10.2
26
±0.3 ±1
25
26
27

Understand first steps of hydration:
• Water binding sites
• Energetics
Hydration
Sites & Energies
for given peptide/protein structure.
However, peptide/protein structure
changes as hydration proceeds.
• Conformation
• Zwitterion formation

HYDRATION OF PEPTIDES
Ionic Groups
The Ammonium Group
The Guanidinium Group
The Carboxylate Group
Several Ionic Groups
Multiply Charged Ions
Salt Bridges
Challenges Ahead
Change
of Conformation
Zwitterion Formation
Entropy

Change of Conformation
H 2 O
Alzheimer amyloid β-peptide
aq

Measure collision cross sections of
hydrated ions in helium
ESI Ion
Source
MS
Drift Cell
(helium)
MS
Detector
form M ±z •(H 2 O) n in the source
Williams, J. Am. Soc. Mass Spectrom. 1997, 8, 565
Beauchamp, J. Am. Chem. Soc. 1998, 120, 11758.
measure cross sections in helium
Wyttenbach, Bowers, Top. Curr. Chem. 2003, 225, 207.

HYDRATION OF PEPTIDES
Ionic Groups
The Ammonium Group
The Guanidinium Group
The Carboxylate Group
Several Ionic Groups
Multiply Charged Ions
Salt Bridges
Challenges Ahead
Change of Conformation
Zwitterion Formation
Entropy

Glycine
O
H 2 O
O
H 2 N CH 2 C
H 3 N CH 2 C
OH
O
aq

Glycine
Gly
Gly•(H 2 O) 2
zwitterion
zwitterion
Theory
Jensen and Gordon
JACS, 117, 8159 (1995)
12 kcal/mol
Photoelectron spectroscopy
Xu, Nilles, Bowen
J.Chem.Phys., 119, 10696 (2003)
Gly•(H 2 O) 5
zwitterion
neutral
kcal/mol
drop per H 2 O

Peptides AARAA
residue
NH
2 N O
NH
H 3 N +
O
O
O
NH
H
NH
+
H 2 N NH 2
NH
O
NH
O
O
DvsL
O
NH
NH
O
O
O –
OH
O
H 3 N CH 2 C
O

AARAA
different
Wyttenbach, Paizs, Barran, residue Breci,
+
Liu, Suhai, Wysocki, Bowers O H 2 N NH 2
JACS 125, 13768 (2003) NH
2 N NH
NH
NH
O
O
O
+
O
O
NH
NH
OR’
RNH
NH
NH
O
O
O
zwitterion
MH
R = Ac
R’= H
100
75
50
25
MH
all
1 H
R = H
R’= H
AARAA
gas-phase
H/D exchange
with D 2 O
R = H
R’=
AARA
CH 3
500 502 504
0
458 460 462 464 466 468 470
m/z
72 474 476 4

AARAA
different
Wyttenbach, Paizs, Barran, residue Breci,
+
Liu, Suhai, Wysocki, Bowers O H 2 N NH 2
JACS 125, 13768 (2003) NH
2 N NH
CAUTION
NH
NH
O
O
O
with interpretation O of
O
NH
NH
OH
H 2 Ngas-phase
NH
NH
O
O
O
H/D exchange
data
(AARAA)H +
Energy (kcal/mol)
AMBER & B3LYP/6-31+G(d,p)
kcal/mol
drop per H 2 O
(AARAA)H +·H 2 O
neutral termini
zwitterion
0.0
+4.8
0.0
+1.8

Wyttenbach, Paizs, Barran, Breci,
Liu, Suhai, Wysocki, Bowers
JACS 125, 13768 (2003)
AARAA
(AARAA)H +···H 2 O
binding energy (kcal/mol)
Theory
B3LYP/6-31+G(d,p)
BSSE & ZPE correction
Experiment
8.9
10.2 ± 0.3

Neutral termini
(AARAA)H + •H 2 O
Wyttenbach, Paizs, Barran, Breci,
Liu, Suhai, Wysocki, Bowers
JACS 125, 13768 (2003)
set up for
H/D exchange
relay mechanism
C-terminus
N-terminus
B3LYP/6-31+G(d,p)

Zwitterion
(AARAA)H + •H 2 O
Wyttenbach, Paizs, Barran, Breci,
Liu, Suhai, Wysocki, Bowers
JACS 125, 13768 (2003)
C-terminus
N-terminus
B3LYP/6-31+G(d,p)

Transition state
(AARAA)H + •H 2 O
Wyttenbach, Paizs, Barran, Breci,
Liu, Suhai, Wysocki, Bowers
JACS 125, 13768 (2003)
C-terminus
N-terminus
B3LYP/6-31+G(d,p)

HYDRATION OF PEPTIDES
Ionic Groups
The Ammonium Group
The Guanidinium Group
The Carboxylate Group
Several Ionic Groups
Multiply Charged Ions
Salt Bridges
Challenges Ahead
Change of Conformation
Zwitterion Formation
Entropy

–∆S°
cal/mol/K
all other data:
• all molecules
• all charge states
• all hydrates 1 st –n th H 2 O
∆S° < 0
loss of 3 translational
and 3 rotational
degrees of freedom
(gain of 6 vibrational
degrees of freedom)
2 nd H 2 O
on small
molecules
1 st H 2 O
on small
molecules
all data
positive and
negative ions
floppy
–∆H° kcal/mol

strong
entropy–enthalpy
correlation
(red data)
tightly bound H 2
O
• large binding energy
• large loss of entropy
exceptions are:
• Addition of 1 st H 2 O to small molecules (blue data)
yields smaller than average loss of entropy
→ floppy hydrates
• Addition of 2 nd H 2 O to small molecules (yellow data)
yields data between blue and red

HYDRATION OF PEPTIDES
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 formation