Directory UMM :wiley:Public:journals:jcc:suppmat:20:
Supplementary Material
A comparative study of global minimum energy
conformations of hydrated peptides
J. L. Klepeis and C. A. Floudas
Department of Chemical Engineering
Princeton University
Princeton, N.J. 08544-5263
Tables SI to SXXI
Figures S1 to S16
S1
Table SI: Free energy density of solvation parameters employed in the RRIGS model. The
second column provides the solvation parameters in cal/(mol
A2 ), and the last two columns
), respectively.
correspond to the van der Waals and hydration radii (A
Atom Type
H hydroxyl, amino
H acid
H amide
H thiol
C aliphatic CH3
C aliphatic CH2
C aliphatic CH
C other aliphatic
C cyclic CH
C aromatic CH
C aromatic CR
C branched aromatic C
C aromatic COH
C carbonyl
N primary amine
N secondary amine
N aromatic
N amide
O hydroxyl, ether
O acid, ester
O ketone, carbonyl
O acid, amide carbonyl
S thiol, disul de
S2
-10.35
-3.206
-7.714
2.709
1.319
0.2374
-1.271
-2.297
0.2890
-0.2137
-1.713
-1.910
-0.6063
2.696
-1.149
-10.28
-10.48
-7.332
-7.396
0.07897
-15.70
-15.56
-4.706
Rv
1.415
1.415
1.415
1.415
2.125
2.225
2.375
2.060
2.375
2.100
1.850
1.850
1.850
1.870
1.755
1.755
1.755
1.755
1.620
1.620
1.560
1.560
2.075
Rh
4.17
4.17
4.17
4.17
5.35
5.35
5.35
5.35
5.35
5.35
5.35
5.35
5.35
5.35
5.05
5.05
5.05
5.05
4.95
4.95
4.95
4.95
5.37
Table SII: Global minimum energies of terminally blocked peptides using the RRIGS solvation model and ASP set. The amino end group is speci ed as N{Acetyl{amino; the carboxyl
end group is speci ed as Carboxyl{CONHCH3 . The total number of dihedral angles is indicated in the column headed by # DA. The total energy, ETOT , is provided along with the
contributions from hydration, EHY D , nonbonded interactions (including hydrogen bonding),
ENB , electrostatic interactions, EES , and torsion, ETOR .
Residue # DA ETOT EHY D ENB
Gly
Ala
Cys
His
Phe
Ser
Trp
Asn
Asp
Thr
Tyr
Val
Gln
Glu
Ile
Leu
Met
Lys
Arg
6
7
7
8
8
8
8
9
9
9
9
9
10
10
10
10
10
11
13
-22.46
-20.82
-23.51
-34.47
-24.72
-28.32
-31.48
-49.07
-39.96
-29.18
-30.11
-18.92
-46.49
-36.11
-17.11
-20.22
-23.93
-28.15
-63.84
-16.14
-15.64
-17.67
-25.57
-16.55
-20.47
-21.92
-26.47
-20.94
-19.59
-21.90
-14.74
-27.70
-20.92
-14.57
-14.53
-17.02
-20.17
-32.38
S3
-3.71
-3.92
-4.66
-6.78
-7.23
-5.40
-8.99
-5.16
-6.29
-5.74
-6.65
-3.11
-5.38
-5.42
-2.80
-4.16
-4.62
-5.91
-6.21
EES ETOR
-2.62
-1.28
-1.21
-2.21
-0.94
-2.49
-0.59
-17.47
-12.74
-4.19
-1.57
-1.16
-13.49
-9.85
-0.52
-1.88
-2.40
-2.17
-25.36
0.01
0.02
0.03
0.09
0.00
0.04
0.02
0.03
0.01
0.34
0.01
0.09
0.08
0.08
0.78
0.35
0.11
0.10
0.11
Table SIII: Global minimum energies of terminally blocked peptides using the WE1 ASP set.
The amino end group is speci ed as N{Acetyl{amino; the carboxyl end group is speci ed
as Carboxyl{CONHCH3 . The total number of dihedral angles is indicated in the column
headed by # DA. The total energy, ETOT , is provided along with the contributions from
hydration, EHY D , nonbonded interactions (including hydrogen bonding), ENB , electrostatic
interactions, EES , and torsion, ETOR.
Residue # DA ETOT EHY D ENB
Gly
Ala
Cys
His
Phe
Ser
Trp
Asn
Asp
Thr
Tyr
Val
Gln
Glu
Ile
Leu
Met
Lys
Arg
6
7
7
8
8
8
8
9
9
9
9
9
10
10
10
10
10
11
13
-12.93
-10.98
-12.80
-19.12
-12.51
-16.46
-16.54
-38.52
-32.68
-16.61
-15.46
-8.89
-34.91
-28.88
-6.80
-9.92
-12.62
-19.56
-51.46
-6.68
-6.59
-8.19
-11.52
-4.38
-11.24
-7.03
-16.03
-14.21
-7.35
-8.66
-5.26
-17.36
-15.08
-4.30
-5.22
-6.50
-13.06
-20.51
S4
-3.71
-3.91
-4.15
-6.59
-7.22
-3.74
-8.98
-6.16
-5.65
-5.55
-5.79
-2.94
-5.01
-5.00
-2.75
-3.79
-4.63
-5.26
-6.39
EES ETOR
-2.54
-0.48
-0.47
-1.02
-0.94
-1.48
-0.56
-16.34
-12.83
-3.98
-1.03
-0.77
-12.67
-8.92
-0.51
-1.07
-1.64
-1.31
-24.62
0.00
0.00
0.01
0.02
0.04
0.00
0.04
0.01
0.01
0.26
0.03
0.07
0.14
0.13
0.76
0.16
0.14
0.07
0.07
Table SIV: Global minimum energies of terminally blocked peptides using the WE2 ASP set.
The amino end group is speci ed as N{Acetyl{amino; the carboxyl end group is speci ed
as Carboxyl{CONHCH3 . The total number of dihedral angles is indicated in the column
headed by # DA. The total energy, ETOT , is provided along with the contributions from
hydration, EHY D , nonbonded interactions (including hydrogen bonding), ENB , electrostatic
interactions, EES , and torsion, ETOR.
Residue # DA ETOT EHY D ENB
Gly
Ala
Cys
His
Phe
Ser
Trp
Asn
Asp
Thr
Tyr
Val
Gln
Glu
Ile
Leu
Met
Lys
Arg
6
7
7
8
8
8
8
9
9
9
9
9
10
10
10
10
10
11
13
-14.46
-12.73
-14.18
-20.97
-15.10
-17.88
-19.11
-39.76
-34.03
-18.48
-19.54
-11.05
-36.14
-30.37
-9.19
-12.28
-14.73
-21.46
-52.94
-8.20
-8.33
-9.54
-13.33
-6.96
-12.58
-9.59
-17.26
-15.52
-9.14
-11.36
-7.37
-17.88
-16.56
-6.68
-7.58
-8.60
-14.90
-21.98
S5
-3.71
-3.92
-4.17
-6.64
-7.22
-3.79
-8.98
-6.16
-5.66
-5.60
-6.64
-2.99
-6.01
-5.02
-2.76
-3.79
-4.64
-5.31
-6.41
EES ETOR
-2.55
-0.48
-0.48
-1.03
-0.94
-1.51
-0.56
-16.35
-12.84
-4.01
-1.57
-0.76
-12.33
-8.92
-0.51
-1.07
-1.64
-1.32
-24.62
0.00
0.00
0.01
0.02
0.03
0.00
0.03
0.01
0.00
0.27
0.03
0.07
0.09
0.13
0.76
0.15
0.14
0.07
0.07
Table SV: Global minimum energies of terminally blocked peptides using the OONS ASP
set. The amino end group is speci ed as N{Acetyl{amino; the carboxyl end group is speci ed
as Carboxyl{CONHCH3 . The total number of dihedral angles is indicated in the column
headed by # DA. The total energy, ETOT , is provided along with the contributions from
hydration, EHY D , nonbonded interactions (including hydrogen bonding), ENB , electrostatic
interactions, EES , and torsion, ETOR.
Residue # DA ETOT EHY D ENB
Gly
Ala
Cys
His
Phe
Ser
Trp
Asn
Asp
Thr
Tyr
Val
Gln
Glu
Ile
Leu
Met
Lys
Arg
6
7
7
8
8
8
8
9
9
9
9
9
10
10
10
10
10
11
13
-7.52 -1.24
-5.59 -1.18
-8.24 -2.61
-15.70 -8.65
-10.49 -2.07
-13.32 -5.53
-15.07 -5.54
-30.84 -8.31
-27.55 -9.07
-13.84 -4.36
-17.64 -9.18
-4.58 -0.51
-26.80 -8.31
-23.36 -8.89
-2.39 0.12
-5.50 0.18
-7.94 -1.83
-14.03 -6.20
-46.79 -15.77
S6
-3.72
-3.93
-4.64
-6.07
-7.55
-5.43
-8.97
-6.14
-5.80
-5.72
-6.94
-3.04
-5.22
-5.95
-2.74
-4.12
-4.63
-5.89
-6.52
EES ETOR
-2.58
-0.48
-1.02
-0.99
-0.88
-2.39
-0.58
-16.41
-12.69
-4.09
-1.52
-1.11
-13.43
-8.60
-0.51
-1.76
-1.63
-2.04
-24.58
0.01
0.01
0.03
0.01
0.00
0.02
0.02
0.02
0.01
0.33
0.00
0.08
0.15
0.08
0.74
0.20
0.14
0.10
0.08
Table SVI: Global minimum energies of terminally blocked peptides using the SCKS ASP
set. The amino end group is speci ed as N{Acetyl{amino; the carboxyl end group is speci ed
as Carboxyl{CONHCH3 . The total number of dihedral angles is indicated in the column
headed by # DA. The total energy, ETOT , is provided along with the contributions from
hydration, EHY D , nonbonded interactions (including hydrogen bonding), ENB , electrostatic
interactions, EES , and torsion, ETOR.
Residue # DA ETOT EHY D ENB
Gly
Ala
Cys
His
Phe
Ser
Trp
Asn
Asp
Thr
Tyr
Val
Gln
Glu
Ile
Leu
Met
Lys
Arg
6
7
7
8
8
8
8
9
9
9
9
9
10
10
10
10
10
11
13
EES ETOR
-0.50 5.82 -3.70 -2.62
2.01 7.18 -3.91 -1.27
-0.50 5.33 -4.66 -1.19
-1.07 7.29 -7.53 -0.86
1.69 10.11 -7.56 -0.87
-1.81 6.04 -5.39 -2.48
0.39 9.92 -8.98 -0.58
-18.37 4.57 -6.33 -16.63
-14.09 5.25 -6.49 -12.85
-2.36 7.22 -5.72 -4.18
0.07 8.54 -6.95 -1.53
4.51 8.65 -3.10 -1.13
-13.53 5.24 -5.38 -13.47
-9.27 5.93 -5.41 -9.87
6.81 9.34 -2.77 -0.51
3.99 9.69 -4.11 -1.80
1.75 8.65 -4.62 -2.38
-0.40 7.58 -5.90 -2.15
-26.07 5.26 -7.11 -24.33
S7
0.00
0.01
0.02
0.04
0.02
0.01
0.03
0.02
0.00
0.32
0.02
0.09
0.08
0.08
0.75
0.20
0.10
0.07
0.11
Table SVII: Global minimum energies of terminally blocked peptides using the JRF ASP set.
The amino end group is speci ed as N{Acetyl{amino; the carboxyl end group is speci ed
as Carboxyl{CONHCH3 . The total number of dihedral angles is indicated in the column
headed by # DA. The total energy, ETOT , is provided along with the contributions from
hydration, EHY D , nonbonded interactions (including hydrogen bonding), ENB , electrostatic
interactions, EES , and torsion, ETOR.
Residue # DA ETOT EHY D ENB
Gly
Ala
Cys
His
Phe
Ser
Trp
Asn
Asp
Thr
Tyr
Val
Gln
Glu
Ile
Leu
Met
Lys
Arg
6
7
7
8
8
8
8
9
9
9
9
9
10
10
10
10
10
11
13
EES ETOR
15.99 14.29 3.01 -1.54 0.23
29.71 24.81 2.36 -0.24 2.78
0.26 -4.22 2.51 -0.21 2.18
-50.22 -42.99 -6.87 -0.46 0.10
-83.47 -86.53 0.12 -0.82 3.76
-5.72 -9.62 2.68 -1.39 2.61
-105.88 -98.00 -7.91 0.03 0.00
-20.76 -20.86 8.13 -16.55 8.52
-41.14 -31.91 2.31 -12.95 1.41
6.56
2.82 0.31 -2.16 5.59
-102.43 -105.52 1.02 -1.43 3.50
46.54 39.84 2.53 -0.86 5.03
-13.89 -6.55 1.93 -12.69 3.42
-33.55 -19.61 -5.18 -8.93 0.17
53.61 56.15 -2.80 -0.52 0.78
47.62 29.61 8.37 -0.54 10.18
26.33 21.35 2.10 -1.61 4.49
26.65 22.85 0.40 -1.45 4.85
-34.88 -4.57 -6.12 -24.39 0.20
S8
Table SVIII: Local minimum energies of terminally blocked peptides using the JRF ASP set
with constrained ! bounds [160,200]. The amino end group is speci ed as N{Acetyl{amino;
the carboxyl end group is speci ed as Carboxyl{CONHCH3 . The total number of dihedral
angles is indicated in the column headed by # DA. The total energy, ETOT , is provided along
with the contributions from hydration, EHY D , nonbonded interactions (including hydrogen
bonding), ENB , electrostatic interactions, EES , and torsion, ETOR .
Residue # DA ETOT EHY D ENB
Ala
Cys
Ser
Asn
Asp
Val
Gln
Leu
Met
Lys
7
7
8
9
9
9
10
10
10
11
32.97
2.34
-4.75
-19.13
-39.35
46.71
-13.51
49.68
27.04
26.96
37.44
7.27
-11.02
3.43
-20.76
50.62
4.20
41.57
32.32
33.71
S9
EES ETOR
-4.00 -0.47
-5.17 0.24
0.69 -0.28
-6.13 -16.43
-6.13 -12.47
-3.26 -0.77
-5.17 -12.74
1.58 -0.66
-4.41 -1.65
-5.51 -1.34
0.00
0.00
5.86
0.00
0.01
0.12
0.20
7.19
0.78
0.10
Table SIX: Comparison of unsolvated components for all accessible area based ASP set global
minima and the RRIGS global minima (of terminally blocked peptides). EPOT = EPOT
ASP POT
ERRIGS at corresponding global minima, for the ASP set as listed.
Residue WE1 WE2 OONS SCKS JRF
Gly
0.07 0.06
0.04 0.00 8.02
Ala
0.79 0.78
0.77 0.00 0.71
Cys
1.22 1.20
0.21 0.01 0.91
His
1.31 1.25
1.85 0.55 1.67
Phe
0.04 0.04 -0.26 -0.25 11.23
Ser
2.64 2.56
0.06 0.00 14.13
Trp
0.04 0.03
0.02 0.02 1.67
Asn
0.10 0.10
0.06 -0.35 0.04
Asp
0.55 0.52
0.55 -0.32 0.44
Thr
0.32 0.25
0.11 0.01 13.32
Tyr
1.42 0.03 -0.24 -0.25 11.30
Val
0.55 0.50
0.11 0.04 0.27
Gln
1.23 0.53
0.29 0.01 1.07
Glu
1.39 1.37
0.71 -0.02 1.24
Ile
0.04 0.03
0.03 0.01 0.00
Leu
1.00 0.99
0.02 -0.01 13.80
Met
0.79 0.78
0.79 0.01 1.63
Lys
1.48 1.43
0.15 0.01 1.23
Arg
0.52 0.50
0.44 0.13 1.15
S10
Table SX: Comparison of unsolvated components for all accessible area based ASP set global
D
minima and the RRIGS global minima (of terminally blocked peptides). EHY D = EHY
ASP D
EHY
RRIGS at corresponding global minima, for the ASP set as listed.
Residue
Gly
Ala
Cys
His
Phe
Ser
Trp
Asn
Asp
Thr
Tyr
Val
Gln
Glu
Ile
Leu
Met
Lys
Arg
WE1
9.46
9.05
9.48
14.05
12.17
9.23
14.89
10.44
6.72
12.25
13.24
9.48
10.35
5.84
10.26
9.31
10.53
7.11
11.87
WE2 OONS SCKS JRF
7.94 14.90 21.96 30.43
7.31 14.46 22.82 53.08
8.13 15.06 23.00 24.94
12.25 16.92 32.86 -17.42
9.59 14.48 26.66 -69.98
7.89 14.93 26.51 9.45
12.33 16.39 31.85 -76.07
9.21 18.16 31.04 29.90
5.41 11.87 26.19 0.17
10.45 15.23 26.81 22.42
10.54 12.72 30.44 -83.62
7.37 14.23 23.39 65.36
9.82 19.40 32.95 31.90
4.37 12.03 26.85 1.32
7.88 14.69 23.91 70.72
6.95 14.71 24.22 56.10
8.43 15.20 25.68 49.34
5.27 13.97 27.75 53.88
10.40 16.61 37.64 27.80
S11
Table SXI: Approximate dihedral angles and nomenclature for { regions.
Conformer
C5
PII
C7
R
,
-150, 150
-80, 150
-80, 80
-80, -50
Protein structure
{sheet
polyproline II
{turn
{helix (right)
Table SXII: Distribution of global minima for terminally blocked amino acids using solvation
model listed in rst column.
Model C5 P
RRIGS
WE1
WE2
OONS
SCKS
JRF
5
13
13
6
6
9
II
0
1
1
2
0
2
C7
14
2
2
8
11
0
R Other
0
2
2
2
2
7
0
1
1
1
0
1
Table SXIII: Dihedral angles at the global minimum energy conformation of unsolvated
leu{enkephalin.
Tyr
Gly
Gly
Phe
Leu
-163.07
65.90
-150.83
-158.73
-77.83
-42.29
-88.33
31.94
157.23
123.31
!
1
2
3
4
182.31 -174.79 90.16 -177.26
174.19
181.29
178.02 53.24 84.40
181.31 -179.81 64.47 172.58 179.43
S12
Table SXIV: Dihedral angles at the global minimum energy conformation of leu{enkephalin,
using the RRIGS model for hydration.
Tyr
Gly
Gly
Phe
Leu
-168.37
78.92
163.21
-150.66
-75.45
-30.66
-87.17
91.51
161.54
105.32
!
1
2
3
4
178.49 -173.40 78.69 -161.13
-177.32
172.72
-178.44 66.75 -86.84
-178.26 179.51 63.84 172.22 179.31
Table SXV: Dihedral angles at the global minimum energy conformation of leu{enkephalin,
using the WE1 model for hydration.
Tyr
Gly
Gly
Phe
Leu
-162.77
66.15
-152.77
-158.33
-86.58
-43.63
-86.15
32.53
156.18
124.93
!
1
2
3
4
-177.55 -174.64 88.60 182.98
173.14
181.90
179.06 51.73 83.41
-179.00 182.65 69.00 54.85 -59.77
Table SXVI: Dihedral angles at the global minimum energy conformation of leu{enkephalin,
using the WE2 model for hydration.
Tyr
Gly
Gly
Phe
Leu
-162.81
66.15
-152.91
-158.47
-86.17
-43.49
-86.18
32.54
156.24
125.26
!
1
2
3
4
-177.59 -174.74 88.48 182.98
173.23
181.81
179.03 51.81 83.50
-178.99 182.37 68.61 54.60 -59.84
S13
Table SXVII: Dihedral angles at the global minimum energy conformation of leu{enkephalin,
using the OONS model for hydration.
Tyr
Gly
Gly
Phe
Leu
-166.40
63.68
-152.32
-159.65
-84.06
-51.73
-85.81
33.95
153.94
148.49
!
1
2
3
4
-175.64 -189.82 75.41 182.41
175.24
181.27
-180.61 51.12 83.54
-179.04 -63.09 160.85 59.05 62.99
Table SXVIII: Dihedral angles at the global minimum energy conformation of leu{enkephalin,
using the SCKS model for hydration.
Tyr
Gly
Gly
Phe
Leu
-162.84
65.94
-150.11
-157.73
-80.71
-43.09
-88.13
31.76
156.45
123.90
!
1
2
3
4
182.46 -174.41 -89.51 2.80
173.67
181.73
178.12 53.21 83.97
181.21 -178.83 65.57 -186.90 -180.38
Table SXIX: Dihedral angles at the global minimum energy conformation of leu{enkephalin,
using the JRF model for hydration.
Tyr
Gly
Gly
Phe
Leu
-84.88
-160.78
144.15
-79.95
-83.98
160.00
140.99
-152.83
71.30
138.62
!
1
2
3
4
178.30 -60.54 100.49 -179.22
-178.01
177.03
-176.06 -60.97 108.26
-179.24 -53.91 176.56 -178.84 69.81
S14
Table SXX: Comparison of hydration energies for leu{enkephalin. The rst column refers
to the hydration model used in the function evaluations, which are performed at the global
solutions for the hydration model listed in the second column. The total energy, ETOT , is
provided along with the contributions from hydration, EHY D , nonbonded interactions (including hydrogen bonding), ENB , electrostatic interactions, EES , and torsion, ETOR. The last
column provides the heavy atom root mean squared deviation between the global minimum
energy structures of the hydration models listed in the rst two columns.
Global of ETOT EHY D ENB
RRIGS RRIGS
WE1
WE2
OONS
SCKS
JRF
WE1 RRIGS
WE1
WE2
OONS
SCKS
JRF
WE2 RRIGS
WE1
WE2
OONS
SCKS
JRF
-46.56
-44.70
-44.75
-43.14
-44.79
-39.10
-24.51
-28.37
-28.36
-26.58
-28.19
-18.76
-28.00
-31.49
-31.50
-29.74
-31.33
-22.35
-39.00
-35.68
-35.69
-35.58
-35.50
-44.27
-16.94
-19.35
-19.31
-19.03
-18.90
-23.92
-20.44
-22.47
-22.44
-22.19
-22.04
-27.51
S15
22.31
22.66
22.67
22.75
22.67
23.77
22.31
22.66
22.67
22.75
22.67
23.77
22.31
22.66
22.67
22.75
22.67
23.77
EES ETOR (RMSD)
-30.95
-32.43
-32.45
-31.55
-32.58
-19.07
-30.95
-32.43
-32.45
-31.55
-32.58
-19.07
-30.95
-32.43
-32.45
-31.55
-32.58
-19.07
1.07
0.75
0.72
1.25
0.62
0.46
1.07
0.75
0.72
1.25
0.62
0.46
1.07
0.75
0.72
1.25
0.62
0.46
0.00
2.56
2.55
2.66
2.60
4.64
2.56
0.00
0.01
0.86
0.77
3.98
2.55
0.01
0.00
0.86
0.77
3.97
Table SXXI: Comparison of hydration energies for leu{enkephalin. The rst column refers
to the hydration model used in the function evaluations, which are performed at the global
solutions for the hydration model listed in the second column. The total energy, ETOT , is
provided along with the contributions from hydration, EHY D , nonbonded interactions (including hydrogen bonding), ENB , electrostatic interactions, EES , and torsion, ETOR. The last
column provides the heavy atom root mean squared deviation between the global minimum
energy structures of the hydration models listed in the rst two columns.
Global of ETOT
OONS RRIGS
WE1
WE2
OONS
SCKS
JRF
SCKS RRIGS
WE1
WE2
OONS
SCKS
JRF
JRF RRIGS
WE1
WE2
OONS
SCKS
JRF
-21.63
-28.61
-28.62
-28.77
-28.37
-19.23
5.57
2.54
2.53
4.15
2.36
18.35
-112.59
-152.64
-152.61
-158.44
-149.29
-263.14
EHY D ENB
-14.06
-19.59
-19.56
-21.21
-19.08
-24.39
13.14
11.56
11.58
11.71
11.65
13.19
-105.02
-143.62
-143.56
-150.88
-140.00
-268.31
S16
22.31
22.66
22.67
22.75
22.67
23.77
22.31
22.66
22.67
22.75
22.67
23.77
22.31
22.66
22.67
22.75
22.67
23.77
EES ETOR (RMSD)
-30.95
-32.43
-32.45
-31.55
-32.58
-19.07
-30.95
-32.43
-32.45
-31.55
-32.58
-19.07
-30.95
-32.43
-32.45
-31.55
-32.58
-19.07
1.07
0.75
0.72
1.25
0.62
0.46
1.07
0.75
0.72
1.25
0.62
0.46
1.07
0.75
0.72
1.25
0.62
0.46
2.66
0.86
0.86
0.00
1.14
3.90
2.60
0.77
0.77
1.14
0.00
4.06
4.64
3.98
3.97
3.90
4.06
0.00
List of gures
Figure S1: Adiabatic { map for unsolvated N{acetyl{N'{methyl{alanineamide. The adiabatic curves de ne regions within a given energy (1, 2, 5, 9 kcal/mole) of the global minimum
value, and the (*) represents the location of the global minimum.
Figure S2: Adiabatic { map for solvated N{acetyl{N'{methyl{alanineamide, using the
RRIGS solvation model. The adiabatic curves de ne regions within a given energy (1, 2, 5,
9 kcal/mole) of the global minimum value, and the (*) represents the location of the global
minimum.
Figure S3: Adiabatic { map for solvated N{acetyl{N'{methyl{alanineamide, using the
WE1 ASP set. The adiabatic curves de ne regions within a given energy (1, 2, 5, 9 kcal/mole)
of the global minimum value, and the (*) represents the location of the global minimum.
Figure S4: Adiabatic { map for solvated N{acetyl{N'{methyl{alanineamide, using the
WE2 ASP set. The adiabatic curves de ne regions within a given energy (1, 2, 5, 9 kcal/mole)
of the global minimum value, and the (*) represents the location of the global minimum.
Figure S5: Adiabatic { map for solvated N{acetyl{N'{methyl{alanineamide, using the
OONS ASP. The adiabatic curves de ne regions within a given energy (1, 2, 5, 9 kcal/mole)
of the global minimum value, and the (*) represents the location of the global minimum.
Figure S6: Adiabatic { map for solvated N{acetyl{N'{methyl{alanineamide, using the
SCKS ASP set. The adiabatic curves de ne regions within a given energy (1, 2, 5, 9
kcal/mole) of the global minimum value, and the (*) represents the location of the global
minimum.
Figure S7: Adiabatic { map for solvated N{acetyl{N'{methyl{alanineamide, using the
JRF ASP set. The adiabatic curves de ne regions within a given energy (1, 2, 5, 9 kcal/mole)
of the global minimum value, and the (*) represents the location of the global minimum.
Figure S8: Plot of met{enkephalin conformation. Global minimum energy of -33.27 kcal/mole
using the WE2 model for hydration.
Figure S9: Plot of met{enkephalin conformation. Global minimum energy of -31.45 kcal/mole
using the OONS model for hydration.
S17
Figure S10: Plot of unsolvated leu{enkephalin conformation. Global minimum energy of
-9.349 kcal/mole.
Figure S11: Plot of leu{enkephalin conformation. Global minimum energy of -46.57 kcal/mole
using the RRIGS model for hydration.
Figure S12: Plot of leu{enkephalin conformation. Global minimum energy of -28.37 kcal/mole
using the WE1 model for hydration.
Figure S13: Plot of leu{enkephalin conformation. Global minimum energy of -31.50 kcal/mole
using the WE2 model for hydration.
Figure S14: Plot of leu{enkephalin conformation. Global minimum energy of -28.77 kcal/mole
using the OONS model for hydration.
Figure S15: Plot of leu{enkephalin conformation. Global minimum energy of 2.35 kcal/mole
using the SCKS model for hydration.
Figure S16: Plot of leu{enkephalin conformation. Global minimum energy of -263.14 kcal/mole
using the JRF model for hydration.
S18
150
1
1 2 5 9
100
9 5
*
5 9
50
0ψ
2
5
9
1
2
9 5
9
9
-100
9
5
-150
-100
9
-50
0
50
φ
Figure S1:
S19
-50
100
150
-150
150
1
1 2 5 9
95
*
50
5 9
1
100
0ψ
2
5
9
1
9 5
9
-100
9
9
5
2
-150
9
9
-100
-50
0
50
φ
Figure S2:
S20
-50
100
150
-150
150
*
1 2 5 9
9 5
100
50
5 9
0ψ
2
9
5
2
1
9 5
9
-100
9
9
9
5
9
2
-150
-100
-50
0
50
φ
Figure S3:
S21
-50
100
150
-150
150
*
9 5
1 2 5 9
100
50
5 9
0ψ
2
9
5
1
-50
2
9 5
9
-100
9
9
9
2
-150
5
9
-100
-50
0
50
φ
Figure S4:
S22
100
150
-150
5
150
*
9 5
12 5 9
100
50
2 5 9
0ψ
2
5
9
2
1
9 5
-50
9
-100
9
9
2
-150
5
5
-100
-50
0
50
φ
Figure S5:
S23
9
100
150
-150
150
1 2 5 9
1
95
100
*
50
2 5 9
0ψ
9
2 5
1
9 5
-50
9
-100
9
9
2
-150
5
5
-100
-50
0
50
φ
Figure S6:
S24
9
100
150
-150
150
*
9 5
1 2
5 9
100
50
9
0ψ
9
2
5
-50
9 5
-100
9
5
-150
9
-100
-50
0
50
φ
Figure S7:
S25
100
150
-150
Figure S8:
S26
Figure S9:
S27
Figure S10:
S28
Figure S11:
S29
Figure S12:
S30
Figure S13:
S31
Figure S14:
S32
Figure S15:
S33
Figure S16:
S34
A comparative study of global minimum energy
conformations of hydrated peptides
J. L. Klepeis and C. A. Floudas
Department of Chemical Engineering
Princeton University
Princeton, N.J. 08544-5263
Tables SI to SXXI
Figures S1 to S16
S1
Table SI: Free energy density of solvation parameters employed in the RRIGS model. The
second column provides the solvation parameters in cal/(mol
A2 ), and the last two columns
), respectively.
correspond to the van der Waals and hydration radii (A
Atom Type
H hydroxyl, amino
H acid
H amide
H thiol
C aliphatic CH3
C aliphatic CH2
C aliphatic CH
C other aliphatic
C cyclic CH
C aromatic CH
C aromatic CR
C branched aromatic C
C aromatic COH
C carbonyl
N primary amine
N secondary amine
N aromatic
N amide
O hydroxyl, ether
O acid, ester
O ketone, carbonyl
O acid, amide carbonyl
S thiol, disul de
S2
-10.35
-3.206
-7.714
2.709
1.319
0.2374
-1.271
-2.297
0.2890
-0.2137
-1.713
-1.910
-0.6063
2.696
-1.149
-10.28
-10.48
-7.332
-7.396
0.07897
-15.70
-15.56
-4.706
Rv
1.415
1.415
1.415
1.415
2.125
2.225
2.375
2.060
2.375
2.100
1.850
1.850
1.850
1.870
1.755
1.755
1.755
1.755
1.620
1.620
1.560
1.560
2.075
Rh
4.17
4.17
4.17
4.17
5.35
5.35
5.35
5.35
5.35
5.35
5.35
5.35
5.35
5.35
5.05
5.05
5.05
5.05
4.95
4.95
4.95
4.95
5.37
Table SII: Global minimum energies of terminally blocked peptides using the RRIGS solvation model and ASP set. The amino end group is speci ed as N{Acetyl{amino; the carboxyl
end group is speci ed as Carboxyl{CONHCH3 . The total number of dihedral angles is indicated in the column headed by # DA. The total energy, ETOT , is provided along with the
contributions from hydration, EHY D , nonbonded interactions (including hydrogen bonding),
ENB , electrostatic interactions, EES , and torsion, ETOR .
Residue # DA ETOT EHY D ENB
Gly
Ala
Cys
His
Phe
Ser
Trp
Asn
Asp
Thr
Tyr
Val
Gln
Glu
Ile
Leu
Met
Lys
Arg
6
7
7
8
8
8
8
9
9
9
9
9
10
10
10
10
10
11
13
-22.46
-20.82
-23.51
-34.47
-24.72
-28.32
-31.48
-49.07
-39.96
-29.18
-30.11
-18.92
-46.49
-36.11
-17.11
-20.22
-23.93
-28.15
-63.84
-16.14
-15.64
-17.67
-25.57
-16.55
-20.47
-21.92
-26.47
-20.94
-19.59
-21.90
-14.74
-27.70
-20.92
-14.57
-14.53
-17.02
-20.17
-32.38
S3
-3.71
-3.92
-4.66
-6.78
-7.23
-5.40
-8.99
-5.16
-6.29
-5.74
-6.65
-3.11
-5.38
-5.42
-2.80
-4.16
-4.62
-5.91
-6.21
EES ETOR
-2.62
-1.28
-1.21
-2.21
-0.94
-2.49
-0.59
-17.47
-12.74
-4.19
-1.57
-1.16
-13.49
-9.85
-0.52
-1.88
-2.40
-2.17
-25.36
0.01
0.02
0.03
0.09
0.00
0.04
0.02
0.03
0.01
0.34
0.01
0.09
0.08
0.08
0.78
0.35
0.11
0.10
0.11
Table SIII: Global minimum energies of terminally blocked peptides using the WE1 ASP set.
The amino end group is speci ed as N{Acetyl{amino; the carboxyl end group is speci ed
as Carboxyl{CONHCH3 . The total number of dihedral angles is indicated in the column
headed by # DA. The total energy, ETOT , is provided along with the contributions from
hydration, EHY D , nonbonded interactions (including hydrogen bonding), ENB , electrostatic
interactions, EES , and torsion, ETOR.
Residue # DA ETOT EHY D ENB
Gly
Ala
Cys
His
Phe
Ser
Trp
Asn
Asp
Thr
Tyr
Val
Gln
Glu
Ile
Leu
Met
Lys
Arg
6
7
7
8
8
8
8
9
9
9
9
9
10
10
10
10
10
11
13
-12.93
-10.98
-12.80
-19.12
-12.51
-16.46
-16.54
-38.52
-32.68
-16.61
-15.46
-8.89
-34.91
-28.88
-6.80
-9.92
-12.62
-19.56
-51.46
-6.68
-6.59
-8.19
-11.52
-4.38
-11.24
-7.03
-16.03
-14.21
-7.35
-8.66
-5.26
-17.36
-15.08
-4.30
-5.22
-6.50
-13.06
-20.51
S4
-3.71
-3.91
-4.15
-6.59
-7.22
-3.74
-8.98
-6.16
-5.65
-5.55
-5.79
-2.94
-5.01
-5.00
-2.75
-3.79
-4.63
-5.26
-6.39
EES ETOR
-2.54
-0.48
-0.47
-1.02
-0.94
-1.48
-0.56
-16.34
-12.83
-3.98
-1.03
-0.77
-12.67
-8.92
-0.51
-1.07
-1.64
-1.31
-24.62
0.00
0.00
0.01
0.02
0.04
0.00
0.04
0.01
0.01
0.26
0.03
0.07
0.14
0.13
0.76
0.16
0.14
0.07
0.07
Table SIV: Global minimum energies of terminally blocked peptides using the WE2 ASP set.
The amino end group is speci ed as N{Acetyl{amino; the carboxyl end group is speci ed
as Carboxyl{CONHCH3 . The total number of dihedral angles is indicated in the column
headed by # DA. The total energy, ETOT , is provided along with the contributions from
hydration, EHY D , nonbonded interactions (including hydrogen bonding), ENB , electrostatic
interactions, EES , and torsion, ETOR.
Residue # DA ETOT EHY D ENB
Gly
Ala
Cys
His
Phe
Ser
Trp
Asn
Asp
Thr
Tyr
Val
Gln
Glu
Ile
Leu
Met
Lys
Arg
6
7
7
8
8
8
8
9
9
9
9
9
10
10
10
10
10
11
13
-14.46
-12.73
-14.18
-20.97
-15.10
-17.88
-19.11
-39.76
-34.03
-18.48
-19.54
-11.05
-36.14
-30.37
-9.19
-12.28
-14.73
-21.46
-52.94
-8.20
-8.33
-9.54
-13.33
-6.96
-12.58
-9.59
-17.26
-15.52
-9.14
-11.36
-7.37
-17.88
-16.56
-6.68
-7.58
-8.60
-14.90
-21.98
S5
-3.71
-3.92
-4.17
-6.64
-7.22
-3.79
-8.98
-6.16
-5.66
-5.60
-6.64
-2.99
-6.01
-5.02
-2.76
-3.79
-4.64
-5.31
-6.41
EES ETOR
-2.55
-0.48
-0.48
-1.03
-0.94
-1.51
-0.56
-16.35
-12.84
-4.01
-1.57
-0.76
-12.33
-8.92
-0.51
-1.07
-1.64
-1.32
-24.62
0.00
0.00
0.01
0.02
0.03
0.00
0.03
0.01
0.00
0.27
0.03
0.07
0.09
0.13
0.76
0.15
0.14
0.07
0.07
Table SV: Global minimum energies of terminally blocked peptides using the OONS ASP
set. The amino end group is speci ed as N{Acetyl{amino; the carboxyl end group is speci ed
as Carboxyl{CONHCH3 . The total number of dihedral angles is indicated in the column
headed by # DA. The total energy, ETOT , is provided along with the contributions from
hydration, EHY D , nonbonded interactions (including hydrogen bonding), ENB , electrostatic
interactions, EES , and torsion, ETOR.
Residue # DA ETOT EHY D ENB
Gly
Ala
Cys
His
Phe
Ser
Trp
Asn
Asp
Thr
Tyr
Val
Gln
Glu
Ile
Leu
Met
Lys
Arg
6
7
7
8
8
8
8
9
9
9
9
9
10
10
10
10
10
11
13
-7.52 -1.24
-5.59 -1.18
-8.24 -2.61
-15.70 -8.65
-10.49 -2.07
-13.32 -5.53
-15.07 -5.54
-30.84 -8.31
-27.55 -9.07
-13.84 -4.36
-17.64 -9.18
-4.58 -0.51
-26.80 -8.31
-23.36 -8.89
-2.39 0.12
-5.50 0.18
-7.94 -1.83
-14.03 -6.20
-46.79 -15.77
S6
-3.72
-3.93
-4.64
-6.07
-7.55
-5.43
-8.97
-6.14
-5.80
-5.72
-6.94
-3.04
-5.22
-5.95
-2.74
-4.12
-4.63
-5.89
-6.52
EES ETOR
-2.58
-0.48
-1.02
-0.99
-0.88
-2.39
-0.58
-16.41
-12.69
-4.09
-1.52
-1.11
-13.43
-8.60
-0.51
-1.76
-1.63
-2.04
-24.58
0.01
0.01
0.03
0.01
0.00
0.02
0.02
0.02
0.01
0.33
0.00
0.08
0.15
0.08
0.74
0.20
0.14
0.10
0.08
Table SVI: Global minimum energies of terminally blocked peptides using the SCKS ASP
set. The amino end group is speci ed as N{Acetyl{amino; the carboxyl end group is speci ed
as Carboxyl{CONHCH3 . The total number of dihedral angles is indicated in the column
headed by # DA. The total energy, ETOT , is provided along with the contributions from
hydration, EHY D , nonbonded interactions (including hydrogen bonding), ENB , electrostatic
interactions, EES , and torsion, ETOR.
Residue # DA ETOT EHY D ENB
Gly
Ala
Cys
His
Phe
Ser
Trp
Asn
Asp
Thr
Tyr
Val
Gln
Glu
Ile
Leu
Met
Lys
Arg
6
7
7
8
8
8
8
9
9
9
9
9
10
10
10
10
10
11
13
EES ETOR
-0.50 5.82 -3.70 -2.62
2.01 7.18 -3.91 -1.27
-0.50 5.33 -4.66 -1.19
-1.07 7.29 -7.53 -0.86
1.69 10.11 -7.56 -0.87
-1.81 6.04 -5.39 -2.48
0.39 9.92 -8.98 -0.58
-18.37 4.57 -6.33 -16.63
-14.09 5.25 -6.49 -12.85
-2.36 7.22 -5.72 -4.18
0.07 8.54 -6.95 -1.53
4.51 8.65 -3.10 -1.13
-13.53 5.24 -5.38 -13.47
-9.27 5.93 -5.41 -9.87
6.81 9.34 -2.77 -0.51
3.99 9.69 -4.11 -1.80
1.75 8.65 -4.62 -2.38
-0.40 7.58 -5.90 -2.15
-26.07 5.26 -7.11 -24.33
S7
0.00
0.01
0.02
0.04
0.02
0.01
0.03
0.02
0.00
0.32
0.02
0.09
0.08
0.08
0.75
0.20
0.10
0.07
0.11
Table SVII: Global minimum energies of terminally blocked peptides using the JRF ASP set.
The amino end group is speci ed as N{Acetyl{amino; the carboxyl end group is speci ed
as Carboxyl{CONHCH3 . The total number of dihedral angles is indicated in the column
headed by # DA. The total energy, ETOT , is provided along with the contributions from
hydration, EHY D , nonbonded interactions (including hydrogen bonding), ENB , electrostatic
interactions, EES , and torsion, ETOR.
Residue # DA ETOT EHY D ENB
Gly
Ala
Cys
His
Phe
Ser
Trp
Asn
Asp
Thr
Tyr
Val
Gln
Glu
Ile
Leu
Met
Lys
Arg
6
7
7
8
8
8
8
9
9
9
9
9
10
10
10
10
10
11
13
EES ETOR
15.99 14.29 3.01 -1.54 0.23
29.71 24.81 2.36 -0.24 2.78
0.26 -4.22 2.51 -0.21 2.18
-50.22 -42.99 -6.87 -0.46 0.10
-83.47 -86.53 0.12 -0.82 3.76
-5.72 -9.62 2.68 -1.39 2.61
-105.88 -98.00 -7.91 0.03 0.00
-20.76 -20.86 8.13 -16.55 8.52
-41.14 -31.91 2.31 -12.95 1.41
6.56
2.82 0.31 -2.16 5.59
-102.43 -105.52 1.02 -1.43 3.50
46.54 39.84 2.53 -0.86 5.03
-13.89 -6.55 1.93 -12.69 3.42
-33.55 -19.61 -5.18 -8.93 0.17
53.61 56.15 -2.80 -0.52 0.78
47.62 29.61 8.37 -0.54 10.18
26.33 21.35 2.10 -1.61 4.49
26.65 22.85 0.40 -1.45 4.85
-34.88 -4.57 -6.12 -24.39 0.20
S8
Table SVIII: Local minimum energies of terminally blocked peptides using the JRF ASP set
with constrained ! bounds [160,200]. The amino end group is speci ed as N{Acetyl{amino;
the carboxyl end group is speci ed as Carboxyl{CONHCH3 . The total number of dihedral
angles is indicated in the column headed by # DA. The total energy, ETOT , is provided along
with the contributions from hydration, EHY D , nonbonded interactions (including hydrogen
bonding), ENB , electrostatic interactions, EES , and torsion, ETOR .
Residue # DA ETOT EHY D ENB
Ala
Cys
Ser
Asn
Asp
Val
Gln
Leu
Met
Lys
7
7
8
9
9
9
10
10
10
11
32.97
2.34
-4.75
-19.13
-39.35
46.71
-13.51
49.68
27.04
26.96
37.44
7.27
-11.02
3.43
-20.76
50.62
4.20
41.57
32.32
33.71
S9
EES ETOR
-4.00 -0.47
-5.17 0.24
0.69 -0.28
-6.13 -16.43
-6.13 -12.47
-3.26 -0.77
-5.17 -12.74
1.58 -0.66
-4.41 -1.65
-5.51 -1.34
0.00
0.00
5.86
0.00
0.01
0.12
0.20
7.19
0.78
0.10
Table SIX: Comparison of unsolvated components for all accessible area based ASP set global
minima and the RRIGS global minima (of terminally blocked peptides). EPOT = EPOT
ASP POT
ERRIGS at corresponding global minima, for the ASP set as listed.
Residue WE1 WE2 OONS SCKS JRF
Gly
0.07 0.06
0.04 0.00 8.02
Ala
0.79 0.78
0.77 0.00 0.71
Cys
1.22 1.20
0.21 0.01 0.91
His
1.31 1.25
1.85 0.55 1.67
Phe
0.04 0.04 -0.26 -0.25 11.23
Ser
2.64 2.56
0.06 0.00 14.13
Trp
0.04 0.03
0.02 0.02 1.67
Asn
0.10 0.10
0.06 -0.35 0.04
Asp
0.55 0.52
0.55 -0.32 0.44
Thr
0.32 0.25
0.11 0.01 13.32
Tyr
1.42 0.03 -0.24 -0.25 11.30
Val
0.55 0.50
0.11 0.04 0.27
Gln
1.23 0.53
0.29 0.01 1.07
Glu
1.39 1.37
0.71 -0.02 1.24
Ile
0.04 0.03
0.03 0.01 0.00
Leu
1.00 0.99
0.02 -0.01 13.80
Met
0.79 0.78
0.79 0.01 1.63
Lys
1.48 1.43
0.15 0.01 1.23
Arg
0.52 0.50
0.44 0.13 1.15
S10
Table SX: Comparison of unsolvated components for all accessible area based ASP set global
D
minima and the RRIGS global minima (of terminally blocked peptides). EHY D = EHY
ASP D
EHY
RRIGS at corresponding global minima, for the ASP set as listed.
Residue
Gly
Ala
Cys
His
Phe
Ser
Trp
Asn
Asp
Thr
Tyr
Val
Gln
Glu
Ile
Leu
Met
Lys
Arg
WE1
9.46
9.05
9.48
14.05
12.17
9.23
14.89
10.44
6.72
12.25
13.24
9.48
10.35
5.84
10.26
9.31
10.53
7.11
11.87
WE2 OONS SCKS JRF
7.94 14.90 21.96 30.43
7.31 14.46 22.82 53.08
8.13 15.06 23.00 24.94
12.25 16.92 32.86 -17.42
9.59 14.48 26.66 -69.98
7.89 14.93 26.51 9.45
12.33 16.39 31.85 -76.07
9.21 18.16 31.04 29.90
5.41 11.87 26.19 0.17
10.45 15.23 26.81 22.42
10.54 12.72 30.44 -83.62
7.37 14.23 23.39 65.36
9.82 19.40 32.95 31.90
4.37 12.03 26.85 1.32
7.88 14.69 23.91 70.72
6.95 14.71 24.22 56.10
8.43 15.20 25.68 49.34
5.27 13.97 27.75 53.88
10.40 16.61 37.64 27.80
S11
Table SXI: Approximate dihedral angles and nomenclature for { regions.
Conformer
C5
PII
C7
R
,
-150, 150
-80, 150
-80, 80
-80, -50
Protein structure
{sheet
polyproline II
{turn
{helix (right)
Table SXII: Distribution of global minima for terminally blocked amino acids using solvation
model listed in rst column.
Model C5 P
RRIGS
WE1
WE2
OONS
SCKS
JRF
5
13
13
6
6
9
II
0
1
1
2
0
2
C7
14
2
2
8
11
0
R Other
0
2
2
2
2
7
0
1
1
1
0
1
Table SXIII: Dihedral angles at the global minimum energy conformation of unsolvated
leu{enkephalin.
Tyr
Gly
Gly
Phe
Leu
-163.07
65.90
-150.83
-158.73
-77.83
-42.29
-88.33
31.94
157.23
123.31
!
1
2
3
4
182.31 -174.79 90.16 -177.26
174.19
181.29
178.02 53.24 84.40
181.31 -179.81 64.47 172.58 179.43
S12
Table SXIV: Dihedral angles at the global minimum energy conformation of leu{enkephalin,
using the RRIGS model for hydration.
Tyr
Gly
Gly
Phe
Leu
-168.37
78.92
163.21
-150.66
-75.45
-30.66
-87.17
91.51
161.54
105.32
!
1
2
3
4
178.49 -173.40 78.69 -161.13
-177.32
172.72
-178.44 66.75 -86.84
-178.26 179.51 63.84 172.22 179.31
Table SXV: Dihedral angles at the global minimum energy conformation of leu{enkephalin,
using the WE1 model for hydration.
Tyr
Gly
Gly
Phe
Leu
-162.77
66.15
-152.77
-158.33
-86.58
-43.63
-86.15
32.53
156.18
124.93
!
1
2
3
4
-177.55 -174.64 88.60 182.98
173.14
181.90
179.06 51.73 83.41
-179.00 182.65 69.00 54.85 -59.77
Table SXVI: Dihedral angles at the global minimum energy conformation of leu{enkephalin,
using the WE2 model for hydration.
Tyr
Gly
Gly
Phe
Leu
-162.81
66.15
-152.91
-158.47
-86.17
-43.49
-86.18
32.54
156.24
125.26
!
1
2
3
4
-177.59 -174.74 88.48 182.98
173.23
181.81
179.03 51.81 83.50
-178.99 182.37 68.61 54.60 -59.84
S13
Table SXVII: Dihedral angles at the global minimum energy conformation of leu{enkephalin,
using the OONS model for hydration.
Tyr
Gly
Gly
Phe
Leu
-166.40
63.68
-152.32
-159.65
-84.06
-51.73
-85.81
33.95
153.94
148.49
!
1
2
3
4
-175.64 -189.82 75.41 182.41
175.24
181.27
-180.61 51.12 83.54
-179.04 -63.09 160.85 59.05 62.99
Table SXVIII: Dihedral angles at the global minimum energy conformation of leu{enkephalin,
using the SCKS model for hydration.
Tyr
Gly
Gly
Phe
Leu
-162.84
65.94
-150.11
-157.73
-80.71
-43.09
-88.13
31.76
156.45
123.90
!
1
2
3
4
182.46 -174.41 -89.51 2.80
173.67
181.73
178.12 53.21 83.97
181.21 -178.83 65.57 -186.90 -180.38
Table SXIX: Dihedral angles at the global minimum energy conformation of leu{enkephalin,
using the JRF model for hydration.
Tyr
Gly
Gly
Phe
Leu
-84.88
-160.78
144.15
-79.95
-83.98
160.00
140.99
-152.83
71.30
138.62
!
1
2
3
4
178.30 -60.54 100.49 -179.22
-178.01
177.03
-176.06 -60.97 108.26
-179.24 -53.91 176.56 -178.84 69.81
S14
Table SXX: Comparison of hydration energies for leu{enkephalin. The rst column refers
to the hydration model used in the function evaluations, which are performed at the global
solutions for the hydration model listed in the second column. The total energy, ETOT , is
provided along with the contributions from hydration, EHY D , nonbonded interactions (including hydrogen bonding), ENB , electrostatic interactions, EES , and torsion, ETOR. The last
column provides the heavy atom root mean squared deviation between the global minimum
energy structures of the hydration models listed in the rst two columns.
Global of ETOT EHY D ENB
RRIGS RRIGS
WE1
WE2
OONS
SCKS
JRF
WE1 RRIGS
WE1
WE2
OONS
SCKS
JRF
WE2 RRIGS
WE1
WE2
OONS
SCKS
JRF
-46.56
-44.70
-44.75
-43.14
-44.79
-39.10
-24.51
-28.37
-28.36
-26.58
-28.19
-18.76
-28.00
-31.49
-31.50
-29.74
-31.33
-22.35
-39.00
-35.68
-35.69
-35.58
-35.50
-44.27
-16.94
-19.35
-19.31
-19.03
-18.90
-23.92
-20.44
-22.47
-22.44
-22.19
-22.04
-27.51
S15
22.31
22.66
22.67
22.75
22.67
23.77
22.31
22.66
22.67
22.75
22.67
23.77
22.31
22.66
22.67
22.75
22.67
23.77
EES ETOR (RMSD)
-30.95
-32.43
-32.45
-31.55
-32.58
-19.07
-30.95
-32.43
-32.45
-31.55
-32.58
-19.07
-30.95
-32.43
-32.45
-31.55
-32.58
-19.07
1.07
0.75
0.72
1.25
0.62
0.46
1.07
0.75
0.72
1.25
0.62
0.46
1.07
0.75
0.72
1.25
0.62
0.46
0.00
2.56
2.55
2.66
2.60
4.64
2.56
0.00
0.01
0.86
0.77
3.98
2.55
0.01
0.00
0.86
0.77
3.97
Table SXXI: Comparison of hydration energies for leu{enkephalin. The rst column refers
to the hydration model used in the function evaluations, which are performed at the global
solutions for the hydration model listed in the second column. The total energy, ETOT , is
provided along with the contributions from hydration, EHY D , nonbonded interactions (including hydrogen bonding), ENB , electrostatic interactions, EES , and torsion, ETOR. The last
column provides the heavy atom root mean squared deviation between the global minimum
energy structures of the hydration models listed in the rst two columns.
Global of ETOT
OONS RRIGS
WE1
WE2
OONS
SCKS
JRF
SCKS RRIGS
WE1
WE2
OONS
SCKS
JRF
JRF RRIGS
WE1
WE2
OONS
SCKS
JRF
-21.63
-28.61
-28.62
-28.77
-28.37
-19.23
5.57
2.54
2.53
4.15
2.36
18.35
-112.59
-152.64
-152.61
-158.44
-149.29
-263.14
EHY D ENB
-14.06
-19.59
-19.56
-21.21
-19.08
-24.39
13.14
11.56
11.58
11.71
11.65
13.19
-105.02
-143.62
-143.56
-150.88
-140.00
-268.31
S16
22.31
22.66
22.67
22.75
22.67
23.77
22.31
22.66
22.67
22.75
22.67
23.77
22.31
22.66
22.67
22.75
22.67
23.77
EES ETOR (RMSD)
-30.95
-32.43
-32.45
-31.55
-32.58
-19.07
-30.95
-32.43
-32.45
-31.55
-32.58
-19.07
-30.95
-32.43
-32.45
-31.55
-32.58
-19.07
1.07
0.75
0.72
1.25
0.62
0.46
1.07
0.75
0.72
1.25
0.62
0.46
1.07
0.75
0.72
1.25
0.62
0.46
2.66
0.86
0.86
0.00
1.14
3.90
2.60
0.77
0.77
1.14
0.00
4.06
4.64
3.98
3.97
3.90
4.06
0.00
List of gures
Figure S1: Adiabatic { map for unsolvated N{acetyl{N'{methyl{alanineamide. The adiabatic curves de ne regions within a given energy (1, 2, 5, 9 kcal/mole) of the global minimum
value, and the (*) represents the location of the global minimum.
Figure S2: Adiabatic { map for solvated N{acetyl{N'{methyl{alanineamide, using the
RRIGS solvation model. The adiabatic curves de ne regions within a given energy (1, 2, 5,
9 kcal/mole) of the global minimum value, and the (*) represents the location of the global
minimum.
Figure S3: Adiabatic { map for solvated N{acetyl{N'{methyl{alanineamide, using the
WE1 ASP set. The adiabatic curves de ne regions within a given energy (1, 2, 5, 9 kcal/mole)
of the global minimum value, and the (*) represents the location of the global minimum.
Figure S4: Adiabatic { map for solvated N{acetyl{N'{methyl{alanineamide, using the
WE2 ASP set. The adiabatic curves de ne regions within a given energy (1, 2, 5, 9 kcal/mole)
of the global minimum value, and the (*) represents the location of the global minimum.
Figure S5: Adiabatic { map for solvated N{acetyl{N'{methyl{alanineamide, using the
OONS ASP. The adiabatic curves de ne regions within a given energy (1, 2, 5, 9 kcal/mole)
of the global minimum value, and the (*) represents the location of the global minimum.
Figure S6: Adiabatic { map for solvated N{acetyl{N'{methyl{alanineamide, using the
SCKS ASP set. The adiabatic curves de ne regions within a given energy (1, 2, 5, 9
kcal/mole) of the global minimum value, and the (*) represents the location of the global
minimum.
Figure S7: Adiabatic { map for solvated N{acetyl{N'{methyl{alanineamide, using the
JRF ASP set. The adiabatic curves de ne regions within a given energy (1, 2, 5, 9 kcal/mole)
of the global minimum value, and the (*) represents the location of the global minimum.
Figure S8: Plot of met{enkephalin conformation. Global minimum energy of -33.27 kcal/mole
using the WE2 model for hydration.
Figure S9: Plot of met{enkephalin conformation. Global minimum energy of -31.45 kcal/mole
using the OONS model for hydration.
S17
Figure S10: Plot of unsolvated leu{enkephalin conformation. Global minimum energy of
-9.349 kcal/mole.
Figure S11: Plot of leu{enkephalin conformation. Global minimum energy of -46.57 kcal/mole
using the RRIGS model for hydration.
Figure S12: Plot of leu{enkephalin conformation. Global minimum energy of -28.37 kcal/mole
using the WE1 model for hydration.
Figure S13: Plot of leu{enkephalin conformation. Global minimum energy of -31.50 kcal/mole
using the WE2 model for hydration.
Figure S14: Plot of leu{enkephalin conformation. Global minimum energy of -28.77 kcal/mole
using the OONS model for hydration.
Figure S15: Plot of leu{enkephalin conformation. Global minimum energy of 2.35 kcal/mole
using the SCKS model for hydration.
Figure S16: Plot of leu{enkephalin conformation. Global minimum energy of -263.14 kcal/mole
using the JRF model for hydration.
S18
150
1
1 2 5 9
100
9 5
*
5 9
50
0ψ
2
5
9
1
2
9 5
9
9
-100
9
5
-150
-100
9
-50
0
50
φ
Figure S1:
S19
-50
100
150
-150
150
1
1 2 5 9
95
*
50
5 9
1
100
0ψ
2
5
9
1
9 5
9
-100
9
9
5
2
-150
9
9
-100
-50
0
50
φ
Figure S2:
S20
-50
100
150
-150
150
*
1 2 5 9
9 5
100
50
5 9
0ψ
2
9
5
2
1
9 5
9
-100
9
9
9
5
9
2
-150
-100
-50
0
50
φ
Figure S3:
S21
-50
100
150
-150
150
*
9 5
1 2 5 9
100
50
5 9
0ψ
2
9
5
1
-50
2
9 5
9
-100
9
9
9
2
-150
5
9
-100
-50
0
50
φ
Figure S4:
S22
100
150
-150
5
150
*
9 5
12 5 9
100
50
2 5 9
0ψ
2
5
9
2
1
9 5
-50
9
-100
9
9
2
-150
5
5
-100
-50
0
50
φ
Figure S5:
S23
9
100
150
-150
150
1 2 5 9
1
95
100
*
50
2 5 9
0ψ
9
2 5
1
9 5
-50
9
-100
9
9
2
-150
5
5
-100
-50
0
50
φ
Figure S6:
S24
9
100
150
-150
150
*
9 5
1 2
5 9
100
50
9
0ψ
9
2
5
-50
9 5
-100
9
5
-150
9
-100
-50
0
50
φ
Figure S7:
S25
100
150
-150
Figure S8:
S26
Figure S9:
S27
Figure S10:
S28
Figure S11:
S29
Figure S12:
S30
Figure S13:
S31
Figure S14:
S32
Figure S15:
S33
Figure S16:
S34