sqrt pk - sci.ccny.cuny.edugunner/pages-lab/papers/bj02-rox-sup.pdf8/14/02 georgescu, alexov, and...

8/14/02 Georgescu, A

lexov, and Gunner Supplem

entary Material Pg 1

Com

bining Conform

ational Flexibility and C

ontinuum E

lectrostatics for Calculating pK

a 's in Proteins

R.E

. Georgescu, E

.G. A

lexov, and M.R

. Gunner

Supplementary m

aterial: Biophysical Journal O

ct. 2002

SM I-X

: Experim

ental and calculated pKa 's for residues w

ith measured p

Ka 's. R

esidue name is underlined if it has electrostatic interactions w

ith

another residue of more than –3 ∆

pK units (–4.08 kcal/m

ol). If the residue name is in bold the ionized form

has lost more than 3 ∆

pK units of

reaction field energy (∆∆

Grxn >

4.08 kcal/mol). O

nly the initial heavy atom conform

er in the starred protein data file is used to determine if a

residue is in either category.

Expt: E

xperimental p

Ka 's: ±: R

eported error of experimental m

easurements; n: reported H

ill coefficient value (underlined, if the n values

were explicitly reported otherw

ise n was estim

ated from the shape of published titration curves).

The colum

ns headed by protein data file name contains the calculated p

Ka 's. E

rr: Difference betw

een calculated and experimental value.

Absolute errors greater than 1 pH

unit in bold while those greater than 2 pH

units are also underlined. #: SCC

E: Single C

onformation C

ontinuum

Electrostatics. A

ll other calculations obtained with M

CC

E. *:R

epresentative calculation for this protein. §: Calculations using N

MR

structures.

All other coordinates obtained by x-ray crystallography. For the N

MR

structures the pK

a is the average value for the ensemble of structures;

RM

SV: R

oot-mean-square-variation of pK

a 's calculated for a given residue (J) in the group of n structures is sqrt( 1npK

av-

pKJ

() 2

J=1 nÂ

) . All

calculations carried out with 0.15 M

ionic strength and eprot =4 except for ¶ w

here eprot =8 and || w

here eprot =20. R

MS: root-m

ean-square error of

computed p

Ka 's for a given protein data file is sqrt( 1N

pKexp -

pKcalc

() 2

i=1 NÂ) w

here N is the num

ber of residues with know

n pK

a 's; Conf:

Num

ber of conformers in the calculation. Several proteins have ions that influence residue pK

a 's. +: Ion included; –: no ion.




SM I. B

acillus amyloliquefaciens barnase.

X-ray structures: 1A

2P (Martin et al., 1999) and 1B

20 (Buckle et al., 1993) and 20 N

MR

structures in 1BN

R (B

ycroft et al., 1991). Experim

entalp

Ka 's (O

liveberg et al., 1995). The pK

a of His18 (L

oewenthal et al., 1993)

Ex

pt

±n

#1A2P

#Err

*1A2P

*Err

1B20

Err

§1BN

R§E

rr§R

MSV

¶1A2P

¶Err

||1A2P

||Err

Asp

83.06

0.10.9

1.1-2.0

1.4-1.7

1.7-1.4

2.0-1.0

1.23.4

0.33.7

0.6A

sp1

23.65

0.10.9

2.6-1.1

3.70.0

3.6-0.1

3.80.2

0.83.4

-0.23.7

0.1A

sp2

23.30

0.10.9

2.5-0.8

2.7-0.6

3.70.4

3.70.4

0.63.5

0.23.7

0.4A

sp4

43.50

0.10.9

4.10.6

4.00.5

3.90.4

3.90.4

0.54.3

0.84.5

1.0A

sp5

4 2.2

0.30.9

-1.1-3.3

2.30.1

2.80.6

1.8-0.4

2.61.3

-1.02.5

0.4A

sp7

53.10

0.2\

3.90.8

4.51.4

4.81.7

4.61.5

2.31.4

-1.81.5

-1.6A

sp8

64.20

0.10.8

5.21.0

4.90.6

4.80.6

5.91.7

1.84.9

0.74.1

-0.1A

sp9

3 2

0.3\

-1.1-3.1

1.4-0.6

2.70.7

1.6-0.4

0.82.4

0.43.3

1.3A

sp1

01

2.000.2

1.0-0.9

-2.93.2

1.23.3

1.33.0

1.01.3

2.60.6

3.51.5

Ctr

1103.30

0.10.9

-0.4-3.7

2.7-0.7

1.9-1.4

3.40.1

1.62.0

-1.31.8

-1.5G

lu2

93.75

0.050.8

1.4-2.4

2.6-1.2

2.3-1.5

4.50.8

0.84.1

0.44.3

0.5G

lu6

03.20

0.10.9

4.10.9

1.8-1.4

2.9-0.3

3.60.4

1.33.1

-0.13.4

0.2G

lu7

32.1

0.11.2

-1.0-3.1

0.6-1.5

-0.8-2.9

3.61.5

3.20.6

-1.52.5

0.4H

is1

87.72

0.051.0

7.0-0.7

6.6-1.1

7.0-0.8

6.8-0.9

0.16.6

-1.16.6

-1.2R

MS

2.111.04

1.260.94

1.630.91

0.89C

onf9

65

26

48

02

91

45

02

99




SM II. B

ovine Pancreatic T

rypsin Inhibitor . X

-ray structures: 4PTI (M

arquart et al., 1983) and 20 NM

R structures in 1PIT

(Berndt et al., 1992). E

xperimental pK

a 's (Brow

n et al., 1976;M

arch et al., 1982)

Expt.

Err.

n#

4P

TI

#Err.

*4

PT

IE

rr§1P

IT§E

rr§R

MSV

¶4P

TI

¶Err

||4PT

I||E

rrA

sp3

3.550.1

\3.8

0.33.9

0.43.7

0.10.3

4.00.5

4.30.7

Asp

50

3.200.0

\3.4

0.22.3

-0.92.6

-0.61.0

2.9-0.3

3.0-0.2

Ctr

58

3.100.3

0.93.4

0.33.7

0.62.7

-0.40.5

3.80.7

3.80.7

Glu

73.85

0.10.8

5.61.7

2.6-1.3

3.1-0.7

1.44.5

0.64.1

0.2G

lu4

93.91

0.1\

3.2-0.7

3.90.0

3.5-0.4

1.14.4

0.54.4

0.5L

ys1

510.43

0.1\

10.90.5

10.90.5

10.4-0.1

0.411.0

0.510.8

0.4L

ys2

610.44

0.1\

10.50.1

10.60.2

10.60.1

0.410.8

0.310.7

0.3L

ys4

110.75

0.1\

12.11.4

11.60.8

11.20.5

1.011.4

0.611.3

0.5L

ys4

610.35

0.2\

10.60.2

10.3-0.0

10.2-0.2

0.610.4

0.110.3

-0.0N

tr1

7.900.2

1.06.5

-1.47.7

-0.28.3

0.40.8

7.8-0.1

7.9-0.0

Ty

r1

09.46

0.00.7

9.0-0.4

9.4-0.0

9.70.3

1.69.4

-0.19.9

0.4T

yr

21

9.940.0

0.810.1

0.210.3

0.410.6

0.60.7

10.20.3

10.40.5

Tyr

23

110.1

\12.0

1.012.1

1.110.6

-0.41.5

11.00.0

10.8-0.2

Tyr

35

10.600.1

0.810.5

-0.110.0

-0.612.4

1.83.9

9.7-0.9

10.4-0.2

RM

S0.80

0.640.62

1.400.47

0.41C

onf5

31

87

14

01

38

13

1




SM-III. Intestinal B

ovine Calcium

-Binding P

rotein (CabD

).X

-ray structure: 3ICB

(Szebenyi and Moffat, 1986) and the 24 N

MR

structures in 1CD

N (A

kke et al., 1995) have calcium bound (holo-enzym

e).T

he 33 NM

R structures in 1C

LB

(Skelton et al., 1995) do not (apo-form). E

xperimental pK

a 's (Kesvatera et al., 1996; 1999). T

he reported errorof experim

ental pKa values is less than 0.08.

pKa

pKa

n3IC

BE

rr*3IC

BE

rr§1C

DN

§Err

§RM

SV§1C

LB

§Err

§RM

SV¶3IC

B¶E

rr||3IC

B||E

rrC

a+

2+

–+

++

–+

+A

sp4

73.00

0.72.9

-0.10.7

Ctr

75

3.201.1

4.61.4

1.8G

lu4

3.800.8

3.5-0.3

0.7G

lu5

3.400.8

3.1-0.3

1.2G

lu1

14.70

0.74.9

0.20.8

Glu

17

3.620.6

4.10.5

2.9G

lu2

64.10

0.92.7

-1.41.8

Glu

48

4.600.6

4.4-0.2

0.9G

lu6

43.80

0.84.3

0.50.7

Lys

110.60

10.600.7

11.00.4

10.80.2

11.30.7

1.39.7

-0.92.2

11.50.9

11.81.2

Lys

711.35

11.390.9

10.9-0.4

10.7-0.7

11.50.2

1.010.9

-0.51.0

11.40.1

11.80.5

Lys

12

10.8211.06

0.710.9

0.110.8

-0.011.2

0.30.5

10.9-0.1

0.511.3

0.411.8

0.9L

ys1

610.09

10.070.7

11.11.0

10.60.5

10.10.0

2.211.2

1.12.2

11.00.9

11.51.4

Lys

25

11.8111.69

0.913.3

1.413.4

1.512.2

0.40.9

11.5-0.1

0.712.7

0.912.7

0.9L

ys2

910.97

11.370.8

9.5-1.5

10.4-0.5

10.5-0.4

1.310.2

-1.21.6

11.00.0

11.30.3

Lys

41

10.8910.93

0.810.9

0.010.9

0.010.8

-0.10.9

10.6-0.3

0.910.9

0.011.0

0.1L

ys5

511.38

12.120.9

10.2-1.2

11.60.2

12.41.0

1.111.7

-0.40.8

11.3-0.0

12.20.9

Lys

71

10.7210.73

0.810.1

-0.69.9

-0.811.1

0.40.7

10.2-0.5

1.310.4

-0.310.7

0.0L

ys7

210.96

11.330.8

10.8-0.2

10.5-0.5

11.20.2

0.910.7

-0.71.3

10.9-0.0

11.30.3

RM

S0.87

0.660.47

1.170.71

1.270.38

0.59C

onf7

22

73

33

62

37

17

51

46




SM-V

I. Rat T

-Lym

phocyte Adhesion G

lycoprotein (CD

2).X

-ray structure 1HN

G (Jones et al., 1992)

Ex

pt

±n

#1HN

G#E

rr*1H

NG

*Err

¶1HN

G¶E

rr||1H

NG

||Err

Asp

23.50

0.020.9

3.1-0.4

3.0-0.5

3.4-0.1

3.80.3

Asp

25

3.530.02

0.93.8

0.33.9

0.44.2

0.64.4

0.8A

sp2

63.58

0.030.9

3.90.4

4.10.5

4.20.7

4.50.9

Asp

28

3.570.06

0.81.5

-2.11.9

-1.72.8

-0.83.0

-0.6A

sp6

24.18

0.030.8

6.52.4

5.81.6

5.21.0

4.80.6

Asp

71

3.200.10

0.83.8

0.63.8

0.63.9

0.74.4

1.2A

sp7

24.14

0.050.8

4.40.2

4.80.7

5.00.9

3.9-0.2

Asp

94

3.830.04

0.83.0

-0.83.4

-0.43.9

0.13.6

-0.2C

tr9

93.11

0.050.8

-1.0-4.1

3.80.7

3.80.7

3.90.8

Glu

29

4.510.10

0.61.8

-2.74.8

0.33.0

-1.53.7

-0.9G

lu3

34.20

0.040.8

4.70.5

4.50.3

4.50.3

4.30.1

Glu

41

6.530.10

0.57.5

0.95.8

-0.75.3

-1.25.0

-1.5G

lu5

63.95

0.020.8

3.9-0.0

4.00.0

4.00.1

3.9-0.0

Glu

99

4.100.05

0.84.6

0.54.0

-0.14.0

-0.13.9

-0.2R

MS

1.620.77

0.760.73

Conf

15

43

98

30

92

85




SM-V

. Hen E

gg-White L

ysozyme (H

EW

L).

X-ray structures: 1B

0D (V

aney et al., 1996); 2LZ

T (R

amanadham

et al., 1981), 1HE

L (W

ilson et al., 1992). NM

R structure 1E

8L (Schw

albe etal., 2001). E

xperimental data (K

uramitsu and H

amaguchi, 1980; B

artik et al., 1994). SCC

E colum

ns show only errors of calculated p

Ka 's for

2LZ

T and 1B

0D.

Ex

pt

±n

#2

LZ

Terr

#1BO

Derr.

*1BO

DE

rr2

LZ

TE

rr2H

EL

Err

§1E8L

§Err

§RM

SV¶2L

ZT

¶Err

||2LZ

T||E

rr

Asp

18

2.660.1

0.8-0.1

0.33.0

0.42.8

0.22.2

-0.53.6

0.90.5

3.61.0

3.50.8

Asp

48

1.600.4

\-0.7

2.10.6

-1.01.7

0.1-0.2

-1.83.2

1.60.2

2.61.0

4.12.5

Asp

52

3.680.1

0.8-3.4

-4.13.9

0.23.0

-0.74.6

0.93.8

0.12.5

4.50.9

3.5-0.2

Asp

66

0.900.5

\1.9

1.91.5

0.62.6

1.71.8

0.92.7

1.80.8

1.40.5

1.91.0

Asp

87

2.070.2

\0.7

3.11.0

-1.11.2

-0.91.2

-0.91.7

-0.30.3

2.70.6

3.51.5

Asp

10

14.08

0.1\

-4.70.5

3.8-0.3

5.11.0

4.30.2

4.10.0

0.24.2

0.14.1

0.1A

sp1

19

3.200.1

\-0.1

-0.34.1

0.92.4

-0.83.8

0.63.3

0.10.4

4.41.2

3.70.5

Ctr

12

92.75

0.1\

-3.80.8

2.4-0.4

2.6-0.1

3.00.2

2.5-0.3

0.62.5

-0.23.0

0.2G

lu7

2.850.3

\1.0

2.43.5

0.62.2

-0.62.2

-0.63.3

0.50.2

3.10.2

3.50.7

Glu

35

6.200.1

\0.8

1.36.2

0.06.2

-0.06.6

0.46.8

0.66.8

5.7-0.5

4.8-1.4

His

15

5.360.1

\-1.5

-1.86.5

1.16.4

1.06.8

1.55.8

0.50.3

5.70.3

5.50.1

Lys

110.80

0.1\

0.8-1.7

10.3-0.5

9.8-1.0

10.2-0.6

10.3-0.5

1.012.1

1.310.3

-0.5L

ys1

310.50

0.1\

3.8-0.9

11.20.7

10.80.3

10.70.2

10.90.4

0.411.2

0.711.2

0.7L

ys3

310.40

0.1\

1.91.3

9.8-0.6

8.9-1.5

9.5-0.9

9.1-1.3

1.410.3

-0.110.2

-0.2L

ys9

610.80

0.1\

0.7-1.4

11.30.5

11.91.1

11.81.0

10.80.0

0.812.2

1.411.5

0.7L

ys9

710.30

0.1\

1.0-0.6

10.50.2

11.10.8

10.80.5

10.60.3

0.710.8

0.511.4

1.1L

ys1

16

10.200.1

\0.2

1.510.0

-0.29.5

-0.79.4

-0.89.8

-0.40.7

10.50.3

10.40.2

Ty

r2

010.30

0.1\

-1.81.3

9.7-0.6

11.10.8

9.6-0.7

9.7-0.6

1.09.5

-0.810.4

0.1T

yr

23

9.800.1

\-0.8

0.59.3

-0.59.3

-0.59.7

-0.19.3

-0.50.7

9.6-0.2

9.90.1

RM

S2.05

1.740.63

0.860.81

0.731.77

0.740.90

Conf

10

44

51

46

64

43

25

33

31

28

8




SM- V

I. Third dom

ain of the turkey ovomucoid inhibitor (O

MT

KY

3).X

-ray structures: 1PPF (Bode et al., 1986), 1C

HO

(Fujinaga et al., 1987) and 3SGB

(Read et al., 1983). T

he 50 NM

R structures in 1O

MU

(Hoogstraten et al., 1995). E

xperimental data (Schaller and R

oberston, 1995; Forsyth et al., 1998)

Ex

pt

±n

#1PP

F#E

rr*1P

PF

Err

1CH

OE

rr3SG

BE

rr§1O

MU

§Err

§RM

SV¶1P

PF

¶Err

||1PP

F||E

rrA

sp7

2.70.1

0.70.4

-2.32.8

0.14.2

1.52.7

-0.02.9

0.30.5

4.01.3

5.02.3

Asp

27

2.30.1

0.93.9

1.63.3

0.92.7

0.42.3

0.03.2

0.90.5

4.01.7

3.61.3

Ctr

56

2.20.2

0.92.7

0.53.2

0.93.2

0.93.2

0.93.3

1.10.9

3.21.0

3.31.1

Glu

10

4.10.2

0.93.7

-0.43.5

-0.63.9

-0.24.2

0.13.7

-0.40.6

3.7-0.4

3.8-0.3

Glu

19

3.20.0

1.1-0.3

-3.51.6

-1.62.9

-0.32.7

-0.52.7

-0.50.6

3.90.7

4.31.1

Glu

43

4.80.2

1.04.6

-0.24.5

-0.34.6

-0.24.6

-0.24.8

-0.00.1

4.6-0.2

4.90.1

His

52

7.5\

0.98.5

1.08.2

0.78.6

1.18.5

1.07.1

-0.40.7

7.5-0.0

6.9-0.6

Lys

13

9.90.0

0.714.3

4.411.5

1.610.1

0.210.0

0.111.2

1.31.6

11.41.5

12.02.1

Lys

29

11.10.1

0.911.7

0.611.2

0.110.9

-0.210.8

-0.310.4

-0.71.1

11.40.3

11.30.2

Lys

34

10.10.1

0.712.4

2.37.2

-2.98.8

-1.310.1

0.07.6

-2.51.3

12.62.5

12.01.9

Lys

55

11.10.1

0.610.3

-0.810.2

-0.910.8

-0.311.7

0.610.8

-0.30.6

10.7-0.4

10.9-0.2

Ntr

18.0

0.00.9

5.9-2.0

7.3-0.7

7.3-0.7

8.40.4

0.57.4

-0.57.6

-0.4T

yr1

110.2

0.10.7

8.9-1.3

11.81.6

13.73.5

14.64.4

12.72.5

1.510.3

0.110.5

0.3T

yr

20

11.10.2

0.69.8

-1.310.1

-1.010.8

-0.39.4

-1.710.6

-0.50.7

9.8-1.3

10.1-1.0

Tyr

31

12.5\

\15.0

3.012.2

-0.314.4

1.913.0

0.512.5

0.00.3

11.4-1.1

13.91.5

RM

S2.06

1.191.24

1.341.10

0.871.10

1.19C

onf5

12

13

21

91

67

16

41

54

12

2




SM-V

II. B1 im

munoglobulin-binding dom

ain of streptococcal protein G.

X-ray structures 1PG

A (G

allagher et al., 1994), 60 NM

R structures in 1G

BL

(Gronenborn et al., 1991). E

xperimental pK

a 's (Khare et al., 1997).

Estim

ated n-values are all in the range 0.9 - 1.

Ex

pt

±#1P

GA

#Err

*1PG

A*E

rr§1G

BL

§Err

§RM

SV1P

GA

Err

||1PGA

||Err

Asp

22

2.90.1

0.5-2.4

2.2-0.7

2.6-0.3

1.03.1

0.23.7

0.8A

sp3

63.8

0.15.3

1.55.0

1.24.7

0.90.7

5.21.4

5.01.2

Asp

40

4.00.2

4.50.5

4.10.1

5.41.4

0.94.7

0.75.0

1.0A

sp4

63.6

0.11.6

-2.03.1

-0.53.7

0.10.3

4.20.6

4.40.8

Asp

47

3.40.3

0.3-3.2

2.3-1.1

4.41.0

0.23.0

-0.43.2

-0.2C

tr5

64.0

0.13.0

-1.03.3

-0.74.3

0.30.9

3.5-0.5

3.7-0.4

Glu

56

4.00.1

3.9-0.1

5.31.3

6.82.8

0.84.9

0.94.7

0.7G

lu1

54.4

0.11.7

-2.73.8

-0.64.3

-0.10.6

3.8-0.6

4.1-0.3

Glu

19

3.70.2

2.7-1.0

3.5-0.2

4.20.5

0.23.9

0.24.0

0.3G

lu2

74.5

0.1-0.5

-5.03.8

-0.74.5

0.00.2

3.9-0.6

3.3-1.2

Glu

42

4.40.1

5.00.6

5.10.7

5.00.6

0.55.0

0.65.2

0.8L

ys1

011.0

\11.9

0.911.4

0.411.1

0.10.4

11.20.2

11.50.5

Lys

13

11.0\

11.0-0.0

10.8-0.2

10.8-0.2

0.611.0

-0.011.5

0.5L

ys2

810.9

\13.4

2.511.7

0.810.2

-0.70.7

11.80.9

12.01.1

Tyr

33

11.0\

10.7-0.3

10.8-0.2

10.3-0.7

0.210.5

-0.510.9

-0.1R

MS

2.130.67

0.650.60

0.630.75

Conf

55

24

02

02

14

31

07




SM-V

III Ribonuclease A

(RN

ase A).

X-ray structures 3R

N3 (H

owlin et al., 1989), 7R

SA (W

lodawer et al., 1988) and the 32 N

MR

structures in 2A

AS (Santoro et al., 1993).

Experim

ental values (Antosiew

icz et al., 1996). His p

Ka values

averages experim

ental data

(Ruterjans

and W

itzel, 1969;

Matthew

s and

Westm

oreland, 1973; Walters and A

llerhand, 1980). Only the pK

a 's of His 12 and 19 are effected by added PO

4 . +: w

ith PO4 . E

xperimental values

from (M

eadows et al., 1969; C

ohen et al., 1973).C

alculations had PO4 dynam

ically equilibrated with the protein during M

onte Carlo sam

pling. –: no PO4 .

Ex

pt

±#3R

N3

#Err.

*3RN

3*E

rr.7R

SAE

rr.§2A

AS

§Err

§RM

SV¶3R

N3

¶Err.

3RN

3E

rr.P

O4

++

+–

++

Asp

14

20.2

-1.0-3.0

0.6-1.4

0.6-1.4

4.92.9

5.51.3

-0.72.8

0.8A

sp3

83.1

0.23.0

-0.13.0

-0.11.7

-1.43.1

0.00.4

3.60.5

3.80.7

Asp

53

3.90.2

3.4-0.5

3.7-0.2

3.4-0.5

4.00.1

1.24.3

0.44.3

0.4A

sp8

33.5

0.26.3

2.83.8

0.33.2

-0.32.7

-0.81.2

3.60.1

3.1-0.4

Asp

1213.1

0.2-1.0

-4.13.2

0.10.5

-2.62.2

-0.91.4

2.7-0.4

3.0-0.1

Ctr

12

42.4

0.2-0.0

-2.41.3

-1.10.9

-1.51.6

-0.81.0

1.7-0.7

2.2-0.2

Glu

22.8

0.2-0.6

-3.41.3

-1.55.6

2.82.4

-0.41.5

2.80.0

3.20.4

Glu

94

0.25.8

1.85.4

1.45.5

1.55.1

1.11.2

5.01.0

4.60.6

Glu

49

4.70.2

5.71.0

5.50.8

5.71.0

7.52.8

2.95.3

0.65.0

0.3G

lu8

64.1

0.24.4

0.34.2

0.15.7

1.64.6

0.50.9

4.80.7

4.50.4

Glu

11

13.5

0.24.4

0.93.9

0.44.3

0.84.8

1.31.6

4.10.6

4.20.7

His

12-5.8

0.05-1.0

-6.84.2

-1.64.2

-1.64.7

-1.12.0

12+7

6.7-0.3

6.7-0.3

6.9-0.1

His

48

6.30.1

3.1-3.2

8.82.5

7.51.2

4.7-1.6

4.48.0

1.76.7

0.4H

is1

05

6.60.15

6.1-0.5

5.9-0.7

6.1-0.5

6.2-0.4

0.46.4

-0.26.3

-0.3H

is119-

6.10.1

6.70.6

5.4-0.7

6.10.0

5.4-0.7

1.2119+

7.16.0

-1.16.7

-0.46.7

-0.3N

tr1

7.60.15

6.0-1.6

7.4-0.2

8.71.1

8.00.4

0.77.5

-0.17.5

-0.1R

MS

2.690.98

1.441.28

2.210.66

0.44C

onf1

23

40

64

22

35

63

50

28

5




SM IX

. Ribonuclease H

i (RN

ase H).

X-ray structure: 2R

N2 (K

atayanagi et al., 1992), 1RN

H (Y

ang et al., 1990), and 1RD

D (K

atayanagi et al., 1993) and 8 NM

R structures in 1R

CH

(Yam

azaki et al., 1997). The experim

ental pK

a 's (in presence or absence of Mg

+2) are from

(Oda et al., 1993; O

da et al., 1994). Experim

entalvalues that differ by m

ore than 0.2 pH units are bold; N

o pKa 's w

ith Mg

+2 are reported for H

is. The reported errors assum

e that these pK

a 's areindependent of added ion. The pK

a 's of Asp 10 are not included in the R

MS calculations. 1R

NH

does not contain coordinates for residues 1-3 and153 through the C

-terminal 155.

Ex

pt

Ex

pt

±#2R

N2

#Err.

*2RN

2*E

rr.1R

NH

Err

1RD

DE

rr.§1rch

§Err

§RM

SV¶2R

N2

¶Err.

||2RN

2||E

rr.M

g+

2–

+–

––

+–

––

Asp

10

6.14.2

10.94.8

10.44.3

15.49.3

8.74.5

14

7.93.1

8.72.6

6.40.3

Asp

70

2.63.4

0.62.4

-0.22.3

-0.33.2

0.62.4

-1.04.0

1.41.1

3.61.0

3.91.3

Asp

94

3.23.3

111.9

8.73.8

0.63.4

0.21.4

-1.93.6

0.40.6

3.60.4

3.70.5

Asp

102 2.0

2.0\

-1.0-3.0

2.0-0.0

1.4-0.6

1.6-0.4

2.30.3

0.51.8

-0.2-0.5

-2.5A

sp1

08

3.23.5

0.91.7

-1.52.0

-1.22.0

-1.24.8

1.34.4

1.21.0

3.1-0.1

3.0-0.2

Asp

13

44.1

4.20.8

1.0-3.1

2.2-1.9

4.40.3

3.8-0.4

4.20.1

0.52.7

-1.43.3

-0.8A

sp148

2.0 2.0

\6.9

4.91.1

-0.93.9

1.9-1.0

-3.04.4

2.33.6

-0.5-2.5

1.3-0.7

Ctr

15

53.4

3.50.8

3.70.3

2.7-0.7

2.2-1.3

2.4-1.0

1.73.7

0.33.4

0.0G

lu6

4.54.5

0.94.1

-0.46.3

1.84.3

-0.25.7

1.25.4

0.91.1

5.10.6

3.9-0.6

Glu

32

3.63.6

0.731.3

-2.32.1

-1.51.6

-2.01.5

-2.13.3

-0.30.5

2.5-1.1

3.5-0.1

Glu

48

4.44.4

0.755.3

0.95.5

1.16.4

2.05.2

0.85.1

0.72.9

5.61.2

4.70.3

Glu

57

3.23.4

11.7

-1.52.5

-0.82.0

-1.22.6

-0.84.5

1.31.5

3.0-0.2

3.30.1

Glu

61

3.94.0

0.91.7

-2.22.9

-1.03.5

-0.40.5

-3.53.5

-0.40.7

3.3-0.6

3.2-0.7

Glu

64

4.44.5

0.94.6

0.24.3

-0.12.9

-1.54.8

0.35.3

0.91.7

4.4-0.0

4.3-0.1

Glu

1194.1

4.30.75

-0.4-4.5

3.1-1.0

4.40.3

5.81.5

5.31.2

1.43.3

-0.83.9

-0.2G

lu129

3.64.0

0.70.0

-3.62.8

-0.82.9

-0.72.5

-1.52.2

-1.41.7

3.2-0.4

3.0-0.6

Glu

13

14.3

4.40.85

5.10.8

5.00.7

3.4-0.9

5.51.1

5.31.0

1.25.0

0.74.8

0.5G

lu1

35

4.34.3

0.94.3

-0.04.3

0.03.5

-0.84.4

0.14.3

-0.00.3

4.60.3

4.60.3

Glu

14

74.2

4.21

4.30.1

4.40.2

4.90.7

4.50.3

4.2-0.0

0.54.7

0.54.7

0.5G

lu1

54

4.44.4

12.6

-1.83.8

-0.66.7

2.34.8

0.40.6

4.0-0.4

4.60.2

His

62

7.00.9

5.7-1.3

6.7-0.3

6.5-0.5

6.4-0.6

6.1-0.9

1.06.6

-0.46.5

-0.5H

is8

35.5

15.4

-0.15.4

-0.14.8

-0.75.8

0.35.4

-0.10.4

5.50.0

5.60.1

His

11

4 5.0

0.94.2

-0.84.5

-0.64.2

-0.85.3

0.32.8

-2.23.1

4.8-0.2

5.70.7

His

12

47.1

0.854.5

-2.64.5

-2.68.7

1.64.9

-2.24.7

-2.42.5

5.2-1.9

5.7-1.4

His

12

77.9

0.98.1

0.27.0

-0.98.7

0.88.8

0.96.5

-1.41.7

7.3-0.6

7.7-0.2

RM

S2.75

1.041.06

1.491.15

1.600.87

0.77C

onf1

33

51

24

56

36

53

96

26

8




SM-X

. Ribonuclease T

1 (RN

ase T).

X-ray structure: 3R

NT

(Kostrew

a et al., 1989). Experim

ental values (Inagaki et al., 1981; McN

utt et al., 1990).

Ex

pt

±n

#3RN

T#E

rr.*3R

NT

*Err.

¶3RN

T¶E

rr.||3R

TN

||Err.

His

27

7.30.1

\12.0

4.78.0

0.77.6

0.37.8

0.5H

is4

07.9

0.2\

13.05.1

9.01.1

8.40.5

7.2-0.7

His

92

7.80.2

\8.0

0.27.1

-0.76.9

-0.97.5

-0.3G

lu5

84.3

0.2\

-0.4-4.7

4.50.2

4.2-0.1

5.20.9

RM

S4.18

0.750.54

0.63C

onf9

53

95

31

62

44




SM X

I. Lennard-Jones param

eters (kcal/mol).

DGij non.el=

Ar 12-

Br6

Ê Ë Á ˆ ¯ ˜ .

Value varies for atom

types. not-H* are heavy atom

s other than H, N

, C, or O

.

Å w

here ∆G

lj=0 is the distance betw

een atom centers w

here DGij non.el=

0,.

Em

in is the energy minim

um for this atom

pair is. N

o Lennard-Jones interactions are determ

ined for atoms in the sam

e side chain or between C

A (in the backbone) and C

B (in the side chain) of the

same residue.

atoms

AB

Em

inÅ

where ∆

Glj=

0H

: H1.33x10

+1

1.81X10

+0

-0.051.40

H : C

1.61X10

+3

6.66X10

+1

-0.541.70

H : O

4.02X10

+2

3.33X10

+1

-0.541.51

H : N

6.27X10

+2

3.73X10

+1

-0.441.60

H : not-H

*1.61X

10+

36.66X

10+

1-0.54

1.70not-H

: not-H2.96X

10+

51.05X

10+

2-0.01

3.76




SM X

II. Reaction field energies (kcal/m

ol) for isolated side chains.E

nergy for transfer from a m

edium w

ith a dielectric constant of eprot of 4, 8, or 20 to a solvent w

ith e=80. ∆∆

Grxn,i (in eqn. 3) is the difference

between this reference value and the reaction field energy for a conform

er in the protein. ∆∆

Grxn,i is constrained to have a m

inimum

of 0.

Resid

ue

e = 4.0

ionized

e = 4.0

neu

tral

e = 8.0

ionized

e =.0

neu

tral

e = 20.0

ionized

e = 20.0

neu

tral

ASP

18.12.1

8.71.1

2.90.3

CT

R16.6

1.57.9

0.82.6

0.2

GL

U18.7

2.28.9

1.12.9

0.4

HIS

11.81.8

5.70.9

2.10.3

LYS

19.61.1

9.80.6

3.20.2

TY

R15.2

1.27.3

1.12.4

0.3

NT

R13.3

1.86.7

0.92.1

0.3

AR

G12.8

3.48.0

1.72.9

0.5

ASN

5.91.7

0.5

GL

N5.9

1.70.5

SER

1.80.8

0.3

TH

R1.8

0.80.2

HO

H3.6

2.41.1

PO

4 -262.1

32.514.8

Mg

+2

17.88.9

4.7

sqrt pk - sci.ccny.cuny.edugunner/pages-lab/papers/bj02-rox-sup.pdf8/14/02 georgescu, alexov, and...

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