Stereoscopic atlas of amino acid structures

Mat. Res. Bull. Vol. 7, pp. 1225-1238, 1972. Pri nt e d in the United States.

P e r g a m o n P r e s s , Inc.

STEREOSCOPIC ATLAS OF AMINO ACID STRUCTURES W. C. Hamilton, M. N. F r e y , L. Goli~, T. F. Koetzle, M. S. Lehmann and J. J. Verbist C h e m i s t r y Department, Brookhaven National Laboratory Upton, New York 11973

(Received S e p t e m b e r 5, 1972)

ABSTRACT S t e r e o s c o p i c drawings and tables of to rsio n angles a r e p res en ted for twenty c o m m o n amino acid s t r u c t u r e s , most of which have been subjected to p r e c i s i o n s t r u c t u r a l r e f i n e m e n t s based on neutron diffraction data. Introduction The d e t e r m i n a t i o n of amino acid s t r u c t u r e s by the c r y s t a l l o g r a p h i c group at the California Institute of Technology (1-6) in the 1940's and 1950's r e s u l t e d in a body of g e o m e t r i c a l data that was e s s e n t i a l to the development of the b r i l l i a n t proposals by Pauling, Corey and c o - w o r k e r s of the basic protein s t r u c t u r e types, which have been co n firmed by the s t r u c t u r a l work of Kendrew, P e r u t z , t h e i r c o - w o r k e r s and a whole new g e n e r a t i o n of c r y s t a l l o g r a p h e r s who have followed them. The x - r a y s t r u c t u r a l work on amino acids has been c o m p r e h e n s i v e l y r e v i e w e d by Marsh and Donohue (7).

In most of the e a r l y x - r a y work, h y d r o -

gen a t oms w e r e not located, and even in the best work available today, h y d r o gen atom positions, although qualitatively c o r r e c t in most c a s e s , a r e a c c u r a t e only to 0. 1 - 0. 2/~.

At the Brookhaven National L a b o r a t o r y and at the Indian

Atomic Energy L a b o r a t o r y at T r o m b a y , w o r k in the past two y e a r s has r e sulted in p r e c i s i o n r e f i n e m e n t s of the s t r u c t u r e s of 16 of the c o m m o n l y occ u r r i n g amino acids.

In these studies hydrogen atom positions have been 1225

1226

AMINO ACID STRUCTURES

g e n e r a l l y d e t e r m i n e d to a p r e c i s i o n of a b o u t 0. 003.~. particularly thermal motion parameters

Vol. 7, No. 11

Heavy a t o m p a r a m e t e r s ,

in a n u m b e r of s t r u c t u r e s sho~7 s o m e

i m p r o v e m e n t o v e r the x - r a y ~,ork. A l t h o u g h d e t a i l e d r e p o r t s of t h e s e s t r u c t u r e d e t e r m i n a t i o n s have a p p e a r e d , it ~,ould s e e m u s e f u l to w o r k e r s in the field of p r o t e i n s t r u c t u r e to have a v a i l a b l e s u m m a r i e s of t h e i n f o r m a t i o n so o b t a i n e d .

We will be p r e s e n t -

ing e l s e ~ , h e r e a d e t a i l e d c o m p a r i s o n of bond l e n g t h s and a n g l e s , and a d i s c u s s i o n of the g e n e r a l f e a t u r e s of the h y d r o g e n bonds w h i c h we h a v e b e e n a b l e to d e s c r i b e a d e q u a t e l y f o r the f i r s t t i m e .

In t h i s p a p e r , r,e p r e s e n t d r a w i n g s of

a l l t h e m o l e c u l a r and c r y s t a l s t r u c t u r e s , TABLE

a s w e l l a s a t a b u l a t i o n of the t o r s i o n angles which

1

Amino acid structures for which stereoscopic drawings are presented in this paper. The literature references are to the neutron diffraction work marked by an asterisk (*) with the exception of those where the best available x-ray parameters have been used in the preparation of the drawings.

are sufficient to d e s c r i b e the c o n f o r -

Compound

Formula

Ref.

mations of

~-Glycine L-AIanine L-Valine. HCl L-Isoleucine L-Serine. H20 DL-Serine L-Threonine DL-Aspartic Acid L-Glutamic Acid (~ form) L-Glutamic Acid. HCI L-Asparagine. tt20 L-Glutamine L-Arginine. 2tt20 L-Lysine. HC1. H20 L-Cystine L-Cystine DL-Methionine (~ +fl) L- Phenylalanine. HC1 L-Tyrosine L-Tyrosine. HC1 L-Tryptophan. HC1 L - Hist id ine 4-Hydroxy-L-Proline

NH3+ CH2CO2(CH3 )CH(NH3 + )CO2 (CH3)2CHCH(NH3+)cOzHC1CH3CH2CH(CH3)CH(NH3+)CO2-

1, 8* 9" 10" 22 11" 6, 11.

the m o l e c u -

{ HOCH2CH(NH3+)CO2CH3CH(OH)CH(NH3+)CO2-O2CCH2CH(NH3+)CO2H HOCO(CH2)2CH(NH3+ )CO2 HOCO(CH2)2CH(NH3 +)cOOHclNH2COCH2CH(NH3+ )CO2NH2CO(CH2)2CH(NH3+)CO2(NH2)2C :NH +(CH2)3CH(NH2)CO2 (NH3)+ (CH2)4CH(NH3)+ CO2ClHSCH2CH(NH3+)CO2[ -O2CCH(NH3+)CH2S- ] 2 CH3S(CH2)2CH(NH3+)CO2C6H5CH2CH(NH3+ )CO2HCIHOC6H4CH2CH(NH3+)CO2HOC6H4CH2CH(NH3+ )COOHCl-

5 23 12" 13. 14., 15. 16" 17" 18" 24 25 26 27 19" 19.

C6H4NHCH:CCH2CH(NH3+ )COOHC1C3N~H(NH3+ )CO2Ct~2NH2+ CH(CO2-)CH2 ~H (OH)

28 20* 21"

lar structures. We a l s o p r e s e n t nearly prepared d r a w i n g s of a few i m p o r t a n t structures for ~,hich n e u t r o n diffraction d a t a a r e not yet available. The structures presented are s u m m a r ized in T a b l e s 1 and 2.

Vol. 7, No. 11

AMINO ACID STRUCTURES

~1

1227

Cxl

c~

I

~

~

0

0

,-~

~

,-I

0

I

0 0 ~ 0

0

O0

I

C'q

CO

I

O'b

~1~

I

I

~

~

I

I

0 v i

ZI o

v

v

•--I

v

v

~

v

v

~

v

0

~

~t ~

L~

0

0~,

L~

~

~

~

~

~

~

~

~

L~

v

v

0

~t~

CO

O~

~

~

~

~

N

~

I

%

I

°~

d

I

4

,.4

M

I

d

I

?

I

~ I

-,B ~

I

I

I

,,6 M

I

I

-e I

.% I

I

/

I

I

I

i-4

I

0I

c..) I

b

=nI

I

I

I

r/l I

0 H .~ I

I

I

---

~o ~ •~

-~

.~

..~

"<

I

0

~

I

I

I

I

0

~

o

I

•

=

'

1228

AMINO ACID STRUCTURES Atlas of amino acid structures.

Vol. 7, No. II

For description, see page 1236.

%

(J

.H U

,-~

.1..I c~ rn -r-

I

I

Vol. 7, No. 11

cx

i

C~

AMINO ACID STRUCTURES

v

o

vb c~

1229

v

x.s

~.J

L)

,-4

!

1230

AMINO ACID STRUCTURES

Vol. 7, No. II

b

b

-r-~,~,~

.,,z.- o~

U U

,--4

""tl~l~ ~

~ _"-,~

c,~

O

Vol. 7, No. I I

AMINO ACID STRUCTURES

1231

j O

°

I

,-~

1232

AMINO ACID STRUCTURES

Vol. 7, No. 11

L) ..J

0 ~4

°

~

- ° ~

L9

°¥

.A

'

Vol.

co

z

7, No.

z

t.J

ll

AMINO ACID STRUCTURES

1233

~

,-I 0

!

C'4

-r

I

1234

AMINO ACID STRUCTURES

Vol.

‘7, No.

11

Vol. 7, No. 11

AMINO ACID STRUCTURES

1235

i.-t

QI

r

co

0

8~

O~

0

[.-4 I

I

~,~ ~ z

~

c~

)

0 q~

•

•

m rO

0

or-.I

4.1

0 °r.I

0 0 I

0

o 0 4-1 0

c~

1236

AMINO ACIDSTRUCTURES

Vol. 7, No. 11

General Description of Figure The individual molecules, most of which a r e in the zwitterion form, a r e drawn ~,ith t h e r m a l ellipsoids enclosing 50% of the scattering density probability. Atoms a r e labelled according to the IUPAC-IUB conventions (29) w i t h A = ~, B = ~, G = 9 ' , D = 5, E = ~, Z = ~, H = ~ , T = 0. The internal hydrogen bonds in hydroxy-proline and histidine are indicated by open lines. The contents of the unit cells are drawn with heavy lines indicating covalent bonds and light lines indicating hydrogen bonds. References 1. G. Albrecht and R. B. Corey, J. A m e r . Chem. Soc. 6_1.1, 1087 (1939). 2. H. A. Levy and R. B. Corey, J. Amer. Chem. Soc. 6..~3, 2095 (1941). 3. J. Donohue, J. Amer. Chem. Soc. 7_.22, 949 (1950). 4. J. Donohue and K. T. Trueblood, Acta Cryst. 5, 419 (1952). 5. D. P. Shoemaker, J. Donohue, V. Schomaker and R. Corey, J. Amer. Chem. Soc. 72, 2328 (1950). 6. D. P. Shoemaker, R. E. Barieau, J. Donohue and Chia-si Lu, Acta Cryst. 6, 241 (1953). 7. R. E. Marsh and J. Donohue, Adv. P r o t e i n Chemistry 22.._, 235 (1967). 8. P-G. JSnsson and/~. Kvick, Acta Cryst. B28, 1827 (1972). 9. M. S. Lehmann, T. F. Koetzle and W. C. Hamilton, J. Amer. Chem. Soc. 94_ 2657 (1972). 10. L. Goli~, W. C. Hamilton and M. S. Lehmann (in preparation). 11. M. N. Frey, M. S. Lehmann, T. F. Koetzle and W. C. Hamilton (in preparation). 12. M. S. Lehmann, T. F. Koetzle and w. C. Hamilton, J. Cryst. Molec. Structure (submitted). 13. A. Sequeira, H. Rajopal and R. Chidambaram, Acta Cryst. (in press). 14. M. Ramanadham, S. K. Sikka and R. Chidambaram, Acta Cryst. (in press). 15. J. J. Verbist, M. S. Lehmann, T. F. Koetzle and W. C. Hamilton, Acta Cryst. (in press). 16. T. F. Koetzle, M. N. Frey, M. S. Lehmann and w. C. Hamilton (in pre paration). 17. M. S. Lehmann, J. J. Verbist, w. C. Hamilton and T. F. Koetzle, J. Chem. Soc. (submitted). 18. T. F. Koetzle, M. S. Lehmann, J. J. Verbist and W. C. Hamilton, Acta Cryst. (submitted).

Vol. 7, No. 11

AMINO ACID STRUCTURES

1237

19. M. N. Frey, T. F. Koetzle, M. S. Lehmann and w. C. Hamilton (in preparation). 20. M. S. Lehmann, T. F. Koetzle and w. C. Hamilton, Int. J. Protein Res e a r c h (in press). 21. T. F. Koetzle, M. S. Lehmann and W. C. Hamilton, Acta Cryst. (submitted). 22. Katzuo T o r i i and Yoichi Iitaka, Acta Cryst. B27, 2237 (1971). 23. S. T h y a g a r a j a Rao, R. Srinivasan and V. Valambal, Indian J. Pure App. Phys. 6, 523 (1968). 24. M. M. Harding and H. A. Long, Acta Cryst. B24, 1096 (1968). 25. B. M. Oughton and P. M. Harrison, Acta Cryst. 12__, 396 (1959). 26. A. McL. Mathieson, Acta Cryst. 5, 332 (1952). 27. G. V. Gurskaya, K r i s t a l l o g r a f i y a 9, 839 (1964). 28. T. Takigawa, T. Ashida, Y. Sasada and M. Kakudo, Bull. Chem. Soc., Japan 39, 2369 (1966). 29. IUPAC-IUB Commission on Biochemical Nomenclature, J. Mol. Biol.

52, 1 (1970).