Glycosciences.de MODELING

Author:	Dorland L; van Halbeek H; Vliegenthart JFG; Lis H; Sharon
Title:	Primary structure of the carbohydrate chain of soybean agglutinin. A reinvestigation by high-resolution 1H-NMR spectroscopy
Citation:	J Biol Chem (1981) 256: 7708-7711
Biological Source / Taxonomy:	(GS) Glycine max, (CN) soybean
Parent Molecule (or Source):	agglutinin
Molecular Type:	N-linked glycoprotein
Analytical Methods:	1H-NMR
Submitted by:	Darvill A; van Halbeek H
Date, update of entry:	22-04-1989
Structure Identifier:	CBank:20400
CCSD accession number:	CCSD:1895

        a-D-Manp-(1-2)-a-D-Manp-(1-6)+
                                     |
                                a-D-Manp-(1-6)+
                                     |        |
        a-D-Manp-(1-2)-a-D-Manp-(1-3)+   b-D-Manp-(1-4)-b-D-GlcpNAc-(1-4)-b-D-GlcpNAc-(1-4)-Asn
                                              |
  a-D-Manp-(1-2)-a-D-Manp-(1-2)-a-D-Manp-(1-3)+

This molecule (generated with SWEET2) in pdb mime format.
This molecule (generated with SWEET2) in pdb text format.
View this molecule with WebMol.

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Several authors have analysed possible conformations of high-mannose N-linked glycans using a combination of NMR methods and computational approaches showing that such molecules are rather flexible, populating normally several conformations for each glycosidic linkage. Here we compare the PHI/PSI torsion angles of the conformation generated by SWEET with other approaches. An exact correspondence of PHI, PSI values calculated with different force fields and varying computational approaches cannot be expected. As pointed out by Rasmussen and Fabricius, a minimum in a two-dimensional conformational map may represent an entire family of points in multidimensional space. Therefore, a "difference in PHI,PSI of 10^o, 10^o is really no difference at all".

Rasmussen, K. and Fabricius, J (1990) in: Computer Modeling of Carbohydrate Molecules. French, A.D. and Brady, J. (Eds.) ACS Symposium Series 439, pp 177-190, American Chemical Siciety, Washington, DC

Comparison between different data from literature

Approach

Crystal data

rigid rotation
minimisation

systematic
search

MD and NMR

Author

Petrescu et al.[0]

This work

Imberty et al.[1]

Woods et al.[2]

Homans et al.[3-5]

Kozar et al.[7]

Quasba et al.[8]

Force Field

natural

MM3 (Tinker)

MM2Carb

Amber-Glycam

Amber-Homans

CFF95

CVFF

b-GalNAc-(1-4)-GlcNAc

47±8/-4±16

43/0

40/10
35/15
30/-55

36±15/-33±23

0/-33
54/-2
27(25)/-17(24)^*
34(27)/-14(22)

49/-4
41/-19
173/1
60/-7
38/-27

46/-7
-16/-52
59/-2
141/0

b-Man-(1-4)-GlcNAc

32±11/-13±20

50/10

45/10
35/15
30/-55

46±13/-10±16

15/-27
15/-5
13(26)/-16(20)
25(30)/-7(18)

49/-170
95/-167
170/2
74/34
50/-7

(around) 55/-5

a-Man-(1-3)-Man

-48±11/6±22

-43/-14
-40/-19

-35/55
-50/-20
30/30

-45/30
-45±10/0±50

-20/30
-20/50
-40(15)/12(27)
-38(17)/2(23)

31/45
8/-61
-8/-171
-33/52
-25/11

(around) -40/5

a-Man-(1-6)-Man

-55±9/182±5/-174±10
-54±11/180±15/-55±15
-53±14/109±13/-37±22

-29/-159/71
-22/-155/-65

-50/-170/?
-45/100/?
-50/-170/?
-45/90/?

-35±15/180±10/?
40±10/145±15/?

-2/81/179
8/59/-52
-8(27)/95(31)/?

-50/178/-45
-167/-53/120
2/-24/-141
34/-51/-164
-7/-42/-174

-55,60/-170,-60,60/60,180,-60

a-Man-(1-2)-Man

-58±8/-55±10
-49±8/16±15

-43/-18
38/-19
40/19
39/25

-30/60
-50/-20
30/30

-39±9/56±14
-42±9/55±14
-39±9/52±22
-46±8/22±14

-40/-20
-40/0

---

^* : Number in parentheses represent angular rms deviation in degrees.

[0] A. J. Petrescu, S. M. Petrescu, R. A. Dwek and M. R. Wormland, (1999), A statistical analysis of N- and O-glycan linkage conformations from crystallographic data, Glycobiology, vol. 9, no. 4, 343-352

[1] Rasmussen, K. and Fabricius, J (1990) in: Computer Modeling of Carbohydrate Molecules. French, A.D. and Brady, J. (Eds.) ACS Symposium Series 439, pp 177-190, American Chemical Society, Washington, DC

[2] Imberty A., Gerber S., Tran V., Perez S. (1990) Data Bank of Three-Dimensional Structure of Disaccharides, A Tool to Build 3D Structure of Oligosaccharide Glycoconjugate J , 7; 27-54

[3] Woods R.J., Pathiaseril A., Wormald M.R., Edge C.J., Dwek R.A. (1998) The high degree of internal flexibility observed for an oligomannose oligosaccharide does not alter the overall topology of the molecule Eur. J. Biochem., 258, 372-386

[4] Homans, S.W, Dwek R.A.,Rademacher T.W.(1987) Tertiary Structure in N-Linked Oligosaccharides, Biochem., 26, 6553-6560

[5] Homans, S.W., Pastore, R.A., Dwek R.A.,Rademacher T.W. (1987) Structure and Dynamics in Oligomannse-Type-Oligosaccharides, Biochem. 26, 6649-6655

[6] Rutherford T.J., Homans S.W. (1994) Restrained vs Free Dynamics Simulation of Oligosaccharides: Application to Solution Dynamica of Biantennary and Bisected Biantennary N-Linked Glycans Biochem. 33, 9609-9614

[7] Kozar T., Tvaroska I., Carver J.P., Studies on the conformational behaviour of GlcNac-Man₃-GlcNac₂ oligosacchrides using molecular dynamics simulations, Glycoconjugate J. (1988), 15, 187-191

[8] Qasba P.K., Balaji P.V., Rao V.S., Molecular dynamics simulation of oligosaccharides and their conformation in the crystal structure of lectin-carbohydrate complex: importance of the torsion angle psi for the orientation of a 1,6-arm, Glycobiology (1994), vol. 4, no. 6, 805-815

Phi:	H1-C1-O1-CX'
Psi:	C1-O1-CX'-HX'
Omega:	H1-C1-O1-C6', C1-O1-C6-C5' and O1-C6'-C5'-H5'

Carbohydrate Chain of Soybean Agglutinin (Given as Carbbank entry)

Carbohydrate Chain of Soybean Agglutinin
(Given as Carbbank entry)