Explanations to the table:
Bacterial strains (column 1) includes the following species abbreviations: P.v. = Proteus vulgaris, P.p. = Proteus penneri, P.m. = Proteus mirabilis.
Program input (column 2) includes monomeric composition and widespread mode either ON or OFF. The experimental spectrum is omitted. The first character in each line is the anomeric configuration, the second is the absolute configuration, rest are the residue name. The question mark stands for unknown configurations. If any substitution constraints were specified, they are recorded before the closing parenthesis like "xx)"
Program output (column 3) includes the list of five (may be from 1 to 100) structures most closely fitting the experimental spectrum. The proper structure is given in bold. Each line contains also schematic representation of topology (e.g. -[x]xxx-) and the deviation of the calculated 13C NMR spectrum from the experimental.
References (column4) are to publications with these structures determined independently.
Additional experiments (column 5) column lists the additional NMR and chemical methods that are required to select the proper structure from the list generated. If a particular experiment is needed to distinguish two certain structures, their numbers are presented in parentheses, e.g. (1 vs. 4).
Bacterial strain |
Program input |
Program output (the proper structure is highlighted) | Ref. | Additional experiments |
---|---|---|---|---|
|
Llys ?Dgaa ?Dgaln ?Dgla ?Dgaln Widespread =ON |
1: [Llys--6)aDgaa] |4 --6)bDgaln--4)bDgla--3)bDgaln-- (-[xx]xxx-) Dev.: 0.272: [Llys--6)aDgaa-] |4 --6)bDgaln--2)bDgla--3)bDgaln-- (-[xx]xxx-) Dev.: 0.33 3: [Llys--6)aDgaa-] |4 --6)bDgaln--3)bDgla--3)bDgaln-- (-[xx]xxx-) Dev.: 0.33 4: [Llys] |6 [bDgla--3)bDgaln--4)aDgaa] |4 --6)bDgaln-- ([xx[x]x]x) Dev.: 0.34 5: [bDgla--3)bDgaln] [Llys] |6 |6 --4)bDgaln--4)aDgaa-- ([xx]x[x]x) Dev.: 0.34 |
[1] |
HMQC-TOCSY or methylation analysis |
|
bDgal bDglcn aletP aDgal bDglc Widespread =ON |
1: [alet--P] |6 --3)aDgal--6)bDglc--3)bDgal—-3)bDglcn-- (-[xx]xxxx-) Dev.: 0.132: [alet--P] |6 --3)aDgal--6)bDglc--3)bDglcn--3)bDgal-- (-[xx]xxxx-) Dev.: 0.13 3: [alet--P] |6 --3)bDgal--3)bDglcn--3)aDgal--6)bDglc-- (-[xx]xxxx-) Dev.: 0.23 4: [alet--P] |6 --3)bDglcn--3)bDgal--3)aDgal--6)bDglc-- (-[xx]xxxx-) Dev.: 0.23 5: [alet--P] |6 --2)aDgal--6)bDglc--3)bDglcn--3)bDgal-- (-[xx]xxxx-) Dev.: 0.23 |
[2] |
NOESY (ROESY) (1 vs. 2) (3), (4), (5) posses much greater deviation |
P.m. O10 |
?Dgla ?Dglcn ?Dgaln aLalta Widespread =ON |
1: [aLalta] |3 --4)aDgaln--3)aDgla--3)aDglcn-- (-[x]xxx-) Dev.: 0.342: [aDglcn] |4 --3)aDgaln--3)aDgla--3)aLalta-- (-[x]xxx-) Dev.: 0.38 3: [aLalta] |3 --4)aDgaln--3)aDgla--4)aDglcn-- (-[x]xxx-) Dev.: 0.41 4: [aLalta] |3 --4)aDgaln--3)aDglcn--3)aDgla-- (-[x]xxx-) Dev.: 0.41 5: [aLalta] |3 --4)aDgaln--4)aDglcn--3)aDgla-- (-[x]xxx-) Dev.: 0.46 |
[3] |
HMQC-TOCSY or methylation analysis (1 vs. 2,3) NOESY (ROESY) (1 vs. 4) (5) posses much greater deviation |
P.m. O13 |
3?)?Dglcn 34)?Dgal ?Dgla Lalys Correction |
1: [Lalys--6)bDgla] |3 --4)aDgal--3)bDglcn-- (-[xx]xx-) Dev.: 1.23 2: [aDgla] [Lalys] |4 |2 --3)aDgal--3)bDglcn-- (-[x]x[x]x-) Dev.: 1.23 3: [Lalys--6)bDgla] |4 --3)aDgal--3)bDglcn-- (-[xx]xx-) Dev.: 1.234: [Lalys--6)aDgla] |4 --3)aDgal--3)bDglcn-- (-[xx]xx-) Dev.: 1.245: [Lalys--6)aDgla] |4 --3)bDgal--3)bDglcn-- (-[xx]xx-) Dev.: 1.28 |
[4] |
HMQC-TOCSY or methylation analysis (4 vs. 2) NOESY (ROESY) (4 vs. 1) 13C Gated (4 vs. 3,5) |
P.m. O14 De-OAc |
bDgaln aDgal bDgaln alet P aDgal Widespread =ON |
1: [alet--P] |6 --4)aDgal--4)bDgaln--3)aDgal--3)bDgaln-- (-[xx]xxxx-) Dev.: 0.202: [alet--P] |6 --4)aDgal--3)bDgaln--3)aDgal--4)bDgaln-- (-[xx]xxxx-) Dev.: 0.20 3: [alet--P] |6 --4)aDgal--3)bDgaln--4)aDgal--4)bDgaln-- (-[xx]xxxx-) Dev.: 0.23 4: [alet--P] |6 --4)aDgal--4)bDgaln--4)aDgal--3)bDgaln-- (-[xx]xxxx-) Dev.: 0.23 5: [alet--P] |6 --4)aDgal--3)bDgaln--2)aDgal--4)bDgaln-- (-[xx]xxxx-) Dev.: 0.24 |
[5] |
NOESY (ROESY) or HMBC |
|
?Dgaln ?Dgaln etnP ?Dglcn ?ribP Widespread =ON |
1: [etnP] |6 --3)aDglcn--4)DribP--6)bDgaln--4)aDgaln-- (-[x]xxxx-) Dev.: 0.282: [etnP] [bDgaln] |6 |6 --4)aDgaln--4)DribP--4)aDglcn-- ([x]xx[x]x) Dev.: 0.31 3: [etnP] |6 --4)aDglcn--4)DribP--6)bDgaln--4)aDgaln-- (-[x]xxxx-) Dev.: 0.32 4: [etnP] |3 --6)aDglcn--4)aDgaln--4)DribP--6)bDgaln-- (-[x]xxxx-) Dev.: 0.32 5: [etnP--6)bDgaln] |6 --3)aDglcn--4)aDgaln--4)DribP-- (-[xx]xxx-) Dev.: 0.32 |
[6] |
{1H-31P} HMQC (1 vs. 2,5) NOESY (ROESY) (1 vs. 3,4) |
P.m. O26 De-OAc |
Llys ?Dgla ?Dgal ?Dgla ?Dglcn Widespread =ON |
1: [Llys] [aDgal] |6 |4 --4)aDgla--3)bDgla--3)bDglcn-- (-[x]xx[x]x-) Dev.: 0.272: [Llys] |6 --4)aDgla--4)aDgal--3)bDgla--3)bDglcn-- (-[x]xxxx-) Dev.: 0.363: [Llys] [aDgal] |6 |3 --4)aDgla--3)bDgla--4)bDglcn-- (-[x]xx[x]x-) Dev.: 0.43 4: [Llys] [aDgal] |6 |4 --3)aDgla--3)bDgla--3)bDglcn-- (-[x]xx[x]x-) Dev.: 0.45 5: [Llys] 6| --4)aDgla--3)bDgla--2)aDgal--3)bDglcn-- (-[x]xxxx-) Dev.: 0.47 |
[7] |
HMQC-TOCSY or methylation analysis or NOESY (ROESY) (2 vs. 1,3) (4), (5) posses much greater deviation |
P.m. O30 |
bDgla aDgaln bDglcn bDglcn Widespread =OFF |
1: --4)bDgla--3)bDglcn--6)aDgaln--6)bDglcn-- (-xxxx-) Dev.: 0.35 2: --4)bDgla--6)aDgaln--6)bDglcn--3)bDglcn-- (-xxxx-) Dev.: 0.37 3: --2)bDgla--3)bDglcn--6)aDgaln--6)bDglcn-- (-xxxx-) Dev.: 0.39 4: [bDglcn--4)bDgla] |3 --6)bDglcn--6)aDgaln-- (-[xx]xx-) Dev.: 0.39 5: [bDglcn--6)aDgaln] |6 --3)bDglcn--4)bDgla-- (-[xx]xx-) Dev.: 0.39 |
[8] |
HMQC-TOCSY or methylation analysis (1,2 vs. 3,4,5) +NOESY (ROESY) (1 vs. 2) |
|
DribP ?Dgal ?Dglcn etnP ?Dglc ?Dglcn Widespread =ON |
1: [DribP] [etnP] |3 |6 --2)bDgal--3)aDglcn--3)bDglc--3)bDglcn-- (-[x]xx[x]xx-) Dev.: 0.332: [DribP] [etnP] |6 |3 --3)bDglc--3)bDglc--2)bDgal--3)aDglcn-- (-[x]xx[x]xx-) Dev.: 0.33 3: [etnP] [DribP] |3 |6 --2)bDgal--3)bDglc--3)aDglcn--3)bDglcn-- (-[x]xxx[x]x-) Dev.: 0.33 4: [DribP] [etnP] |3 |6 --2)bDgal--3)bDglc--3)aDglcn--3)bDglcn-- (-[x]xxx[x]x-) Dev.: 0.33 5: [DribP] [etnP] |3 |6 --2)bDgal--3)aDglcn--3)bDglc--3)bDglcn-- (-[x]xxx[x]x-) Dev.: 0.33 |
[9] |
{1H-31P} HMQC + NOESY (ROESY) (1 vs. 2) |
P.p. 1 |
bDglc bDgaln bDgaln aDgal Widespread =OFF |
1: [bDgaln] |3 --4)aDgal--6)bDglc--3)bDgaln-- (-[x]xxx-) Dev.: 0.18 2: [bDgaln] |4 --3)aDgal--6)bDglc--3)bDgaln-- (-[x]xxx-) Dev.: 0.18 3: [bDglc--3)bDgaln] |4 --3)aDgal--6)bDgaln-- (-[xx]xx-) Dev.: 0.23 4: [bDglc--3)bDgaln] |3 --4)aDgal--6)bDgaln-- (-[xx]xx-) Dev.: 0.23 5: --6)bDglc--3)bDgaln--4)bDgaln--3)aDgal-- (-xxxx-) Dev.: 0.34 |
[10] |
NOESY (ROESY) |
P.p. 2 |
?Dr23n ?Dglc ??ta6d ?Dglcn Widespread =ON |
1: [bDr23n] |3 --4)aDglc--3)aLta6d--3)bDglcn-- (-[x]xxx-) Dev.: 0.412: [bDr23n] |4 --2)aDglc--3)aLta6d--4)bDglcn-- (-[x]xxx-) Dev.: 0.44 3: [bDr23n] |4 --3)aDglc--3)aLta6d--3)bDglcn-- (-[x]xxx-) Dev.: 0.44 4: -4)bDr23n--4)bDglcn--3)aDglc--3)bLta6d-- (-xxxx-) Dev.: 0.44 5: [bDr23n] |3 --4)aDglc--3)aLta6d--4)bDglcn-- (-[x]xxx-) Dev.: 0.44 |
[11] |
HMQC-TOCSY or methylation analysis (1 vs. 2,4,5) +NOESY (ROESY) (1 vs. 3) |
P.p. 4 |
bDglc bDgaln bDgaln aDgal aDglc Widespread =ON |
1: [aDglc--6)bDgaln] |4 --3)aDgal--6)bDglc--3)bDgaln-- (-[xx]xxx-) Dev.: 0.21 2: [aDglc--6)bDgaln] |3 --4)aDgal--6)bDglc--3)bDgaln-- (-[xx]xxx-) Dev.: 0.21 3: [bDgaln] [aDglc] |4 |6 --3)aDgal--6)bDglc--3)bDgaln-- (-[x]xx[x]x-) Dev.: 0.22 4: [bDgaln] [aDglc] |3 |6 --4)aDgal--6)bDglc--3)bDgaln-- (-[x]xx[x]x-) Dev.: 0.22 5: [bDgaln] |4 --3)aDgal--6)bDglc--2)aDglc--6)bDgaln-- (-[x]xxxx-) Dev.: 0.28 |
[10] |
HMQC-TOCSY or methylation analysis (1,2,5 vs. 3,4) +NOESY (ROESY) (3 vs. 4) |
P.p.15 De-Pyr |
aDgal bDgal bDglcn Widespread =OFF |
Linear: 1a: --3)aDgal--4)bDgal--3)bDglcn-- (-xxx-) Dev.: 0.23 2a: --2)aDgal--4)bDgal--3)bDglcn-- (-xxx-) Dev.: 0.30 3a: --4)aDgal--4)bDgal--3)bDglcn-- (-xxx-) Dev.: 0.31 Widespread branched (with 1 or 2 sugars in side chains): 1b: [bDgal--3)bDglcn] |2 --4)aDgal-- (-[xx]x-) Dev.: 0.28 2b: [bDgal--3)bDglcn] |3 --4)aDgal-- (-[xx]x-) Dev.: 0.28 3b: [bDgal] |3 --4)bDglcn--3)aDgal-- (-[x]xx-) Dev.: 0.38 Rarely occurring branched (with more than 2 sugars in side chains): absent |
[12] |
HMQC-TOCSY or methylation analysis |
P.p.17 |
bDmaan aDglcn aDfu4n Widespread =OFF |
1: --4)bDmaan--4)aDglcn--3)aDfu4n-- (-xxx-) Dev.: 0.272: [aDglcn--3)aDfu4n] |3 --4)bDmaan-- (-[xx]x-) Dev.: 0.55 3: --4)bDmaan--3)aDglcn--3)aDfu4n-- (-xxx-) Dev.: 0.56 4: [aDglcn] |3 --2)aDfu4n--4)bDmaan-- (-[x]xx-) Dev.: 0.56 5: [bDmaan-] |3 --4)aDglcn--3)aDfu4n-- (-[x]xx-) Dev.: 0.68 |
[*] |
(2), (3), (4), (5) posses much greater deviation |
P.p. 63 |
?Dglcn ?Dglc ?Lfucn etnP ?Dglcn ?Dglc Widespread =ON |
1: [etnP] [bDglc] |6 |4 --3)bDglcn--2)bDglc--6)aDglcn--3)aLfucn-- (-[x]xxx[x]x-) Dev.: 0.102: [etnP--2)bDglc] |4 --3)aLfucn--3)bDglcn--2)bDglc--6)aDglcn-- (-[xx]xxxx-) Dev.: 0.18 3: [etnP] [bDglc] |6 |4 --2)bDglc--6)aDglcn--3)aLfucn--3)bDglcn-- (-[x]xx[x]xx-) Dev.: 0.21 4: [etnP] [aDglcn] |6 |3 --3)bDglcn--2)bDglc--6)bDglc--4)aLfucn-- (-[x]xxx[x]x-) Dev.: 0.21 5: [etnP--6)aDglcn] |4 --3)aLfucn--3)bDglcn--2)bDglc--6)bDglc-- (-[xx]xxxx-) Dev.: 0.26 |
[13] |
(2), (3), (4), (5) posses much greater deviation |
P.p. 71 |
bDglcn bDglcn aDgal Widespread =OFF |
1: --3)bDglcn--4)bDglcn--3)aDgal-- (-xxx-) Dev.: 0.34 2: --4)bDglcn--3)aDgal--3)bDglcn-- (-xxx-) Dev.: 0.34 3: [aDgal] |3 --4)bDglcn--4)bDglcn-- (-[x]xx-) Dev.: 0.42 4: --3)bDglcn--4)bDglcn--2)aDgal-- (-xxx-) Dev.: 0.43 5: --4)bDglcn--2)aDgal--3)bDglcn-- (-xxx-) Dev.: 0.43 |
[14] |
NOESY (ROESY) or HMBC (1 vs. 2) (3), (4), (5) posses much greater deviation |
P.p. 103 |
?Dglc ?Dgal ?Dgaln ?ribP etnP Widespread =ON |
1: [DetnP] |6 --4)bDglc--3)bDgal--3)bDgaln--2)DribP-- (-[x]xxxx-) Dev.: 0.422: [DetnP] |4 --6)bDglc--3)bDgal--3)bDgaln--2)DribP-- (-[x]xxxx-) Dev.: 0.42 3: [DetnP] |6 --3)bDgal--3)bDgaln--2)DribP--4)bDglc-- (-[x]xxxx-) Dev.: 0.42 4: [DetnP-4)bDglc] |3 --6)bDgal--3)bDgaln--2)DribP-- (-[xx]xxx-) Dev.: 0.42 4: [DetnP-6)bDglc] |3 --2)bDgal--3)bDgaln--2)DribP-- (-[xx]xxx-) Dev.: 0.42 |
[15] |
HMQC-TOCSY or methylation analysis (1,2) vs. (3,4,5) + {1H-31P} HMQC (1 vs. 2) |
P.v. O17 De-P |
?Dglc ?Dglcn ??fu3n ?DglcA Dbut Widespread =ON |
1: [Dbut] |2 --6)aDglcn--2)bDfu3n--3)aDglc--4)bDgla-- (-[x]xxxx-) Dev.: 0.342: [Dbut] |3 --2)bDfu3n--6)aDglc--4)bDgla--3)aDglcn-- (-[x]xxxx-) Dev.: 0.353: [Dbut--3)bLfu3n] |3 --2)aDglc--4)bDgla--6)aDglcn-- (-[xx]xxx-) Dev.: 0.36 4: [Dbut--3)bDfu3n] |3 --2)aDglc--4)bDgla--6)aDglcn-- (-[xx]xxx-) Dev.: 0.37 5: [Dbut--3)bLfu3n] |4 --3)aDglcn--6)aDglc--4)bDgla-- (-[xx]xxx-) Dev.: 0.37 |
[16] |
HMQC-TOCSY (Fuc3N C-3 displacement) (2) vs. (1) +methylation analysis or HMQC-TOCSY (2 vs. 3,4,5) |
P.v. O22 De-OAc |
?Dqu3n ??rha ??rha ?Dgla ?Dglcn Widespread =ON |
1: [aDqu3n] |2 --3)bLrha--4)aLrha--4)bDgla--3)bDglcn-- (-[x]xxxx-) Dev.: 0.242: [aDqu3n] |3 --4)aLrha--4)bDgla--3)bDglcn--4)bDrha-- (-[x]xxxx-) Dev.: 0.24 3: [aDqu3n] |3 --2)bLrha--4)aLrha--4)bDgla--3)bDglcn-- (-[x]xxxx-) Dev.: 0.25 4: [aDqu3n--3)aLrha] |2 --4)bDrha--3)bDglcn--4)bDgla-- (-[xx]xxx-) Dev.: 0.25 5: [aDqu3n--3)aLrha] |2 --3)bLrha--3)bDglcn--4)bDgla-- (-[xx]xxx-) Dev.: 0.29 |
[17] |
NOESY (ROESY) |
P.v. OX19 |
??quin 34)?Dgaln 4x)?Dgal ??quin 3x)?Dglcn P Widespread =ON Correction -0.1ppm |
1: [aLquin] |3 --4)aDgaln--4)aDgal--P--4)aLquin--3)bDglcn-- (-[x]xxxxx-) Dev.: 0.392: [aLquin--3)bDglcn] |4 --3)aDgaln--4)aDgal--P--4)aLquin-- (-[xx]xxxx-) Dev.: 0.39 3: [aLquin] |3 --4)aDgaln--4)aDgal--P--4)aLquin--3)aDglcn-- (-[x]xxxxx-) Dev.: 0.43 4: [aLquin--3)aDglcn] |4 --3)aDgaln--4)aDgal--P--4)aLquin-- (-[xx]xxxx-) Dev.: 0.43 5: [aLquin] [P] |4 |4 --3)aLquin--3)aDglcn--4)aDgal--3)aDgaln-- ([x]xxx[x]x) Dev.: 0.43 |
[18] |
13C Gated (1) vs. (3) + NOESY (ROESY) (1) vs. (2,4,5) |
E.coli O28 |
?Dglcn b?galf ?Dglcn ?gro P Widespread =OFF |
1: -4)bDglcn--3)bDgalf--3)aDglcn--2)Lgro--P-- (xxxxx) Dev.: 0.542: -4)bDglcn--3)bDgalf--3)aDglcn--2)Dgro--P-- (xxxxx) Dev.: 0.54 3: [bDglcn--3)bDgalf--2)Dgro--P] |4 --3)aDglcn-- ([xxxx]x) Dev.: 0.55 4: [bDglcn--3)bDgalf--2)Lgro--P] |4 --3)aDglcn-- ([xxxx]x) Dev.: 0.55 5: [bDglcn--3)bDgalf] |4 --3)aDglcn--2)Dgro--P-- ([xx]xxx) Dev.: 0.57 |
[19] |
optical rotation measurement (1 vs. 2) HMQC-TOCSY or methylation analysis (1 vs. 3,4,5) |
The resulting deviation is significantly sensitive to absolute configurations of input residues (which means that in most cases the absolute configurations are predicted with high accuracy), e.g. specifying (bLgal bDglcn Dalet P aDgal bDglc) as a monomeric composition in stead of (bDgal bDglcn Dalet P aDgal bDglc) leads to the following list of five best structures for the polysaccharide of P.mirabilis O3:
1: [P] [alet] |4 |3 --2)bDglc--3)bDglcn--6)aDgal--6)bLgal-- (-[x]xxx[x]x-) Dev.: 0.32 2: [alet--P] |6 --3)aDgal--6)bLgal--2)bDglc--3)bDglcn-- (-[xx]xxxx-) Dev.: 0.33 3: [alet--3)bLgal] |6 --3)aDgal--P--6)bDglc--3)bDglcn-- (-[xx]xxxx-) Dev.: 0.34 4: [alet] [P] |3 |6 --6)bLgal--2)bDglc--3)bDglcn--2)aDgal-- (-[x]xxx[x]x-) Dev.: 0.35 5: [alet] [P] |3 |3 --6)bLgal--2)bDglc--3)bDglcn--4)aDgal-- (-[x]xxx[x]x-) Dev.: 0.35
as compared to the primary (all monosaccharides have D configuration) list:
1: [alet--P] |6 --3)aDgal--6)bDglc--3)bDglcn--3)bDgal-- (-[xx]xxxx-) Dev.: 0.13
2: [alet--P] |6 --3)aDgal--6)bDglc--3)bDgal—3)bDglcn-- (-[xx]xxxx-) Dev.: 0.13
3: [alet--P] |6 --3)bDgal--3)bDglcn--3)aDgal--6)bDglc-- (-[xx]xxxx-) Dev.: 0.23 4: [alet--P] |6 --3)bDglcn--3)bDgal--3)aDgal--6)bDglc-- (-[xx]xxxx-) Dev.: 0.23 5: [alet--P] |6 --2)aDgal--6)bDglc--3)bDglcn--3)bDgal-- (-[xx]xxxx-) Dev.: 0.23
As it can be seen from these two lists of structures, the deviation of the best-fitting structure increased from 0.13 to 0.32 after changing the absolute configuration of one of residues to the value not corresponding to the proper structure. Thus BIOPSEL is the reliable way to determine absolute configurations of monosaccharides basing on the thorough differences in glycosylation effects in DD and DL pairs of monomers.