glycosciences.de - LINUCS - LInear Notation for Unique description of Carbohydrate Sequences

LINUCS: LInear Notation for Unique description of Carbohydrate Sequences

Introduction

LINUCS was chosen to fulfil to following conditions: Input of extended, non-graphic nomenclature to describe carbohydrate structures. Resulting linear code is closely related to notations and abbreviations recommended by IUPAC. Number of additional rules to define the priority of the branches is low Extended nomenclature of complex carbohydrates contains all information to define the hierarchy. LINUCS is applicable to all types of carbohydrates (macrocyclic system are currently not implemented) . Remaining unassigned linkage information are tolerated
Input:	A structure using the extended, non-graphic nomenclature (in ASCII writing) to describe complex carbohydrates as recommended by IUPAC
Output:	A linear, unique notation

Contact: Andreas Bohne

References

Service
	If you want to convert your own structure to a uniqe you can use this service. Just click the Input/Work button:
	We prepared an example for you if you want to see how the system works. Just click the Example button:

Why do we need a unique description: The following structures illustrates the problem
Saccharide taken from CarbBank	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)+
Variation 1	a-D-Manp-(1-2)-a-D-Manp-(1-3)+ \| a-D-Manp-(1-6)+ \| \| a-D-Manp-(1-2)-a-D-Manp-(1-6)+ 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)+
Variation 2	a-D-Manp-(1-2)-a-D-Manp-(1-2)-a-D-Manp-(1-3)+ \| a-D-Manp-(1-2)-a-D-Manp-(1-6)+ b-D-Manp-(1-4)-b-D-GlcpNAc-(1-4)-b-D-GlcpNAc-(1-4)-Asn \| \| a-D-Manp-(1-6)+ \| a-D-Manp-(1-2)-a-D-Manp-(1-3)+
Variation 3	a-D-Manp-(1-2)-a-D-Manp-(1-2)-a-D-Manp-(1-3)+ \| 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-(1-6)+ \| a-D-Manp-(1-2)-a-D-Manp-(1-6)+
Description:	Dorland L; van Halbeek H; Vliegenthart JFG; Lis H; Sharon Primary structure of the carbohydrate chain of soybean agglutinin. A reinvestigation by high-resolution 1H-NMR spectroscopy J Biol Chem (1981) 256: 7708-7711

In the example you can see four times the same chemical structure but with another
notation. Only the following notation can describe the structure unique:

The first step is to transform the carbohydrate in SWEET-notation and
the second step is to make it unique.

[][Asn]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{
[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{
[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}

In a tab'd writing you can see the nested structure better:

[][Asn]{
  [(4+1)][b-D-GlcpNAc]{
    [(4+1)][b-D-GlcpNAc]{
      [(4+1)][b-D-Manp]{
        [(3+1)][a-D-Manp]{
          [(2+1)][a-D-Manp]{
            [(2+1)][a-D-Manp]{}
            }
          }
        [(6+1)][a-D-Manp]{
          [(3+1)][a-D-Manp]{
            [(2+1)][a-D-Manp]{}
            }
          [(6+1)][a-D-Manp]{
            [(2+1)][a-D-Manp]{}
            }
          }
        }
      }
    }
  }

The blue marked connections are points where the sorting makes the
structure unique. The structure starts with the reducing end. This is the same point where nature
starts building the complex carbohydrate structure. It garantes the there is only one end.

You can transform the structure back to IUPAC nomenclature by reversing the structure. In this case
the example structure is identical with variation no. 3.

References

[1]	Dorland L, van Halbeek H, Vleigenthart JF, Lis H, Sharon N: Primary structure of the carbohydrate chain of soybean agglutinin. A reinvestigation by high resolution 1H NMR spectroscopy J Biol Chem 1981, 256(15): 7708-11.

When citing LINUCS, please refer to:

Bohne-Lang A, Lang E, Forster T, von der Lieth CW:
LINUCS: linear notation for unique description of carbohydrate sequences.
Carbohydr Res 2001, 336: 1-11.