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GLYCOSYLATION manual

glycosylation

Written by J.M. Franklin.
Post all your questions about GLYCOSYLATION to the ATSAS Forum.

© ATSAS Team, 2001-2012

This is the manual for GLYCOSYLATION, a program to be used in conjunction with SASREF for rigid body modeling of glycosylated structures. Glycan groups are added onto PDB structures for improved modeling against experimental scattering data of glycosylated proteins.

Table of Contents

Manual

Introduction

GLYCOSYLATION adds glycan groups to asparagine (ASN) or serine (SER) residues of protein structures. The glycan groups are selected from a database of 50 precomputed structures found on glycosylated proteins ranging from 320 to 6820 Da. The structures were generated using Sweet2 which models the 3D structure of saccharides.

The program can be run automatically, where the residues and glycan structures are determined by the program, given the number of glycans to be added and the total molecular weight of the glycans.

Alternatively, expert mode can be used to specify exactly which glycan goes to which residue. This mode offers no detection of buried residues.

NOTE: Only ASN residues are considered in the automatic mode.

Running

Usage:

$ glycosylation <input pdb file> <output pdb file> [OPTIONS]

Here, the input pdb file is the protein structure to be glycosylated and the output pdb file is the glycosylated structure. OPTIONS are described in the following section.

Command-Line Arguments and Options

GLYCOSYLATION recognizes the following command-line options. Mandatory arguments to long options are mandatory for short options too.

Short Option Long Option Default Description
-k -keepASN False (optional) whether to keep the ASN residue from the glycan structure. This means there will be an additional amino acid residue to the corresponding protein residue. This is meant to be used for modeling the glycan as a separate rigid body.
-n -nsugars <number of gylcans> N/A The number of glycans to be added to the structure.
-m -mw <total molecular weight> N/A The total molecular weight of the glycan groups to be added.
-e -expert N/A Run in expert mode. NOTE: only the number of glycans needs to be specified at the command line, not the MW.
-v -version N/A Print version information and exit.
-h -help N/A Print the help text and exit.

Output files

The output file contains the atoms in pdb format with a new header. The header is formatted as follows:

 Parent PDB file:                   <input pdb file>
 Number of glycans requested:       <number of gylcans>
 Total molecular weight requested:  <total molecular weight>
 Keep ASN residues from glycans     <T or F>
 								   
 Glycan ASN  chain   Glycan ID      name             MW
 -----------------------------------------------------------
   1     60G   B          6      complex_5_1       1141.0
   2     78    F         28      hm_6_1            1155.0
   3    204B   F          8      complex_6_2       1141.0
   4     78    H         27      hm_5_2             992.9
     Total molecular weight of glycans added:      4429.8

Examples

Automatic

Glycosylate 1XMN.pdb with 4 glycans about 1000 Da each.

$ glycosylation 1XMN.pdb gly_1XMN.pdb -n 4 -mw 4000

 Glyco data successfully loaded.
 input PDB FILE: 1XMN.pdb
 output PDB FILE: gly_auto_1XMN.pdb
IGNORED 1XMN.pdb A (less than 5 residues)
 Found (          28 ) non-buried ASN residues out of (          42 ) ASN residues.
 Calculated approximately   1000.0000000000000       Daltons per glycosylation.
 Found           7  glyco structures available for glycosylation.
   CA  ASN B  60G
 Placing glycan complex_5_1      on residue   CA  ASN B  60G
   CA  ASN F  78 
 Placing glycan hm_6_1           on residue   CA  ASN F  78 
   CA  ASN B  62 
 WARNING: Glyco molecule moved more than 8 Angstroms. Could be a missed buried residue. Reinitializing with another ASN residue.
   CA  ASN H 143 
 WARNING: Glyco molecule moved more than 8 Angstroms. Could be a missed buried residue. Reinitializing with another ASN residue.
   CA  ASN B  78 
 WARNING: Glyco molecule moved more than 8 Angstroms. Could be a missed buried residue. Reinitializing with another ASN residue.
   CA  ASN H  60G
 WARNING: Glyco molecule moved more than 8 Angstroms. Could be a missed buried residue. Reinitializing with another ASN residue.
   CA  ASN B  95 
 WARNING: Glyco molecule moved more than 8 Angstroms. Could be a missed buried residue. Reinitializing with another ASN residue.
   CA  ASN F  60G
 WARNING: Glyco molecule moved more than 8 Angstroms. Could be a missed buried residue. Reinitializing with another ASN residue.
   CA  ASN B 147D
 WARNING: Glyco molecule moved more than 8 Angstroms. Could be a missed buried residue. Reinitializing with another ASN residue.
   CA  ASN F 204B
 Placing glycan complex_6_2      on residue   CA  ASN F 204B
   CA  ASN B 159 
 WARNING: Glyco molecule moved more than 8 Angstroms. Could be a missed buried residue. Reinitializing with another ASN residue.
   CA  ASN H  78 
 Placing glycan hm_5_2           on residue   CA  ASN H  78 
 Pdb file written:  gly_1XMN.pdb

Expert

Glycosylate 1XMN.pdb with 4 glycans and run in expert mode.

$> glycosylation 1XMN.pdb gly_1XMN.pdb -n 4 -e 

 Entering expert mode.
 Glyco data successfully loaded.
 input PDB FILE: 1XMN.pdb
 output PDB FILE: gly_1XMN.pdb
 Found (         105 ) non-buried ASN residues out of (         105 ) ASN residues.
 Choose from the following ASN and SER residues:
<  1>  CA  SER B  20  
<  2>  CA  SER B  27  
<  3>  CA  SER B  36A 
<  4>  CA  SER B  45  
<  5>  CA  SER B  48  
<  6>  CA  ASN B  60G 
<  7>  CA  ASN B  62  
<  8>  CA  SER B  72  
<  9>  CA  ASN B  78  
< 10>  CA  SER B  83  
< 11>  CA  ASN B  95  
< 12>  CA  ASN B  98  
< 13>  CA  SER B 115  
< 14>  CA  SER B 129B 
< 15>  CA  ASN B 143  
.
.
.
<105>  CA  SER H 214  
Enter residue choices one at a time:
6
7
37
51
 For each of the chosen ASN residues, choose a  
 sugar by first giving molecular weight range   
 then selecting from the available structures.

Enter approximate MW (Da):
1000
 Found           7  glyco structures available for glycosylation.
 
Structure <  1>
Molecular weight:  1141.0
 Name:complex_5_1                                       
 
                  A-D-MANP-(1-6)+                                                                                                                                                                        
                                |                                                                                                                                                                        
            A-D-MANP-(1-3)-B-D-MANP-(1-4)-B-D-GLCPNAC-(1-4)-B-D-GLCPNAC-(1-4)-ASN                                                                                                                        
                                |                                                                                                                                                                        
                  B-D-XYLP-(1-2)+                                                                                                                                                                        
 
 
 
Structure <  2>
Molecular weight:  1141.0
 Name:complex_6_2                                       
 
                  A-D-MANP-(1-6)+                                                                                                                                                                        
                                |                                                                                                                                                                        
            A-D-MANP-(1-3)-B-D-MANP-(1-4)-B-D-GLCPNAC-(1-4)-B-D-GLCPNAC-(1-4)-ASN                                                                                                                        
                                |                                                                                                                                                                        
                  B-D-XYLP-(1-2)+                                                                                                                                                                        
 
 
 
Structure <  3>
Molecular weight:   846.7
 Name:hm_4_1                                            
 
 a-D-Manp-(1-3)-b-D-Manp-(1-4)-b-D-GlcpNAc-(1-4)-b-D-GlcpNAc-(1-4)-Asn                                                                                                                                   
 
 
 
Structure <  4>
Molecular weight:  1008.9
 Name:hm_5_1                                            
 
            A-D-MANP-(1-6)+                                                                                                                                                                              
                          |                                                                                                                                                                              
                     B-D-MANP-(1-4)-B-D-GLCPNAC-(1-4)-B-D-GLCPNAC-(1-4)-ASN                                                                                                                              
                          |                                                                                                                                                                              
            A-D-MANP-(1-3)+                                                                                                                                                                              
 
 
 
Structure <  5>
Molecular weight:   992.9
 Name:hm_5_2                                            
 
                                   a-L-Fucp-(1-6)+                                                                                                                                                       
                                                 |                                                                                                                                                       
                                            b-D-GlcpNAc-(1-4)-Asn                                                                                                                                        
                                                 |                                                                                                                                                       
  a-D-Manp-(1-6)-b-D-Manp-(1-4)-b-D-GlcpNAc-(1-4)+                                                                                                                                                       
 
 
 
Structure <  6>
Molecular weight:  1155.0
 Name:hm_6_1                                            
 
                                       A-L-FUCP-(1-6)+                                                                                                                                                   
                                                     |                                                                                                                                                   
            A-D-MANP-(1-6)+                  B-D-GLCPNAC-(1-4)-ASN                                                                                                                                       
                          |                          |                                                                                                                                                   
                     B-D-MANP-(1-4)-B-D-GLCPNAC-(1-4)+                                                                                                                                                   
                          |                                                                                                                                                                              
            A-D-MANP-(1-3)+                                                                                                                                                                              
 
 
 
Structure <  7>
Molecular weight:  1171.0
 Name:hm_6_2                                            
 
            A-D-MANP-(1-3)-A-D-MANP-(1-6)+                                                                                                                                                               
                                         |                                                                                                                                                               
                                    B-D-MANP-(1-4)-B-D-GLCPNAC-(1-4)-B-D-GLCPNAC-(1-4)-ASN                                                                                                               
                                         |                                                                                                                                                               
                           A-D-MANP-(1-3)+                                                                                                                                                               
 
 
 
 Choose from the following structures:
1 

Repeat selection process for other glycans...

 Placing glycan complex_5_1      on residue   CA  ASN B  60G
 Placing glycan complex_5_1      on residue   CA  ASN B  62 
 WARNING: Glyco molecule moved more than 8 Angstroms. Could be a missed buried residue.
 Placing glycan complex_5_1      on residue   CA  ASN D  78 
 Placing glycan complex_5_1      on residue   CA  ASN D 204B
 Pdb file written:  gly_1XMN.pdb

  Last modified: February 25, 2015

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