Protein-glycosaminoglycan interactions: computational approaches

Here you can download home-made libraries for monomeric saccharide residues which are building blocks of natural and artificial GAG. The libraries are compatible with AMBER molecular dynamics package [1]. All of them were built using already existing libraries for their non-sulfated derivatives from GLYCAM06 [2]. Sulfate groups were added with the charges obtained from ab initio calculations [3], and the charges on respective oxygens were adjusted so that the charge of the residue was modified by -1 per each sulfate group when compared to the source library used for its construction.


In order to use these libraries for production of topology and coordinate files to be further used for AMBER simulations do the following in tleap or xleap:


Source GLYCAM06 force field: source $AMBERHOME/dat/leap/cmd/leaprc.GLYCAM_06j-1

Load the library (LIB.lib) you need: loadoff LIB.lib

Now you can either use sequence command to build your GAG: new_unit=sequence { … LIB …}

Or you can read the data from the pdb, where the residues are already renamed to be compatible with the nomenclature of the libraries:new_unit=loadpdb my_pdb_which_includes_residue_LIB.pdb


Be careful Ido2UA residues:if you want to build a heparin molecule or a molecule, which contains Ido2UA, pay attention to the fact that this residue rather exists in 1C4and 2S0 conformations. In our libraries, however, ALL the residues are in 4C1 conformation. Therefore, DO NOT use sequence command to build your GAG. Instead you can use these two prepared files with heparin dp10 with Ido2SUA in 1C4 and 2S0 conformations and read them by loadpdb command. These structures originate from the experimental structure (PDB ID: 1HPN) and contain already renamed residues/atoms to be compatible with our libraries. If you use an experimental structure of a protein complex with heparin, just rename the residues according to the nomenclature in our libraries and read them in. The same applies to the residues, for which you know that their conformations are not 4C1.


1. Case DA, Berryman JT, Betz RM, Cerutti DS, Cheatham TE, Darden TA, Duke RE, Giese TJ, Gohlke H, Goetz AW, Homeyer N, Izadi S, Janowski P, Kaus J, Kovalenko A, Lee TS, LeGrand S, Li P, Luchko T, Luo R, Madej B, Merz KM, Monard G, Needham P, Nguyen H, Nguyen HT, Omelyan I, Onufriev A, Roe DR, Roitberg A, Salomon-Ferrer R, Simmerling CL, Smith W, Swails J, Walker RC, Wang J, Wolf RM, Wu X, York DM, Kollman PA. AMBER 14. San Francisco: University of California; 2015.

2. Kirschner K, Yongye A, Tschampel S, González-Outeiriño J, DaNon-terminalls C, Foley L, Woods R. GLYCAM06: a generalizable biomolecular force field. carbohydrates. J. Comput. Chem. 2008;29:622–655.

3. Huige C, Altona C. Force field parameters for sulfates and sulfamates based on Ab initio calculations: extensions of AMBER and CHARMm Fields. J. Comput. Chem. 1995;16:56–79.


AMBER library

(residue name)

Chemical formula

Terminal

/non-terminal

Carbon participating

in glycosidic linkage

Sulfation pattern

01G α-D-Glc(2S,3S,6S) Terminal - 2S, 3S, 6S
02u α-L-IdoA(2S) Terminal - 2S
02Y α-D-Glc(NS) Terminal - NS
02Z β-D-GlcA(2S) Terminal - 2S
03u α-L-IdoA(3S) Terminal - 3S
03Z β-D-GlcA(3S) Terminal - 3S
04B β-D-GlcNAc(4S) Terminal - 4S
04V β-D-GalNAc(4S) Terminal - 4S
04Y α-D-GlcNAc(4S) Terminal - 4S
06B α-D-GlcNAc(6S) Terminal - 6S
06L β-D-Gal(6S) Terminal - 6S
06V β-D-GalNAc(6S) Terminal - 6S
06Y α-D-GlcNAc(6S) Terminal - 6S
07B α-D-GlcNAc(4S,6S) Terminal - 4S,6S
07u α-L-IdoA(2S,3S) Terminal - 2S,3S
07V β-D-GalNAc(4S,6S) Terminal - 4S,6S
07Y α-D-Glc(6S,NS) Terminal - 6S,NS
07Z β-D-GlcA(2S,3S) Terminal - 2S,3S
08G α-D-Glc(2S,6S) Terminal - 2S,6S
09G α-D-Glc(3S,6S) Terminal - 3S,6S
S7Z β-D-GlcA(2S,3S,4S) Terminal - 2S,3S,4S
34B β-D-GlcNAc(4S) Non-Terminal 3 4S
34V β-D-GalNAc(4S) Non-Terminal 3 4S
36B α-D-GlcNAc(6S) Non-Terminal 3 6S
36L β-D-Gal(6S) Non-Terminal 3 6S
36V β-D-GalNAc(6S) Non-Terminal 3 6S
36Y α-D-GlcNAc(6S) Non-Terminal 3 6S
37B β-D-GlcNAc(4S,6S) Non-Terminal 3 4S,6S
37V β-D-GalNAc(4S,6S) Non-Terminal 3 4S,6S
39Y α-D-GlcNAc(4S,6S) Non-Terminal 3 4S,6S
41G β-D-Glc(2S,3S,6S) Non-Terminal 4 2S,3S,6S
42u α-L-IdoA(2S) Non-Terminal 4 2S
42Y α-D-Glc(NS) Non-Terminal 4 NS
42Z β-D-GlcA(2S) Non-Terminal 4 2S
43u α-L-IdoA(3S) Non-Terminal 4 3S
43Z α-D-GlcA(3S) Non-Terminal 4 3S
46V β-D-GalNAc(6S) Non-Terminal 4 6S
46Y α-D-GlcNAc(6S) Non-Terminal 4 6S
47u α-L-IdoA(2S,3S) Non-Terminal 4 2S,3S
47Y α-D-Glc(6S,NS) Non-Terminal 4 6S,NS
47Z β-D-GlcA(2S,3S) Non-Terminal 4 3S,3S
48G α-D-Glc(2S,6S) Non-Terminal 4 2S,6S
49G α-D-Glc(3S,6S) Non-Terminal 4 3S,6S
46B α-D-GlcNAc(6S) Non-Terminal 4 6S
49Y α-D-Glc(2S,6S,NS) Non-Terminal 4 2S,6S,NS
ROS SO3- Non-Terminal 4 2S,6S,NS

Biomolecular modelling: methodology and case studies in computational biology


Introduction to the course. Force field. Docking: Lecture1

Molecular Dynamics (MD): Lecture2

Solvent in biomolecular modelling: Lecture3

Protein Folding: Lecture4

Computational glycobiology: Lecture5

Basics of QM: Lecture6

MD, QM and NMR Lecture7


Introduction to Molecular and Cellular Biology


Introduction to cell chemistry and biosynthesis: Lecture1, Lecture2, Lecture3-4, Lecture5-6

Cell organization: Lecture7-8, Lecture9, Lecture10-11

Cellular nucleus: Lecture12-13

Cell membrane: Lecture14-16

Vesicular transport: Lecture17-18

Cellular signaling: Lecture19-20

Cell cycle: Lecture21-22, Lecture23-24

Cell junctions and adhesion: Lecture25-26

This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 665778.