Supplementary Information
Hierarchical sampling for metastable conformers determine biomolecular recognition:
The case of Malectin and Di-glucosylated-N-glycan interactions
M. Ashalatha Sreshty and Avadhesha Surolia*
Affliations:
Molecular Biophysics Unit, Indian Institute of Science, Bangalore – 560012, India
*To whom correspondence should be addressed:
Prof. Avadhesha Surolia
Molecular Biophysics Unit,
Indian Institute of Science,
Bangalore – 560012, India
Email: surolia@mbu.iisc.ernet.in
Running Title: Metastable conformations reveal Malectin’s specificity
b)
Figure S1: (a) Malectin structure is shown in cartoon representation and was prepared using Pymol v1.5 and
(b) Glc3Man9GlcNAc2-N shown with three terminal glucose units in red, nine mannose units in green and two
N-acetylglucosamine units in blue, which are covalently attached to Asparagine residue (NSA) was constructed
using the ChemBioDraw Ultra 13.0.
Figure S2. RMSD plots of free structures in aqueous solution
Figure S3. Plot showing radius of gyration of malectin (green) and its four complexes over a time period of 110ns
Figure S4. Color coded Matrix plot of RMSIP computed for Mlec-DiG-N-glycan complex between four
windows of MD simulations. (i) Scale for RMSIP calculated using MD trajectories obtained from different
windows of time period and (ii) scale for the RMSIP calculated using the same trajectory
Figure S5. Three-dimensional free energy landscapes (FELs) were obtained from different PCAs at multiple
levels of heirarchial sampling. FELs for Mlec-MonoG complex was obtained by (a) cPCA, (b) dPCAb, (c)
dPCAcrd and (d) dPCAgly
Figure S6. Gibbs free energy landscapes represent energy minima of Mlec-DiG complex obtained by (a) cPCA,
(b) dPCAb, (c) dPCAcrd and (d) dPCAgly
Figure S7. Gibbs free energy landscapes represent energy minima of Mlec-TriG complex obtained by (a) cPCA,
(b) dPCAb, (c) dPCAcrd and (d) dPCAgly
Figure S8. Cluster validity indices computed on k-means geometrical partitioning of MonoG-N-glycan
Figure S9. Cluster validity indices computed on PAM geometrical partitioning of MonoG-N-glycan
Figure S10. Cluster validity indices computed on k-means geometrical partitioning of Mlec-MonoG-N-glycan
complex
Figure S11. Cluster validity indices computed on PAM geometrical partitioning of Mlec-MonoG-N-glycan
complex
Figure S12. Cluster validity indices computed on k-means geometrical partitioning of Mlec-TriG-N-glycan
complex
Figure S13. Cluster validity indices computed on PAM geometrical partitioning of Mlec-TriG-N-glycan
complex
Figure S14. Bar plot representing the cosine content of four PCs from the nine trajectories of molecular systems
containing metastable conformations
Figure S15. Hydropathy versus size (ΔASAt) for the four malectin-N-glycan interfaces. The hydropathy index
calculated for polar surface area (fp) is represented as triangle and non-polar surface (fnp) as square.
Figure S16. Plot showing the values of gap indices (GI) for the three malectin-N-glycan complexes
Figure S17. Occurrence of hydrogen bonds in Mlec-DiG complex, as a function of time
Figure S18. Schematic representation of sugar-aromatic interactions showing geometries considered in this
study. (a) Stacking interactions between the sugar and aromatic amino-acids are shown. T he distance between
the centroids of two rings is represented as Rcen, the interplanar dihedral angle as  and the shortest distance
between the carbons of the pair is represented as Rclo, (b) Schematic representation of CH-π interactions is
shown. The distance between hydrogen donor (C) and the centroid of the aromatic ring is denoted as d c-x and the
angle between donor-hydrogen-acceptor as C-H-x
Figure S19. Plot showing the distance calculated between the center of mass of malectin-CRD and the three Nglycans without any position restraint between their atoms
Figure SV1: Video showing the dynamics of metastable conformations of MlecDiG complex
Figure SV2: Animation detailing the sequential binding event of malectin upon recognizing DiG-N-glycan