IMSc Webinar

Structural and functional insights into biological systems through molecular modelling and simulations

Kanagasabai Balamurugan

Biotechnologisches Zentrum (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Germany.

Computational biomolecular simulations are highly useful scientific methodology for understanding the biomolecular systems at an extremely precise length and time scales. Most of the biomolecular structure and function are dictated by the changes in the non-covalent interactions existing between the interacting molecular systems, and thus the computational methodologies like modelling, docking and molecular dynamics simulation were demonstrated to be an ideal tool to understand the biomolecular structure and function. The results of the following research topics are discussed in this presentation. (1) the structure and stability of the protein secondary structural element α-helix on interaction with carbon nano materials.1-3
(2) interaction of PET (positron emission tomography) tracers with amyloid beta peptides(Aβ42) for the diagnosis of Alzheimer’s disease.4,5 (3) interaction of glycosaminoglycans (GAGs) with various growth factors pertaining to the skin and bone degeneration.6-10

References:
(1) K. Balamurugan, R. Gopalakrishnan, S. Sundar Raman, and V. Subramanian. Exploring the changes in the structure of α-helical peptides
adsorbed onto a single walled carbon nanotube using classical molecular dynamics simulation. J. Phys. Chem. (B), 114, (2010) 14048–14058
(Published as Cover Article).
(2) K. Balamurugan, E. R. Azhagiya Singam and V. Subramanian. Effect of curvature on the α-helix breaking tendency of carbon
nanomaterials. J. Phys. Chem. (C), 115, (2011), 8886–8892. (Published as Cover Article)
(3) K. Balamurugan and V. Subramanian. Length dependent stability of α-helical peptide upon adsorption to single walled carbon nanotube.
Biopolymers, 99, (2013), 357-369.
(4) K. Balamurugan*, N.A. Murugan and H. Ågren. Multistep modeling strategy to improve the binding affinity prediction of PET tracers to
Aβ42: case study with styrylbenzoxazole derivatives. ACS Chem. Neurosci., (2016), 7, 1698–1705. *Published as corresponding author
(5) K. Balamurugan*, N. A. Murugan*, B. Långström, A. Nordberg, and H. Ågren*. Effect of Alzheimer familial chromosomal mutations on
the amyloid fibril interaction with different PET tracers: Insight from molecular modeling studies. ACS Chem. Neurosci., (2017), 8, 2655–
2666. *Published as corresponding author
(6) S. Thönes#, S. Rother#, T. Wippold# , J. Blaszkiewicz , K. Balamurugan , G. Ruiz-Gómez, S. Moeller, M. Schnabelrauch, D. Scharnweber,
J. Rademann, A. Saalbach , M. Teresa Pisabarro , V. Hintze and U. Anderegg. Hyaluronan/collagen hydrogels containing sulfated hyaluronan
improve wound healing by sustained release of heparin-binding EGF-like growth factor. Acta Biomaterialia, (2019), 86, 135-147. #authors
contributed equally
(7) L. Koehler#, G. Ruiz-Gómez#, K. Balamurugan, S. Rother, S. Möller, M. Schnabelrauch, J. Blaszkiewicz, S. Köhling, S. Djordjevic, J.
Rademann, D. Scharnweber, M. Teresa Pisabarro and V. Hintze. Dual Action of sulfated hyaluronan on angiogenic processes in relation to
vascular endothelial growth factor-A. Scientific Reports, (2019), 9, 1-18. #authors contributed equally
(8) . other . uiz- mez K. Balamurugan, L. Koehler, K. M. Fiebig, V. D. Galiazzo, U. Hempel, S. Moeller, M. Schnabelrauch, J.
Waltenberger, M. T. Pisabarro, D. Scharnweber and V. Hintze. Hyaluronan/Collagen Hydrogels with Sulfated Glycosaminoglycans Maintain
VEGF165 Activity and Fine-Tune Endothelial Cell Response. ACS Applied Bio Materials, (2021), 4, 494-506.
(9) K. Balamurugan, L. Koehler, J. Dürig, U. Hempel, J. Rademann, V. Hintze and M. T. Pisabarro. Structural insights into the modulation of
PDGF/PDGFR-β complexation by hyaluronan derivatives. Biol. Chem. (2021), 402, 1441–1452.
(10) K. Balamurugan and M. T. Pisabarro. Role of water solvation in stabilizing the anion-π interaction in proteins. AC Omega (2021), 6,
25350–25360.

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