Computational insights into dynamics of protein aggregation and enzyme-substrate interactions

Mehmet Ozbil, Arghya Barman, Ram Prasad Bora, Rajeev Prabhakar

Research output: Contribution to journalArticlepeer-review

4 Scopus citations


In this Perspective, the roles of protein dynamics have been discussed in the aggregation of amyloid beta (Aβ) peptides and formation of enzyme-substrate complexes of beta-secretase (BACE1) and insulin-degrading enzyme (IDE). The studies regarding the influence of individual amino acid residues and specific regions on the structures and oligomerization of early Aβ aggregates and computations of their translational and rotational diffusion coefficients and order parameters exhibited that even the short-time-scale molecular dynamics simulations can reproduce certain experimental parameters with reasonable accuracy. The simulations elucidating the enzyme-substrate interactions of BACE1 and IDE successfully showed that the chemical nature and length of the substrates influence the dynamics and plasticity of both the enzyme and substrate. An atomic-level understanding of these processes will advance our efforts to develop therapeutic strategies for several deadly diseases through the design of small molecules with antiaggregation properties and substrate-specific designer forms of enzymes.

Original languageEnglish (US)
Pages (from-to)3460-3469
Number of pages10
JournalJournal of Physical Chemistry Letters
Issue number23
StatePublished - Dec 6 2012

ASJC Scopus subject areas

  • Materials Science(all)
  • Physical and Theoretical Chemistry


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