Interaction of arginine, lysine, and guanidine with surface residues of lysozyme: Implication to protein stability

Dhawal Shah, Abdul Rajjak Shaikh

Research output: Contribution to journalArticlepeer-review

11 Citations (Scopus)

Abstract

Additives are widely used to suppress aggregation of therapeutic proteins. However, the molecular mechanisms of effect of additives to stabilize proteins are still unclear. To understand this, we herein perform molecular dynamics simulations of lysozyme in the presence of three commonly used additives: arginine, lysine, and guanidine. These additives have different effects on stability of proteins and have different structures with some similarities; arginine and lysine have aliphatic side chain, while arginine has a guanidinium group. We analyze atomic contact frequencies to study the interactions of the additives with individual residues of lysozyme. Contact coefficient, quantified from contact frequencies, is helpful in analyzing the interactions with the guanidine groups as well as aliphatic side chains of arginine and lysine. Strong preference for contacts to the additives (over water) is seen for the acidic followed by polar and the aromatic residues. Further analysis suggests that the hydration layer around the protein surface is depleted more in the presence of arginine, followed by lysine and guanidine. Molecular dynamics simulations also reveal that the internal dynamics of protein, as indicated by the lifetimes of the hydrogen bonds within the protein, changes depending on the additives. Particularly, we note that the side-chain hydrogen-bonding patterns within the protein differ with the additives, with several side-chain hydrogen bonds missing in the presence of guanidine. These results collectively indicate that the aliphatic chain of arginine and lysine plays a critical role in the stabilization of the protein.

Original languageEnglish
Pages (from-to)104-114
Number of pages11
JournalJournal of Biomolecular Structure and Dynamics
Volume34
Issue number1
DOIs
Publication statusPublished - Jan 2 2016

Keywords

  • Additives
  • contact coefficient
  • lysozyme
  • molecular dynamics simulations

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology

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