Interaction of an ionic complementary peptide with a hydrophobic graphite surface

Abstract

Protein adsorption on a surface plays an important role in biomaterial science and medicine. It is strongly related to the interaction between the protein residues and the surface. Here we report all-atom molecular dynamics simulations of the adsorption of an ionic complementary peptide, EAK16-II, to the hydrophobic highly ordered pyrolytic graphite surface. We find that, the hydrophobic interaction is the main force to govern the adsorption, and the peptide interchain electrostatic interaction affects the adsorption rate. Under neutral pH condition, the interchain electrostatic attraction facilitates the adsorption, whereas under acidic and basic conditions, because of the protonation and deprotonation of glutamic acid and lysine residues, respectively, the resulting electrostatic repulsion slows down the adsorption. We also found that under basic condition, during the adsorption peptide Chain II will be up against a choice to adsorb to the surface through the hydrophobic interaction or to form a temporary hydrophobic core with the deposited peptide Chain I. These results provide a basis for understanding some of the fundamental interactions governing peptide adsorption on the surface, which can shed new light on novel applications, such as the design of implant devices and drug delivery materials.

Efficient and Unbiased Sampling of Biomolecular Systems in the Canonical Ensemble: A Review of Self‐Guided Langevin Dynamics

“…In an SGMD simulation, the system undergoes an accelerated systematic motion, which is defined by the local averaging time, t L , while maintaining a desired temperature. Many applications have demonstrated that SGMD simulations have an enhanced conformational search ability (Choudhary & Clancy 2005a; 2005b; Lung et al 2001; Sheng et al 2010a; 2010b; Varady et al 2002; Wu & Wang 2000; 2001; Wu et al 2002). Shinoda and Mikami extended SGMD to the NPT ensemble (Shinoda & Mikami 2001) and later combined it with the rigid body dynamics (Shinoda & Mikami 2003).…”

“…The enhanced conformational searching ability of SGMD and SGLD are demonstrated by their many applications in protein folding (Lee & Chang 2010; Lee & Olson 2010; Wu & Wang 2000; 2001; Wu et al 2002), ligand binding (Lung et al 2001; Varady et al 2002; Yang et al 2004), conformational transitions (Damjanovic et al 2009; Damjanovic et al 2008a; Damjanovic et al 2008b; Pendse et al 2010), phase transitions (Abe & Jitsukawa 2009; Choudhary & Clancy 2002; Chowdhury et al 2003; Tsuru et al 2010; Wu & Wang 1999), and surface adsorption (Sheng et al 2010a; 2010b). There are several method developments along the same concept of SGLD.…”

“…The self-guided molecular dynamics (SGMD) (Wu & Wang 1998; 1999) and the self-guided Langevin dynamics (SGLD) (Wu & Brooks 2003; Wu & Brooks 2011a; 2011b) simulation methods were developed for an efficient conformational search and have found many applications to study rare events, such as protein folding (Lee & Chang 2010; Lee & Olson 2010; Wen et al 2004; Wen & Luo 2004; Wu & Sung 1999; Wu & Brooks 2004; Wu & Wang 2000; 2001; Wu et al 2002), and ligand binding (Lung et al 2001; Varady et al 2002; Yang et al 2004), docking (Chandrasekaran et al 2009), conformational transitions (Damjanovic et al 2009; Damjanovic et al 2008a; Damjanovic et al 2008b; Pendse et al 2010), crystallization (Abe & Jitsukawa 2009; Choudhary & Clancy 2005a; 2005b; Tsuru et al 2010; Wu & Wang 1999), and surface absorption (Sheng et al 2010a; 2010b)…”

“…36)(Sheng et al 2010a; 2010b). Protein adsorption plays an important role in bioactive implant devices and drug delivery materials design.…”

Force-momentum-based self-guided Langevin dynamics: A rapid sampling method that approaches the canonical ensemble

“…3) simulation methods were developed for efficient conformational searching and have found many applications for the study of rare events such as protein folding, [4][5][6][7][8][9][10][11][12] ligand binding, 13 docking, 14 conformational transition, [15][16][17] and surface absorption. [18][19][20][21] While SGMD/SGLD can accelerate slow events to an affordable time scale, the perturbation in conformational distribution due to the self-guiding force was not quantitatively understood until recently. 22 A common practice for SGMD or SGLD simulations is to limit the guiding factor to a small range so that the effect on conformational distribution is very small and can be neglected.…”