Molecular Simulation Studies of the Orientation and Conformation of Cytochrome c Adsorbed on Self-Assembled Monolayers

Abstract

Cytochrome c (Cyt-c) is an important membrane electron-transfer protein. To maximize its electron transfer, adsorbed Cyt-c should have a preferred orientation with its heme ring close and perpendicular to the surface. Moreover, the adsorbed Cyt-c should keep its native conformation. In this work, the orientation and conformation of Cyt-c adsorbed on carboxyl-terminated self-assembled monolayers (SAMs) are investigated by a combined Monte Carlo and molecular dynamics simulation approach. The root-mean-square deviation, radius of gyration, eccentricity, dipole moment, heme orientation, and superimposed structures of Cyt-c were calculated. Simulation results show that the desired orientation of Cyt-c with its heme group perpendicular to the surface could be obtained on a negatively charged surface. The direction of the dipole of Cyt-c, contributed significantly by both lysine residues near the surface and glutamic acid residues far away from the surface, determines the final orientation of Cyt-c adsorbed on a charged surface. Lysine residues Lys25, Lys27, Lys72, and Lys79 are responsible for the strong electrostatic interactions with the surface. A possible electron-transfer pathway is proposed (i.e., iron−His18−Cys17−Gln16−surface and iron−Met80−Lys79−surface). The effect of the strength of negatively charged surfaces on the conformation of adsorbed Cyt-c is studied. Although higher surface charge density of a negatively charged surface favors its preferred orientation, too high a surface charge density will cause a severe conformational change of the adsorbed protein, resulting in the loss of bioactivity of the adsorbed protein.

Modeling and simulation of protein–surface interactions: achievements and challenges

“…However, a recent study (Utesch et al 2013) reporting a titration curve of an amino-terminated alkanethiol SAM showed that the level of ionization was very sensitive at pH values around 6 (with 16 ± 5% protonation at pH 7 and 52 ± 9% at pH 6). A positive correlation between the ionization level of a SAM and the strength of adsorption of charged proteins was found (Zhou et al 2004;Utesch et al 2013). Therefore, it is crucial to compute and model the surface ionization to obtain reliable results compatible with experiments.…”

“…Therefore, it is crucial to compute and model the surface ionization to obtain reliable results compatible with experiments. The protonation states of SAMs in modeling studies are mostly represented by random assignment of protonated and deprotonated groups (Alvarez-Paggi et al 2013;Utesch et al 2012;Zhou et al 2004). In several studies, they are represented either by a uniform distribution of small partial charges (Sun et al 2005) or by large partial charges being assigned to functional groups in neutral surfaces (Wang et al 2010b).…”

“…Examples include simulations for structural refinement of docked complexes (Aliaga et al 2011;Alvarez-Paggi et al 2013;Brancolini et al 2012Brancolini et al , 2015Imamura et al 2007), and for the investigation of the binding orientations of proteins on surfaces (Alvarez-Paggi et al 2010;Boughton et al 2010;Coppage et al 2013); the kinetic mechanisms of adsorption (Raffaini & Ganazzoli, 2010); the ET pathways and properties of adsorbed proteins (Bizzarri, 2006;Siwko & Corni, 2013;Utesch et al 2012;Zanetti-Polzi et al 2014;Zhou et al 2004); the effects of pH (Emami et al 2014b;Imamura et al 2003;Tosaka et al 2010;Utesch et al 2013) and ionic strength (Bizzarri, 2006) on adsorption; the role of ions in mediating adsorption ; and structural and energetic aspects of adsorption of proteins on surfaces (Apicella et al 2013;Jose & Sengupta, 2013;Hoefling et al 2011;Hung et al 2011;Kubiak-Ossowska & Mulheran, 2010a, b;O'Mahony et al 2013;Vila Verde et al 2009Wang et al 2010a, b;Yu et al 2012a;Steckbeck et al 2014;Sun et al 2014a;Sun et al 2014b). Further, conventional MD can be used to simulate physical perturbations, such as mechanical or electrical forces exerted on molecules in experiments.…”

5-(4-pyridinyl)-1,3,4-oxadiazole-2-thiol on gold: SAM Formation and electroactivity

“…31 Also, the observation of such potential suggests that there is no change in the protein conformation in consequence of the SAM-Cyt c molecular recognition process. 32,33 Based on the Nicholson's method, 34 the dependence of the difference between the anodic and cathodic peak potentials ( E p ) on the scan rate allows one to estimate the kinetic parameter, . Based on equation 3 with f = F/RT, the heterogeneous electron transfer rate constant, k 0 , was determined from the slope of the curve presented in the plot of 2 vs. the reciprocal of the scan rate, v -1 (Figure 3c).…”

Direct Electron Transfer to Cytochrome c Induced by a Conducting Polymer

“…This difficulty has been overcome by using electrode modifiers such as metal oxides, advanced carbon materials, DNA or lipid membranes [20][21][22][23][24][25][26] . In particular, the modification of surfaces with organic thin films like self-assembled monolayers (SAM), has been extensively used to manipulate the electrode surface, promoting the appropriate orientation of the protein and thus enhancing its electroactivity [27][28][29][30][31][32][33][34][35][36] .…”