25 research outputs found
Multiprotein Interactions during Surface Adsorption: a Molecular Dynamics Study of Lysozyme Aggregation at a Charged Solid Surface
Multiprotein adsorption of hen egg white lysozyme at a model charged ionic surface is studied using fully atomistic molecular dynamics simulations. Simulations with two, three, and five proteins, in various orientations with respect the surface, are performed over a 100 ns time scale. Mutated proteins with point mutations at the major (Arg128 and Arg125) and minor (Arg68) surface adsorption sites are also studied. The 100 ns time scale used is sufficient to observe protein translations, rotations, adsorption, and aggregation. Two competing processes of particular interest are observed, namely surface adsorption and protein–protein aggregation. At low protein concentration, the proteins first adsorb in isolation and can then reorientate on the surface to aggregate. At high concentration, the proteins aggregate in the solution and then adsorb in nonspecific ways. This work demonstrates the role of protein concentration in adsorption, indicates the residues involved in both types of interaction (protein–protein and protein–surface), and gives an insight into processes to be considered in the development of new functionalized material systems
Protein Diffusion and Long-Term Adsorption States at Charged Solid Surfaces
The diffusion pathways of lysozyme adsorbed to a model
charged
ionic surface are studied using fully atomistic steered molecular
dynamics simulation. The simulations start from existing protein adsorption
trajectories, where it has been found that one particular residue,
Arg128 at the N,C-terminal face, plays a crucial role in anchoring
the lysozyme to the surface [Langmuir 2010, 26, 15954−15965]. We first investigate
the desorption pathway for the protein by pulling the Arg128 side
chain away from the surface in the normal direction, and its subsequent
readsorption, before studying diffusion pathways by pulling the Arg128
side chain parallel to the surface. We find that the orientation of
this side chain plays a decisive role in the diffusion process. Initially,
it is oriented normal to the surface, aligning in the electrostatic
field of the surface during the adsorption process, but after resorption
it lies parallel to the surface, being unable to return to its original
orientation due to geometric constraints arising from structured water
layers at the surface. Diffusion from this alternative adsorption
state has a lower energy barrier of ∼0.9 eV, associated with
breaking hydrogen bonds along the pathway, in reasonable agreement
with the barrier inferred from previous experimental observation of
lysozyme surface clustering. These results show the importance of
studying protein diffusion alongside adsorption to gain full insight
into the formation of protein clusters and films, essential steps
in the future development of functionalized surfaces
Multiprotein Interactions during Surface Adsorption: a Molecular Dynamics Study of Lysozyme Aggregation at a Charged Solid Surface
Multiprotein adsorption of hen egg white lysozyme at a model charged ionic surface is studied using fully atomistic molecular dynamics simulations. Simulations with two, three, and five proteins, in various orientations with respect the surface, are performed over a 100 ns time scale. Mutated proteins with point mutations at the major (Arg128 and Arg125) and minor (Arg68) surface adsorption sites are also studied. The 100 ns time scale used is sufficient to observe protein translations, rotations, adsorption, and aggregation. Two competing processes of particular interest are observed, namely surface adsorption and protein–protein aggregation. At low protein concentration, the proteins first adsorb in isolation and can then reorientate on the surface to aggregate. At high concentration, the proteins aggregate in the solution and then adsorb in nonspecific ways. This work demonstrates the role of protein concentration in adsorption, indicates the residues involved in both types of interaction (protein–protein and protein–surface), and gives an insight into processes to be considered in the development of new functionalized material systems
Protein Diffusion and Long-Term Adsorption States at Charged Solid Surfaces
The diffusion pathways of lysozyme adsorbed to a model
charged
ionic surface are studied using fully atomistic steered molecular
dynamics simulation. The simulations start from existing protein adsorption
trajectories, where it has been found that one particular residue,
Arg128 at the N,C-terminal face, plays a crucial role in anchoring
the lysozyme to the surface [Langmuir 2010, 26, 15954−15965]. We first investigate
the desorption pathway for the protein by pulling the Arg128 side
chain away from the surface in the normal direction, and its subsequent
readsorption, before studying diffusion pathways by pulling the Arg128
side chain parallel to the surface. We find that the orientation of
this side chain plays a decisive role in the diffusion process. Initially,
it is oriented normal to the surface, aligning in the electrostatic
field of the surface during the adsorption process, but after resorption
it lies parallel to the surface, being unable to return to its original
orientation due to geometric constraints arising from structured water
layers at the surface. Diffusion from this alternative adsorption
state has a lower energy barrier of ∼0.9 eV, associated with
breaking hydrogen bonds along the pathway, in reasonable agreement
with the barrier inferred from previous experimental observation of
lysozyme surface clustering. These results show the importance of
studying protein diffusion alongside adsorption to gain full insight
into the formation of protein clusters and films, essential steps
in the future development of functionalized surfaces
Multiprotein Interactions during Surface Adsorption: a Molecular Dynamics Study of Lysozyme Aggregation at a Charged Solid Surface
Multiprotein adsorption of hen egg white lysozyme at a model charged ionic surface is studied using fully atomistic molecular dynamics simulations. Simulations with two, three, and five proteins, in various orientations with respect the surface, are performed over a 100 ns time scale. Mutated proteins with point mutations at the major (Arg128 and Arg125) and minor (Arg68) surface adsorption sites are also studied. The 100 ns time scale used is sufficient to observe protein translations, rotations, adsorption, and aggregation. Two competing processes of particular interest are observed, namely surface adsorption and protein–protein aggregation. At low protein concentration, the proteins first adsorb in isolation and can then reorientate on the surface to aggregate. At high concentration, the proteins aggregate in the solution and then adsorb in nonspecific ways. This work demonstrates the role of protein concentration in adsorption, indicates the residues involved in both types of interaction (protein–protein and protein–surface), and gives an insight into processes to be considered in the development of new functionalized material systems
Protein Diffusion and Long-Term Adsorption States at Charged Solid Surfaces
The diffusion pathways of lysozyme adsorbed to a model
charged
ionic surface are studied using fully atomistic steered molecular
dynamics simulation. The simulations start from existing protein adsorption
trajectories, where it has been found that one particular residue,
Arg128 at the N,C-terminal face, plays a crucial role in anchoring
the lysozyme to the surface [Langmuir 2010, 26, 15954−15965]. We first investigate
the desorption pathway for the protein by pulling the Arg128 side
chain away from the surface in the normal direction, and its subsequent
readsorption, before studying diffusion pathways by pulling the Arg128
side chain parallel to the surface. We find that the orientation of
this side chain plays a decisive role in the diffusion process. Initially,
it is oriented normal to the surface, aligning in the electrostatic
field of the surface during the adsorption process, but after resorption
it lies parallel to the surface, being unable to return to its original
orientation due to geometric constraints arising from structured water
layers at the surface. Diffusion from this alternative adsorption
state has a lower energy barrier of ∼0.9 eV, associated with
breaking hydrogen bonds along the pathway, in reasonable agreement
with the barrier inferred from previous experimental observation of
lysozyme surface clustering. These results show the importance of
studying protein diffusion alongside adsorption to gain full insight
into the formation of protein clusters and films, essential steps
in the future development of functionalized surfaces
What Governs Protein Adsorption and Immobilization at a Charged Solid Surface?
The adsorption of hen egg white lysozyme at a model charged surface is studied using fully atomistic molecular dynamics simulations. The simulations are performed over a 90 ns time scale which is sufficient to observe rotational and translational steps in the adsorption process. Electrostatics is found to play a key role in guiding the protein to the favorable binding orientation with the N,C-terminal face against the substrate. However, full immobilization appears to only occur through the strong interaction of Arg128 with the surface, facilitated by the protein’s flexibility at the terminal face. Simulated mutation at this residue confirms its crucial role. This work demonstrates that electrostatics alone might not be sufficient to guide the development of material systems that exploit protein adsorption and immobilization
Protein Diffusion and Long-Term Adsorption States at Charged Solid Surfaces
The diffusion pathways of lysozyme adsorbed to a model
charged
ionic surface are studied using fully atomistic steered molecular
dynamics simulation. The simulations start from existing protein adsorption
trajectories, where it has been found that one particular residue,
Arg128 at the N,C-terminal face, plays a crucial role in anchoring
the lysozyme to the surface [Langmuir 2010, 26, 15954−15965]. We first investigate
the desorption pathway for the protein by pulling the Arg128 side
chain away from the surface in the normal direction, and its subsequent
readsorption, before studying diffusion pathways by pulling the Arg128
side chain parallel to the surface. We find that the orientation of
this side chain plays a decisive role in the diffusion process. Initially,
it is oriented normal to the surface, aligning in the electrostatic
field of the surface during the adsorption process, but after resorption
it lies parallel to the surface, being unable to return to its original
orientation due to geometric constraints arising from structured water
layers at the surface. Diffusion from this alternative adsorption
state has a lower energy barrier of ∼0.9 eV, associated with
breaking hydrogen bonds along the pathway, in reasonable agreement
with the barrier inferred from previous experimental observation of
lysozyme surface clustering. These results show the importance of
studying protein diffusion alongside adsorption to gain full insight
into the formation of protein clusters and films, essential steps
in the future development of functionalized surfaces
What Governs Protein Adsorption and Immobilization at a Charged Solid Surface?
The adsorption of hen egg white lysozyme at a model charged surface is studied using fully atomistic molecular dynamics simulations. The simulations are performed over a 90 ns time scale which is sufficient to observe rotational and translational steps in the adsorption process. Electrostatics is found to play a key role in guiding the protein to the favorable binding orientation with the N,C-terminal face against the substrate. However, full immobilization appears to only occur through the strong interaction of Arg128 with the surface, facilitated by the protein’s flexibility at the terminal face. Simulated mutation at this residue confirms its crucial role. This work demonstrates that electrostatics alone might not be sufficient to guide the development of material systems that exploit protein adsorption and immobilization
Impact of the Crystal Structure of Silica Nanoparticles on Rhodamine 6G Adsorption: A Molecular Dynamics Study
Understanding the
mechanism of adsorption of Rhodamine 6G (R6G)
to various crystal structures of silica nanoparticles (SNPs) is important
to elucidate the impact of dye size when measuring the size of the
dye–SNP complex via the time-resolved fluorescence anisotropy
method. In this work, molecular dynamics (MD) simulations were used
to get an insight into the R6G adsorption process, which cannot be
observed using experimental methods. It was found that at low pH,
α-Cristobalite structured SNPs have a strong affinity to R6G;
however, at high pH, more surface silanol groups undergo ionization
when compared with α-Quartz, preventing the adsorption. Therefore,
α-Quartz structured SNPs are more suitable for R6G adsorption
at high pH than the α-Cristobalite ones. Furthermore, it was
found that stable adsorption can occur only when the R6G xanthene
core is oriented flat with respect to the SNP surface, indicating
that the dye size does not contribute significantly to the measured
size of the dye–SNP complex. The requirement of correct dipole
moment orientation indicates that only one R6G molecule can adsorb
on any sized SNP, and the R6G layer formation on SNP is not possible.
Moreover, the dimerization process of R6G and its competition with
the adsorption has been explored. It has been shown that the highest
stable R6G aggregate is a dimer, and in this form, R6G does not adsorb
to SNPs. Finally, using steered molecular dynamics (SMD) with constant-velocity
pulling, the binding energies of R6G dimers and R6G complexes with
both α-Quartz and α-Cristobalite SNPs of 40 Å diameter
were estimated. These confirm that R6G adsorption is most stable on
40 Å α-Quartz at pH 7, although dimerization is equally
possible