It is important to remember that there are subtleties in the real world that simulations won't capture.  If you're doing a simulation in explicit solvent, the dielectric constant of the water around your protein is a fixed aspect of the water model.  Most water models are rigid with fixed point charges.  You can't alter their bulk properties.  If you do implicit solvent simulations, likely you can alter the implicit dielectric constant, but there are a whole host of deficiencies in implicit solvent simulations that make tuning the dielectric less important.  Moreover, even if experimental reality dictates that solvent effects can alter pKa values, again most force fields have fixed charges, so your simulation inherently cannot reflect these effects or the subtle changes that arise from changes in microenvironment.  Polarizable models can do this, though by and large, people continue to use fixed-charge force fields because they are faster to simulate, if less accurate.

I call your attention to my paper with Sushkin "N. Sushkin and G. D. J. Phillies, Charged Dielectric Spheres in Electrolyte Solutions: Induced Dipoles and Counterion Exclusion Effects", Journal of Chemical Physics, 103, 4600-4612 (1995)" which is a followon to the work of Kirkwood and collaborators on dielectric contributions to the pK of amino acids.  In short, the dielectric constant of a protein interior at low frequency is something around 4 give or take, water is more than an order of magnitude larger, and therefore a charge in water tends to repel a nearby protein via the induced dipole effects.  These effects are large.  The series approximations Sushkin generated represent the upper limit of what could be done locally in-period with computer algebra, but numerical checks indicated that the approximations were reasonably accurate.  I would expect that the answer to your question is "yes".  For starters, the dielectric effect swill modify the pKs of all charged groups, and structure is certainly sensitive to charge.

Thank you George sir.. I got the very important concept regarding the implication of dielectric constant on the structure of a biomolecule in a very scientific manner. I will go through one of the research article you have mentioned in your comment.  I have one more small doubt regarding the invitro studies, while performing the molecular dynamics simulation  do i have an option to include dielectric value directly or indirectly and which force field is good for my studies which is related to interaction studies in the purification system and not related to any drug discovery.. Thank you in advance

It is important to remember that there are subtleties in the real world that simulations won't capture.  If you're doing a simulation in explicit solvent, the dielectric constant of the water around your protein is a fixed aspect of the water model.  Most water models are rigid with fixed point charges.  You can't alter their bulk properties.  If you do implicit solvent simulations, likely you can alter the implicit dielectric constant, but there are a whole host of deficiencies in implicit solvent simulations that make tuning the dielectric less important.  Moreover, even if experimental reality dictates that solvent effects can alter pKa values, again most force fields have fixed charges, so your simulation inherently cannot reflect these effects or the subtle changes that arise from changes in microenvironment.  Polarizable models can do this, though by and large, people continue to use fixed-charge force fields because they are faster to simulate, if less accurate.

Justin Lemkul Sir,

I'm asking a different approach here. In NAMD we generate a water box around our system. Similarly we can put ion and thus change the PH values. Can the method be extended to generate a box of dielectric materials, say benzene? Can we change the dielectric environment of the simulation with this? Can we explore properties of our system with this kind of model?

Adding an ion (assuming you mean hydronium) does not change the pH in a simulation.  In the absence of true titration (i.e. a changing topology), the concept of pH is ill defined in classical MD simulations.  Besides, if you add one hydronium to a typical simulation cell, you've (on an extremely simplistic level) modeled a concentration reflective of pH = 1 since the box is so small.

You can, of course, do simulations in different solvents.  People do this routinely.  The key point here is that in explicit-solvent MD simulations (regardless of what that solvent is), the dielectric constant is not an independent variable; it is a fixed property of the model(s) used in the simulation.