Date of Award

8-2015

Document Type

Thesis

Degree Name

Master of Science (MS)

Legacy Department

Chemical Engineering

Advisor

Sarupria, Sapna

Committee Member

Blenner, Mark A

Committee Member

Getman, Rachel

Committee Member

Podila, Ramakrishna

Abstract

Over the past few years there has been a rise in the number of nanomaterials engineered for a wide array of applications because of their unique properties. This rise in the development of engineered nanomaterials (ENMs) and its growing usage has also raised questions about its potential impact on the biological environment. Recent experimental studies suggest that these ENMs could be toxic due to the formation of a protein corona. Therefore, understanding the formation of a protein corona would provide some insights into the toxic behavior of ENMs. This requires understanding the interactions between proteins and ENMs. We employ molecular dynamics simulations to explore the factors and governing forces influencing interactions between carbon nanomaterials (CNMs) and proteins. We first study the interactions between bovine serum albumin (BSA) and a set of CNMs that are of varying shape and surface chemistry. These CNMs include a single walled carbon nanotube (SWCNT), a graphene nanoribbon (GNR) and a graphene oxide nanoribbon (GONR). Our results indicate that BSA interacted with all the three CNMs and its interaction strength follows the order GNR>SWCNT~GONR. During this interaction, we found a strong correlation between the interaction energy and the number of heavy atoms of BSA near the CNM. However, there are no significant changes in the secondary structure content and all α helices are stable during this interaction in the timescales of our simulations. We have also not observed any one or two types of amino acids that are dominant during the interactions of BSA with the CNMs to identify the driving forces. In order to determine the role of various factors such as i) aromatic residues ii) arginine iii) water and also iv) neighboring residues of an aromatic residue or arginine in the interactions of proteins with CNMs, we have designed a set of tripeptide-CNM systems. We used an advanced sampling method, umbrella-sampling method in order to determine the free energy of interaction between the tripeptides and CNM, which will enable us to quantify the contributions of different factors to the interactions. Our initial results show that the influence of the neighboring residues (Val/Leu/Thr/Ser/Gly) in the free energy of interactions for the tripeptide-graphene system where the central residue is Phe is not significant. However, barriers appear during the interactions for the larger and polar side chains. We hypothesize this is due to conformational changes that the larger side chains need to make as the tripeptide associates with the CNMs.

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Engineering Commons

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