Regulation of Permeation in Aquaporins

Regulation of Permeation in Aquaporins

Shreyas Sanjay Kaptan

Doctoral thesis

Date of Examination: 2015-03-23

Date of issue: 2016-02-19

Advisor: Groot, Bert De Prof. Dr.

Referee: Mueller, Marcus Prof. Dr.

Referee: Bennati, Marina Prof. Dr.

Persistent Address: http://hdl.handle.net/11858/00-1735-0000-0028-86CE-E

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Abstract

English

Regulation of water permeation is an essential aspect of homeostasis in living organisms. Proteins of the ubiquitous aquaporin family act as trans-membrane tetrameric channels through which water may permeate under osmotic gradients in a bidirectional manner. These channels are highly specific in the choice of the conducting molecules, but at the same time several members of this family allow permeation of alternative solutes. In the last two decades, the structures of several aquaporin proteins have been unveiled through x-ray and electron crystallography and have helped us understand the features of this protein family that make so- lute permeation across bio-membranes possible. Molecular Dynamics (MD) simulations have contributed substantially to the understanding of the mechanisms that govern the efficiency and the specificity of the aquaporin family of protein. These simulations have helped shed light on the finer mechanical details of the process of water permeation at the atomistic level. MD simulations add a new dimension, that of the dynamics, to the ensemble of available knowledge. This added information is crucial to understand the inherently dynamic nature of the permeation process. In this study we explore the molecular mechanisms that regulate the permeability in three aquaporin proteins, namely, AQP4, AQP0 and TIP2;1. We find that the permeability of AQP4 protein can be modulated with an extrinsic parameter such as pH. We provide an explanation for the native low permeability of the protein AQP0 and suggest means to manipulate this protein through mutations so it can be made more water permeable. Finally, we study the permeability of ammonia through the plant aquaporin TIP2;1 and explore the origin of the modified specificity of this protein. To achieve the results stated above, we use a variety of techniques related to MD simulations and highlight several aspects of regulation of permeation that could be general features of the protein family as a whole.

Keywords: Molecular Simulations; Aquaporins; Computational Biophysics; Molecular Dynamics