Neutron Scattering Studies of Water in Biomolecules and Biomaterials

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Abstract

It is increasingly important to identify the nature of the interfacial water in biology in order to explain how biological functions and systems work. It is not simply a matter of which biomolecules are present in a cell, but also of how these biomolecules interact with one another. This body of work uses neutron scattering techniques to explain the nature of the vibrational dynamics of water interacting with biomolecules and systems that mimic the biological molecular crowding environment of a cell.Recent work in science has seen the synthesis of periodic mesoporous organosilicas with organic groups attached. In the first paper in this thesis, the use of one of these materials is highlighted to look at confined water, equivalent to the water found in a crowded cellular environment. Here it is shown that the properties of the water within the pores and water molecules around the surface were shown to be different and then identified as interfacial and bulk water respectively. In order to develop the investigation of interfacial water with biological matter, it seemed appropriate to start with the most basic molecules, amino acids. The second paper presents a complete survey of the 20 biologically important amino acids using one of the world’s highest resolution neutron scattering spectrometer (TOSCA at ISIS, Rutherford Appleton Laboratory). Computer simulation of the experimental work through molecular dynamics, allows many vibrational modes to be assigned for the first time and correlated with the broader vibrational peaks previously observed for proteins. Comparison of the dry states with the hydrated states of amino acids, gives some insight into the sites within the amino acid side chains where water molecules are likely to bind. For serine this is the hydroxyl group in the side chain. The third paper focuses on IINS data of serine in more detail and discusses several low energy vibrational modes that have been assigned and for the first time, shows how the presence of water molecules changes the dynamic behaviour of librational and torsional modes differently. The combination of these studies allows a clearer picture of how water in biology interacts with biomolecules and of the importance of water to our existence.

Layman's Abstract

Water provides the environment for organisms to live in, it is the most abundant substance on our planet and it is the main component (by mass) of living things. It is increasingly important to identify the nature of water in biology in order to explain how biological functions and systems work. It isn’t simply a matter of which biomolecules are present in a cell, but also of how these biomolecules interact with one another. Since water is so abundant within biology, it is important to use a technique which can reflect these interactions well. Neutrons are very susceptible to the presence of hydrogen atoms and since there are two hydrogen atoms present per water molecule, a technique such as neutron scattering is ideal for this type of investigation and is widely used in studies about water. This thesis features 3 papers, each of which looks at different aspects of water interactions in biology. The first investigates water within cells through mimicking the cell environment by a silica-based compound. The behaviour of water molecules trapped within the small pores (interfacial water) is more restricted to those that are around the surface of this material which behave similarly to that of free water (bulk water). In order to develop the investigation of interfacial water with biological matter, it seemed appropriate to start with the most basic molecules, amino acids. The second paper studies the molecular dynamics of amino acids in dry and hydrated states. With the use of computer simulation work, for the first time, many interactions can be described as vibrational modes within the side-chains of the amino acid structure and associated with other studies of larger biomolecules such as proteins. The third paper focuses on the amino acid, serine, and studies where water molecules are likely to bind within the side-chains. The first descriptions of water interactions on several low energy vibration modes are assigned. The combination of these studies allows a clearer picture of how water in biology interacts with biomolecules and of the importance of water to our existence.

Additional content not available electronically

Supplementary Electronic Data (CD attached to Thesis)Using Jmol: Word document advising of the installation, running and use of the program to view the movies from the simulation of serine and proline.Jmol Program: Version 12.2.17-binaryFolder 1 : Supplementary Data for “Inelastic incoherent neutron scattering spectroscopy of amino acids and bound water of hydration.”Table of amino acid peaks (Excel Worksheet)Table listing the location of each spectral peak of all 20 amino acids from the IINS spectra.IINS spectra of all 20 amino acids (Graphs)Normalised IINS spectra of the 20 biologically important amino acids with hydrations where available. All spectra were recorded on TOSCA at ISIS, Rutherford Appleton Laboratory.Simulation files of the vibrational modes of serine (Movie Files)Movie files of each vibrational mode of serine obtained from molecular dynamics computer simulations (DMOL3). Requires JMOL software to view the files.Simulation files of the vibrational modes of proline (Movie Files)Movie files of each vibrational mode of proline obtained from molecular dynamics computer simulations (DMOL3). Requires JMOL software to view the files.Folder 2 : Supplementary Data for “Inelastic incoherent neutron scattering study of the Debye-Waller effects on dry and hydrated serine.”Simulation files of the low energy vibrational modes of serine (Movie Files)Movie files of some low energy vibrational modes of serine obtained from molecular dynamics computer simulations (DMOL3). Requires JMOL software to view the files.

Keyword(s)

amino acid; hydration; neutron scattering; serine; silica gel; vibrational spectroscopy; water

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