The electrostatic field created by the inward pointing dipole moments of an oriented membrane leaflet has never been measured directly, but is thought to have an important influence on membrane function. Here we present the first direct measurement of the membrane dipole field in lipid bicelles using vibrational Stark effect spectroscopy which is based on the sensitivity of a nitrile oscillator’s vibrational frequency to its local electrostatic environment. The nitrile probe was introduced as the artificial amino acid p-cyanophenylalanine (CN-Phe) in four different locations of a α-helical peptide composed of alternating alanine and leucine residues. This peptide was intercalated into bicelles composed of mixtures of the long chain lipids 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), or 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), and the short chain lipid 1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC) formed in two different sizes, 5 nm and 15 nm in radius. Formation of the bicelle above the phase transition temperature of the lipid mixture was confirmed by ³¹P NMR, and the structure of the [alpha]-helix within the bicelle was confirmed by circular dichroic spectroscopy. The absorption energy of the nitrile probe at 4 positions along the helical axis was measured by Fourier transform infrared spectroscopy, from which we estimate the magnitude of the membrane dipole electrostatic field to be -6 MV/cm. Then we successfully manipulated the dipole field in q = 0.5 DMPC/DHPC bicelles by incorporating the small molecule phloretin into the membrane and measured the corresponding ratiometric fluorescence signal of the co-intercalated voltage gated dye di-8-ANEPPS. We measured 0.7 ± 0.2 cm⁻¹ blue shift in absorption energy of the nitrile probe due to the decrease in dipole field caused by phloretin, corresponding to a dipole field of -4.2 MV/cm. This change was essentially identical to what has been estimated through ratiometric fluorescence methods, indicating that VSE spectroscopy will be useful tool for measurement of the biological effects of electrostatic fields in lipid membranes. / text

The functional aspects of proteins are largely dictated by highly selective protein- protein and protein-ligand interactions, even in situations of high structural homology, where electrostatic factors are the major contributors to selectivity. The vibrational Stark effect (VSE) allows us to measure electrostatic fields in complex environments, such as proteins, by the introduction of a vibrational chromophore whose vibrational absorption energy is linearly sensitive to changes in the local electrostatic field. The works presented here seek to computationally quantify electrostatic fields measured via VSE, with the eventual goal of being able to quantitatively predict electrostatic fields, and therefore Stark shifts, for any given protein-interaction. This is done using extensive molecular dynamics in the Amber03 and AMOEBA force fields to generate large ensembles the GTPase Rap1a docked to RalGDS and [superscript p]²¹Ras docked to RalGDS. We discuss how side chain orientations contribute to the differential binding of different mutations of Rap1a binding to RalGDS, where it was found that a hydrogen-bonding pocket is disrupted by the mutation of position 31 from lysine to glutamic acid. We then show that multi-dimensional umbrella sampling of the probe orientations yields a wider range of accessible structures, increasing the quality of the ensembles generated. A large variety of methods for calculating electrostatic fields are presented, with Poisson- Boltzmann electrostatics yielding the most consistent, reliable results. Finally, we explore using AMOEBA for both ensemble-generation as well as the electrostatic description of atoms for field calculations, where early results suggest that the electrostatic field due to the induce dipole moment of the probe is responsible for predicting qualitatively correct Stark shifts.

Mineral oxide/aqueous interfaces play an important role in the transport of water through aquafers and streams, erosion, the formation of beaches and river deltas, nuclear waste storage, the sequestration and filtration of small ions, and are widely used in industrial scale catalysis. Unlike metal or semiconductor electrodes, the surface charge resulting from the protonation or deprotonation of insulating mineral oxides is highly localized and heterogeneous in nature. While the unique acid/base chemistry associated with different mineral oxide surfaces leads to their wide variety of applications, the extent to which surface groups found on mineral oxides partake in acid/base chemistry is still controversial due to the difficulty associated with experimentally probing them. Surface specific spectroscopic techniques, such as vibrational Sum Frequency Generation (vSFG), provide an opportunity to investigate how the surface architecture and corresponding chemical nature of various mineral oxide surfaces orient the interfacial solvent at a variety of solvent compositions and surface charges. Although vSFG has been used as a tool to measure the orientation and composition of interfacial O-H species originating from the surface and solvent for many mineral oxide/aqueous interfaces since the late 1990’s, controversy still exists in the assignment of vSFG spectra in the O-H stretching region of SiO2, Al2O3, CaF2, and TiO2/aqueous interfaces. The first section of this dissertation focuses on how the nonlinear optics and computational community’s understanding of the structure associated with mineral oxide/aqueous interfaces has evolved and where it stands now. Of particular interest is how the addition of electrolyte and variation of bulk pH allow modulation of the depth of the interfacial region and surface charge. Electrolyte solutions can vary the length of the interface by screening interfacial charges through non-specific adsorption at the interface, or generating surface charge if accumulation is facilitated by specific adsorption. The specific interaction of small ions with mineral oxide surfaces is relevant in geochemistry and filtration technology, and can also aid in prediction of contaminant mobility in ground water systems. Chapters two and three discuss the theory and application of vSFG, and the experimental setup used to capture vSFG spectra in this work, respectively. The fourth chapter investigates how monovalent or divalent cations accumulate at alpha-Al2O3(0001)/H2O interfaces and reorganize the interfacial solvent structure. The reactivity of these interfaces is strongly impacted by the presence of ions. Thus, it is critical to understand how ions alter the interfacial environment. This is achieved by measuring the changes in the structure and vibrational dynamics of interfacial water induced by the presence of ions in close vicinity to the mineral surface. The alpha-Al2O3(0001) surface represents a flexible platform to study the effect of ions on interfacial aqueous environments at positive, neutral and negative surface charge. Using vibrational sum frequency generation (vSFG) in the frequency and time domain, we investigate how monovalent and divalent cations affect the hydrogen bonding environment of the first few layers of interfacial water next to an alpha-Al2O3(0001) surface. Our results indicate that monovalent cations, such as Li+, Na+, K+, and Cs+, appear to have lower adsorption affinities for the interface compared to Ca2+, Sr2+, and Ba2+. This leads to an interfacial region that is structured in a cation valence dependent manner. Time resolved vSFG measurements reveal that the O-H vibrational lifetime (T1) of interfacial species at pH 10 conditions in the presence of NaCl and BaCl2 remains similar, but restructuring of the surface seen in steady state vSFG is manifested in the degree to which strongly hydrogen bonded species recover to their original populations post excitation. By tracking the accumulation of ions at the interface via the vSFG response, we can characterize the unique surface arrangements of interfacial water molecules induced by a range of monovalent and divalent cations at the alpha-Al2O3(0001)/water interface. In the fifth chapter the Stark active C ≡ N stretch of potassium thiocyanate is used as a molecular probe of interfacial electrostatic potential at the alpha-Al2O3(0001)/H2O interface. We confirm the presence of the thiocyanate ion in the interfacial region via reorganization of surface waters in the O-H stretching region. Changes in electrostatic potential are then tracked via Stark shifts of the vibrational frequency of the C ≡ N stretch. Our vSFG measurements show that we can simultaneously measure the SFG response of SCN- ions experiencing charged and neutral surface sites and assign a local potential of + 308 mV and -154 mV to positively and negatively charged aluminol groups, respectively. Thiocyanate anions at charged surface sites adopt similar relative orientations independent of surface charge, but adopt an opposite orientation at neutral surface sites. MD-DFT simulations of SCN- near the neutral alpha-Al2O3(0001)//H2O interface show that the vSFG response in the C ≡ N stretch region originates from a SCN-H-O-Al complex, suggesting the surface site specificity of these experiments. By tracking how this molecular probe responds to local surface charges we offer insight into the local electrostatic potential at neutral and charged surface aluminol groups. Chapter six investigates the vibrational dynamics of potassium thiocyanate at the alumina/water interface. Here, we leverage the sensitivity of the C ≡ N stretch vibrational lifetime of potassium thiocyanate to measure the local electrostatic potential at the alpha-Al2O3(0001)/H2O interface. To accomplish this, KSCN was investigated using free induction decay vSFG (FID-vSFG) and time resolved pump probe (TR-vSFG) measurements, which measure the total dephasing time and vibrational lifetime of the excited C ≡ N stretch, respectively. Our FID-vSFG spectra suggest that at all surface charges the total dephasing time of SCN- is on the order of ~300-600 fs. TR-vSFG characterizations of potassium thiocyanate report the vibrational lifetime of the excited C ≡ N stretch between ~0.5-2 ps. TR-vSFG measurements show two distinct vibrational relaxation rates, which are assigned the CN stretch and the HOH bend plus libration combination band of interfacial water. The variation in the T1 lifetime of the CN stretch with bulk pH show that changes in the SCN- net orientation measured using steady-state vSFG can be correlated to the vibrational dynamics in the interfacial region. The energy transfer to the bend plus libration combination band of water is also sensitive to the surface charge, as the lifetime of this species becomes shorter as the bulk pH is increased. Lastly, in chapter seven this thesis is summarized, and future directions of the experiments presented here are discussed. / Chemistry

This examines the interplay of structure and local electrostatic fields in protein-protein and protein-solvent interactions. The partial charges of the protein amino acids and the polarization of the surrounding solvent create a complex system of electrostatic fields at protein-protein and protein-solvent interfaces. An approach incorporating vibrational Stark effect (VSE) spectroscopy, dissociation constant measurements, and molecular dynamics (MD) simulations was used to investigate the electrostatic interactions in these interfaces. Proteins p21Ras (Ras) and Rap1A (Rap) have nearly identical amino acid sequences and structures along the effector-binding region but bind with different affinities to Ral guanine nucleotide dissociation stimulator (RalGDS). A charge reversion mutation at position 31 alters the binding affinity of Ras and Rap with RalGDS from 0.1 [mu]M and 1 [mu]M, to 1 [mu]M and 0.5 [mu]M, respectively. A spectral probe was placed at various locations along the binding interface on the surface of RalGDS as it was docked with Ras and Rap single (position 30 or 31) and double mutants (both positions). By comparing the probes' absorption energies with the respective wild-type (WT) analogs, VSE spectroscopy was able to measure molecular-level electrostatic events across the protein-protein interface. MD simulations provided a basis for deconvoluting the structural and electrostatic changes observed by the probes. The mutation at position 31 was found to be responsible for both structural and electrostatic changes compared to the WT analogs. Furthermore, previous identification of positions N27 and N29 on RalGDS as "hot spots" that help discriminate between structurally similar GTPases was supported. The RalGDS probe-containing variants and three model compounds were placed in aqueous solvents with varying dielectric constants to measure changes in absorption energy. We investigated the ability of the Onsager solvent model to describe the solvent induced changes in absorption energy, while MD simulations were employed to determine the location and solvation of the probes at the protein-solvent interface. The solvent accessible-surface area, a measure of hydration, was determined to correlate well with the change in magnitude of the probe's absorption energy and the displaced solvent by the probe. / text

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