Chemical-scale studies of G protein-coupled receptors and ligand-gated ion channels

This dissertation describes studies of G protein-coupled receptors (GPCRs) and ligand-gated ion channels (LGICs) using unnatural amino acid mutagenesis to gain high precision insights into the function of these important membrane proteins.

Chapter 2 considers the functional role of highly conserved proline residues within the transmembrane helices of the D2 dopamine GPCR. Through mutagenesis employing unnatural α-hydroxy acids, proline analogs, and N-methyl amino acids, we find that lack of backbone hydrogen bond donor ability is important to proline function. At one proline site we additionally find that a substituent on the proline backbone N is important to receptor function.

In Chapter 3, side chain conformation is probed by mutagenesis of GPCRs and the muscle-type nAChR. Specific side chain rearrangements of highly conserved residues have been proposed to accompany activation of these receptors. These rearrangements were probed using conformationally-biased β-substituted analogs of Trp and Phe and unnatural stereoisomers of Thr and Ile. We also modeled the conformational bias of the unnatural Trp and Phe analogs employed.

Chapters 4 and 5 examine details of ligand binding to nAChRs. Chapter 4 describes a study investigating the importance of hydrogen bonds between ligands and the complementary face of muscle-type and α4β4 nAChRs. A hydrogen bond involving the agonist appears to be important for ligand binding in the muscle-type receptor but not the α4β4 receptor.

Chapter 5 describes a study characterizing the binding of varenicline, an actively prescribed smoking cessation therapeutic, to the α7 nAChR. Additionally, binding interactions to the complementary face of the α7 binding site were examined for a small panel of agonists. We identified side chains important for binding large agonists such as varenicline, but dispensable for binding the small agonist ACh.

Chapter 6 describes efforts to image nAChRs site-specifically modified with a fluorophore by unnatural amino acid mutagenesis. While progress was hampered by high levels of fluorescent background, improvements to sample preparation and alternative strategies for fluorophore incorporation are described.

Chapter 7 describes efforts toward a fluorescence assay for G protein association with a GPCR, with the ultimate goal of probing key protein-protein interactions along the G protein/receptor interface. A wide range of fluorescent protein fusions were generated, expressed in Xenopus oocytes, and evaluated for their ability to associate with each other.

High-energy ion emission from cooled deuterium clusters in 20 TW laser fields

High-energy ion emission from intense-ultrashort (30fs) laser-pulse- cooled deuterium-cluster (80K) interaction is measured. The deuterium ions have an average energy 20keV, which greatly exceeds Zweiback's expectation [Phys. Rev. Lett. 84 (2000) 2634]. These fast deuterium ions can be used to drive fusion and have a broad prospect.

Temperature effects on the activity coefficient of the bicarbonate ion

Natural waters may be chemically studied as mixed electrolyte solutions. Some important equilibrium properties of natural waters are intimately related to the activity-concentration ratios (i.e., activity coefficients) of the ions in solution. An Ion Interaction Model, which is based on Pitzer's (1973) thermodynamic model, is proposed in this dissertation. The proposed model is capable of describing the activity coefficient of ions in mixed electrolyte solutions. The effects of temperature on the equilibrium conditions of natural waters and on the activity coefficients of the ions in solution, may be predicted by means of the Ion Interaction Model presented in this work.

The bicarbonate ion, HCO₃^-, is commonly found in natural waters. This anion plays an important role in the chemical and thermodynamic properties of water bodies. Such properties are usually directly related to the activity coefficient of HCO₃^- in solution. The Ion Interaction Model, as proposed in this dissertation, is used to describe indirectly measured activity coefficients of HCO₃^- in mixed electrolyte solutions.

Experimental pH measurements of MCl-MHCO₃ and MCl-H₂CO₃ solutions at 25°C (where M = K⁺, Na⁺, NH₄⁺, Ca²⁺ or Mg²⁺) are used in this dissertation to evaluate indirectly the MHCO₃ virial coefficients. Such coefficients permit the prediction of the activity coefficient of HCO₃^- in mixed electrolyte solutions. The Ion Interaction Model is found to be an accurate method for predicting the activity coefficient of HCO₃^- within the experimental ionic strengths (0.2 to 3.0 m). The virial coefficients of KHCO₃ and NaHCO₃ and their respective temperature variations are obtained from similar experimental measurements at 10° and 40°C. The temperature effects on the NH₄HCO₃, Ca(HCO₃)₂, and Mg(HCO₃)₂ virial coefficients are estimated based on these results and the temperature variations of the virial coefficients of 40 other electrolytes.

Finally, the Ion Interaction Model is utilized to solve various problems of water chemistry where bicarbonate is present in solution.

Studies of the serotonin type 3A receptor and the chemical preparation of tRNA

This thesis describes studies surrounding a ligand-gated ion channel (LGIC): the serotonin type 3A receptor (5-HT₃AR). Structure-function experiments using unnatural amino acid mutagenesis are described, as well as experiments on the methodology of unnatural amino acid mutagenesis. Chapter 1 introduces LGICs, experimental methods, and an overview of the unnatural amino acid mutagenesis.

In Chapter 2, the binding orientation of the clinically available drugs ondansetron and granisetron within 5-HT₃A is determined through a combination of unnatural amino acid mutagenesis and an inhibition based assay. A cation-π interaction is found for both ondansetron and granisetron with a specific tryptophan residue (Trp183, TrpB) of the mouse 5-HT₃AR, which establishes a binding orientation for these drugs.

In Chapter 3, further studies were performed with ondansetron and granisetron with 5-HT₃A. The primary determinant of binding for these drugs was determined to not include interactions with a specific tyrosine residue (Tyr234, TyrC2). In completing these studies, evidence supporting a cation-π interaction of a synthetic agonist, meta-chlorophenylbiguanide, was found with TyrC2.

In Chapter 4, a direct chemical acylation strategy was implemented to prepare full-length suppressor tRNA mediated by lanthanum(III) and amino acid phosphate esters. The derived aminoacyl-tRNA is shown to be translationally competent in Xenopus oocytes.

Appendix A.1 gives details of a pharmacological method for determining the equilibrium dissociation constant, K_B, of a competitive antagonist with a receptor, known as Schild analysis. Appendix A.2 describes an examination of the inhibitory activity of new chemical analogs of the 5-HT₃A antagonist ondansetron. Appendix A.3 reports an organic synthesis of an intermediate for a new unnatural amino acid. Appendix A.4 covers an additional methodological examination for the preparation of amino-acyl tRNA.

A fundamental approach to phase noise reduction in hybrid Si/III-V lasers

Spontaneous emission into the lasing mode fundamentally limits laser linewidths. Reducing cavity losses provides two benefits to linewidth: (1) fewer excited carriers are needed to reach threshold, resulting in less phase-corrupting spontaneous emission into the laser mode, and (2) more photons are stored in the laser cavity, such that each individual spontaneous emission event disturbs the phase of the field less. Strong optical absorption in III-V materials causes high losses, preventing currently-available semiconductor lasers from achieving ultra-narrow linewidths. This absorption is a natural consequence of the compromise between efficient electrical and efficient optical performance in a semiconductor laser. Some of the III-V layers must be heavily doped in order to funnel excited carriers into the active region, which has the side effect of making the material strongly absorbing.

This thesis presents a new technique, called modal engineering, to remove modal energy from the lossy region and store it in an adjacent low-loss material, thereby reducing overall optical absorption. A quantum mechanical analysis of modal engineering shows that modal gain and spontaneous emission rate into the laser mode are both proportional to the normalized intensity of that mode at the active region. If optical absorption near the active region dominates the total losses of the laser cavity, shifting modal energy from the lossy region to the low-loss region will reduce modal gain, total loss, and the spontaneous emission rate into the mode by the same factor, so that linewidth decreases while the threshold inversion remains constant. The total spontaneous emission rate into all other modes is unchanged.

Modal engineering is demonstrated using the Si/III-V platform, in which light is generated in the III-V material and stored in the low-loss silicon material. The silicon is patterned as a high-Q resonator to minimize all sources of loss. Fabricated lasers employing modal engineering to concentrate light in silicon demonstrate linewidths at least 5 times smaller than lasers without modal engineering at the same pump level above threshold, while maintaining the same thresholds.

Steady state ion acceleration by a circularly polarized laser pulse

The steady state ion acceleration at the front of a cold solid target by a circularly polarized flat-top laser pulse is studied with one-dimensional particle-in-cell (PIC) simulation. A model that ions are reflected by a steady laser-driven piston is used by comparing with the electrostatic shock acceleration. A stable profile with a double-flat-top structure in phase space forms after ions enter the undisturbed region of the target with a constant velocity. (C) 2007 Elsevier B.V. All rights reserved.

Multistaged acceleration of ions by circularly polarized laser pulse: Monoenergetic ion beam generation

A multiple-staged ion acceleration mechanism in the interaction of a circularly polarized laser pulse with a solid target is studied by one-dimensional particle-in-cell simulation. The ions are accelerated from rest to several MeV monoenergetically at the front surface of the target. After all the plasma ions are accelerated, the acceleration process is repeated on the resulting monoenergetic ions. Under suitable conditions multiple repetitions can be realized and a high-energy quasi-monoenergetic ion beam can be obtained.

Effect of plasma temperature on electrostatic shock generation and ion acceleration by laser

The effect of plasma temperature on electrostatic shock generated by a circularly polarized laser pulse in overdense plasma is studied by particle-in-cell simulation. Ion reflection and transmission in the collisionless electrostatic shock (CES) are investigated analytically. As the initial ion temperature is varied, a distinct transition from the laser-driven piston scenario with all ions being reflected to the CES scenario with partial ion reflection is found. The results show that at low but finite temperatures the ions are much more accelerated than if they were cold.

Efficient GeV ion generation by ultraintense circularly polarized laser pulse

The interaction of an ultraintense circularly polarized laser pulse and a solid target is studied by one-dimensional particle-in-cell simulations. Ions at the front of the target are reflected by a moving quasisteady electrostatic field and obtain a relativistic velocity. At a laser intensity of 10(22) W/cm(2), almost half of the laser energy is transferred to ions and GeV ions are obtained. Effects of laser polarization state and target thickness on the laser energy conversion are investigated. It is found that a circularly polarized laser pulse can accelerate ions more efficiently than a linearly polarized laser pulse at the same laser and target parameters. A monoenergetic ion bunch is obtained for the ultrathin target, which is accelerated as a single entity. (c) 2007 American Institute of Physics.

Bubble regime for ion acceleration in a laser-driven plasma

Proton trapping and acceleration by an electron bubble-channel structure in laser interaction with high-density plasma is investigated by using three-dimensional particle-in-cell simulations. It is shown that protons can be trapped, bunched, and efficiently accelerated for appropriate laser and plasma parameters, and the proton acceleration is enhanced if the plasma consists mainly of heavier ions such as tritium. The observed results are analyzed and discussed in terms of a one-dimensional analytical three-component-plasma wake model.

Expressão do colágeno I, III e metaloproteinase nos diferentes graus de Gleason e estadio patológico do câncer prostático

O objetivo deste trabalho foi avaliar se a expressão do colágeno tipo I, III e metaloproteinase podem estar relacionadas com o grau de Gleason, estadio patológico e PSA pré-operatório, e se isto poderia servir como prognóstico de doença. O grupo de estudo incluiu espécimes de prostatectomia radical de 33 pacientes com adenocarcinoma submetidos à cirurgia no período de 2001 a 2009. Os pacientes foram divididos em 3 grupos: grau de Gleason = 6 (13 pacientes), escore de Gleason = 7 (10 pacientes), escore de Gleason ≥ 8 (10 pacientes). O tecido prostático benigno adjacente à area de câncer nos graus de Gleason foi utilizado como grupo controle. As áreas de adenocarcinoma e de tecido benigno foram selecionados sob análise microscópica e processados para colágeno I e III sob análise do gene por PCR em Tempo Real. Dez seções desparafinadas de cada grupo foram utilizados para avaliar o colágeno I, III e a imunoexpressão de metaloproteinase. Os resultados foram relacionados com o grau de Gleason, PSA pré-operatório e estadio patológico. Apesar da diferença significativa na expressão gênica de ambos colágeno I e III entre as áreas de tecido prostático benigno e tumor nas amostras de próstata Gleason = 6 (colágeno I = 0,4 0,2 vs 5 2,4, p<0,05; colágeno III = 0,2 0,06 vs 0,7 0,1, p<0,05) e grau de Gleason ≥ 8 (I = 8 3,4 vs 1,4 0,8, p<0,05; colágeno III = 1,8 0,5 vs 0,6 0,1, p<0,05), não houve correlação com grau de Gleason, PSA pré-operatório ou estadio patológico. Houve uma correlação positiva entre a expressão de metaloproteinases e grau de Gleason (r2 = 0,47). Concluindo, tem-se que a correlação positiva entre a expressão de metaloproteinases e o grau de Gleason sugere que a metaloproteinase pode ser um fator promissor para melhorar o grau de Gleason. Sua expressão e regulação não parecem estar relacionados com a degradação do colágeno. Não há correlação entre expressão de colágeno e grau de Gleason, nem a nível gênico nem protéico.