Synthetic molecular machines for active self-assembly : prototype algorithms, designs, and experimental study

Computer science and electrical engineering have been the great success story of the twentieth century. The neat modularity and mapping of a language onto circuits has led to robots on Mars, desktop computers and smartphones. But these devices are not yet able to do some of the things that life takes for granted: repair a scratch, reproduce, regenerate, or grow exponentially fast–all while remaining functional.

This thesis explores and develops algorithms, molecular implementations, and theoretical proofs in the context of “active self-assembly” of molecular systems. The long-term vision of active self-assembly is the theoretical and physical implementation of materials that are composed of reconfigurable units with the programmability and adaptability of biology’s numerous molecular machines. En route to this goal, we must first find a way to overcome the memory limitations of molecular systems, and to discover the limits of complexity that can be achieved with individual molecules.

One of the main thrusts in molecular programming is to use computer science as a tool for figuring out what can be achieved. While molecular systems that are Turing-complete have been demonstrated [Winfree, 1996], these systems still cannot achieve some of the feats biology has achieved.

One might think that because a system is Turing-complete, capable of computing “anything,” that it can do any arbitrary task. But while it can simulate any digital computational problem, there are many behaviors that are not “computations” in a classical sense, and cannot be directly implemented. Examples include exponential growth and molecular motion relative to a surface.

Passive self-assembly systems cannot implement these behaviors because (a) molecular motion relative to a surface requires a source of fuel that is external to the system, and (b) passive systems are too slow to assemble exponentially-fast-growing structures. We call these behaviors “energetically incomplete” programmable behaviors. This class of behaviors includes any behavior where a passive physical system simply does not have enough physical energy to perform the specified tasks in the requisite amount of time.

As we will demonstrate and prove, a sufficiently expressive implementation of an “active” molecular self-assembly approach can achieve these behaviors. Using an external source of fuel solves part of the the problem, so the system is not “energetically incomplete.” But the programmable system also needs to have sufficient expressive power to achieve the specified behaviors. Perhaps surprisingly, some of these systems do not even require Turing completeness to be sufficiently expressive.

Building on a large variety of work by other scientists in the fields of DNA nanotechnology, chemistry and reconfigurable robotics, this thesis introduces several research contributions in the context of active self-assembly.

We show that simple primitives such as insertion and deletion are able to generate complex and interesting results such as the growth of a linear polymer in logarithmic time and the ability of a linear polymer to treadmill. To this end we developed a formal model for active-self assembly that is directly implementable with DNA molecules. We show that this model is computationally equivalent to a machine capable of producing strings that are stronger than regular languages and, at most, as strong as context-free grammars. This is a great advance in the theory of active self- assembly as prior models were either entirely theoretical or only implementable in the context of macro-scale robotics.

We developed a chain reaction method for the autonomous exponential growth of a linear DNA polymer. Our method is based on the insertion of molecules into the assembly, which generates two new insertion sites for every initial one employed. The building of a line in logarithmic time is a first step toward building a shape in logarithmic time. We demonstrate the first construction of a synthetic linear polymer that grows exponentially fast via insertion. We show that monomer molecules are converted into the polymer in logarithmic time via spectrofluorimetry and gel electrophoresis experiments. We also demonstrate the division of these polymers via the addition of a single DNA complex that competes with the insertion mechanism. This shows the growth of a population of polymers in logarithmic time. We characterize the DNA insertion mechanism that we utilize in Chapter 4. We experimentally demonstrate that we can control the kinetics of this re- action over at least seven orders of magnitude, by programming the sequences of DNA that initiate the reaction.

In addition, we review co-authored work on programming molecular robots using prescriptive landscapes of DNA origami; this was the first microscopic demonstration of programming a molec- ular robot to walk on a 2-dimensional surface. We developed a snapshot method for imaging these random walking molecular robots and a CAPTCHA-like analysis method for difficult-to-interpret imaging data.

Mechanistic aspects of the Ziegler-Natta polymerization

The isotope effect on propagation rate was determined for four homogeneous ethylene polymerization systems. The catalytic system Cp_2Ti(Et)Cl + EtA1Cl_2 has a k^H_p/k^D_p = 1.035 ± 0.03. This result strongly supports an insertion mechanism which does not involve a hydrogen migration during the rate determining step of propagation (Cossee mechanism). Three metal-alkyl free systems were also studied. The catalyst I_2 (PMe_3)_3Ta(neopentylidene)(H) has a k^H_p/k^D_p = 1.709. It is interpreted as a primary isotope effect involving a non-linear a-hydrogen migration during the rate determining step of propagation (Green mechanism). The lanthanide complexes Cp*_2LuMe•Et_2O and Cp*_2YbMe•Et_2O have a k^H_p/k^D_p = 1.46 and 1.25, respectively. They are interpreted as primary isotope effects due to a partial hydrogen migration during the rate determining step of propagation.

The presence of a precoordination or other intermediate species during the polymerization of ethylene by the mentioned metal-alkyl free catalysts was sought by low temperature NMR spectroscopy. However, no evidence for such species was found. If they exist, their concentrations are very small or their lifetimes are shorter than the NMR time scale.

Two titanocene (alkenyl)chlorides (hexenyl 1 and heptenyl 2 were prepared from titanocene dichloride and a THF solution of the corresponding alkenylmagnesium chloride. They do not cyclize in solution when alone, but cyclization to their respective titanocene(methyl(cycloalkyl) chlorides occurs readily in the presence of a Lewis acid. It is demonstrated that such cyclization occurs with the alkenyl ligand within the coordination sphere of the titanium atom. Cyclization of 1 with EtAlCl_2 at 0°C occurs in less than 95 msec (ethylene insertion time), as shown by the presence of 97% cyclopentyl-capped oligomers when polymerizing ethylene with this system. Some alkyl exchange occurs (3%). Cyclization of 2 is slower under the same reaction conditions and is not complete in 95 msec as shown by the presence of both cyclohexyl-capped oligomers (35%) and odd number α-olefin oligomers (50%). Alkyl exchange is more extensive as evidenced by the even number n-alkanes (15%).

Cyclization of 2-d_1 (titanocene(hept-6-en-1-yl-1-d_1)chloride) with EtA1Cl_2 demonstrated that for this system there is no α-hydrogen participation during said process. The cyclization is believed to occur by a Cossee-type mechanism. There was no evidence for precoordination of the alkenyl double bond during the cyclization process.

Mechanism and applications of the photochemistry of Bis(η^5-cyclopentadienyl)titanacyclobutanes

The photochemically induced reductive elimination of cyclopropanes from bis(η⁵-cyclopentadienyl)titanacyclobutanes has been examined. Stereochemical labelling studies indicate that the cyclopropane is initially formed in a 6±1:1, ratio favoring retention of stereochemistry. The starting titanacyclobutane is isomerized during the course of the reaction. The isomerization of the starting material results from metal-carbon bond homolysis to yield a 1,4-biradical, which can either close to give the starting material or generate cyclopropane. The 1,4-biradical can be observed through a cyclopropyl carbinyl rearrangement employing 2-bis(η⁵- cyclopentadienyl)titana-5,5-dimethylbicyclo[2.1.0]pentane, to give the titanium alkylidene, 1-bis(η⁵-cyclopentadienyl)titana-3,3-dimethyl-1,4- pentadiene, which can be observed directly by NMR at low temperature.

The oxidation of titanacyclobutanes by chemical and electrochemical methods also yields cyclopropanes. Reduction of the metal center does not yield cyclopropanes. Depending on the oxidant, stereochemically labelled titanacyclobutanes yield cyclopropanes that are between 7:1 and 100:1 retention:isomerization. The fragmentation reaction resembles the photochemically induced reductive elimination. Both result from formal oxidation of a metal-carbon bond, which then results in very rapid formation of cyclopropane.

The titanocene generated photochemically reacts with a variety of substrates even at low temperature. Titanocene can be generated in a glass at 77 K. The titanocene can be trapped in noncoordinating solvents in high yield with bulky internal acetylenes to give monoacetylene adducts of titanocene. Less bulky acetylenes give the titanacyclopentadienes. The titanocene can be trapped with olefins to give less stable adducts, which appear by NMR analysis to be intermediate in structure between a titanacyclopropane and an η² olefin adduct of titanocene. Reaction of titanocene with butadiene gives a stable product, which appears to be the s-trans butadiene adduct of titanocene. It does not isomerize on heating. Titanocene reacts with epoxides to give titanocene-µ-oxo polymer and olefin. Stereochemically labelled epoxides and episulfides yield isomerized olefin upon deoxygenation by titanocene. The observations are rationalized as a result of a 1,4-biradical formed by stepwise insertion of titanocene into a carbon-oxygen bond.

Single cell proteomics microchip to profile immune function, with applications in stem cell biology, translational disease mechanism study and clinical therapeutics monitoring

In response to infection or tissue dysfunction, immune cells develop into highly heterogeneous repertoires with diverse functions. Capturing the full spectrum of these functions requires analysis of large numbers of effector molecules from single cells. However, currently only 3-5 functional proteins can be measured from single cells. We developed a single cell functional proteomics approach that integrates a microchip platform with multiplex cell purification. This approach can quantitate 20 proteins from >5,000 phenotypically pure single cells simultaneously. With a 1-million fold miniaturization, the system can detect down to ~100 molecules and requires only ~104 cells. Single cell functional proteomic analysis finds broad applications in basic, translational and clinical studies. In the three studies conducted, it yielded critical insights for understanding clinical cancer immunotherapy, inflammatory bowel disease (IBD) mechanism and hematopoietic stem cell (HSC) biology.

To study phenotypically defined cell populations, single cell barcode microchips were coupled with upstream multiplex cell purification based on up to 11 parameters. Statistical algorithms were developed to process and model the high dimensional readouts. This analysis evaluates rare cells and is versatile for various cells and proteins. (1) We conducted an immune monitoring study of a phase 2 cancer cellular immunotherapy clinical trial that used T-cell receptor (TCR) transgenic T cells as major therapeutics to treat metastatic melanoma. We evaluated the functional proteome of 4 antigen-specific, phenotypically defined T cell populations from peripheral blood of 3 patients across 8 time points. (2) Natural killer (NK) cells can play a protective role in chronic inflammation and their surface receptor – killer immunoglobulin-like receptor (KIR) – has been identified as a risk factor of IBD. We compared the functional behavior of NK cells that had differential KIR expressions. These NK cells were retrieved from the blood of 12 patients with different genetic backgrounds. (3) HSCs are the progenitors of immune cells and are thought to have no immediate functional capacity against pathogen. However, recent studies identified expression of Toll-like receptors (TLRs) on HSCs. We studied the functional capacity of HSCs upon TLR activation. The comparison of HSCs from wild-type mice against those from genetics knock-out mouse models elucidates the responding signaling pathway.

In all three cases, we observed profound functional heterogeneity within phenotypically defined cells. Polyfunctional cells that conduct multiple functions also produce those proteins in large amounts. They dominate the immune response. In the cancer immunotherapy, the strong cytotoxic and antitumor functions from transgenic TCR T cells contributed to a ~30% tumor reduction immediately after the therapy. However, this infused immune response disappeared within 2-3 weeks. Later on, some patients gained a second antitumor response, consisted of the emergence of endogenous antitumor cytotoxic T cells and their production of multiple antitumor functions. These patients showed more effective long-term tumor control. In the IBD mechanism study, we noticed that, compared with others, NK cells expressing KIR2DL3 receptor secreted a large array of effector proteins, such as TNF-α, CCLs and CXCLs. The functions from these cells regulated disease-contributing cells and protected host tissues. Their existence correlated with IBD disease susceptibility. In the HSC study, the HSCs exhibited functional capacity by producing TNF-α, IL-6 and GM-CSF. TLR stimulation activated the NF-κB signaling in HSCs. Single cell functional proteome contains rich information that is independent from the genome and transcriptome. In all three cases, functional proteomic evaluation uncovered critical biological insights that would not be resolved otherwise. The integrated single cell functional proteomic analysis constructed a detail kinetic picture of the immune response that took place during the clinical cancer immunotherapy. It revealed concrete functional evidence that connected genetics to IBD disease susceptibility. Further, it provided predictors that correlated with clinical responses and pathogenic outcomes.

Synthetic, structural and mechanistic studies of interactions of carbon, nitrogen, and oxygen nucleophiles with bis-pentamethylcyclopentadienyl zirconium and hafnium derivatives

The reactivity of permethylzirconocene and permethylhafnocene complexes with various nucleophiles has been investigated. Permethylzirconocene reacts with sterically hindered ketenes and allenes to afford metallacycle products. Reaction of these cummulenes with permethylzirconocene hydride complexes affords enolate and σ-allyl species, respectively. Reactions which afford enolate products are nonstereospecific, whereas reactions which afford allyl products initially give a cis-σ-allyl complex which rearranges to its trans isomer. The mechanism of these reactions is proposed to occur either by a Lewis Acid-Lewis Base interaction (ketenes) or by formation of a π-olefin intermediate (allenes).

Permethylzirconocene haloacyl complexes react with strong bases such as lithium diisopropylamide or methylene trimethylphosphorane to afford ketene compounds. Depending on the size of the alkyl ketene substituent, the hydrogenation of these compounds affords enolate-hydride products with varying degrees of stereoselectivity. The larger the substituent, the greater is the selectivity for cis hydrogenation products.

The reaction of permethylzirconocene dihydride and permethylhafnocene dihydride with methylene trimethylphosphorane affords methyl-hydride and dimethyl derivatives. Under appropriate conditions, the metallated-ylide complex 1, (η^5-C_5(CH_3)_5)_2 Zr(H)CH_2PMe_2CH_2, is also obtained and has been structurally characterized by X-ray diffraction techniques. Reaction of 1 with CO affords (η^5-C_5(CH_3)_5)_2 Zr(C,O-η^2 -(PMe_3)HC=CO)H which exists in solution as an equilibrium mixture of isomers. In one isomer (2), the η^2-acyl oxygen atom occupies a lateral equatorial coordination position about zirconium, whereas in the other isomer (3), the η-acyl oxygen atom occupies the central equatorial position. The equilibrium kinetics of the 2→3 isomerization have been studied and the structures of both complexes confirmed by X-ray diffraction methods. These studies suggest a mechanism for CO insertion into metal-carbon bonds of the early transition metals.

Permethylhafnocene dihydride and permethylzirconocene hydride complexes react with diazoalkanes to afford η^2-N, N' -hydrazonido species in which the terminal nitrogen atom of the diazoalkane molecule has inserted into a metal-hydride or metal-carbon bond. The structure of one of these compounds, Cp*_2Zr(NMeNCTol_2)OH, has been determined by X-ray diffraction techniques. Under appropriate conditions, the hydrazonido-hydride complexes react with a second equivalent of diazoalkene to afford η' -N-hydrazonido-η^2-N, N' -hydrazonido species.

Essays in mechanism design

This dissertation contains three essays on mechanism design. The common goal of these essays is to assist in the solution of different resource allocation problems where asymmetric information creates obstacles to the efficient allocation of resources. In each essay, we present a mechanism that satisfactorily solves the resource allocation problem and study some of its properties. In our first essay, ”Combinatorial Assignment under Dichotomous Preferences”, we present a class of problems akin to time scheduling without a pre-existing time grid, and propose a mechanism that is efficient, strategy-proof and envy-free. Our second essay, ”Monitoring Costs and the Management of Common-Pool Resources”, studies what can happen to an existing mechanism — the individual tradable quotas (ITQ) mechanism, also known as the cap-and-trade mechanism — when quota enforcement is imperfect and costly. Our third essay, ”Vessel Buyback”, coauthored with John O. Ledyard, presents an auction design that can be used to buy back excess capital in overcapitalized industries.

Exploration of new drug delivery pathways: I. Mechanism of folate uptake in cultured human cells. II. Role of nuclear localization signal peptides in the delivery of oligonucleotide into reconstituted nuclei

The roles of the folate receptor and an anion carrier in the uptake of 5- methyltetrahydrofolate (5-MeH_4folate) were studied in cultured human (KB) cells using radioactive 5-MeH_4folate. Binding of the 5-MeH_4folate was inhibited by folic acid, but not by probenecid, an anion carrier inhibitor. The internalization of 5-MeH_4folate was inhibited by low temperature, folic acid, probenecid and methotrexate. Prolonged incubation of cells in the presence of high concentrations of probenecid appeared to inhibit endocytosis of folatereceptors as well as the anion carrier. The V_(max) and K_M values for the carrier were 8.65 ± 0.55 pmol/min/mg cell protein and 3.74 ± 0.54µM, respectively. The transport of 5-MeH4folate was competitively inhibited by folic acid, probenecid and methotrexate. The carrier dissociation constants for folic acid, probenecid and methotreate were 641 µM, 2.23 mM and 13.8 µM, respectively. Kinetic analysis suggests that 5-MeH_4folate at physiological concentration is transported through an anion carrier with the characteristics of the reduced-folate carrier after 5-MeH_4folate is endocytosed by folate receptors in KB cells. Our data with KB cells suggest that folate receptors and probenecid-sensitive carriers work in tandem to transport 5-MeH_4folate to the cytoplasm of cells, based upon the assumption that 1 mM probenecid does not interfere with the acidification of the vesicle where the folate receptors are endocytosed.

Oligodeoxynucleotides designed to hybridize to specific mRNA sequences (antisense oligonucleotides) or double stranded DNA sequences have been used to inhibit the synthesis of a number of cellular and viral proteins (Crooke, S. T. (1993) FASEB J. 7, 533-539; Carter, G. and Lemoine, N. R. (1993) Br. J. Cacer 67, 869-876; Stein, C. A. and cohen, J. S. (1988) Cancer Res. 48, 2659-2668). However, the distribution of the delivered oligonucleotides in the cell, i.e., in the cytoplasm or in the nucleus has not been clearly defined. We studied the kinetics of oligonucleotide transport into the cell nucleus using reconstituted cell nuclei as a model system. We present evidences here that oligonucleotides can freely diffuse into reconstituted nuclei. Our results are consistent with the reports by Leonetti et al. (Proc. Natl. Acad. Sci. USA, Vol. 88, pp. 2702-2706, April 1991), which were published while we were carrying this research independently. We also investigated whether a synthetic nuclear localization signal (NLS) peptide of SV40 T antigen could be used for the nuclear targeting of oligonucleotides. We synthesized a nuclear localization signal peptide-conjugated oligonucleotide to see if a nuclear localization signal peptide can enhance the uptake of oligonucleotides into reconstituted nuclei of Xenopus. Uptake of the NLS peptide-conjugated oligonucleotide was comparable to the control oligonucleotide at similar concentrations, suggesting that the NLS signal peptide does not significantly enhance the nuclear accumulation of oligonucleotides. This result is probably due to the small size of the oligonucleotide.

Insights into the mechanism of human erythrocyte hexose transport : a transferred NOE study of glucose binding to GLUT1

This study examines binding of α- and β-D-glucose in their equilibrium mixture to the glucose transporter (GLUT1) in human erythrocyte membrane preparations by an ^1H NMR method, the transferred NOE (TRNOE). This method is shown theoretically and experimentally to be a sensitive probe of weak ligand-macromolecule interactions. The TRNOEs observed are shown to arise solely from glucose binding to GLUT1. Sites at both membrane faces contribute to the TRNOEs. Binding curves obtained are consistent with a homogeneous class of sugar sites, with an apparent K_D which varies (from ~30 mM to ~70 mM for both anomers) depending on the membrane preparation examined. Preparations with a higher proportion of the cytoplasmic membrane face exposed to bulk solution yield higher apparent KK_Ds. The glucose transport inhibitor cytochalasin B essentially eliminates the TRNOE. Nonlinearity was found in the dependence on sugar concentration of the apparent inhibition constant for cytochalasin B reversal of the TRNOE observed in the α anomer (and probably the β anomer); such nonlinearity implies the existence of ternary complexes of sugar, inhibitor and transporter. The inhibition results furthermore imply the presence of a class of relatively high-affinity (K_D < 2mM) sugar sites specific for the α anomer which do not contribute to NMR-observable binding. The presence of two classes of sugar-sensitive cytochalasin B sites is also indicated. These results are compared with predictions of the alternating conformer model of glucose transport. Variation of apparent K_D in the NMR-observable sites, the formation of ternary complexes and the presence of an anomer-specific site are shown to be inconsistent with this model. An alternate model is developed which reconciles these results with the known transport behavior of GLUT1. In this model, the transporter possesses (at minimum) three classes of sugar sites: (i) transport sites, which are alternately exposed to the cytoplasmic or the extracellular compartment, but never to both simultaneously, (ii) a class of sites (probably relatively low-affinity) which are confined to one compartment, and (iii) the high-affinity α anomer-specific sites, which are confined to the cytoplasmic compartment.

Bimetallic olefin polymerization catalysis : mechanisms and applications of proximal effects

This dissertation covers progress with bimetallic polymerization catalysts. The complexes we have designed were aimed at expanding the capabilities of homogeneous polymerization catalysts by taking advantage of multimetallic effects. Such effects were examined in group 4 and group 10 bimetallic complexes; proximity and steric repulsion were determined to be major factors in the effects observed.

Chapters 2 and 3 introduce the rigid p-terphenyl dinucleating framework utilized in most of this thesis. The permethylation of the central arene allows for the separation of syn and anti atropisomers of the terphenyl compounds. Kinetic studies were carried out to examine the isomerization of the dinucleating bis(salicylaldimine) ligand precursors. Metallation of the syn and anti bis(salicylaldimine)s using Ni(Me)2(tmeda) and excess pyridine afforded dinickel bisphenoxyiminato complexes with a methyl and a pyridyl ligand on each nickel. The syn and anti atropisomers of the dinickel complexes were structurally characterized and utilized in ethylene and ethylene/α-olefin polymerizations. Monometallic analogues were also synthesized and tested for polymerization activity. Ethylene polymerizations were performed in the presence of primary, secondary, and tertiary amines – additives that generally deactivate nickel polymerization catalysts. Inhibition of this deactivation was observed with the syn atropisomer of the bimetallic species, but not with the anti or monometallic analogues. A mechanism was proposed wherein steric repulsion of the substituents on proximal nickel centers disfavors simultaneous ligation of base to both of the metal centers. The bimetallic effect has been explored with respect to size and binding ability of the added base.

Chapter 4 presents the optimization of the bisphenoxyimine ligand synthesis and synthesis of syn and anti m-terphenyl analogues. Metallation with NiClMe(PMe₃)₂ yielded phosphine-ligated dinickel complexes, which have been structurally characterized. Ethylene/1-hexene copolymerizations in the presence of amines using Ni(COD)₂ as a phosphine scavenger showed significantly improved activity relative to the pyridine-ligated analogues. Incorporation of amino olefins in copolymerizations with ethylene was accomplished, and a mechanism was proposed based on proximal effects. Copolymerization trials with a variety of amino olefins and ethylene/1-hexene/amino olefin terpolymerizations were completed.

Early transition metal complexes based on the rigid p-terphenyl framework were designed with a variety of donor sets (Chapter 5 and Appendix B). Chapter 5 details the use of syn dizirconium di[amine bis(phenolate)] complexes for isoselective 1-hexene and propylene homopolymerizations. Ligand variation and monometallic complexes were studied to determine the origin of tacticity control. A mechanistic proposal was presented based on the symmetry at zirconium and the steric effects of the proximal metal center. Appendix B covers additional studies of bimetallic early transition metal complexes based on the p-terphenyl. Dititanium, dizirconium, and asymmetric complexes with bisphenoxyiminato ligands and derivatives thereof were targeted. Progress toward the synthesis of these complexes is described along with preliminary polymerization data. 1-hexene/diene copolymerizations and attempted polymerizations in the presence of ethers and esters with the syn dizirconium di[amine bis(phenolate)] complexes demonstrate the potential for further applications of this system in catalysis.

Appendix A includes work toward palladium catalysts for insertion polymerization of polar monomers. These complexes were based on dioxime and diimine frameworks with the intent of binding Lewis acidic metals at the oxime oxygens, at pendant phenolic donors, or at pendant aminediol moieties. The synthesis and structural characterization of a number of palladium and Lewis acid complexes is presented. Due to the instability of the desired species, efforts toward isolation of the desired complexes proved unsuccessful, though preliminary ethylene/methyl acrylate copolymerizations using in situ activation of the palladium species were attempted.

Neuronal mechanism of state control in Drosophila melanogaster

The changes in internal states, such as fear, hunger and sleep affect behavioral responses in animals. In most of the cases, these state-dependent influences are “pleiotropic”: one state affects multiple sensory modalities and behaviors; “scalable”: the strengths and choices of such modulations differ depending on the imminence of demands; and “persistent”: once the state is switched on the effects last even after the internal demands are off. These prominent features of state-control enable animals to adjust their behavioral responses depending on their internal demands. Here, we studied the neuronal mechanisms of state-controls by investigating energy-deprived state (hunger state) and social-deprived state of fruit flies, Drosophila melanogaster, as prototypic models. To approach these questions, we developed two novel methods: a genetically based method to map sites of neuromodulation in the brain and optogenetic tools in Drosophila.

These methods, and genetic perturbations, reveal that the effect of hunger to alter behavioral sensitivity to gustatory cues is mediate by two distinct neuromodulatory pathways. The neuropeptide F (NPF) – dopamine (DA) pathway increases sugar sensitivity under mild starvation, while the adipokinetic hormone (AKH)- short neuropeptide F (sNPF) pathway decreases bitter sensitivity under severe starvation. These two pathways are recruited under different levels of energy demands without any cross interaction. Effects of both of the pathways are mediated by modulation of the gustatory sensory neurons, which reinforce the concept that sensory neurons constitute an important locus for state-dependent control of behaviors. Our data suggests that multiple independent neuromodulatory pathways are underlying pleiotropic and scalable effects of the hunger state.

In addition, using optogenetic tool, we show that the neural control of male courtship song can be separated into probabilistic/biasing, and deterministic/command-like components. The former, but not the latter, neurons are subject to functional modulation by social experience, supporting the idea that they constitute a locus of state-dependent influence. Interestingly, moreover, brief activation of the former, but not the latter, neurons trigger persistent behavioral response for more than 10 min. Altogether, these findings and new tools described in this dissertation offer new entry points for future researchers to understand the neuronal mechanism of state control.

Reactions of oxygen containing ligands in the coordination sphere of permethylhafnocene and permethyltantalocene

A series of terl-butylperoxide complexes of hafnium, Cp*₂Hf(R)(OOCMe₃) (Cp* = ((η⁵-C₅Me₅); R = Cl, H, CH₃, CH₂CH₃, CH₂CH₂CH₃, CH₂CH₂CH₂CH₃, CH₂CHMe₂, CH=CHCMe₃, C₆H₅, meta-C₆H₃(CH₂)2) and Cp*(η⁵-C₅(CH₃)₄CH₂CH₂CH₂)Hf(OOCMe₃), has been synthesized. One example has been structurally characterized, Cp*₂Hf(OOCMe₃)CH₂CH₃ crystallizes in space group P2₁/c, with a = 19.890(7)Å, b = 8.746(4)Å, c = 17.532(6)Å, β = 124.987(24)°, V = 2498(2)ų, Z = 4 and R_F = 0.054 (2222 reflections, I > 0). Despite the coordinative unsaturation of the hafnium center, the terl-butylperoxide ligand is coordinated in a mono-dentate ligand. The mode of decomposition of these species is highly dependent on the substituent R. For R = H, CH₂CH₃, CH₂CH₂CH₃, CH₂CH₂CH₂CH₃, CH₂CHMe₂ a clean first order conversion to Cp*₂Hf(OCMe₃)(OR) is observed (for R CH₂CH₃, ΔHǂ = 19.6 kcal•mol^-1, ΔSǂ = -13 e.u.). These results are discussed in terms of a two step mechanism involving η²-coordination of the terl-butylperoxide ligand. Homolytic O-O bond cleavage is observed upon heating of Cp*₂Hf(OOCMe₃) R (R = C₆H₆, meta-C₆H₃(CH₃)₂). In the presence of excess 9,10-dihydroanthracene thermolysis of Cp*₂Hf(OOCMe₃)C₆H₆ cleanly affords Cp*₂Hf(C₆H₆)OH and HOCMe₃ (ΔHǂ = 22.6 kcal•mol^-1, ΔSǂ = -9 e.u.). The O-O bond strength in these complexes is thus estimated to be 22 kcal•mol^-1.

Cp*₂Ta(CH₂)H, Cp*₂Ta(CHC₆H₅)H, Cp*₂Ta(C₆H₄)H, Cp*₂Ta(CH₂=CH₂)H and Cp*₂Ta(CH₂=CHMe)H react, presumably through Cp*₂Ta-R intermediates, with H₂O to give Cp*₂Ta(O)H and alkane. Cp*₂Ta(O)H was structurally characterized: space group P2₁/n, a= 13.073(3)Å, b = 19.337(4)Å, c = 16.002(3)Å, β = 108.66(2)°, V = 3832(1)ų, Z = 8 and R_F = 0.0672 (6730 reflections). Reaction of terlbutylhydroperoxide with these same starting materials ultimately yields Cp*₂Ta(O)R and HOCMe₃. Cp*₂Ta(CH₂=CHR)OH species are proposed as intermediates in the olefin hydride reactions. Cp*₂Ta(O₂)R species can be generated from the reaction of the same starting materials and O₂. Lewis acids have been shown to promote oxygen insertion in these complexes.

Molecular mechanism of sulfated carbohydrate recognition: structural and biochemical studies of the cysteine-rich domain of mannose receptor

Mannose receptor (MR) is widely expressed on macrophages, immature dendritic cells, and a variety of epithelial and endothelial cells. It is a 180 kD type I transmembrane receptor whose extracellular region consists of three parts: the amino-terminal cysteine-rich domain (Cys-MR); a fibronectin type II-like domain; and a series of eight tandem C-type lectin carbohydrate recognition domains (CRDs). Two portions of MR have distinct carbohydrate recognition properties: Cys-MR recognizes sulfated carbohydrates and the tandem CRD region binds terminal mannose, fucose, and N-acetyl-glucosamine (GlcNAc). The dual carbohydrate binding specificity allows MR to interact with sulfated and nonsulfated polysaccharide chains, and thereby facilitating the involvement of MR in immunological and physiological processes. The immunological functions of MR include antigen capturing (through binding non-sulfated carbohydrates) and antigen targeting (through binding sulfated carbohydrates), and the physiological roles include rapid clearance of circulatory luteinizing hormone (LH), which bears polysaccharide chains terminating with sulfated and non-sulfated carbohydrates.

We have crystallized and determined the X-ray structures of unliganded Cys-MR (2.0 Å) and Cys-MR complexed with different ligands, including Hepes (1.7 Å), 4SO_4-N-Acetylgalactosamine (4SO_4-GalNAc; 2.2 Å), 3SO_4-Lewis^x (2.2 Å), 3S04-Lewis^a (1.9 Å), and 6SO_4-GalNAc (2.5 Å). The overall structure of Cys-MR consists of 12 anti-parallel β-strands arranged in three lobes with approximate three fold internal symmetry. The structure contains three disulfide bonds, formed by the six cysteines in the Cys-MR sequence. The ligand-binding site is located in a neutral pocket within the third lobe, in which the sulfate group of ligand is buried. Our results show that optimal binding is achieved by a carbohydrate ligand with a sulfate group that anchors the ligand by forming numerous hydrogen bonds and a sugar ring that makes ring-stacking interactions with Trpll7 of CysMR. Using a fluorescence-based assay, we characterized the binding affinities between CysMR and its ligands, and rationalized the derived affinities based upon the crystal structures. These studies reveal the mechanism of sulfated carbohydrate recognition by Cys-MR and facilitate our understanding of the role of Cys-MR in MR recognition of its ligands.

Phospholipids and a protein-conducting channel regulate cotranslational protein targeting

Signal recognition particle (SRP) and signal recognition particle receptor (SR) are evolutionarily conserved GTPases that deliver secretory and membrane proteins to the protein-conducting channel Sec61 complex in the lipid bilayer of the endoplasmic reticulum in eukaryotes or the SecYEG complex in the inner membrane of bacteria. Unlike the canonical Ras-type GTPases, SRP and SR are activated via nucleotide-dependent heterodimerization. Upon formation of the SR•SRP targeting complex, SRP and SR undergo a series of discrete conformational changes that culminate in their reciprocal activation and hydrolysis of GTP. How the SR•SRP GTPase cycle is regulated and coupled to the delivery of the cargo protein to the protein-conducting channel at the target membrane is not well-understood. Here we examine the role of the lipid bilayer and SecYEG in regulation of the SRP-mediated protein targeting pathway and show that they serve as important biological cues that spatially control the targeting reaction.

In the first chapter, we show that anionic phospholipids of the inner membrane activate the bacterial SR, FtsY, and favor the late conformational states of the targeting complex conducive to efficient unloading of the cargo. The results of our studies suggest that the lipid bilayer acts as a spatial cue that weakens the interaction of the cargo protein with SRP and primes the complex for unloading its cargo onto SecYEG.

In the second chapter, we focus on the effect of SecYEG on the conformational states and activity of the targeting complex. While phospholipids prime the complex for unloading its cargo, they are insufficient to trigger hydrolysis of GTP and the release of the cargo from the complex. SecYEG modulates the conformation of the targeting complex and triggers the GTP hydrolysis from the complex, thus driving the targeting reaction to completion. The results of this study suggest that SecYEG is not a passive recipient of the cargo protein; rather, it actively releases the cargo from the targeting complex. Together, anionic phospholipids and SecYEG serve distinct yet complementary roles. They spatially control the targeting reaction in a sequential manner, ensuring efficient delivery and unloading of the cargo protein.

In the third chapter, we reconstitute the transfer reaction in vitro and visualize it in real time. We show that the ribosome-nascent chain complex is transferred to SecYEG via a stepwise mechanism with gradual dissolution and formation of the contacts with SRP and SecYEG, respectively, explaining how the cargo is kept tethered to the membrane during the transfer and how its loss to the cytosol is avoided.

In the fourth chapter, we examine interaction of SecYEG with secretory and membrane proteins and attempt to address the role of a novel insertase YidC in this interaction. We show that detergent-solubilized SecYEG is capable of discriminating between the nascent chains of various lengths and engages a signal sequence in a well-defined conformation in the absence of accessory factors. Further, YidC alters the conformation of the signal peptide bound to SecYEG. The results described in this chapter show that YidC affects the SecYEG-nascent chain interaction at early stages of translocation/insertion and suggest a YidC-facilitated mechanism for lateral exit of transmembrane domains from SecYEG into the lipid bilayer.

Chemical studies of viral entry mechanisms: I. Hydrophobic protein-lipid interactions during sendai virus membrane fusion. II. Kinetics of bacteriophage λ DNA injection.

Viruses possess very specific methods of targeting and entering cells. These methods would be extremely useful if they could also be applied to drug delivery, but little is known about the molecular mechanisms of the viral entry process. In order to gain further insight into mechanisms of viral entry, chemical and spectroscopic studies in two systems were conducted, examining hydrophobic protein-lipid interactions during Sendai virus membrane fusion, and the kinetics of bacteriophage λ DNA injection.

Sendai virus glycoprotein interactions with target membranes during the early stages of fusion were examined using time-resolved hydrophobic photoaffinity labeling with the lipid-soluble carbene generator3-(trifluoromethyl)-3-(m-^(125 )I] iodophenyl)diazirine (TID). The probe was incorporated in target membranes prior to virus addition and photolysis. During Sendai virus fusion with liposomes composed of cardiolipin (CL) or phosphatidylserine (PS), the viral fusion (F) protein is preferentially labeled at early time points, supporting the hypothesis that hydrophobic interaction of the fusion peptide at the N-terminus of the F_1 subunit with the target membrane is an initiating event in fusion. Correlation of the hydrophobic interactions with independently monitored fusion kinetics further supports this conclusion. Separation of proteins after labeling shows that the F_1 subunit, containing the putative hydrophobic fusion sequence, is exclusively labeled, and that the F_2 subunit does not participate in fusion. Labeling shows temperature and pH dependence consistent with a need for protein conformational mobility and fusion at neutral pH. Higher amounts of labeling during fusion with CL vesicles than during virus-PS vesicle fusion reflects membrane packing regulation of peptide insertion into target membranes. Labeling of the viral hemagglutinin/neuraminidase (HN) at low pH indicates that HN-mediated fusion is triggered by hydrophobic interactions, after titration of acidic amino acids. HN labeling under nonfusogenic conditions reveals that viral binding may involve hydrophobic as well as electrostatic interactions. Controls for diffusional labeling exclude a major contribution from this source. Labeling during reconstituted Sendai virus envelope-liposome fusion shows that functional reconstitution involves protein retention of the ability to undergo hydrophobic interactions.

Examination of Sendai virus fusion with erythrocyte membranes indicates that hydrophobic interactions also trigger fusion between biological membranes, and that HN binding may involve hydrophobic interactions as well. Labeling of the erythrocyte membranes revealed close membrane association of spectrin, which may play a role in regulating membrane fusion. The data show that hydrophobic fusion protein interaction with both artificial and biological membranes is a triggering event in fusion. Correlation of these results with earlier studies of membrane hydration and fusion kinetics provides a more detailed view of the mechanism of fusion.

The kinetics of DNA injection by bacteriophage λ. into liposomes bearing reconstituted receptors were measured using fluorescence spectroscopy. LamB, the bacteriophage receptor, was extracted from bacteria and reconstituted into liposomes by detergent removal dialysis. The DNA binding fluorophore ethidium bromide was encapsulated in the liposomes during dialysis. Enhanced fluorescence of ethidium bromide upon binding to injected DNA was monitored, and showed that injection is a rapid, one-step process. The bimolecular rate law, determined by the method of initial rates, revealed that injection occurs several times faster than indicated by earlier studies employing indirect assays.

It is hoped that these studies will increase the understanding of the mechanisms of virus entry into cells, and to facilitate the development of virus-mimetic drug delivery strategies.

I. The rate and mechanism of the vapor-phase reaction between water and parts-per-million concentrations of nitrogen dioxide. II. The rate and mechanism of the air oxidation of parts-per-million concentrations of nitric oxide in the presence of water vapor.

Part I

A study of the thermal reaction of water vapor and parts-per-million concentrations of nitrogen dioxide was carried out at ambient temperature and at atmospheric pressure. Nitric oxide and nitric acid vapor were the principal products. The initial rate of disappearance of nitrogen dioxide was first order with respect to water vapor and second order with respect to nitrogen dioxide. An initial third-order rate constant of 5.5 (± 0.29) x 10⁴ liter² mole^-2 sec^-1 was found at 25˚C. The rate of reaction decreased with increasing temperature. In the temperature range of 25˚C to 50˚C, an activation energy of -978 (± 20) calories was found.

The reaction did not go to completion. From measurements as the reaction approached equilibrium, the free energy of nitric acid vapor was calculated. This value was -18.58 (± 0.04) kilocalories at 25˚C.

The initial rate of reaction was unaffected by the presence of oxygen and was retarded by the presence of nitric oxide. There were no appreciable effects due to the surface of the reactor. Nitric oxide and nitrogen dioxide were monitored by gas chromatography during the reaction.

Part II

The air oxidation of nitric oxide, and the oxidation of nitric oxide in the presence of water vapor, were studied in a glass reactor at ambient temperatures and at atmospheric pressure. The concentration of nitric oxide was less than 100 parts-per-million. The concentration of nitrogen dioxide was monitored by gas chromatography during the reaction.

For the dry oxidation, the third-order rate constant was 1.46 (± 0.03) x 10⁴ liter² mole^-2 sec^-1 at 25˚C. The activation energy, obtained from measurements between 25˚C and 50˚C, was -1.197 (±0.02) kilocalories.

The presence of water vapor during the oxidation caused the formation of nitrous acid vapor when nitric oxide, nitrogen dioxide and water vapor combined. By measuring the difference between the concentrations of nitrogen dioxide during the wet and dry oxidations, the rate of formation of nitrous acid vapor was found. The third-order rate constant for the formation of nitrous acid vapor was equal to 1.5 (± 0.5) x 10⁵ liter² mole^-2 sec^-1 at 40˚C. The reaction rate did not change measurably when the temperature was increased to 50˚C. The formation of nitric acid vapor was prevented by keeping the concentration of nitrogen dioxide low.

Surface effects were appreciable for the wet tests. Below 35˚C, the rate of appearance of nitrogen dioxide increased with increasing surface. Above 40˚C, the effect of surface was small.