Single Molecule Techniques Can Distinguish the Photophysical Processes Governing Metal-Enhanced Fluorescence

<p>Plasmonic metal nanoparticles can impact the behaviour of organic molecules in a number of ways, including enhancing or quenching fluorescence. Only through a comprehensive understanding of the fundamental photophysical processes regulating nano-molecular interactions can these effects be controlled, and exploited to the fullest extent possible. Metal-enhanced fluorescence (MEF) is governed by two underlying processes, increased rate of fluorophore excitation and increased fluorophore emission, the balance between which has implications for optimizing hybrid nanoparticle-molecular systems for various applications. We report groundbreaking work on the use of single molecule fluorescence microscopy to distinguish between the two mechanistic components of MEF, in a model system consisting of two analogous boron dipyrromethene (BODIPY) fluorophores and triangular silver nanoparticles (AgNP). We demonstrate that the increased excitation MEF mechanism occurs to approximately the same extent for both dyes, but that the BODIPY with the higher quantum yield of fluorescence experiences a greater degree of MEF via the increased fluorophore emission mechanism, and higher overall enhancement, as a result of its superior ability to undergo near-field interactions with AgNP. We foresee that this knowledge and methodology will be used to tailor MEF to meet the needs of different applications, such as those requiring maximum enhancement of fluorescence intensity or instead prioritizing excited-state photochemistry. </p>

Single Molecule Techniques Can Distinguish the Photophysical Processes Governing Metal-Enhanced Fluorescence

<p>Plasmonic metal nanoparticles can impact the behaviour of organic molecules in a number of ways, including enhancing or quenching fluorescence. Only through a comprehensive understanding of the fundamental photophysical processes regulating nano-molecular interactions can these effects be controlled, and exploited to the fullest extent possible. Metal-enhanced fluorescence (MEF) is governed by two underlying processes, increased rate of fluorophore excitation and increased fluorophore emission, the balance between which has implications for optimizing hybrid nanoparticle-molecular systems for various applications. We report groundbreaking work on the use of single molecule fluorescence microscopy to distinguish between the two mechanistic components of MEF, in a model system consisting of two analogous boron dipyrromethene (BODIPY) fluorophores and triangular silver nanoparticles (AgNP). We demonstrate that the increased excitation MEF mechanism occurs to approximately the same extent for both dyes, but that the BODIPY with the higher quantum yield of fluorescence experiences a greater degree of MEF via the increased fluorophore emission mechanism, and higher overall enhancement, as a result of its superior ability to undergo near-field interactions with AgNP. We foresee that this knowledge and methodology will be used to tailor MEF to meet the needs of different applications, such as those requiring maximum enhancement of fluorescence intensity or instead prioritizing excited-state photochemistry. </p>

Sequence Divergence and Functional Specializations of the Ancient Spliceosomal SF3b: Implications in Flexibility and Adaptations of the Multi-Protein Complex

Multi-protein assemblies are complex molecular systems that perform highly sophisticated biochemical functions in an orchestrated manner. They are subject to changes that are governed by the evolution of individual components. We performed a comparative analysis of the ancient and functionally conserved spliceosomal SF3b complex, to recognize molecular signatures that contribute to sequence divergence and functional specializations. For this, we recognized homologous sequences of individual SF3b proteins distributed across 10 supergroups of eukaryotes and identified all seven protein components of the complex in 578 eukaryotic species. Using sequence and structural analysis, we establish that proteins occurring on the surface of the SF3b complex harbor more sequence variation than the proteins that lie in the core. Further, we show through protein interface conservation patterns that the extent of conservation varies considerably between interacting partners. When we analyze phylogenetic distributions of individual components of the complex, we find that protein partners that are known to form independent subcomplexes are observed to share similar profiles, reaffirming the link between differential conservation of interface regions and their inter-dependence. When we extend our analysis to individual protein components of the complex, we find taxa-specific variability in molecular signatures of the proteins. These trends are discussed in the context of proline-rich motifs of SF3b4, functional and drug binding sites of SF3b1. Further, we report key protein-protein interactions between SF3b1 and SF3b6 whose presence is observed to be lineage-specific across eukaryotes. Together, our studies show the association of protein location within the complex and subcomplex formation patterns with the sequence conservation of SF3b proteins. In addition, our study underscores evolutionarily flexible elements that appear to confer adaptive features in individual components of the multi-protein SF3b complexes and may contribute to its functional adaptability.

Local Phonon Environment as a Design Element for Long-lived Excitonic Coherence: Dithia-anthracenophane Revisited

Excitonic energy transfer in light harvesting complexes, the primary process of photosynthesis, operates with near-unity efficiency. Experimental and theoretical studies suggest that quantum mechanical wave-like motion of excitons in the pigment-protein complex may be responsible for this quantum efficiency. Observed coherent exciton dynamics can be modelled completely only if we consider the interaction of the exciton with its complex environment. While it is known that the relative orientation of the chromophore units and reorganisation energy are important design elements, the role of a structured phonon environment is often not considered. The purpose of this study is to investigate the role of a structured immediate phonon environment in determining the exciton dynamics and the possibility of using it as an optimal design element. Through the case study of dithia-anthracenophane, a bichromophore using the Hierarchical Equations Of Motion formalism, we show that the experimentally observed coherent exciton dynamics can be reproduced only by considering the actual structure of the phonon environment. While the slow dephasing of quantum coherence in dithia-anthracenophane can be attributed to strong vibronic coupling to high-frequency modes, vibronic quenching is the source of long oscillation periods in population transfer. This study sheds light on the crucial role of the structure of the immediate phonon environment in determining the exciton dynamics. We conclude by proposing some design principles for sustaining long-lived coherence in molecular systems.

Quantum harmonic free energies for biomolecules and nanomaterials

Obtaining the free energy of large molecules from quantum mechanical energy functions is a longstanding challenge. We describe a method that allows us to estimate, at the quantum mechanical level, the harmonic contributions to the thermodynamics of molecular systems of unprecedented size, with modest cost. Using this approach, we compute the vibrational thermodynamics of a series of diamond nanocrystals, and show that the error per atom decreases with system size in the limit of large systems. We further show that we can obtain the vibrational contributions to the binding free energies of prototypical protein-ligand complexes where the exact computation is too expensive to be practical. Our work raises the possibility of routine quantum mechanical estimates of thermodynamic quantities in complex systems.

The Mitochondrial RNA Granule is Necessary for Parkinsonism-Associated Metal Toxicity

Manganese exposure causes a parkinsonian disorder, manganism, which is viewed as a neurodegenerative disorder minimally related to Parkinson s disease. We tested this hypothesis asking if there is phenotypic and mechanistic overlap between two genetic models of these diseases. We targeted for study the plasma membrane manganese efflux transporter SLC30A10 and the mitochondrial Parkinson gene PARK2. We performed comparative molecular systems studies and found that SLC30A10 and PARK2 mutations compromised the mitochondrial RNA granule as well as mitochondrial transcript processing. These shared RNA granule defects led to impaired assembly and function of the mitochondrial respiratory chain. Notably, CRISPR gene editing of subunits of the mitochondrial RNA granule, FASTKD2 and DHX30, or pharmacological inhibition of mitochondrial transcription-translation were protective rather than deleterious for survival of cells acutely exposed to manganese. Similarly, adult Drosophila mutants with defects in the mitochondrial RNA granule component scully were safeguarded from manganese-induced mortality. We conclude that the downregulation of the mitochondrial RNA granule function is a protective mechanism for acute metal toxicity. We propose that initially adaptive mitochondrial dysfunction caused by manganese exposure, when protracted, causes neurodegeneration

The emergence of molecular systems neuroscience

Systems neuroscience is focused on how ensemble properties in the brain, such as the activity of neuronal circuits, gives rise to internal brain states and behavior. Many of the studies in this field have traditionally involved electrophysiological recordings and computational approaches that attempt to decode how the brain transforms inputs into functional outputs. More recently, systems neuroscience has received an infusion of approaches and techniques that allow the manipulation (e.g., optogenetics, chemogenetics) and imaging (e.g., two-photon imaging, head mounted fluorescent microscopes) of neurons, neurocircuits, their inputs and outputs. Here, we will review novel approaches that allow the manipulation and imaging of specific molecular mechanisms in specific cells (not just neurons), cell ensembles and brain regions. These molecular approaches, with the specificity and temporal resolution appropriate for systems studies, promise to infuse the field with novel ideas, emphases and directions, and are motivating the emergence of a molecularly oriented systems neuroscience, a new discipline that studies how the spatial and temporal patterns of molecular systems modulate circuits and brain networks, and consequently shape the properties of brain states and behavior.

Complex Energies and Transition-Dipoles for the Uracil anion Shape-type Resonances from stabilization curves via Padé

Absorption of slow moving electrons by neutral ground state nucleobases have been known to produce resonance, metastable, states. There are indications that such metastable states may play a key-role in DNA/RNA damage. Therefore, herein, we present an ab-initio, non-Hermitian investigation of the resonance positions and decay rates of the low lying shape-type states of the uracil anion. In addition, we calculate the complex transition dipoles between these resonance states. We employ the resonance via Padé (RVP) method to calculate these complex properties from real stabilization curves by analytical dilation into the complex plane. This method has al-ready been successfully applied to many small molecular systems and herein we present the first application of RVP to a medium-size system. The presented resonance energies are converged with respect to the size of the basis set and compared with previous theoretical works and experimental findings. Complex transition dipoles between the shape-type resonances are computed using the energy-converged basis set. The ability to calculate ab-initio energies and lifetimes of biologically relevant systems opens the door for studying reactions of such systems in which autoionization takes place. While the ability to also calculate their complex transition dipoles open the door for studying photo induced dynamics of such biological molecules.

Anion-Cation Contrast of Small Molecule Solvation in Salt Solutions

Salts are inseparable in their perturbation of molecular systems by experimental and computational methods, rendering it difficult to dissect the effects exerted by the anions and cations individually. Here we...