Peptide–protein interactions are among the most prevalent and important interactions in the cell, but a large fraction of those interactions lack detailed structural characterization. The Rosetta FlexPepDock web server (http://flexpepdock.furmanlab.cs.huji.ac.il/) provides an interface to a high-resolution peptide docking (refinement) protocol for the modeling of peptide–protein complexes, implemented within the Rosetta framework. Given a protein receptor structure and an approximate, possibly inaccurate model of the peptide within the receptor binding site, the FlexPepDock server refines the peptide to high resolution, allowing full flexibility to the peptide backbone and to all side chains. This protocol was extensively tested and benchmarked on a wide array of non-redundant peptide–protein complexes, and was proven effective when applied to peptide starting conformations within 5.5 Å backbone root mean square deviation from the native conformation. FlexPepDock has been applied to several systems that are mediated and regulated by peptide–protein interactions. This easy to use and general web server interface allows non-expert users to accurately model their specific peptide–protein interaction of interest.

Quantum dot (QD) solids and arrays hold a great potential for novel applications which are aimed at exploiting quantum properties in room-temperature devices. Careful tailoring of the QD energy levels and coupling between dots could lead to efficient energy-harvesting devices. Here, we used a self-assembly method to create a disordered layered structure of QDs, coupled by covalently bonded organic molecules. Energy transfer rates from small (donor) to large (acceptor) QDs are measured. Best tailoring of the QDs energy levels and the length of the linking molecules results in an energy transfer rate as high as 30 ps–1. Such rates approach energy transfer rates of the highly efficient photosynthesis complexes and are compatible with a coherent mechanism of energy transfer. These results may pave way for new controllable building blocks for future technologies.

The design of new complex structures containing semiconductor quantum dots offers a means to create a variety of new meso-solids and molecules. The control of the coupling properties between the dots, accompanied by the energetic tunability of the dots themselves, paves the way toward the application and use of novel quantum properties. Here we present our approach to alteration of interdot coupling using organic linking molecules in a system of covalently bonded, aggregated quantum dots. We used ultrafast transient absorption measurements to identify marks of exciton delocalization over nearest neighbors to some extent. In linking molecules incorporating a benzene ring, the delocalized electron cloud displayed a profound influence over the interdot effects, leading the way to easy coupling control in quantum-based devices, under ambient conditions.

In this paper we propose an energy dissipation mechanism that is completely reliant on changes in the aggregation state of the phycobilisome light-harvesting antenna components. All photosynthetic organisms regulate the efficiency of excitation energy transfer (EET) to fit light energy supply to biochemical demands. Not many do this to the extent required of desert crust cyanobacteria. Following predawn dew deposition, they harvest light energy with maximum efficiency until desiccating in the early morning hours. In the desiccated state, absorbed energy is completely quenched. Time and spectrally resolved fluorescence emission measurements of the desiccated desert crust Leptolyngbya ohadii strain identified (i) reduced EET between phycobilisome components, (ii) shorter fluorescence lifetimes, and (iii) red shift in the emission spectra, compared with the hydrated state. These changes coincide with a loss of the ordered phycobilisome structure, evident from small-angle neutron and X-ray scattering and cryo-transmission electron microscopy data. Based on these observations we propose a model where in the hydrated state the organized rod structure of the phycobilisome supports directional EET to reaction centers with minimal losses due to thermal dissipation. In the desiccated state this structure is lost, giving way to more random aggregates. The resulting EET path will exhibit increased coupling to the environment and enhanced quenching.eserts cover almost half of the Earth's terrestrial surface, and although desert conditions may seem unfavorable, they are home for diverse ecosystems. Many of these ecosystems are founded on biological desert crusts, which play an essential role in stabilizing shifting sands and enriching them with nutrients (1, 2). Cyanobacteria are among the first microorganisms to inhabit these crusts where one of the major sources of water is often dew deposited before dawn (3, 4). However, as temperatures elevate, water quickly evaporates. Such conditions can be extremely harmful for photosynthetic organisms and require adaptations on all cellular levels (3-9). These include shifts in metabolic profiles and the accumulation of compatible solutes. A key issue is the adaptation of the photosynthetic apparatus because continued photosynthetic activity under high light, and especially in combination with desiccation, may lead to the production of reactive oxygen species that will cause damage to the entire cell (10-12). The cyanobacteria that colonize sand crusts evolved strategies for coping with these daily cycles of hydration using mechanisms that enable extensive quenching of absorbed light energy. The extent of quenching in these organisms far exceeds that of common laboratory model organisms (13, 14).Our studies focused on Leptolyngbya ohadii, a crust cyanobacterium isolated from the Nizzana region of the NW Negev desert in Israel (3,6). This is a keystone organism in this environment (4). To maintain L. ohadii cells in a viable state the desiccation process must be gradual (3). Recovery o...

Hybrid nanostructures are attractive for future use in a variety of electronic components. Self-assembled hybrid organic/nanocrystals can couple quantum properties to semiconductor working devices and modify their functionality. For example, light absorption in some core quantum dot (QD)-based self-assembled detectors induces a large dipole. These dipole moments may change the current of a shallow field effect transistor on which the QDs’ layer is assembled. In order to improve the absorption and quantum efficiency of such devices, multiple self-assembled layers are used. In such layers the charge transfer, excitonic energy transfer, surface trap passivation, and oxidation mechanisms are not fully understood. Therefore, establishing new tools for characterizing multilayer devices is essential. In the present work we have used confocal fluorescence microscopy to examine the photophysical properties of multilayered self-assembled organic molecules and QDs. We studied the interlayer coupling and surface-related mechanisms. By changing the coupling molecules and using photoinduced processes that gradually change the system, we were able to compare different binding groups and molecules under different conditions. Importantly, we found that in layered structures the binding group greatly contribute to the electronic coupling and luminescence, a contribution stronger than the linker’s molecular length. Consequently, we propose that proper illumination of core QD-based detectors be used for activation and yield improvement.