Analytical Rebridging Monte Carlo: Application to cis/trans Isomerization in Proline-Containing, Cyclic Peptides

We present a new method, the analytical rebridging scheme, for Monte Carlo simulation of proline-containing, cyclic peptides. The cis/trans isomerization is accommodated by allowing for two states of the amide bond. We apply our method to five peptides that have been previously characterized by NMR methods. Our simulations achieve effective equilibration and agree well with experimental data in all cases. We discuss the importance of effective equilibration and the role of bond flexibility and solvent effects on the predicted equilibrium properties.Comment: 29 pages, 8 PostScript figures, LaTeX source. to appear in J. Chem. Phys., 199

Improving Resolution and Resolvability of Single Particle CryoEM using Gaussian Mixture Models

Cryogenic electron microscopy is widely used in structural biology, but the resolution it achieves is often limited by the dynamics of the macromolecule. Here, we developed a refinement protocol based on Gaussian mixture models that integrate particle orientation and conformation estimation, and improves the alignment for flexible domains of protein structures. We demonstrated this protocol on multiple datasets, resulting in improved resolution and resolvability by visual and quantitative measures

A tail-like assembly at the portal vertex in intact herpes simplex type-1 virions

Herpes viruses are prevalent and well characterized human pathogens. Despite extensive study, much remains to be learned about the structure of the genome packaging and release machinery in the capsids of these large and complex double-stranded DNA viruses. However, such machinery is well characterized in tailed bacteriophage, which share a common evolutionary origin with herpesvirus. In tailed bacteriophage, the genome exits from the virus particle through a portal and is transferred into the host cell by a complex apparatus (i.e. the tail) located at the portal vertex. Here we use electron cryo-tomography of human herpes simplex type-1 (HSV-1) virions to reveal a previously unsuspected feature at the portal vertex, which extends across the HSV-1 tegument layer to form a connection between the capsid and the viral membrane. The location of this assembly suggests that it plays a role in genome release into the nucleus and is also important for virion architecture

Removing subordinate species in a biodiversity experiment to mimic observational field studies

Background: Positive effects of plant species richness on community biomass in biodiversity experiments are often stronger than those from observational field studies. This may be because experiments are initiated with randomly assembled species compositions whereas field communities have experienced filtering. Methods: We compared aboveground biomass production of randomly assembled communities of 2–16 species (controls) with experimentally filtered communities from which subordinate species were removed, resulting in removal communities of 1–8 species. Results: Removal communities had (1) 12.6% higher biomass than control communities from which they were derived, that is, with double species richness and (2) 32.0% higher biomass than control communities of equal richness. These differences were maintained along the richness gradient. The increased productivity of removal communities was paralleled by increased species evenness and complementarity. Conclusions: Result (1) indicates that subordinate species can reduce community biomass production, suggesting a possible explanation for why the most diverse field communities sometimes do not have the highest productivity. Result (2) suggests that if a community of S species has been derived by filtering from a pool of 2S randomly chosen species it is more productive than a community derived from a pool of S randomly chosen species without filtering

Electron Cryomicroscopy of Biological Machines at Subnanometer Resolution

Advances in electron cryomicroscopy (cryo-EM) have made possible the structural determination of large biological machines in the resolution range of 6–9 Å. Rice dwarf virus and the acrosomal bundle represent two distinct types of machines amenable to cryo-EM investigations at subnanometer resolutions. However, calculating the density map is only the first step, and much analysis remains to extract structural insights and the mechanism of action in these machines. This paper will review the computational and visualization methodologies necessary for analysis (structure mining) of the computed cryo-EM maps of these machines. These steps include component segmentation, averaging based on local symmetry among components, density connectivity trace, incorporation of bioinformatics analysis, and fitting of high-resolution component data, if available. The consequences of these analyses can not only identify accurately some of the secondary structure elements of the molecular components in machines but also suggest structural mechanisms related to their biological functions

Ultrafast Photo-Induced Charge Transfer Unveiled by Two-Dimensional Electronic Spectroscopy

The interaction of exciton and charge transfer (CT) states plays a central role in photo-induced CT processes in chemistry, biology and physics. In this work, we use a combination of two-dimensional electronic spectroscopy (2D-ES), pump-probe measurements and quantum chemistry to investigate the ultrafast CT dynamics in a lutetium bisphthalocyanine dimer in different oxidation states. It is found that in the anionic form, the combination of strong CT-exciton interaction and electronic asymmetry induced by a counter-ion enables CT between the two macrocycles of the complex on a 30 fs timescale. Following optical excitation, a chain of electron and hole transfer steps gives rise to characteristic cross-peak dynamics in the electronic 2D spectra, and we monitor how the excited state charge density ultimately localizes on the macrocycle closest to the counter-ion within 100 fs. A comparison with the dynamics in the radical species further elucidates how CT states modulate the electronic structure and tune fs-reaction dynamics. Our experiments demonstrate the unique capability of 2D-ES in combination with other methods to decipher ultrafast CT dynamics.Comment: 14 pages, 11 figures, and Supporting informatio

Zernike Phase Contrast Cryo-Electron Microscopy and Tomography for Structure Determination at Nanometer and Subnanometer Resolutions

Zernike phase contrast cryo-electron microscopy (ZPC-cryoEM) is an emerging technique that is capable of producing higher image contrast than conventional cryoEM. By combining this technique with advanced image processing methods, we achieved subnanometer resolution for two biological specimens: 2D bacteriorhodopsin crystal and epsilon15 bacteriophage. For an asymmetric reconstruction of epsilon15 bacteriophage, ZPC-cryoEM can reduce the required amount of data by a factor of ~3, compared with conventional cryoEM. The reconstruction was carried out to 13 Å resolution without the need to correct the contrast transfer function. New structural features at the portal vertex of the epsilon15 bacteriophage are revealed in this reconstruction. Using ZPC cryo-electron tomography (ZPC-cryoET), a similar level of data reduction and higher resolution structures of epsilon15 bacteriophage can be obtained relative to conventional cryoET. These results show quantitatively the benefits of ZPC-cryoEM and ZPC-cryoET for structural determinations of macromolecular machines at nanometer and subnanometer resolutions.National Institutes of Health (U.S.) (Grant P41RR002250)National Institutes of Health (U.S.) (Grant R01AI0175208)National Institutes of Health (U.S.) (Grant PN1EY016525)Robert Welch Foundation (Q1242

Technical note: A collision prediction tool using Blender.

Non-coplanar radiotherapy treatment techniques on C-arm linear accelerators have the potential to reduce dose to organs-at-risk in comparison with coplanar treatment techniques. Accurately predicting possible collisions between gantry, table and patient during treatment planning is needed to ensure patient safety. We offer a freely available collision prediction tool using Blender, a free and open-source 3D computer graphics software toolset. A geometric model of a C-arm linear accelerator including a library of patient models is created inside Blender. Based on the model, collision predictions can be used both to calculate collision-free zones and to check treatment plans for collisions. The tool is validated for two setups, once with and once without a full body phantom with the same table position. For this, each gantry-table angle combination with a 2° resolution is manually checked for collision interlocks at a TrueBeam system and compared to simulated collision predictions. For the collision check of a treatment plan, the tool outputs the minimal distance between the gantry, table and patient model and a video of the movement of the gantry and table, which is demonstrated for one use case. A graphical user interface allows user-friendly input of the table and patient specification for the collision prediction tool. The validation resulted in a true positive rate of 100%, which is the rate between the number of correctly predicted collision gantry-table combinations and the number of all measured collision gantry-table combinations, and a true negative rate of 89%, which is the ratio between the number of correctly predicted collision-free combinations and the number of all measured collision-free combinations. A collision prediction tool is successfully created and able to produce maps of collision-free zones and to test treatment plans for collisions including visualisation of the gantry and table movement