Hybrid Approaches to Structural Characterization of Conformational Ensembles of Complex Macromolecular Systems Combining NMR Residual Dipolar Couplings and Solution X‑ray Scattering

Solving structures or structural ensembles of large macromolecular systems in solution poses a challenging problem. While NMR provides structural information at atomic resolution, increased spectral complexity, chemical shift overlap, and short transverse relaxation times (associated with slow tumbling) render application of the usual techniques that have been so successful for medium sized systems (\u3c50 \u3ekDa) difficult. Solution X-ray scattering, on the other hand, is not limited by molecular weight but only provides low resolution structural information related to the overall shape and size of the system under investigation. Here we review how combining atomic resolution structures of smaller domains with sparse experimental data afforded by NMR residual dipolar couplings (which yield both orientational and shape information) and solution X-ray scattering data in rigid-body simulated annealing calculations provides a powerful approach for investigating the structural aspects of conformational dynamics in large multidomain proteins. The application of this hybrid methodology is illustrated for the 128 kDa dimer of bacterial Enzyme I which exists in a variety of open and closed states that are sampled at various points in the catalytic cycles, and for the capsid protein of the human immunodeficiency virus

The Structure of Pre-transitional Protoplanetary Disks I: Radiative Transfer Modeling of the Disk+Cavity in the PDS 70 system

Through detailed radiative transfer modeling, we present a disk+cavity model to simultaneously explain both the SED and Subaru H-band polarized light imaging for the pre-transitional protoplanetary disk PDS 70. Particularly, we are able to match not only the radial dependence, but also the absolute scale, of the surface brightness of the scattered light. Our disk model has a cavity 65 AU in radius, which is heavily depleted of sub-micron-sized dust grains, and a small residual inner disk which produces a weak but still optically thick NIR excess in the SED. To explain the contrast of the cavity edge in the Subaru image, a factor of ~1000 depletion for the sub-micron-sized dust inside the cavity is required. The total dust mass of the disk may be on the order of 1e-4 M_sun, only weakly constrained due to the lack of long wavelength observations and the uncertainties in the dust model. The scale height of the sub-micron-sized dust is ~6 AU at the cavity edge, and the cavity wall is optically thick in the vertical direction at H-band. PDS 70 is not a member of the class of (pre-)transitional disks identified by Dong et al. (2012), whose members only show evidence of the cavity in the millimeter-sized dust but not the sub-micron-sized dust in resolved images. The two classes of (pre-)transitional disks may form through different mechanisms, or they may just be at different evolution stages in the disk clearing process.Comment: 28 pages (single column), 7 figures, 1 table, ApJ accepte

New Techniques for High-Contrast Imaging with ADI: the ACORNS-ADI SEEDS Data Reduction Pipeline

We describe Algorithms for Calibration, Optimized Registration, and Nulling the Star in Angular Differential Imaging (ACORNS-ADI), a new, parallelized software package to reduce high-contrast imaging data, and its application to data from the SEEDS survey. We implement several new algorithms, including a method to register saturated images, a trimmed mean for combining an image sequence that reduces noise by up to ~20%, and a robust and computationally fast method to compute the sensitivity of a high-contrast observation everywhere on the field-of-view without introducing artificial sources. We also include a description of image processing steps to remove electronic artifacts specific to Hawaii2-RG detectors like the one used for SEEDS, and a detailed analysis of the Locally Optimized Combination of Images (LOCI) algorithm commonly used to reduce high-contrast imaging data. ACORNS-ADI is written in python. It is efficient and open-source, and includes several optional features which may improve performance on data from other instruments. ACORNS-ADI requires minimal modification to reduce data from instruments other than HiCIAO. It is freely available for download at www.github.com/t-brandt/acorns-adi under a BSD license.Comment: 15 pages, 9 figures, accepted to ApJ. Replaced with accepted version; mostly minor changes. Software update

Constraining the Movement of the Spiral Features and the Locations of Planetary Bodies within the AB Aur System

We present new analysis of multi-epoch, H-band, scattered light images of the AB Aur system. We used a Monte Carlo, radiative transfer code to simultaneously model the system's SED and H-band polarized intensity imagery. We find that a disk-dominated model, as opposed to one that is envelope dominated, can plausibly reproduce AB Aur's SED and near-IR imagery. This is consistent with previous modeling attempts presented in the literature and supports the idea that at least a subset of AB Aur's spirals originate within the disk. In light of this, we also analyzed the movement of spiral structures in multi-epoch H-band total light and polarized intensity imagery of the disk. We detect no significant rotation or change in spatial location of the spiral structures in these data, which span a 5.8 year baseline. If such structures are caused by disk-planet interactions, the lack of observed rotation constrains the location of the orbit of planetary perturbers to be >47 AU.Comment: 8 pages, 3 figures, 1 table, Accepted to Ap

Target 2035-update on the quest for a probe for every protein

Twenty years after the publication of the first draft of the human genome, our knowledge of the human proteome is still fragmented. The challenge of translating the wealth of new knowledge from genomics into new medicines is that proteins, and not genes, are the primary executers of biological function. Therefore, much of how biology works in health and disease must be understood through the lens of protein function. Accordingly, a subset of human proteins has been at the heart of research interests of scientists over the centuries, and we have accumulated varying degrees of knowledge about approximately 65% of the human proteome. Nevertheless, a large proportion of proteins in the human proteome (∼35%) remains uncharacterized, and less than 5% of the human proteome has been successfully targeted for drug discovery. This highlights the profound disconnect between our abilities to obtain genetic information and subsequent development of effective medicines. Target 2035 is an international federation of biomedical scientists from the public and private sectors, which aims to address this gap by developing and applying new technologies to create by year 2035 chemogenomic libraries, chemical probes, and/or biological probes for the entire human proteome