Describing protein conformational ensembles: beyond static snapshots

Protein molecules are not static but are in varying degrees of motion. Of course, the breadth of structural arrangements in an ensemble will vary tremendously. Some proteins are like ‘rocks’ and are very tightly constrained in terms of deviations of their coordinates from their averages. Others are ‘writhing snakes’, with little recognized persistent structure, and then there is everything in between. Through the work of many, there is an increasing awareness of the role of dynamics in the biological function of proteins, and new computational and experimental methods are allowing us to make these connections. A personal perspective on the state of affairs is offered with examples primarily from the author's own work

Clark County Cultural Site Stewardship Program: Final Project Report

Cooperative Conservation: Increasing Capacity through Community Partnerships – Cultural Site Stewardship Program is a Round 4 Southern Nevada Public Land Management Act (SNPLMA)- funded project implemented by the University of Nevada, Las Vegas Public Lands Institute on behalf of and in cooperation with four Federal agencies. This project resulted in the design, development, and implementation of an Interagency Cultural Site Stewardship Program. The program: Was recognized with Department of the Interior Cooperative Conservation Service Award (2007). Was modeled after the successful Arizona Site Steward Program developed and implemented with the following components: ─ recruitment activities ─ required classroom and field training and optional courses ─ recognition events ─ volunteer service totaling 10,929 hours by 288 Cultural Site Stewards and seven regional coordinators who identified, documented, and reported 94 significant impacts and 200 lesser impacts Developed Standard Operating Procedures (SOP) describing recruitment, training, recognition, and retention of volunteers, site steward operations, relevant laws, and a protocol for interfacing with law enforcement personnel. Conducted research on the viability of establishing a certificate program for cultural site stewards. Developed, distributed, and analyzed training program effectiveness survey. Designed, developed and implemented a hybrid relational database for the Cultural Site Stewardship Program. Built and maintained relationships with the public through: ─ outreach activities at community events ─ membership and participation in professional societies ─ multiple formal and informal presentations ─ timely response to inquiries through telephone, electronic, and mail correspondenc

Protein structural variation in computational models and crystallographic data

Normal mode analysis offers an efficient way of modeling the conformational flexibility of protein structures. Simple models defined by contact topology, known as elastic network models, have been used to model a variety of systems, but the validation is typically limited to individual modes for a single protein. We use anisotropic displacement parameters from crystallography to test the quality of prediction of both the magnitude and directionality of conformational variance. Normal modes from four simple elastic network model potentials and from the CHARMM forcefield are calculated for a data set of 83 diverse, ultrahigh resolution crystal structures. While all five potentials provide good predictions of the magnitude of flexibility, the methods that consider all atoms have a clear edge at prediction of directionality, and the CHARMM potential produces the best agreement. The low-frequency modes from different potentials are similar, but those computed from the CHARMM potential show the greatest difference from the elastic network models. This was illustrated by computing the dynamic correlation matrices from different potentials for a PDZ domain structure. Comparison of normal mode results with anisotropic temperature factors opens the possibility of using ultrahigh resolution crystallographic data as a quantitative measure of molecular flexibility. The comprehensive evaluation demonstrates the costs and benefits of using normal mode potentials of varying complexity. Comparison of the dynamic correlation matrices suggests that a combination of topological and chemical potentials may help identify residues in which chemical forces make large contributions to intramolecular coupling.Comment: 17 pages, 4 figure

Instability of the salinity profile during the evaporation of saline groundwater

We investigate salt transport during the evaporation and upflow of saline groundwater. We describe a model in which a sharp evaporation-precipitation front separates regions of soil saturated with an air-vapour mixture and with saline water. We then consider two idealised problems. We first investigate equilibrium configurations of the fresh-water system when the depth of the soil layer is finite, obtaining results for the location of the front and for the upflow of water induced by the evaporation. Motivated by these results, we develop a solution for a propagating front in a soil layer of infinite depth, and we investigate the gravitational stability of the salinity profile which develops below the front, obtaining marginal linear stability conditions in terms of a Rayleigh number and a dimensionless salt saturation parameter. Applying our findings to realistic parameter regimes, we predict that salt fingering is unlikely to occur in low-permeability soils, but is likely in high-permeability (sandy) soils under conditions of relatively low evaporative upflow

Loop Dynamics of Thymidine Diphosphate-Rhamnose 3\u27-\u3cem\u3eO\u3c/em\u3e-Methyltransferase (CalS11), an Enzyme in Calicheamicin Biosynthesis

Structure analysis and ensemble refinement of the apo-structure of thymidine diphosphate (TDP)-rhamnose 3\u27-O-methyltransferase reveal a gate for substrate entry and product release. TDP-rhamnose 3\u27-O-methyltransferase (CalS11) catalyses a 3\u27-O-methylation of TDP-rhamnose, an intermediate in the biosynthesis of enediyne antitumor antibiotic calicheamicin. CalS11 operates at the sugar nucleotide stage prior to glycosylation step. Here, we present the crystal structure of the apo form of CalS11 at 1.89 Å resolution. We propose that the L2 loop functions as a gate facilitating and/or providing specificity for substrate entry or promoting product release. Ensemble refinement analysis slightly improves the crystallographic refinement statistics and furthermore provides a compelling way to visualize the dynamic model of loop L2, supporting the understanding of its proposed role in catalysis

INTEGRAL and XMM-Newton Spectral Studies of NGC 4388

We present first INTEGRAL and XMM-Newton observations of a Seyfert galaxy, the type 2 AGN NGC 4388. Several INTEGRAL observations performed in 2003 allow us to study the spectrum in the 20 - 300 keV range. In addition two XMM-Newton observations give detailed insight into the 0.2 - 10 keV emission. The measurements presented here and comparison with previous observations by BeppoSAX, SIGMA and CGRO/OSSE show that the overall spectrum from soft X-rays up to the gamma-rays can be described by a highly absorbed (N_H = 2.7e23 1/cm^2) and variable non-thermal component in addition to constant non-absorbed thermal emission (T = 0.8 keV) of low abundance (7% solar), plus a constant Fe K-alpha and K-beta line. The hard X-ray component is well described by a simple power law with a mean photon index of 1.7. During the INTEGRAL observations the 20 - 100 keV flux increased by a factor of 1.4. The analysis of XMM-Newton data implies that the emission below 3 keV is decoupled from the AGN and probably due to extended emission as seen in Chandra observations. The constant iron line emission is apparently also decoupled from the direct emission of the central engine and likely to be generated in the obscuring material, e.g. in the molecular torus.Comment: 11 pages, 5 figures, accepted for publication in Ap

Fantasies of subjugation: a discourse theoretical account of British policy on the European Union

The decision by the UK government to hold a referendum on Britain’s membership of the European Union (EU) marks an important development in policy towards the EU. Policy changes of this kind must be understood in the historical and political context in which they occur. This includes the framing of the policy issues within public discourse. In the UK, policies are formed in a discursive environment which is overwhelmingly hostile towards the EU. Debates are structured by a predominantly Euroskeptic discourse which emphasizes the UK’s separation and heterogeneity from the rest of the EU. Drawing on the logics of critical explanation, this article examines the structure and affective power of Euroskeptic discourses which dictate the terms of the EU debate. It presents a case study of the recent EU treaty revision process, culminating in the Treaty of Lisbon. In so doing, it enables a deeper understanding of recent policy developments

Successful Flash-Cooling of Xenon Derivatized Myoglobin Crystals

This paper demonstrates for the first time a method for preparing cryocooled xenon-derivatized protein crystals. The method is based upon the hypothesis and subsequent observation that the diffusion of a xenon atom from a tight binding site following depressurization occurs on a timescale of minutes. We have observed significant changes in diffraction intensities from myoglobin crystals for up to 5 min following depressurization from 1 MPa of xenon. In accordance with this observation, a xenon-derivatized myoglobin crystal was cryocooled at ~95 K within 20 s of complete depressurization. A crystallographic data set was then collected to 2.0 Å resolution and isomorphous and anomalous difference Patterson maps revealed the presence of a well ordered xenon site with an occupancy of approximately 0.5. Phasing statistics for this site were of good quality and demonstrate the practicality of this method. The ability to cryocool xenon-derivatized crystals will make this heavy-atom substitution method even more useful for single-isomorphous-replacement and multiple-isomorphous-replacement phasing of macromolecules

Effect of Primary Power Source on the Load Voltage Relationship in Load Cells from an Instrumented Scrum Machine

To measure force generated by rugby union players during the scrum, we instrumented a scrum machine using S-type load cells for voltage force data collection. Data collection may take place in a variety of settings with varying access to primary power. The voltage outputs from electronic equipment may change when using battery versus AC power. Purpose: To compare the load-voltage relationship in S-type load cells between wall outlet AC power and a lithium ion battery pack and inverter. Methods: Dead weight calibrations of two load cells under two power supply conditions were performed up to 200kg. Voltage data was obtained using 1) outlet power from the lab, and 2) using a lithium ion battery pack and inverter (Yeti 1500x Goal Zero, South Bluffdale, UT). A linear model was created to estimate the influence of power source (battery vs wall plug) on the load-voltage relationship (i.e. voltage = β0 + β1•load + β2•load.cell(7) + β3•power.source(plug) + β4•time + β5•load • power.source(plug)). Results: The linear model indicated a main effect of the power source was present (p = 0.003) but not a load x power source interaction effect (p = 0.085). On average, voltage values from the load cell were about 0.001 volts greater than when using the battery. Conclusion: The lithium ion battery pack reliably produces voltage outputs greater than wall AC outlet power. Thus field data collection using the lithium ion battery pack is permitted, providing the volt difference is accounted for when analyzing data

CrysFormer: Protein Structure Prediction via 3d Patterson Maps and Partial Structure Attention

Determining the structure of a protein has been a decades-long open question. A protein's three-dimensional structure often poses nontrivial computation costs, when classical simulation algorithms are utilized. Advances in the transformer neural network architecture -- such as AlphaFold2 -- achieve significant improvements for this problem, by learning from a large dataset of sequence information and corresponding protein structures. Yet, such methods only focus on sequence information; other available prior knowledge, such as protein crystallography and partial structure of amino acids, could be potentially utilized. To the best of our knowledge, we propose the first transformer-based model that directly utilizes protein crystallography and partial structure information to predict the electron density maps of proteins. Via two new datasets of peptide fragments (2-residue and 15-residue) , we demonstrate our method, dubbed \texttt{CrysFormer}, can achieve accurate predictions, based on a much smaller dataset size and with reduced computation costs