To gain insight into how the POP scaffold might give rise to the observed ArM selectivity, molecular dynamics simulations were conducted on models of 5-G that involved different starting coordination states of dirhodium cofactor 1. Three starting coordination states (5-G apo, 5-G with parameterized Rh-His bond, 5-G without Rh-His bond) were studied. The initial structure of 5-G apo was constructed from the crystal structure of POP, with the following amino acids mutations made using VMD17: S477F/E104A/F146A/K199A/D202A/S301G/G99S/Y326H/Q98P/S99H/V71G/E283G. The 5-G with Rh-His and 5-G without Rh-His bond models were constructed by mutating S477Z (Z is azidophenylalanine, where dirhodium cofactor 1 covalently links to the protein), which is the only other mutation from 5-G apo. No other changes where made to the model without a Rh-His bond. The Rh-His model contains a parameterized H326 bond to one of the dirhodium atoms, as shown in Figure 2D.
MD simulations were performed for the 5-G apo, with Rh-His and no Rh-His POP enzymes. All three structures were bathed in a 0.15M KCl solution using the Solution Builder Module in CHARMM-GUI.18 These systems were roughly 100 100 100 Å3 in dimension and contained ~ 110,000 atoms. The periodic boundary conditions were counted using the particle-mesh Ewald method with an automatic generated grid size.
Once the simulation systems were generated, they were subjected to equilibration at 358.15 K. The system was first equilibrated in an NVT ensemble for 10 ns. The equilibration simulations were performed using NAMD2.14 GPU acceleration version package19 on Nvidia’s P100 GPUs. After equilibration, the systems were simulated for 1000 ns each in an NPT ensemble with temperature set to 358.15 K and the isotropic pressure set to 1 atm. Langevin thermostats with a damping coefficient of 1 ps-1 were used to keep the temperature constant. The cutoff of the van der Waals interactions and short-range electrostatic interactions were set to ~25 Å as suggested by the guesser script. The additive C36 force field was used in all the simulations performed here.20,21,22,23 The force field parameters for the covalently linked dirhodium cofactor 1 were generated using the GAAMP server.24
The Quaternary Geology of the Indiana Portion of the Eastern Extent of the South Bend 30- x 60-Minute Quadrangle was created to provide digital access to the Quaternary geology of the eastern extent of the South Bend 30- x 60-minute quadrangle in Indiana. This geodatabase presents basic Quaternary geological information that contributes to the development of a three-dimensional framework of the state of Indiana. The data are synthesized from archived public domain geological data obtained from many different sources, original data obtained from fieldwork conducted by the authors, and contract drilling supported by project funds. Archive data sources include water-well records, refraction seismic surveys, borehole descriptions and geophysical logs, and the geological literature. Project data includes observations and measurements from drilled and sampled boreholes and estimated bedrock depths from analysis of horizontal-vertical spectral ratios (HVSR) seismic measurements. This database is, in large part, the result of a cooperative mapping agreement between the U.S. Geological Survey (USGS) and the Indiana Geological and Water Survey through the STATEMAP program of the USGS.
Antinao, J. L., and Rupp, R. F., 2021, Quaternary geology of the Indiana portion of the eastern extent of the South Bend 30- x 60-minute quadrangle: Indiana Geological and Water Survey, Indiana Journal of Earth Sciences, v. 3, scale 1:100,000. doi: 10.14434/ijes.v3i0.31698
Quaternary Geology of the Indiana Portion of the Eastern Extent of the South Bend 30- x 60-Minute Quadrangle
The Bedrock Geologic Map of the Southern Half of the Knox 30- X 60-Minute Quadrangle was created to provide digital access to the bedrock geology of southern half of the Knox quadrangle in northern Indiana. This geodatabase presents basic bedrock geological information that contributes to the characterization of potential mineral resources and bedrock aquifer systems. The data are synthesized from archived public domain geological data obtained from many different sources, original data obtained from fieldwork conducted by the authors, and contract drilling supported by project funds. Archive data sources include petroleum-well records, water-well records, refraction seismic surveys, and the geological literature. Project data includes measurements from quarry exposures, drill cores, drill cuttings, geophysical logs, chemostratigraphic analysis via portable X-ray fluorescence and stable isotope ratio mass spectrometry, conodont biostratigraphy, and horizontal-to-vertical spectral ratio geophysical surveys. This database is, in large part, the result of a cooperative mapping agreement between the U.S. Geological Survey (USGS) and the Indiana Geological and Water Survey through the STATEMAP program of the USGS.
These matlab files were produced by a Macintosh computer running Matlab version 2015. Files with the extension *.m are unformatted text files that can be opened with any text editor. They are Matlab scripts and functions that can be opened and executed by Matlab. Files with the extension *.mat are binary data files that can be opened only by Matlab. These Matlab files are intended for readers of the monograph “Fourier Analysis for Beginners” who wish to review numerical examples and exercises mentioned in the text. The full text of the book can be downloaded at http://hdl.handle.net/2022/21365 .
Date derived from a sample of OCLC records. Data was collected for research published by "Cataloging & Classification Quarterly." Full citation of the paper is: Park, Taemin Kim & Andrea M. Morrison (2017). The Nature and Characteristics of Bibliographic Relationships in RDA Cataloging Records in OCLC at the Beginning of RDA Implementation. Cataloging & Classification Quarterly, vol. 55, issue 6. http://www.tandfonline.com/doi/full/10.1080/01639374.2017.1319451. A post-print of the paper is available here: http://hdl.handle.net/2022/21657.
Dataset for "Comparing Transaction Logs to ILL requests to Determine the Persistence of Library Patrons In Obtaining Materials" article.
Excel file contains all data in four worksheets
Zip file contains four csv files, one for each worksheet:
- Comparing Transaction Logs to ILL - 2016 ILL Raw Data.csv
- Comparing Transaction Logs to ILL - 2015 ILL Raw Data.csv
- Comparing Transaction Logs to ILL - 2016 Zero Search Raw Data.csv
- Comparing Transaction Logs to ILL - 2015 Zero Search Raw Data.csv
Data transcribed from authority records matching relevant search criteria submitted to OCLC. MARC records retrieved July 11, 2017 via OCLC Connexion Client. Data entry completed September, 12, 2017. Data entered in exact transcription, retaining any errors or typos found in the retrieved records.
Polly, P.D. and A. Goswami. 2010. Modularity for Mathematica, Version 1.0. Goswami, A. & Polly, P. D. 2010 Methods for studying morphological integration, modularity and covariance evolution. In Quantitative Methods in Paleobiology. Paleontological Society Short Course, October 30th, 2010, vol. The Paleontological Society Papers (ed. J. Alroy & G. Hunt), pp. 213-243. Chicago: The Paleontological Society.
Initial Jetstream Featured image. Based on CentOS 6 (6.7) Development. Patched up to date as of 3/29/16, turned off the following from default startup in GNOME: Bluetooth Power Manager Volume Control PulseAudio Package Manager
ZIP file approximately 95MB; CONTENTS: ExpArchive_Across Ss.xlsx; ExpArchive_Individual Ss; ExpArchive_Reference Files; README.pdf with instructions and key to coding; Software: Excel: Mac 2011; Adobe Acrobat XI Pro PDF/A; NOTE: It is imperative to retain Lucida Grande font to preserve the integrity of phonetic transcriptions.
ZIP file approximately 158MB; CONTENTS: PhonArchive_Individual Ss (folder with individual .xlsx files); PhonArchive_Reference Files; README.pdf with instructions for use and keys to coding; SOFTWARE: Excel: Mac 2011; Adobe Acrobat XI Pro PDF/A; NOTE: It is imperative to retain Lucida Grande font to preserve the integrity of phonetic transcriptions.
ZIP file approximately 1MB; CONTENTS: DemogArchive_Across Ss.xlsx; DemogArchive_Reference File.pdf; README.pdf with instructions for use and keys to coding; SOFTWARE: Excel: Mac 2011; Adobe Acrobat XI Pro PDF/A; NOTE: It is imperative to retain Lucida Grande font to preserve the integrity of phonetic transcriptions.
Savaryn, Toby, et al. Comparative top down proteomics of peripheral blood mononuclear cells from kidney transplant recipients with normal kidney biopsies or acute rejection, Proteomics xxx (2016) xxx-xxx
Comparative top down proteomics of peripheral blood mononuclear cells from kidney transplant recipients with normal kidney biopsies or acute rejection
Castillo, DM, AK Gibson, and LC Moyle. 2016. Assortative mating and self-fertilization differ in their contributions to reinforcement, cascade speciation, and diversification. Current Zoology 62(2):169-181. doi.org/10.1093/cz/zow004
Assortative mating and self-fertilization differ in their contributions to reinforcement, cascade speciation, and diversification.
The data are stored in two formats: a single EXCEL 2010 file with two worksheets (one for each phase of data collection) and two csv files (one for each phase of data collection; data are identical to those in the corresponding Excel file worksheets). A Codebook (pdf format) describes the variables in detail.
Study population is described in: Bedwell RM, Spielvogel H, Bellido D, Vitzthum VJ. 2017. "Factors influencing the use of biomedical health care by rural Bolivian anemic women: structural barriers, reproductive status, gender roles, and concepts of anemia." PLOS ONE (in press).
All data are organized and named after their figure numbers in the main text or the supplemental information. The .txt files contain xyz coordinates for all computationally optimized geometries of chemical structures. The .csv files contain other raw data associated with the figures in the main text, in which labels of the x and y axes are also described.
Please direct any questions regarding the data, data collection, methods used in the administration of this survey and/or the summarization of responses provided in this document (or the corresponding report) to Julie Wernert at Indiana University, firstname.lastname@example.org.
To access the coded interview transcripts and description of codes (i.e., codebook), you need NVivo for Mac Version 11.3.2 (1888). To access the raw dataset that lists the frequency with which each benefit was mentioned by DSA board members and non-DSA board members, you need IBM SPSS Statistics 24. To access the processed/analysed data from the Mann-Whitney U tests, you need IBM SPSS Statistics 24 to access the .spv file and Microsoft Word to access the .doc file.