This codebook.txt file was generated on 20201124 by wilsonkm ------------------- GENERAL INFORMATION ------------------- 1. Title of Dataset Proton and amide chemical shift list files of wild-type cAMP-dependent protein kinase a (PKA-C) and the chimeric mutant (PKA-JC) and MATLab scripts for the chemical shift analysis 2. Author Information Principal Investigator Contact Information Name: Gianluigi Veglia Institution: University of Minnesota Associate or Co-investigator Contact Information Name: Cristina Olivieri Institution: University of Minnesota Email: colivier@umn.edu Associate or Co-investigator Contact Information Name: Caitlin Walker Institution: University of Minnesota Associate or Co-investigator Contact Information Name: Manu Veliparambil Subrahmanian Institution: University of Minnesota 3. Date of data collection: July 2016 to December 2018 4. Geographic location of data collection (where was data collected?): All the NMR experiments were acquired at Minnesota NMR Facility, University of Minnesota Twin-Cities, MN, 55455 5. Information about funding sources that supported the collection of the data: Sponsorship: NIH GM 100310 to G.V -------------------------- SHARING/ACCESS INFORMATION -------------------------- 1. Licenses/restrictions placed on the data: Attribution 3.0 United States 2. Links to publications that cite or use the data: The data set is part of the following pubblication "Defective Internal Allosteric Network Imparts Dysfunctional ATP/Substrate 1 Binding Cooperativity in Oncogenic Chimera of Protein Kinase A", that is under review in Communication Biology journal. 3. Links to other publicly accessible locations of the data: N/A 4. Links/relationships to ancillary data sets: http://hdl.handle.net/11299/217206 5. Was data derived from another source? N/A 6. Recommended citation for the data: Veglia, Gianluigi; Cristina, Olivieri; Caitlin, Walker; Manu, Veliparambil Subrahmanian. (2020). Proton and amide chemical shift list files of wild-type cAMP-dependent protein kinase a (PKA-C) and the chimeric mutant (PKA-JC) and MATLab scripts for the chemical shift analysis. Retrieved from the Data Repository for the University of Minnesota, https://doi.org/10.13020/7DB9-VD97. --------------------- DATA & FILE OVERVIEW --------------------- 1. File List A. Filename: CHESCA.m Short description: Matlab script coding for the CHEmical Shift Covariance Analysis was used to analyze the proton and amide chemical shift of PKA-C and PKA-JC free and bound to nucleotides and pseudo-substrate. Veliparambil Subrahmanian converted the R script to Matlab format. CHESCA was developed by Melacini lab. The script is available in the SI of the following publication: Selvaratnam R, Chowdhury S, VanSchouwen B, Melacini G. Mapping allostery through the covariance analysis of NMR chemical shifts. Proc Natl Acad Sci U S A. 2011 Apr 12;108(15):6133-8. doi: 10.1073/pnas.1017311108. Epub 2011 Mar 28. PMID: 21444788; PMCID: PMC3076865. B. Filename: CONCISE.m Short description: Matlab script coding for the COordiNated ChemIcal Shifts bEhavior (CONCISE) program used to analyze the proton and amide chemical shift of PKA-C and PKA-JC free and bound to nucleotides and pseudo-substrate. Veliparambil Subrahmanian converted the R script to Matlab format. CONCISE was developed in Veglia Lab (Cembran A, Kim J, Gao J, Veglia G. NMR mapping of protein conformational landscapes using coordinated behavior of chemical shifts upon ligand binding. Phys Chem Chem Phys. 2014 Apr 14;16(14):6508-18. doi: 10.1039/c4cp00110a. Epub 2014 Mar 7. PMID: 24604024; PMCID: PMC41176820, and can be download from the lab website (http://veglia.chem.umn.edu/software-downloads). C. Filename: Chemical_Shifts_list_file.rar Short description: Chemical shift list files; .list files can be opened using a text editor D. Filename: Domain_and_community_CHESCA.m Short description: Program developed by Veliparambil Subrahmanian. This Matlab script allows the analysis of the chemical shift behavior of the Community of PKA-C. The Community classification is based on the following publication McClendon CL, Kornev AP, Gilson MK, Taylor SS. Dynamic architecture of a protein kinase. Proc Natl Acad Sci U S A. 2014 Oct 28;111(43):E4623-31. doi: 10.1073/pnas.1418402111. Epub 2014 Oct 15. Erratum in: Proc Natl Acad Sci U S A. 2014 Nov 25;111(47):16973. PMID: 25319261; PMCID: PMC4217441. E. Filename: deCONCISE.m Short description: Domain&Community-CONCISE 2. Relationship between files: The file in C are the list file (raw data) used to run all the Matlab script deposit in A, B, D, and E 3. Additional related data collected that was not included in the current data package: 4. Are there multiple versions of the dataset? no -------------------------- METHODOLOGICAL INFORMATION -------------------------- 1. Description of methods used for collection/generation of data: Proton and amide chemical shift list files of wild-type cAMP-dependent protein kinase a (PKA-C) and the chimeric mutant (PKA-JC) and MatLab scripts used for the CHESCA and CONCISE analysis. The chemical shift lists were obtained using standard NMR experiments (1H-15N -TROSY-HSQC). The MatLab scripts were used for the CHESCA and CONCISE analysis of the amide chemical shift. These files are part of a publication on Communication biology: "Defective Internal Allosteric Network Imparts Dysfunctional ATP/Substrate Binding Cooperativity in Oncogenic Chimera of Protein Kinase A". 2. Methods for processing the data: The NMR data were converted and processed using NMRPipe, and the assignment of each resonance was transferred using NMRFAM-Sparky that also has been used to generate the list file (C) 3. Instrument- or software-specific information needed to interpret the data: MatLAB 4. Standards and calibration information, if appropriate: The spectrometer used to acquire the 1H-15N TROSY experiments was calibrated using the standard NMR calibration compound. All the spectra of PKA-C were aligned using the residue Ser262, while the spectra of PKA-JC were aligned using the residue Glu311 5. Environmental/experimental conditions: All the NMR experiment were recorded at 300K 6. Describe any quality-assurance procedures performed on the data: 7. People involved with sample collection, processing, analysis and/or submission: Cristina Olivieri (collecting, processing,alaysis, interpretation, submission) Caitlin Walker (collecting, processing,alaysis, interpretation); Manu Veliparambil Subrahmanian (analysis)