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PINE-SPARKY.2 for automated NMR-based protein structure research

Woonghee Lee, John L Markley, Alfonso Valencia
2017 Bioinformatics  
As a means for facilitating the handling and analysis of spectra involved in these types of NMR studies, we have developed PINE-SPARKY.2, a software package that integrates and automates discrete tasks  ...  The graphical user interface of PINE-SPARKY.2 simplifies chemical shift assignment and verification, automated detection of secondary structural elements, predictions of flexibility and hydrophobic cores  ...  Acknowledgements PINE-SPARKY.2 utilizes the CS-Rosetta web server service provided by BioMagResBank (; we are grateful to Jon Wedell for its maintenance.  ... 
doi:10.1093/bioinformatics/btx785 pmid:29281006 pmcid:PMC5925765 fatcat:xxagdsyjarad7a577o2d34gsii

Integrative NMR for biomolecular research

Woonghee Lee, Gabriel Cornilescu, Hesam Dashti, Hamid R. Eghbalnia, Marco Tonelli, William M. Westler, Samuel E. Butcher, Katherine A. Henzler-Wildman, John L. Markley
2016 Journal of Biomolecular NMR  
NMR spectroscopy is a powerful technique for determining structural and functional features of biomolecules in physiological solution as well as for observing their intermolecular interactions in real-time  ...  We introduce an NMR platform that makes biomolecular NMR spectroscopy much more accessible by integrating tools, databases, web services, and video tutorials that can be launched by simple installation  ...  Frans Mulder from Aarhus University for permitting their contributions to be included in NMRFAM-SPARKY.  ... 
doi:10.1007/s10858-016-0029-x pmid:27023095 pmcid:PMC4861749 fatcat:tktkhzb4xncntf4l4jxos52e4e

ADAPT-NMR Enhancer: complete package for reduced dimensionality in protein NMR spectroscopy

W. Lee, A. Bahrami, J. L. Markley
2012 Bioinformatics  
As an example, we show how ADAPT-NMR Enhancer was used to extend the automated data collection and assignment results for the protein Aedes aegypti sterol carrier protein 2.  ...  ADAPT-nuclear magnetic resonance (ADAPT-NMR) offers an automated approach to the concurrent acquisition and processing of protein NMR data with the goal of complete backbone and side chain assignments.  ...  Funding: National Center for Research Resources (5P41RR002301-27) and National Institute of General Medical Sciences (8 P41 GM103399-27) from the National Institutes of Health.  ... 
doi:10.1093/bioinformatics/bts692 pmid:23220573 pmcid:PMC3570218 fatcat:wkw6jroz6nhx5huikzjgigd6bi

CONNJUR R: an annotation strategy for fostering reproducibility in bio-NMR—protein spectral assignment

Matthew Fenwick, Jeffrey C. Hoch, Eldon Ulrich, Michael R. Gryk
2015 Journal of Biomolecular NMR  
Here we describe an approach for capturing missing metadata during the assignment of protein NMR spectra that can be generalized to arbitrary workflows, different software packages, other biomolecules,  ...  A general solution to this problem has been elusive, in part because of the wide range of approaches and software packages employed in the analysis of protein NMR spectra.  ...  Mark Maciejewski for kindly providing time-domain data of the Samp3 protein and Dr. Woonghee Lee for adding the reproducibility extensions to the NMRFam release of Sparky.  ... 
doi:10.1007/s10858-015-9964-1 pmid:26253947 pmcid:PMC4864978 fatcat:g7n5up2n5vbstc3l3th4o6cxlm

Solution NMR Determination of the CDHR3 Rhinovirus-C Binding Domain, EC1

Woonghee Lee, Ronnie O. Frederick, Marco Tonelli, Ann C. Palmenberg
2021 Viruses  
We now report the solution NMR determination of CDHR3 EC1, showing that this protein, in fact, is mostly inflexible, particularly in the virus-binding face.  ...  responsible for virus interactions.  ...  Acknowledgments: We thank Kelly Watters for the initial EC1 plasmids and for critical reading of the manuscript. Robert Kirchdoerfer suggested critical cis-Pro functionality.  ... 
doi:10.3390/v13020159 pmid:33499226 pmcid:PMC7911512 fatcat:fp7rwneir5elxe445vzenfrmtq

Modern Technologies of Solution Nuclear Magnetic Resonance Spectroscopy for Three-dimensional Structure Determination of Proteins Open Avenues for Life Scientists

Toshihiko Sugiki, Naohiro Kobayashi, Toshimichi Fujiwara
2017 Computational and Structural Biotechnology Journal  
Nuclear magnetic resonance (NMR) spectroscopy is a powerful technique for structural studies of chemical compounds and biomolecules such as DNA and proteins.  ...  Here, we describe the practical aspects, workflow and key points of modern NMR techniques used for solution structure determination of proteins.  ...  This work was supported in part by the Platform Project for Supporting Drug Discovery and Life Science Research, and AMED-CREST from MEXT and AMED, Japan. Appendix A.  ... 
doi:10.1016/j.csbj.2017.04.001 pmid:28487762 pmcid:PMC5408130 fatcat:uwvcokyfxndbne5uy7cksalryi

Probabilistic Interaction Network of Evidence Algorithm and its Application to Complete Labeling of Peak Lists from Protein NMR Spectroscopy

Arash Bahrami, Amir H. Assadi, John L. Markley, Hamid R. Eghbalnia, David Cowburn
2009 PLoS Computational Biology  
PINE-NMR achieves robust and consistent results that have been shown to be effective in subsequent steps of NMR structure determination.  ...  of NMR signals (chemical shifts) to sequence-specific backbone and aliphatic side chain atoms plus a probabilistic determination of the protein secondary structure.  ...  Acknowledgments We thank the members of NMRFAM and CESG who provided NMR data for this study and are pleased to acknowledge the many users of the PINE-NMR server, who provided useful feedback on its operation  ... 
doi:10.1371/journal.pcbi.1000307 pmid:19282963 pmcid:PMC2645676 fatcat:s6zqy7o3xvgx3m5zjgc6k2rgoy

1H, 15N, 13C resonance assignments of the reduced and active form of human Protein Tyrosine Phosphatase, PRL-1

Andria L. Skinner, Jennifer S. Laurence
2009 Biomolecular NMR Assignments  
Because the reduced form is active, we sought to identify a stable mutant that would resist oxidation and be useful for facilitating drug screening and development using NMR-based assays.  ...  We present here NMR assignments for a full-length, reduced and active form of PRL-1, PRL-1-C170S-C171S, that is well suited for this purpose.  ...  Todd Williams for collecting and analyzing the MS data and Dr. Dave Vander Velde for his help with the NMR instrument.  ... 
doi:10.1007/s12104-008-9142-4 pmid:19636948 pmcid:PMC2719816 fatcat:5n3ld2a6vvdg7kuypql367ggum

Automated and assisted RNA resonance assignment using NMR chemical shift statistics

Thomas Aeschbacher, Elena Schmidt, Markus Blatter, Christophe Maris, Olivier Duss, Frédéric H.-T. Allain, Peter Güntert, Mario Schubert
2013 Nucleic Acids Research  
The three-dimensional structure determination of RNAs by NMR spectroscopy relies on chemical shift assignment, which still constitutes a bottleneck.  ...  This is the first automated approach for chemical shift assignment of non-exchangeable protons of RNA and their corresponding 13 C resonances, which provides an important step toward automated structure  ...  Also, we thank Dr Peter Lukavsky for helpful comments and discussions. Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkt665 pmid:23921634 pmcid:PMC3794610 fatcat:44i3lauubncuxaungtyk5kmugm

Automated NMR resonance assignments and structure determination using a minimal set of 4D spectra

Thomas Evangelidis, Santrupti Nerli, Jiří Nováček, Andrew E. Brereton, P. Andrew Karplus, Rochelle R. Dotas, Vincenzo Venditti, Nikolaos G. Sgourakis, Konstantinos Tripsianes
2018 Nature Communications  
Automated methods for NMR structure determination of proteins are continuously becoming more robust.  ...  Automated methods for NMR structure determination of proteins are continuously becoming more robust.  ...  The current version (3.4) of CS-Rosetta also supports conversion of data to NMR Exchange Format for deposition to the wwPDB.  ... 
doi:10.1038/s41467-017-02592-z pmid:29374165 pmcid:PMC5786013 fatcat:3gof7uol7fev5em3rhdbo26wom

Structural basis of RNA recognition by the SARS-CoV-2 nucleocapsid phosphoprotein [article]

Dhurvas Chandrasekaran Dinesh, Dominika Chalupska, Jan Silhan, Vaclav Veverka, Evzen Boura
2020 bioRxiv   pre-print
SARS-CoV-2, like other coronaviruses, has an unusually large genome for a +RNA virus that encodes four structural proteins - the matrix (M), small envelope (E), spike (S) and nucleocapsid phosphoprotein  ...  Here, we characterized the structure of the N-NTD and its interaction with RNA using NMR spectroscopy.  ...  We used I-PINE assignment tool (9) implemented in NMRFAM-SPARKY (10) for initial automatic assignment. 1 H-1 H distance restraints were derived from 3D 15 N/ 1 H NOESY-HSQC and 13 C/ 1 H NOESY-HMQC, which  ... 
doi:10.1101/2020.04.02.022194 fatcat:nqanvjtosncqnh55q6b6gezktq

REDCRAFT: A computational platform using residual dipolar coupling NMR data for determining structures of perdeuterated proteins in solution

Casey A. Cole, Nourhan S. Daigham, Gaohua Liu, Gaetano T. Montelione, Homayoun Valafar, Alexander MacKerell
2021 PLoS Computational Biology  
Finally, we compare the accuracy of structure determination from RDCs alone with traditional NOE-based methods for the structurally novel PF.2048.1 protein.  ...  Nuclear Magnetic Resonance (NMR) spectroscopy is one of the three primary experimental means of characterizing macromolecular structures, including protein structures.  ...  NMR spectra were analyzed by consensus automated backbone assignment analysis using PINE [93] and AutoAssign [94] software, and then extended by manual analysis to complete the resonance assignments  ... 
doi:10.1371/journal.pcbi.1008060 pmid:33524015 fatcat:bjtq54knrveldfrxwrirtyylem

Solution structures of Mengovirus Leader protein, its phosphorylated derivatives, and in complex with nuclear transport regulatory protein, RanGTPase

V. R. Bacot-Davis, J. J. Ciomperlik, H. A. Basta, C. C. Cornilescu, A. C. Palmenberg
2014 Proceedings of the National Academy of Sciences of the United States of America  
Leader protein | NMR | phosphorylation | RanGTPase | cardiovirus  ...  A model of Ran:L M :Crm1, based on the new structures suggests L M phosphorylation status may mediate Ran's selection of exportin(s) and cargo(s), perverting these native trafficking elements into the  ...  Peak lists and peak tables were imported from CARA into SPARKY (11) for figure visualization and assignment verification with PINE-SPARKY (19) .  ... 
doi:10.1073/pnas.1411098111 pmid:25331866 pmcid:PMC4226078 fatcat:w2si4m5h25d6zb5q7osvxtm4ja

Exploiting image registration for automated resonance assignment in NMR

Madeleine Strickland, Thomas Stephens, Jian Liu, Nico Tjandra
2015 Journal of Biomolecular NMR  
For example, the 265-residue RalBP1 protein was 95.4% correctly assigned in 10 seconds.  ...  Analysis of protein NMR data involves the assignment of resonance peaks in a number of multidimensional data sets.  ...  Acknowledgments This work was supported by the Intramural Research Program of the NIH, National Heart, Lung, and Blood Institute.  ... 
doi:10.1007/s10858-015-9926-7 pmid:25828257 pmcid:PMC4452424 fatcat:7as5cd6yyvanpna6xsbc5mzuea

Molecular Insights into the Recognition of N-Terminal Histone Modifications by the BRPF1 Bromodomain

Amanda Poplawski, Kaifeng Hu, Woonghee Lee, Senthil Natesan, Danni Peng, Samuel Carlson, Xiaobing Shi, Stefan Balaz, John L. Markley, Karen C. Glass
2014 Journal of Molecular Biology  
We used chemical shift perturbation data from NMR titration experiments to map the BRPF1 bromodomain ligand binding pocket and identified key residues responsible for coordination of the post-translationally  ...  The MOZ HAT functions as a quaternary complex with the bromodomain-PHD finger protein 1 (BRPF1), inhibitor of growth 5 (ING5), and hEaf6 subunits.  ...  for Research Resources) and P41GM66326 (National Institute of General Medical Sciences).  ... 
doi:10.1016/j.jmb.2013.12.007 pmid:24333487 pmcid:PMC3969779 fatcat:fecgpflmlrhkxfvya3wfvphhsm
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