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PINE-SPARKY.2 for automated NMR-based protein structure research
2017
Bioinformatics
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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 (https://csrosetta.bmrb.wisc.edu/csrosetta); 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
2016
Journal of Biomolecular NMR
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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
2012
Bioinformatics
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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
2015
Journal of Biomolecular NMR
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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
2021
Viruses
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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
2017
Computational and Structural Biotechnology Journal
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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
2009
PLoS Computational Biology
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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
2009
Biomolecular NMR Assignments
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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
2013
Nucleic Acids Research
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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
2018
Nature Communications
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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]
2020
bioRxiv
pre-print
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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
2021
PLoS Computational Biology
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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
2014
Proceedings of the National Academy of Sciences of the United States of America
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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
2015
Journal of Biomolecular NMR
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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
2014
Journal of Molecular Biology
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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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