Tips and Tricks of collecting good NMR data
Online workshop held on Nov 18th 2022
Presented by Debashish Sahu, Director of BioNMR core, University of Michigan
Protein Backbone Assignments using CCPNMR AnalysisAssign
Online workshop held on July 29th 2022
Presented by Dr. Minli Xing, Senior Lab Specialist of BioNMR Core Facility, University of Michigan.
NMR data collection and chemical shift assignments for uniformly labeled well folded proteins (using Sparky)
Online workshop held on May 6th 2022
Presented by Debashish Sahu, Director of BioNMR core, University of Michigan
Collecting and analyzing protein backbone dynamics using T1/T2/NOE NMR based relaxation techniques
Online workshop held on December 8th 2021
Presented by Debashish Sahu, Director of BioNMR core, University of Michigan
1D and 2D NMR methods for small molecules
Online workshop held on July 29th 2021
Presented by Dr. Minli Xing, Senior Lab Specialist of BioNMR Core Facility, University of Michigan.
Newsletter Mar 2020
Announcements
- Due to recent support generously contributed from our funding units (LSA, LSI, COP, and Med), BioNMR core is no longer charging users from University of Michigan for consultation time. However, we will continue to log the time that we spend with each user as a way of demonstrating service to users in the different units.
- Faculty and graduate student recruitment season is continuing, so users should be aware that tour groups will be in instrument spaces.
- The 600 MHz NMR in 3214A LSI will be completely upgraded to Prodigy cryo-probe with NEO console during April 2020. This will significantly upgrade the capability, sensitivity, and throughput of this instrument for our users. Delivery and preparation for the install will happen during the last week of March 2020. We expect this instrument to be down Mar 23rd – April 20th 2020, so please plan experiments accordingly.
- The University of Michigan‘s Biosciences Initiative Core Lab program recently funded a complete renovation of the Varian 600 MHz NMR 600 in 1047 Chemistry. Read more here. The existing magnet will be converted to a Bruker instrument with a NEO console and the latest helium cooled TCI CryoProbe. As a result, this instrument will have similar capabilities and the same software as the 800 MHz instrument, facilitating usage across instruments and increasing availability. Down time for this install is anticipated in Aug 2020.
- The BioNMR core has a new program to provide instrument time for junior faculty collecting preliminary NMR data for external grant proposals. Supported by the College of Literature, Sciences and Arts; Life Sciences Institute; College of Pharmacy; and the Medical School, application details are below.
BioNMR core’s Exploration Funds
BioNMR core’s exploration funds will be used to provide NMR instrument time to UM junior faculty (research assistant professors and assistant professors) who need to collect preliminary data for new external grant applications. The application (https://forms.gle/ndgwQRtcDsH9w8i17) requires:
- Qualifications of the investigator(s): Assistant professor / research assistant professor
- Objectives and scientific/technical significance of the proposed project (1-2 paragraphs)
- Riskiness/feasibility of methods employed
- Details of the NMR experiments proposed (e.g. list of experiments) ~1 paragraph
- Suitability of the methods employed
- Amount of NMR time and instrument requested to carry out proposed projects
Applications will be reviewed by BioNMR core staff and evaluated by the BioNMR advisory committee on a quarterly basis.
Upcoming NMR Conferences
- ICMRBS 2020 XXIX International Conference on Magnetic Resonance in Biological Systems, Aug 23-28 2020, Boston, MA (details: http://icmrbs2020.org)
- Gateway NMR Meeting 2020, Sep 18-19 2020, Vanderbilt University, Nashville, TN (details: https://www.vanderbilt.edu/csb/gateway-nmr-2020/)
NMRlib 2.0 : IBS pulse sequence tools for Bruker spectrometers available on NMR 800
The NMRlib package contains a suite of jython-based tools designed for Bruker spectrometers (TopSpin versions 3.2–4.0) that allow easy setup, management, and exchange of NMR experiments. A NMR experiment can be set up and executed in a few clicks by navigating through the NMRlib GUI tree structure, without any further parameter adjustment. We now have working versions of all sequences mentioned in the latest paper A Favier and B Brutscher. NMRlib: user-friendly pulse sequence tools for Bruker NMR spectrometers (2019) J Biomol NMR. 73(5), 199-211. (details: https://link.springer.com/article/10.1007%2Fs10858-019-00249-1) Please contact BioNMR core staff to get help with setting up these experiments.
NMR Technique Highlight: A better isotopically labeled NMR Sample preparation protocol
The authors here present a modified minimal medium and a simple protocol that can increase the protein yield up to fourfold in a pH-stabilized LB medium and up to seven-fold in a modified M9+ medium. Details of the paper can be found in the link below:Cai M., Huang Y., Craigie R., Clore G.M. A simple protocol for expression of isotope-labeled proteins in Escherichia coli grown in shaker flasks at high cell density (2019) J Biomol NMR. https://link.springer.com/article/10.1007/s10858-019-00285-x
BioNMR core acknowledgement in scientific publications
A reminder to all users of BioNMR core facility users, please acknowledge the BioNMR core facility for all publications that use data collected in our facility.
Research reported in this publication was supported by the University of Michigan BioNMR Core Facility (U-M BioNMR). U-M BioNMR Core is grateful for support from U-M including the College of Literature, Sciences and Arts, Life Sciences Institute, College of Pharmacy and the Medical School along with the U-M Biosciences Initiative.
This helps us to keep track of our facility usage that leads to publications and justification for securing future funding for instrument upgrades
BioNMR core receives Biosciences Initiative Award to upgrade 600 MHz spectrometer housed in 1047 Chemistry
The University of Michigan‘s Biosciences Initiative has funded the upgrade of this instrument via the Biosciences Core Lab Funding Program read more: here. This will be updated to the latest helium cooled TCI CryoProbe with NEO console offered by Bruker Biospin
The BioNMR core assumed operations of three older NMR instruments, including a Varian 600 MHz instrument. As Varian is no longer in business, parts are more and more difficult to find and the instrument and software are no longer supported. In order to overcome this, our proposal to Biosciences Core Lab Funding program was to reuse the newer Varian magnet at the core of this instrument and replace the console, probe, and control units to transition this to a Bruker instrument, currently the only other practical supplier of such instruments. This would ensure long-term instrument availability for the U-M research community while being a good steward of prior investment.
BioNMR core facility has been selected as one of the awardees of the Biosciences Core Lab Funding program and has been granted funds to update/upgrade the Agilent/Varian 600 MHz spectrometer with cryo-probe located in 1047 chemistry to the latest Helium cooled TCI CryoProbe, along with NEO console by Bruker. The accompanying software with this console will be Topspin 4, which can take advantage of the latest capabilities of the NEO console. In order to handle multiple samples along with automation in ICON interface, we will be equipping this instrument with Bruker’s SampleJet sample handling system. This upgrade is in the works and we will post updates as we get delivery updates from Bruker.
BioNMR core’s 600 MHz spectrometer housed in 3214 LSI building is getting an upgrade in the coming months
The University of Michigan‘s Biosciences Initiative has funded the upgrade of 600 MHz instrument via the Biosciences Research Initiative Program awarded to Natural Products Discovery Core read more: here. This will be updated to the latest nitrogen cooled Prodigy CryoProbe with NEO console offered by Bruker Biospin
In 2018, Drs. David H. Sherman and Ashootosh Tripathi (part of Natural Products Discovery Core) received funding from the Biosciences Research Initiative Program to upgrade the room temperature broadband probe connected to 600 MHz NMR spectrometer to Bruker’s latest nitrogen cooled Prodigy CryoProbe with NEO console and 24 SampleCase sample handling system.
The Prodigy CryoProbe will be ideal for routine small molecule NMR experiments, with broadband technology that covers large number of nuclei and 2-3x boost to signal as compared to room temperature probes. The ICON automation interface allows users to setup multiple experiments across many samples, and current users will be retrained to use this interface in order to use this spectrometer. This upgrade is in the works and delivery of the components from Bruker are scheduled for March/April 2020. During the upgrade users will be redirected to use the BioNMR core instruments in chemistry building.
Big Secrets of Tiny Phenomena
We have been featured in the University of Michigan Literature Science and Arts News. Feel free to contact us if you have any NMR needs for your research projects.
Newsletter
Announcements
- We welcome Dr. Minli Xing to BioNMR core facility. Minli is a protein NMR spectroscopist, her research interests include studying protein structure and function using NMR spectroscopy. Prior to joining the University of Michigan, Minli was the lab manager of the Biomolecular NMR Lab at the University of Kansas, where she operated and maintained a 600 MHz and an 800 MHz NMR spectrometer. During her work at the University of Kansas, she has developed extensive experience in protein structure determination, protein-protein and protein-ligand interaction, and STD-NMR fragment screening.
Senior Lab Specialist
BioNMR Core Facility
University of Michigan
Life Sciences Institute #3214
210 Washtenaw Ave, Ann Arbor MI 48109
Email: mlxing@umich.edu
Phone:734-647-1905
- NMR 600 (LSI) will be upgraded to Prodigy cryo-probe with NEO console in the coming year, stay tuned for updates.
Gateway NMR Meeting
This year University of Michigan will be hosting the Gateway NMR Meeting (details: https://sites.google.com/umich.edu/gatewaynmr2019) on Sep 21-22, 2019. Please try to attend this meeting to meet and learn about the exciting NMR research in the area.
NMR Seminars
- Dr. Charles Sanders from Vanderbilt School of Medicine Basic Sciences will talk about “Destabilization of the Human KCNQ1 Potassium Channel is the Most Common Cause of Long QT Syndrome Cardiac Arrhythmia” using NMR techniques on Sep 20th 2019 at 10AM in LSI library (details: https://www.lsi.umich.edu/events/2019-09/um-structure-seminar-destabilization-human-kcnq1-potassium-channel-most-common-cause-long-qt)
- Dr. Haribabu Arthanari from Harvard University & Dana-Farber Cancer Institute will be presenting a seminar titled ” Emerging methods in solution NMR and applications to illuminate blind spots in human biology” on Sep 20th 2019 at noon in 1400 Chem (details: https://lsa.umich.edu/biophysics/news-events/all-events.detail.html/64267-16274479.html)
- I will present a talk on advanced NMR techniques and newer methods to analyze NMR data on Oct 18th 2019 at 10AM in LSI library (details: https://www.lsi.umich.edu/events/2019-10/u-m-structure-seminar-debashish-sahu-phd)
Advanced Capabilities of NEO console on 800 Mhz NMR instrument
The NEO console has the capability of acquiring nested NMR experiments (combining up to five conventional NMR pulse sequences into one supersequence). We have working versions of all sequences mentioned in the latest paper Kupče Ē, Claridge TDW. New NOAH modules for structure elucidation at natural isotopic abundance (2019) J Magn Reson. 307 106568. (https://www.sciencedirect.com/science/article/pii/S1090780719301855?via%3Dihub)
NMR Technique Highlight: Accelerating 2D NMR relaxation dispersion experiments using iterated maps
Conventionally relaxation dispersion data would require collection of data using the full Nyquist grid. The authors had previously developed Fourier-based reconstruction method using iterated maps according to the Difference Map algorithm of Veit Elser (DiffMap), which has been further developed to exploit the strong correlations between 2D data slices in a pseudo-3D experiment. Details of the paper can be found in the link below:
Rovny, J., Blum, R.L., Loria, J.P., Barrett S,E. Accelerating 2D NMR relaxation dispersion experiments using iterated maps (2019) J Biomol NMR. https://doi.org/10.1007/s10858-019-00263-3
BioNMR core acknowledgement in scientific publications
A reminder to all users of BioNMR core facility users, please acknowledge the BioNMR core facility for all publications that use data collected in our facility.
Research reported in this publication was supported by the University of Michigan BioNMR Core Facility (U-M BioNMR). U-M BioNMR Core is grateful for support from U-M including the College of Literature, Sciences and Arts, Life Sciences Institute, College of Pharmacy and the Medical School along with the U-M Biosciences Initiative.
This helps us to keep track of our facility usage that leads to publications and justification for securing future funding for instrument upgrades.