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
Online workshop held on Nov 18th 2022
Presented by Debashish Sahu, Director of BioNMR core, University of Michigan
Online workshop held on May 6th 2022
Presented by Debashish Sahu, Director of BioNMR core, University of Michigan
Online workshop held on December 8th 2021
Presented by Debashish Sahu, Director of BioNMR core, University of Michigan
Announcements
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:
Applications will be reviewed by BioNMR core staff and evaluated by the BioNMR advisory committee on a quarterly basis.
Upcoming NMR Conferences
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
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.
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.
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.
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.
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)
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
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.
Announcements
Recharge Rate
NMR users of BioNMR core facility, please note the latest rates for instrument usage and consultation. The rates listed below are effective Nov 20th 2018.
Instrument | U-M Rate ($/hr) | External Academic Rate ($/hr) | Corporate Rate ($/hr) |
NMR 400 (LSI) | $11 | $16.50 | $33 |
NMR 600 (LSI) | $11 | $16.50 | $33 |
NMR 600 CP (Chem) | $9.50 | $14.25 | $28.50 |
NMR 800 (Chem) | $11.50 | $17.25 | $34.50 |
NMR Core Labor/ Consultation | $61 | $91.50 | $183 |
Seminar on advanced metabolomics analysis on NMR data
Rafael Bruschweiler from Ohio State University is presenting his recent work where they employ advanced metabolomics tools on NMR data to study protein interactions. Dr. Bruschweiler is credited for the development of Covariance NMR, which reduces the NMR measurement time for multidimensional spectra of both solution and solid-state NMR. For more details on the seminar please see the flyer below.
Guide: Connecting remotely to NMR 800CP
As a convenience for the users of NMR 800CP, users can remotely monitor the progress of their experiments using VNC servers. Users have to manually start the X11VNC server and access using VNC viewers (like RealVNC viewer). Instructions on this process is available here: http://bionmrcore.umich.edu/wp-content/uploads/2018/11/Accessing-the-Bruker-800CP-machine-in-Chem-1047-using-VPN.pdf
NMR Technique Highlight: BEST and SOFAST NMR for assigning His & Tyr side-chains
In the following paper, the authors present a NMR technique that uses time-efficient resonance assignment of histidine and tyrosine side chains in uniformly 13C/15N-labeled proteins. The use of band-selective 13C pulses allows to deal with linear chains of coupled spins, thus avoiding signal loss that occurs in branched spin systems during coherence transfer. Details of the paper can be found in the link below:
Christou NE, Brutscher B, BEST and SOFAST experiments for resonance assignment of histidine and tyrosine side chains in 13C/15N labeled proteins (2018) J. Biomol NMR doi: 10.1007/s10858-018-0216-z Link: https://link.springer.com/article/10.1007/s10858-018-0216-z
NMR Webinars by Bruker
Bruker has various webinars on advanced NMR techniques and technologies.
Link: https://www.bruker.com/service/education-training/webinars/nmr-webinars.html
NMR Conferences
Here are a few conferences (deadlines are fast approaching) that current BioNMR users will find useful:
NMRFAM-Sparky tutorial videos
Sparky is the most popular NMR analysis tool for biomolecules for more than a decade. NMRFAM has taken over the original Sparky from UCSF for the continuous development to implement advances in biomolecular NMR field. This software is very useful for biological NMR community for NMR resonance assignment, structure prediction, semi-automatic structure calculation, etc. For details on the updated NMRFAM-Sparky software can be found here: https://nmrfam.wisc.edu/nmrfam-sparky-distribution/
There is a YouTube playlist of video tutorials on NMRFAM-Sparky software:
NMR Staff
Debashish Sahu, Ph. D.
Director, Biomolecular NMR Research Lab
LSA/LSI Core Facility
University of Michigan
Chemistry Building Room # 4015
930 N University Ave, Ann Arbor MI 48109
Email: debsahu@umich.edu
Phone: 734-647-3872
Wendy Feng, Ph. D.
Senior Lab Specialist
BioNMR Core Facility
University of Michigan
Life Sciences Institute # 3214
210 Washtenaw Ave, Ann Arbor MI 48109
Email: wendyfen@umich.edu
Phone: 734-615-5516
Emily Scott, Ph.D.
Professor, Medicinal Chemistry/Pharmacology/Biophysics
Faculty Director, BioNMR Core Lab
University of Michigan
428 Church Street
Ann Arbor, MI 48109-1065
Email: scottee@med.umich.edu
Phone: 734-764-3530
Lab webpage: http://scottlab.info
Cathy Andrews
Director of Operations
BioNMR Core Lab
University of Michigan
Life Sciences Institute # 3119
210 Washtenaw Ave, Ann Arbor MI 48109
Email: cathyand@umich.edu
Phone: 734-763-1200
In order to assist with chemical shift assignments of proteins, here are two plots of aliphatic chemical shifts based on BMRB data as of 10/17/2018.
For assignments of Cα and Cβ present in proteins, we usually run HNCACB and CBCA(CO)NH. Some residues such as Gly, Leu, Ala, Thr, Ser etc can be used as anchor points for starting assignments due to their unique distribution of aliphatic carbon chemical shift as shown below. Once can use this interactive map of chemical shifts below for chemical shift assignment.
A similar graph has been generated for assignments of aliphatic protons below. HCCH-TOCSY and H(CCCO)NH-TOCSY experiments give rise to chemical shifts of aliphatic protons, where this interactive distribution of chemical shift can be used for assignment purposes.