Debashish Sahu

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

Announcements

• All NMR users need to use iLabs (https://bionmrcore.umich.edu/index.php/reservations/) to reserve time and use the instrument. Please note that providing short-codes directly to BioNMR core staff will not grant access to the instruments.
• NMR 400 (LSI) is currently down due to a sample breaking on the probe. Please use the NMR 600 (LSI) in the meantime.
• NMR 600CP (Chem) has issues with tuning to Nitrogen and the stability of the cryo-system causing issues for experiments longer than 2 hours. The NMR facility is in touch with Varian about this issue and will update the impacted users as things get sorted out.

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 20^th 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:

1. Biophysical Society 63nd Annual Meeting (March 2-6, 2019) at Baltimore, Maryland Link: http://www.biophysics.org/2019meeting
   
2.  PANIC 2019 Practical Applications of NMR in Industry Conference (March 3-7, 2019) at Hilton Head, South Carolina Link: http://www.panicnmr.com/
   
3. 60th Experimental Nuclear Magnetic Resonance Conference (April 7 – 12, 2019) at Asilomar Conference Center, Pacific Grove, California
   
4. Computational Aspects of Biomolecular NMR – Gordon Research Seminar (June 8-9, 2019) at Les Diablerets, Switzerland Link: https://www.grc.org/computational-aspects-of-biomolecular-nmr-grs-conference/2019/
   
5. ISMAR 2019 21st International Society of Magnetic Resonance Conference joint with EUROMAR 2019 (August 25-30, 2019) at Berlin, Germany Link: http://www.ismar2019.org/

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