e-Newsletter

Congratulations to NMRFAM! We have secured a 5 years NIH funding titled NMR Technologies for Integrating Structure, Function and Disease. We strive to provide state-of-the-art NMR equipment, technologies and service to assist in NMR solution and solid-state research needs of academic institutions and industries.

NMRFAM eNewsletter – February 2021 

  • NMRFAM is ramping back up to near-normal operations with our spectrometers. However, no outside users are allowed in the building. External user access via samples shipped or dropped off to the facility and remote user access have resumed.
  • 900 MHz (Fleckvieh) is currently configured for solid-state NMR until 2/22/2021, when it will switch back to solution (cryoprobe) NMR.  It will remain in solution probe until end of March. Please plan ahead if you have any needs so we can help schedule your time.
  • As we transition to iLab (see below), please submit NMR time requests to Lai Bergeman to enter in the new system until your research group has been transitioned into iLab.
  • For the latest updates on UW-Madison Smart Restart and support services please visithttps://covid19.wisc.edu/

iLab

  • NMRFAM has transitioned to iLabto streamline the process of scheduling and billing for user requests. iLab requires a one-time registration. Please contact Lai Bergeman for assistance with this process. Once you are registered, the system will enable you to complete new project forms, request spectrometer time, place service requests and provide required approvals.
  • NMRFAM will also transition in 2021 to real-time sharing of experimental NMR data via the Shared Drive hosted by DoIT. For access, users will be registered with wisc.edu domain accounts. Please inquire with Lai Bergeman if you are interested in this capability.

New User/Collaborator Information:

  • Please note that if you would like to collaborate with our facility you will need to submit an abstract providing some detail to Lai Bergeman, coordinator, who will bring it up for review at our weekly staff meeting for approval. Please visit the NMRFAM website for more information.

Solid state NMR spectrometers at NMRFAM:

  • NMRFAM has completed installation of several new systems and upgrades for magic-angle spinning solid-state NMR
  • Vosges: 600 MHz Bruker Avance III with 3.2 mm Efree CPMAS – operational for users
  • Taurus: 600 MHz Varian InfinityPlus with 1.6 mm T3 HXY — operational for users, including 1H, 13C, 15N, 23Na, 27Al, 29Si, 31P, 51V, 69Ga/71Ga, 79Br and other nuclei at request of users
  • Ribeye: 600 MHz Varian InfinityPlus with 3.2 mm Varian T3 HXY and 1.6 mm Phoenix HXY — operational for users, primarily configured for triple resonance HCN
  • Ayrshire: 750 MHz wide bore Varian VNMRS Direct Drive with range of probes — magnet at field, console commissioning near completion, accepting user requests in early 2021
  • Fleckvieh: 900 MHz Bruker Avance III with Bruker 3.2 mm E-FREE HCN, Bruker 1.3 mm HCN, and 1.6 Phoenix HFXY probes — accepting requests for Jan.-Feb. 2021

NMRFAM Software News:

We have developed an algorithm and software package called Cheminformatics Tools for Probabilistic Identification of Carbohydrates (CTPIC) that analyzes the covalent structure of a compound to yield a probabilistic measure for distinguishing saccharides and saccharide-derivatives from non-saccharides. Check out our recent Nature paper.

GISSMO.nmrfam.wisc.edu:

GISSMO enables the efficient calculation and refinement of spin system matrices (chemical shift and coupling constants) against experimental 1D-1H NMR spectra of small molecules. The library of compounds parameterized by GISSMO contains more than 1286 compounds, including many key mammalian metabolites and a library of drug-like molecular fragments used in ligand screening.

ALATIS.nmrfam.wisc.edu:

Unique and reproducible molecule and atom identifiers are required to ensure the correct cross-referencing of properties associated with compounds archived in databases. The best approach to this requirement is the International Chemical Identifier (InChI). ALATIS is an adaptation of InChI that provides unique and reproducible atom numbering for all atoms including hydrogens.

NMRFAM-SPARKY new features:

* Noticeably updated features

– More colors available (ct, cr)

– Move labels to peak centers (lc)

– Help manual updates for two-letter codes (hn / hI)

– NMRPipe, NMRView, TopSpin files can be directly opened in here.

– A new conversion script for importing NMRView to UCSF (nv2ucsf)

– An easy GUI program for modifying ucsf spectrum (easy_ucsfdata)

– Mouse wheel (mw) and/or + – , . arrow key integration

– Contour shortcuts added (shift ) ; ‘ [ ] 

– Very large data support (>10GB) for 64bits (Linux 64 / Mac)

– Completeness counter (cm)

– Chemical shift reference views and versatile assigner (ir / va)

– Advanced selection tool (AS) from Rienstra group

– PluqIn-Sparky (pq) inspired from Rienstra’s plugin and PINE-SPARKY.2

– Transfer and simulate (ta) also supports aromatic experiments

– Improved APES peak picker (ae)- full automation to I-PINE/PONDEROSA

– I-PINE/PINE-SPARKY.2 (ep) also supports some 4D experiments

– Improved PONDEROSA structure calculation plugin (c3)

– RDC-SPARKY analysis tool for ARTSY, IPAP and coupled HSQC (rd)

– mmCIF <-> PDB (Pm / Pp)

– Move to a specific place by frequencies or an assignment label(tc)

– Detect proline isomerization state (dp)

– Uniformly formatting PostScripts generated by NMRFAM-SPARKY (fP)

– PyMOL integration in Perturbation Analysis tool (np)

– Uniformly set contour gaps and thresholds using current view (uc)

– Draw center vertical (dv) and horizontal (dh) lines in current view

– Interactive oriented solid-state NMR fitting by PISA-SPARKY (PS)

– Triple strip plots and their enhancements (sp / SP / Sp)

– Save files have absolute paths as well in case relative paths fail

– Line thickness is adjustable (oz)

– View list (pv), Filterable View List (PV) and Tree View (tv)

– Frequencies at cursor position are displayed (fc)

– Ctrl+c/v/a/o/s/z/p/r (general) ctrl+d (delete)

– Ctrl+n/m (label size) ctrl+j/k (peak size)

– Ctrl+drag works as find/add peaks while in selection mode

– Holding a ctrl key while drawing a line turns tilt line mode on

– 760 colors supported in contours (ct) and ornament colors (cr)

– Atoms are suggested when the residue is assigned (at)

– Command finder (cf)

– Fonts, colors, panel sizes, locale adjustable (LF)

– Lecture videos from NMRFAM for protein NMR (LC)

– Transfer/assign peaks (TP)

– CHESCA/CHESPA automated allosteric network analysis (ch/cH)

 To share the thoughts, visit Sparky user forum (Type SF)

Below is a listing of the available software on our website that you are free to use or download and some associated publications:
1 – NMRFAM-SPARKY
2 – NMRbot
3 – HIFI-NMR
4 – LACS / PECAN
5 – PINE
6 – PINE-Sparky
7 – ADAPT-NMR
8 – ADAPT-NMR Enhancer
9 – Newton
10 – PACSY
11 – PONDERSOSA
12- PONDEROSA-C/S
13 – SPIDER
14 – RNA-PAIRS
15 – NMR Structure Tools
16 – COMPASS

Please visit the NMRFAM software website for more information on the above listed software.

Donate to NMRFAM:

US deductible donations can be made to NMRFAM. Please write check payable to:

UW Foundation, Account 112152802 and mail to:

Attn: Sarah Lynn Traver Saunders

Associate Administrative Program Specialist

University of Wisconsin-Madison

Department of Biochemistry

433 Babcock Dr.

Madison WI 53706

For further information, please contact Ms. Saunders, Tel: 608-265-2507 or email.

References for recent publications are:

Structure and dynamics of drug-bound bacterial transporter EmrE in lipid bilayers. Shcherbakov AA, Hisao G, Mandala VS, Thomas NE, Soltani M, Davis JH Jr, Henzler-Wildman KA, Hong M. Jan 2021. Nat Commun. PMID:33420032.

1H, 13C, and 15N backbone and side chain chemical shift assignments of the SARS-CoV-2 non-structural protein 7. Tonelli M, Rienstra C. Anderson TK, Kirchdoerfer R, Henzler-Wildman K. 2020 Nov. Biomol NMR Assign. PMID:33219414

Structural Insights into the Recognition of Mono- and Diacetylated Histones by the ATAD2B Bromodomain. Lloyd JT, McLaughlin K, Lubula MY, Gay JC, Dest A, Gao C, Philips M, Tonelli M, Cornilescu G, Marunde MR, Evans CM, Boyson SP, Carlson S, Keogh MC, Markley JL, Frietze S, Glass KC. 2020 Nov. J Med Chem. PMID:330844328

CHESPA/CHESCA-SPARKY : automated NMR data analysis plugins for SPARKY to map protein allostery. Shao H, Boulton S, Olivieri C, Mohamed H, Akimoto M, Subrahmanian MV, Veglia G, Markley JL, Melacini G, Lee W. 2020 Sep. Bioinformatics. PMID:32926121

Uncovering a membrane-distal conformation of KRAS available to recruit RAF to the plasma membrane. Van QN, Lopez CA, Tonelli M, Taylor T, Niu B, Stanley CB, Bhowmik D, Tran TH, Frank PH, Messing S, Alexander P, Scott D, Ye X, Drew M, Chertov O, Losche M, Ramanathan A, Gross ML, Hengartner NW, Westler WM, Markley JL, Simanshu DK, Nissley DV, Gillette WK, Espasito D, McCormick F, Gnanakaran S, Heinrich F, Stephen AG. 2020 Sep. Proc Natl Acad Sci USA. PMID:32620933

 

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