Frequently Asked Questions

Wondering if NMR is an appropriate method for your project?
Want more information about the use of NMRFAM?

What is NMR?

Nuclear Magnetic Resonance (NMR) spectroscopy takes advantage of the natural magnetism present in certain atomic nuclei. The nuclei most often studied in biological applications of NMR are: ¹H, ¹³C, ¹⁵N, and ³¹P. All of these nuclei are stable (non-radioactive) isotopes. When a molecule is placed in a magnetic field, these nuclei act like tiny little bar magnets and align like iron filings. The nuclear bar magnets can align either in the same direction (up) or in the opposite direction (down) as the external magnetic field; these two alignments have different energies. An analogy of this energy difference can be physically experienced by holding the north poles of two magnets together versus holding the north and south poles together. In the first case, they repel and in the latter they attract. It is the difference in energy between these two alignments of the nuclei in the magnetic field that is the fundamental quantity measured by NMR. The great strength of the technique comes from the fact that the energy difference between the up and down states (a.k.a. the chemical shift) is exquisitely sensitive to the molecular environment of the nucleus. Virtually every nucleus in a molecule experiences a different environment and thus has a chemical shift different from that of every other nucleus. For example, the chemical shift of a C atom bonded to another C and three H atoms will be different from that of a C bonded to two C and two H atoms. This means the structure of a molecule is encoded in the chemical shifts of the nuclei. By using rather sophisticated experiments, the chemical shift of every nucleus in the molecule and its physical location in the molecule can be determined.

Just as the nuclear bar magnets in a molecule interact with the external magnetic field, they also interact with each other. The strength of this interaction depends on the distance between the nuclei. This feature makes it possible to use NMR to determine distances between nuclei that are closer than about 5?. Thus NMR can be used to determine the folded conformation of a protein or nucleic acid or to discover how a drug binds to its receptor molecule. Three-dimensional structures of molecules are determined by combining information on chemical shifts assigned to particular atoms with internuclear distances estimated from NMR experiments. Specialized NMR experiments can be used to determine how rapidly the molecule or parts of the molecule are moving in solution. The time scale of motions over which NMR is sensitive covers an enormous range: 10^-11s to >1s. In the picosecond to nanosecond time range, effects of librations, vibrations, and overall molecular tumbling can be quantified. The microsecond to the second time frame includes motions involved in conformational changes, ligand binding, and catalysis.

Diffusion measurements, kinetics, metabolism, oil well logging, imaging, fluid flow, analysis of foodstuffs, analysis of zeolite catalysts, clinical quantification of serum cholesterol, combinatorial chemistry, and quantum computing are among the far-ranging applications of NMR. All of this versatility comes at a cost. NMR spectroscopy is an insensitive spectroscopic technique. The problem arises from the very small energy differences between the up and down states of alignment. The experimental problem is the detection of the weak absorption of photons that excite the excess population in the ground state. Due to the lack of sensitivity, liquid state NMR requires micromoles of compound at relatively high concentration (1 mM) and detection by very expensive equipment. NMRFAM supplies the equipment and expertise necessary to do these types of experiments.
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NMR seems very complicated. Do I need a complete understanding of NMR in order to use the facility and obtain data?

No. The theory behind NMR is very complicated, but you do not need to have an in-depth understanding of it in order to collect data to answer a particular biochemical question or obtain a structure. This is analogous to an MRI scan in a hospital – the doctor does not need to understand the theory of the instrument in order to do the scan and interpret the data. The NMRFAM staff includes experts in multiple areas of NMR spectroscopy who can train you to run the samples and analyze the data. The staff is also available to answer questions. Eight hours of training are provided for new users free of charge. If additional training is needed, the fee is $50/hour. The training occurs on-site, although questions can be answered via phone or e-mail. If you need training or have questions, please contact the facility (gillian@nmrfam.wisc.edu); training can be requested through NMRFAM?s on-line scheduling software ?Sundial? <http://www.sesame.wisc.edu/Sundial/sundial_main.html>

If you have a small molecule and do not want to perform the experiment yourself, you can submit a sample to NMRFAM, and we will collect standard spectra for you (details are on the NMRFAM website).
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What types of questions can I answer with NMR?

Questions that can be addressed by NMR vary broadly from determining the structure of small molecules to characterizing the interaction between proteins and their ligands. One of the strengths of NMR is that it looks at proteins and other biomolecules in solution, which is their natural state; a second strength is that it can measure dynamic events. Some of the questions we have addressed at NMRFAM include:

THREE DIMENSIONAL STRUCTURE DETERMINATION OF BIOMACROMOLECULES IN SOLUTION

Song, Jikui; Tyler, Robert C.; Lee, Min S.; Tyler, Ejan M.; Markley, John L. "Solution Structure of Isoform 1 of Roadblock/LC7, a Light Chain in the Dynein Complex". Journal of Molecular Biology (2005), 354(5), 1043-1051

Singh, Shanteri; Cornilescu, Claudia C.; Tyler, Robert C.; Cornilescu, Gabriel; Tonelli, Marco; Lee, Min S.; Markley, John L. "Solution structure of a late embryogenesis abundant protein (LEA14) from Arabidopsis thaliana, a cellular stress-related protein". Protein Science (2005), 14(10), 2601-2609.

Tamm, Lukas K.; Abildgaard, Frits; Arora, Ashish; Blad, Heike; Bushweller, John H. "Structure, dynamics and function of the outer membrane protein A (OmpA) and influenza hemagglutinin fusion domain in detergent micelles by solution NMR". FEBS Letters (2003), 555(1), 139-143.

Kuloglu, E. Sonay; McCaslin, Darrell R.; Kitabwalla, Moiz; Pauza, C. David; Markley, John L.; Volkman, Brian F. Monomeric Solution Structure of the Prototypical 'C' Chemokine Lymphotactin. Biochemistry (2001), 40(42), 12486-12496.

Skjeldal, Lars; Peterson, Francis C.; Doreleijers, Jurgen F.; Moe, Luke A.; Pikus, Jeremie D.; Westler, William M.; Markley, John L.; Volkman, Brian F.; Fox, Brian G. "Solution structure of T4moC, the Rieske ferredoxin component of the toluene 4-monooxygenase complex". Journal of Biological Inorganic Chemistry (2004), 9(8), 945-953.

DYNAMICS OF BIOMACROMOLECULES IN SOLUTION

Blad, Heike; Reiter, Nicholas J.; Abildgaard, Frits; Markley, John L.; Butcher, Samuel E.

"Dynamics and Metal Ion Binding in the U6 RNA Intramolecular Stem-Loop as Analyzed by NMR". Journal of Molecular Biology (2005), 353(3), 540-555.

Song, Jikui; Markley, John L. "Protein inhibitors of serine proteinases: Role of backbone structure and dynamics in controlling the hydrolysis constant". Biochemistry (2003), 42(18), 5186-5194.

BIOMACROMOLECULAR INTERACTIONS

Ligand binding, determination of pKa values of individual residues, etc.

Song, Jikui; Laskowski, Michael, Jr.; Qasim, M. A.; Markley, John L. "NMR Determination of pKa Values for Asp, Glu, His, and Lys Mutants at Each Variable Contiguous Enzyme-Inhibitor Contact Position of the Turkey Ovomucoid Third Domain". Biochemistry (2003), 42(10), 2847-2856.

Zhao, Qin; Song, Jikui; Jin, Zheyuan; Danilova, Vicktoria; Hellekant, Goeran; Markley, John L.. "Probing the sweet determinants of brazzein: Wild-type brazzein and a tasteless variant, brazzein-ins(R18a-I18b), exhibit different pH-dependent NMR chemical shifts". Biochemical and Biophysical Research Communications (2005), 335(1), 256-263.

Protein-protein, Nucleic acid-nucleic acid, and Protein-Nucleic acid, etc.

Davis, Jared H.; Tonelli, Marco; Scott, Lincoln G.; Jaeger, Luc; Williamson, James R.; Butcher, Samuel E. "RNA Helical Packing in Solution: NMR Structure of a 30 kDa GAAA Tetraloop-Receptor Complex." Journal of Molecular Biology (2005), 351(2), 371-382.

Song, Jikui; Markley, John L. "NMR chemical shift mapping of the binding site of a protein proteinase inhibitor: changes in the 1H, 13C and 15N NMR chemical shifts of turkey ovomucoid third domain upon binding to bovine chymotrypsin A". Journal of Molecular Recognition (2001), 14(3), 166-171.

Hydrogen bonding

Markley, John L.; Westler, William M. "Protonation-State Dependence of Hydrogen Bond Strengths and Exchange Rates in a Serine Protease Catalytic Triad: Bovine Chymotrypsinogen A". Biochemistry (1996), 35(34), 11092-11097.

Westler, William M.; Frey, Perry A.; Lin, Jing; Wemmer, David E.; Morimoto, Hiromi; Williams, Phillip G.; Markley, John L.. "Evidence for a Strong Hydrogen Bond in the Catalytic Dyad of Transition-State Analogue Inhibitor Complexes of Chymotrypsin from Proton-Triton NMR Isotope Shifts". Journal of the American Chemical Society (2002), 124(16), 4196-4197.

Assadi-Porter, Fariba M.; Abildgaard, Frits; Blad, Heike; Markley, John L. "Correlation of the Sweetness of Variants of the Protein Brazzein with Patterns of Hydrogen Bonds Detected by NMR Spectroscopy". Journal of Biological Chemistry (2003), 278(33), 31331-31339.

Lin, I-Jin; Gebel, Erika B.; Machonkin, Timothy E.; Westler, William M.; Markley, John L. "Correlation between Hydrogen Bond Lengths and Reduction Potentials in Clostridium pasteurianum Rubredoxin". Journal of the American Chemical Society (2003), 125(6), 1464-1465.

INVESTIGATION OF PARAMAGNETIC INTERACTIONS IN BIOMOLECULES – The general aim of these investigations is to examine the structure and electronic properties of proteins that contain paramagnetic centers (paramagnetic molecules have unpaired electrons).

Lin, I-Jin; Gebel, Erika B.; Machonkin, Timothy E.; Westler, William M.; Markley, John L. "Changes in hydrogen-bond strengths explain reduction potentials in 10 rubredoxin variants". Proceedings of the National Academy of Sciences of the United States of America (2005), 102(41), 14581-14586.

Goodfellow, Brian J.; Nunes, Sofia G.; Rusnak, Frank; Moura, Isabel; Ascenso, Carla; Moura, Jose J. G.; Volkman, Brian F.; Markley, John L. "Zinc-substituted Desulfovibrio gigas desulforedoxins: resolving subunit degeneracy with nonsymmetric pseudocontact shifts". Protein Science (2002), 11(10), 2464-2470.

Machonkin, Timothy E.; Westler, William M.; Markley, John L. "Strategy for the Study of Paramagnetic Proteins with Slow Electronic Relaxation Rates by NMR Spectroscopy: Application to Oxidized Human [2Fe-2S] Ferredoxin". Journal of the American Chemical Society (2004), 126(17), 5413-5426.

OTHER

Metabolomics – The general aim of metabolomics is to identify, measure, and interpret the complex time-related concentration, activity and flux of endogenous metabolites in cells, tissues, and other biosamples such as blood, urine, and saliva.

Schleucher, J.; Vanderveer, P.; Markley, J. L.; Sharkey, T. D. "Intramolecular deuterium distributions reveal disequilibrium of chloroplast phosphoglucose isomerase". Plant, Cell and Environment (1999), 22(5), 525-533.

Structure determination of small organic molecules

Song, Jiasheng; Clagett-Dame, Margaret; Peterson, Richard E.; Hahn, Mark E.; Westler, William M.; Sicinski, Rafal R.; DeLuca, Hector F. "A ligand for the aryl hydrocarbon receptor isolated from lung". Proceedings of the National Academy of Sciences of the United States of America (2002), 99(23), 14694-14699.

Determination of diffusion coefficients

Kuloglu, E. Sonay; McCaslin, Darrell R.; Kitabwalla, Moiz; Pauza, C. David; Markley, John L.; Volkman, Brian F. "Monomeric Solution Structure of the Prototypical 'C' Chemokine Lymphotactin". Biochemistry (2001), 40(42), 12486-12496.

Kinetics

Vidugiris, Gediminas A. J.; Truckses, Dagmar M.; Markley, John L.; Royer, Catherine A. "High-pressure denaturation of staphylococcal nuclease proline-to-glycine substitution mutants". Biochemistry (1996), 35(12), 3857-64.

Imaging

Kornguth S; Anderson M; Markley J L; Shedlovsky A "Near-microscopic magnetic resonance imaging of the brains of phenylalanine hydroxylase-deficient mice, normal littermates, and of normal BALB/c mice at 9.4 Tesla". NeuroImage (1994), 1(3), 220-9.
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Is there a way to find out if my biomacromolecule is amenable to NMR analysis?

Yes, Several questions that should be addressed first:
1) What problem do you want to study? NMR is very good at some and poor at others.
2). What is the molecular mass of your biomacromolecule, and does it dimerize or oligimerize? If it is ~20 kDa or more, there may be limits on what can be studied.
3). How much sample can you produce; is it soluble at the concentration needed by NMR, and can you incorporate stable isotopes?
Our staff can help you determine the best experimental approach for your particular question.
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Is there limit to how large my biomacromolecule can be?

It generally depends on the type of information that is desired. Structural studies are the most limited case. The molecular mass of most biomacromolecules under investigation by NMR are less than ~20-25 kDa with the majority < 20 kDa. If you want to investigate the binding of ligands or determine the binding surface in a protein-protein interaction, molecules with much higher masses can be studied.

New techniques and stable isotope labeling methods have greatly increased the maximum molecular mass of biomacromolecules available for study by NMR. The structures of several b-barrel membrane spanning proteins inserted in a micelle have been determined. These systems had an aggregate molecular mass of ~50-60 kDa. Generally, structure determinations of proteins have been limited to molecules with less than ~400 amino acid residues, however, the global fold for a 82 kDa single chain protein in solution has been recently reported [Tugarinov et al PNAS 102 622-627 (2005)] and there are some reported studies of protein complexes with molecular masses between 200 and 800 kDa. For reviews see: Tugarinov, et al Ann. Rev. Biochem. 73 107-146 (2004); Riek et al TIBS 25 462-468 (2000).
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How much sample do I need?

NMR is not a particularly sensitive technique; however, recent advances in the technology have improved the ability to detect signals from samples at fairly low concentrations. NMRFAM makes use of cryogenic probe technology and modern consoles to provide state-of-the-art NMR sensitivity. To obtain a 3D structure of a biomacromolecule generally requires at least 300μM (eg. ~1.5 mg of a 15,000 Da protein) in 300μl solvent. For other experiments, such as ligand binding or pK_a determinations, concentrations of 10-50μM in 300μl solvent can be used. In general, the more sample, the better with the caveat that if is the molecule dimerizes or oligomerizes at high concentration, it may be better to go with a lower concentration.

The lowest practical concentration for the simplest experiments on small molecules (< 1000 Da) is about 0.1μM in 300 μl solvent. For a structure determination of a small molecule (e.g. 260Da), as little as 5μg in 300μl can been used. however with this amount of material, structure determination is far from routine.
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What do I need to take into consideration when preparing my sample?

Initial steps: The first step is to be sure that you can synthesize and purify a sufficient quantity of protein (or other biomacromolecule) and that it can be solubilized. Many different solvent systems are acceptable, but you should be aware that NMR signal-to-noise is degraded by high salt concentrations and that NMR lines become broad if the solvent viscosity is high. The NMR instrumentation at NMRFAM collects data only on liquid samples. Owing to the low natural abundance of ¹³C and ¹⁵N, observation of these nuclei usually requires that they be enriched. In some limited cases, natural abundance levels of the isotopes are sufficient.
Testing: NMR studies of biomolecules usually take at least one day; a week or two of data collection may be required for a structure determination of a protein or nucleic acid. The first criterion for success is that the sample must remain stable over this time period. The spectrometers have variable temperature capabilities, and the temperature of the sample can be adjusted between 0?C and 50?C to optimize the stability of your system. Raising the temperature above ambient typically gives higher quality spectra (because molecules tumble more rapidly) while lowering it may lead to lowered resolution. A second criterion for success is the spectral quality achieved with the sample under the solution conditions used (pH, buffer, additives, temperature).

Although it may be possible to determine the stability and spectral quality of a sample without labeling, more definitive results can be obtained with a sample labeled uniformly with ¹⁵N. A solution of a few milligrams of protein is prepared, and an initial test spectrum (a HSQC spectrum that takes 0.5-24 hr) is collected. This spectrum generally is diagnostic of further success. It may be necessary to adjust the sample conditions (pH, salt, buffers) to improve the quality of the spectrum. Sometimes, a redesigned molecule (protein or nucleic acid with altered sequence) will yield better quality spectra. Once a high quality spectrum is obtained, the sample is retested a week or other suitable time later to establish the stability of the sample. Obviously, the length of time that the sample must remain stable must be long enough to collect the data. Therefore, if you want to determine the structure of a large biomacromolecule, it must remain stable for a week or longer.

Once it is determined that the protein is suitable for 3D structure determination, a ¹³C and ¹⁵N labeled sample (double labeled) is prepared for data collection. If you have a large (>20-30kDa) biomacromolecule or a large (>20-30kDa) biomacromolecular complex, you may need to also replace carbon bound hydrogens with deuterium in addition to ¹³C and ¹⁵N labeling (triple labeling).

Special labeling schemes (selective, ¹³C, ¹⁵N, or both) may be used for assignments, dynamics, ligand binding, pH titration, and other studies. If you contact the facility, our experienced staff can help you determine the best labeling scheme for your experiment.
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How do I label my protein?

There are several ways to label the proteins. If you are expressing proteins in E. coli, you can grow the bugs in minimal media supplemented with labeled glucose, ammonium chloride, and/or amino acids. Labeled samples also can be prepared in yeast, baculovirus, and insect cells. Some biomacromolecules can also be chemically synthesized with labeled compounds. NMRFAM also has the capability of preparing labeled protein samples by cell free synthesis.

There are also more specialized ways of labeling your protein: selective amino acid labeling, segmental labeling, or SAIL labeling (specially labeled amino acids) with cell free synthesis. If you contact the facility, we can help you determine the best approach for labeling your protein.
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I see the facility has spectrometers ranging from 400 to 900 MHz. How do I know which one to use?

The fundamental reason for choosing a higher frequency spectrometer is to obtain increased resolution (linear increase with frequency) and higher sensitivity (~frequency ^3/2). NMRFAM staff will help you choose the proper spectrometer for your project. We recommend that you contact us before beginning a project for a consultation on the best experimental strategy for your project.
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How long does it take to run an experiment?

The amount of time it takes to run an experiment depends upon the particular problem that you are studying, the amount of data that must be collected, and the concentration of the sample. For a simple 1D spectrum of a small molecule, the experimental time is usually less than 15 minutes. To collect all of the data for the determination of a protein structure may take 2-3 weeks and this does not include the time required to analyze the data. One core project at NMRFAM is an attempt to reduce both the required spectrometer and data analysis time for structure determinations.
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Is there someone who can train me to use NMR and to analyze data?

Yes, our staff consists of many NMR experts who can help you not only use the spectrometers and analyze your data but can also help you design and set up your experiment. Because analyzing the data from a protein or nucleic acid is fairly time consuming, you need to have a scientist dedicated to this project and we can help train that person. NMRFAM staff members also collaborate with outside users, especially if the project is compatible with one of the NMRFAM core research projects. "Hands-on" training is encouraged. Contact Anne Lynn Gillian-Daniel at gillian@nmrfam.wisc.edu or (608)262-3173 to arrange training. Training can also be requested through the time request software Sundial.

Before independent use of any of the facility instruments, all users must be trained. Facility staff will oversee this training, and solo use on a particular class of experiment will not be permitted until the staff is satisfied that a minimum competency level is reached. New users receive up to 8 hours of free training. The cost for training is $50 per hr (minimum 1 hr)
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Can I have someone run a sample for me?

Yes, NMRFAM offers routine service spectroscopy of submitted samples twice weekly on a first-come-first-serve basis on the DMX 400 ($53/hr - most samples can be run in less than 30 minutes). See the schedule via Sundial. www.sesame.wisc.edu/Sundial/sundial_main.html. This service is generally only for obtaining ¹H or ¹³C spectra of small molecules (< 1000 Da). Application forms and detailed instructions for submitting service spectroscopy samples can be found on the NMRFAM web site at www.nmrfam.wisc.edu/NMRFAM/service.htm. An abstract describing the proposed project must be submitted with the time request (or already be on file at NMRFAM).
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How do I become a user of NMRFAM?

There are two kinds of NMRFAM members: principal investigators (PIs) and users. PIs are the heads of research groups and the users are members of their group. A PI can also be a user. The PI is responsible for paying for the used spectrometer time.

The first thing both a PI and a user must do is register in Sundial www.sesame.wisc.edu/Sundial/sundial_main.html. The PI information will include funding sources so that we know where to send your bills. Once a PI has registered, he/she can invite users into his/her group and issue dated permits to the users; the permits allow users to request spectrometer time. Detailed instructions for registering both as a PI and a user can be found at www.sesame.wisc.edu. All registered users and PIs may submit time requests. Requests are due by 4:00 pm on the 19th of the month prior to the requested time (e.g. time requests for March are due by 4:00 pm February 19). If the 19^th falls on a Saturday, requests are due by 4:00 pm on Friday the 18^th. If the 19^th falls on a Sunday, requests are due by 4:00 pm on Monday the 20^th. Late requests will be given lowest scheduling priority. Detailed instructions for submitting a time request can be found at www.sesame.wisc.edu . After the 19^th the site administrator (SA) will create the schedule. You will receive an e-mail if you have received time and you can go to Sundial to view the schedule. An alternative to submitting a time request is to sign up for open time on the schedule once it has been posted. Detailed instructions for signing up for open time can be found at www.sesame.wisc.edu. Please keep in mind that many of the spectrometers are heavily utilized, so there may not be open time once the schedule has been made. Therefore, we recommend that you sign up for time in advance whenever possible.

For high demand instruments, the combined time requested by all users may be greater than what is available that month. NMRFAM will do its best to accommodate all users, either on the requested instrument or an alternative spectrometer (with the users permission). However, some users may need to be deferred until the following month. A deferral log is kept by the facility, and users interested in this information should contact Dr. Anne Lynn Gillian-Daniel at gillian@nmrfam.wisc.edu or (608)262-3173 or download the NMRFAM 'overage log' from the web site at http://www.nmrfam.wisc.edu/NMRFAM/files/overage_log.xls. Users who have been deferred should resubmit a time request for the following month. NMRFAM cannot make assumptions about a user?s continued need to access a particular instrument across time.
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Do I acknowledge NMFAM in my publications?

It is very important that you acknowledge the facility in all of your publications that benefited from NMRFAM. The main reason for this is that the NIH Biomedical Technology Program scans all publications for grant numbers and uses this information to justify their budget. This, in turn, has an impact on the funds they can make available to support our facility. Your acknowledgment should contain the following information:

This study made use of the National Magnetic Resonance Facility at Madison, which is supported by National Institutes of Health grants P41RR02301 (Biomedical Research Technology Program, National Center for Research Resources) and P41GM66326 (National Institute of General Medical Sciences). Equipment in the facility was purchased with funds from the University of Wisconsin, the National Institutes of Health (P41GM66326, P41RR02301, RR02781, RR08438), the National Science Foundation (DMB-8415048, OIA-9977486, BIR-9214394), and the U.S. Department of Agriculture.
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How do I set up a collaboration with NMRFAM?

If you have a biomacromolecule structure that you want to solve or other involved project, you may be interested in setting up a collaboration with NMRFAM. If you are interested in a collaboration, please contact Dr. Anne Lynn Gillian-Daniel at gillian@nmrfam.wisc.edu or (608)262-3173.

NMRFAM scientific collaborators generally expect to be intellectually engaged in these studies and included as authors on resulting publications.
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How much does it cost?

NMRFAM charges hourly fees for data collection. The rate depends on the field strength and whether the instrument has a cryogenic probe. The table below lists the spectrometers and their per hour rate. We bill the spectrometers in 0.5 hr increments

If you choose to send us your sample or need to have our staff set up your experiment and run it, we apply a surcharge for the time it takes to set up your experiment (typically 0.5-1 hr at $50/hr) and then the charge drops to the per hour rate for the remainder of the experimental time. This does not include data analysis. Data analysis is usually done by the user or a collaborator, who may be a NMRFAM staff member. If the project is a collaboration with a staff member, there is no surcharge, but the cost of the spectrometer time will be charged as in the table below.

Fees will be waived if problems develop as the result of equipment failure, but not for problems resulting from sample quality, quantity, or outside operator error.

IMPORTANT: If you sign up for time and then do not use it or arrange for someone else to use it, you will be billed for that time. If you know that you will not use time you have signed up for then you can cancel it but you must do so at least 24 hours in advance to avoid being charged for the time.

There is no charge for the use of the computers and software at NMRFAM.

Spectrometer system	Data collection rate
	Academic
Bruker DMX 400 WB	$3/hr
Bruker DMX 500i	$3/hr
Bruker DMX 500ii with CryoprobeTM	$6/hr
Bruker DMX 600i with CryoprobeTM	$8/hr
Varian Unity Inova 600ii with Cold ProbeTM	$8/hr
Varian NMR System 600iii with Cold ProbeTM	$8/hr
Bruker DMX 750 with CryoprobeTM	$10/hr
Varian Unity Inova 800 with Cold ProbeTM	$10/hr
Varian Unity Inova 900 with Cold ProbeTM	$12/hr

Spectrometer system	Industrial (proprietary only)
Bruker DMX 400 WB	$100/hr
Bruker DMX 500i	$100/hr
Bruker DMX 500ii with CryoprobeTM	$200/hr
Bruker DMX 600i with CryoprobeTM	$250/hr
Varian Unity Inova 600ii with Cold ProbeTM	$250/hr
Varian NMR System 600iii with Cold ProbeTM	$250/hr
Bruker DMX 750 with CryoprobeTM	$250/hr
Varian Unity Inova 800 with Cold ProbeTM	$250/hr
Varian Unity Inova 900 with Cold ProbeTM	$350/hr

If an industrial user plans on publishing the data collected at NMRFAM within one year, then the academic rate is charged.
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Do I have to come to Madison to run my sample? Can I log-on to the spectrometers from another location?

Inexperienced users should plan to come to the facility to receive training. Trained spectroscopists can sign up for time on a spectrometer using Sundial (link here) and then FedEx us your sample. One of our staff members will place the sample in the magnet, tune and match the probe and contact you when the spectrometer is ready for remote data collection. Detailed instructions for remote log-on can be found at remote user instructions. We strongly recommend that you follow these remote log-on instructions to prevent a loss of data collection in the event that the internet connection is disrupted. If you choose to log-on via a different method and you lose data, we will still charge you for spectrometer time. If you choose to send us your samples, please contact us (Anne Lynn Gillian-Daniel at gillian@nmrfam.wisc.edu or (608)262-3173) so we know when your sample will be arriving and can have someone available to set up the spectrometer.
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If I come to Madison, where can I stay?

The listing of a hotel does not constitute an endorsement in any shape or form. These places just happen to be rather close to campus (or are part of the campus in the case of the Extension Conference Center and the Union buildings).

Below is housing provided for visitors through the University Extension and the University Union.

On Campus Accommodations		Wisconsin Union Guest Rooms
The Friedrick Center 1950 Willow Drive (608) 231-1341 jffred@ecc.uwex.edu	The Lowell Center 610 Langdon Street (608) 256-2621 lowell@ecc.uwex.edu	Memorial Union (East campus) 800 Langdon Street (608) 262-1583	Union South (West campus) 227 N. Randall (608) 263-2600
The following is a list of local hotels near the campus area. One could also contact the Greater Madison Convention and Visitors Bureau (1-800-373-6376) or the Wisconsin Innkeepers Association.
Best Western Inn on the Park 22 South Carroll Street 800-279-8811	Best Western InnTowner 2424 University Avenue (608) 233-8778 or (800) 528-1234	The Edgewater Hotel 666 Wisconsin Avenue 800-922-5512	Hilton Madison at Monona Terrace 9 East Wilson St (608) 255-5100
Double-Tree Hotel 525 West Johnson Street (608) 251-5511	University Inn 441 N. Frances Street 1-608-285-8040	The Madison Concourse Hotel 1 West Dayton Street 800-356-8293	Arbor House B&B 3402 Monroe St. 608-23

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Where is NMRFAM located?

Having trouble finding us? Our facilities are located in the Biochemistry Addition (433 Babcock Dr.) on the campus of the University of Wisconsin-Madison. If you need some help orienting yourself try looking at a Madison map. Or check out the Campus map. The University also has a very nice Expandable map.
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What are NMRFAM's core research projects?

1: Fast data collection and automated data analysis for determining structures of small proteins

Aims: To reduce the time required for routine structure determinations (proteins <20 kD) to one week. This process would involve the collection and analysis of data with deposition of the resonance assignments at the Biological Magnetic Resonance Bank (BMRB) and deposition of the structure at the protein structure database (Protein Data Bank (PDB)) in one week. We will accomplish this by automating the steps in structure determinations. A figure of merit for the final structure will be provided by probabilistic evaluation and validation at each step.

2: Advanced methods for investigations of RNA and RNA complexes

Aims: To develop approaches for determining structures of larger RNA molecules. To develop methods for investigating tertiary interactions in RNA molecules. To develop approaches to the investigation of metal-ion:nucleic acid interactions.

3: Technology for metabolomics

Aims: To develop technology to identify and quantitate metabolites in a variety of organisms and to develop a large database of standard compounds.

4: Technology for challenging systems: larger protieins and complexes, paramagnetic proteins, membrane proteins, dynamics

Aims: To develop technology that will enable routine NMR structure determinations of proteins up to 40 kD with fast data collection and automation of assignments and structure determinations. To enable routine NMR investigations of stereo array isotope labeled (SAIL) proteins by lowering costs of protein production and by optimizing data collection, processing, and analysis methods. To develop robust approaches for applying underutilized information from the PDB and BMRB databases determining structures of larger proteins in cases where extensive NOE data are difficult or impossible to obtain. To apply these new methods to biologically important proteins and complexes.

To develop experimental and computational methods for the structural refinement of paramagnetic centers in iron-sulfur proteins. To investigate the role of hydrogen bonds in tuning the redox potential of electron transport proteins.

To develop a comprehensive strategy for dynamic analyses of larger biomolecules through data collected at multiple field strengths. To develop methods for reducing data collection times for relaxation studies by a factor of 10. To create and release user-friendly software for the analysis of relaxation data. To apply this approach to high-value targets to test its merit in structure-function investigations.

Who can I contact if I have more questions?

Please contact the NMRFAM administrator: Dr. Anne Lynn Gillian-Daniel at gillian@nmrfam.wisc.edu or (608)262-3173.
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The NMRFAM Protein Structure Determination Workshop will be June 3-8, 2007

MMCD – Madison Metabolomics Consortium Database – a freely-available database containing information about small chemical compounds of biological interest.

New instructions for Remote Users are now available.

The new PINE server incorporates PISTACHIO (assignments), LACS (checking of carbon-13 chemical shift referencing and possible outliers), and PECAN (secondary structure determination) to yield results consistent with all three.