An Overview of Protein NMR Spectroscopy - Doing Science (2023)

An Overview of Protein NMR Spectroscopy - Doing Science (1)

  • laboratory techniques,Historic,Science

An overview of protein NMR spectroscopy

  • anjali singh
  • 13.04.2021

Spectroscopy is "the study of the study and measurement of the absorption and emission of light or electromagnetic radiation by matter as a function of its wavelength and frequency"[8]🇧🇷 Simply put, it is the study of the interaction of light with a matter or substance.

Based on the nature of the interaction between energy and material, spectroscopy is divided into subcategories including: absorption spectroscopy, emission spectroscopy, elastic reflection and scattering spectroscopy, impedance spectroscopy, resonance spectroscopy, and nuclear spectroscopy.[13].

Spectroscopy is also divided according to the type of radiant energy and the type of interacting material.

This article discusses the principle, operation and applications of protein NMR spectroscopy. But before we get to that, let's take a quick look at the basics of NMR spectroscopy.

NMR spectroscopy

Nuclear magnetic resonance (NMR) spectroscopy techniques are used to study the molecular structure of chemical compounds by exploiting the magnetic field around their atomic nuclei. This is done by determining the different local electronic environments of atoms such as hydrogen, carbon, chlorine, etc. into a chemical compound.

It is the only method that generates the three-dimensional structure of the molecule in the solution phase. The electromagnetic resonance phenomenon that occurs provides detailed information about the structure, dynamics, reaction state and chemical environment of molecules such as proteins.

You can read more about terms, advantages and disadvantages of NMR spectroscopy in the article "Spectroscopic nuclear magnetic resonance.“

(Video) Methods for Determining Atomic Structures: NMR Spectroscopy (from PDB-101)

The principle of NMR spectroscopy and the calculations needed to study NMR data from proteins (or other biomolecules).

NMR spectroscopy works on the principle of changing the energy state and orientation of an atomic nucleus in a magnetic field. The change depends on the presence or absence of electrons around the atomic nuclei of a molecule.

This phenomenon pulls all atomic nuclei in the same direction and is called a resonance state. And the energy transfer and the state of the atomic nuclei are indicated by the different signal levels on the screen.

Furthermore, signals from NMR spectra are processed and the amount of energy needed to bring atomic nuclei to the higher state is calculated. Several machines are needed to produce the structure of the molecule in solution.

The formula for calculating the amount of energy required to bring atomic nuclei to their highest state is:

𝚫E = hv

wo =change energy

h = Planck's constant

v = frequency of light

The NMR operating frequency is calculated[4]:

v = ( 𝜸 /2π ) * secondÖ

Onde 𝜸 =Gyromagnetic relationship that differs in different nuclei.

Bo = the strength of the magnetic field applied by NMR

This equation means that the higher the frequency of light, the greater the applied magnetic field strength. The frequency is therefore directly proportional to the strength of the applied magnetic field.

Resonance spectra are obtained from the chemical shifts of nuclei. Different atomic nuclei show different chemical shifts in the presence of magnetic fields due to the shielding effect of surrounding electrons. This causes the nuclei to resonate at slightly different frequencies.

The formula[4]used to calculate this:v = ( 𝜸 /2π ) * secondÖ* (1-𝛔)

here𝛔is the shielding effect.

NMR protein spectroscopy

NMR spectroscopy has revealed many mysteries about the behavior of molecules. NMR spectroscopy of proteins helps to study conformational changes, denaturation and internal mobility of proteins, pH titration of individual ionizable amino acid side chains in active sites of enzymes, observation of hydrogen bonded iminos of protons in tRNA, study of paramagnetic centers in metalloproteins etc.[1].

This method measures the short distances and angles between different protons and then computationally derives the structure of the protein. Modern protein spectroscopy requires multidimensional experiments with1H,13C,yfifteenN-nuclei and isotopically labeled proteins[1].

The NMR spectroscopy apparatus consists of nine main parts, a sample holder, magnetic coils, a permanent magnet, a scanning generator, a radio frequency transmitter, a radio frequency detector, a recorder and a reading system. All these parts organize their functions to achieve the desired results.

Steps to determine protein structure using NMR spectroscopy

The different steps to determine protein structure include: sample preparation, NMR measurements, resonance mapping, and structure determination from NMR data. The steps are discussed below.

1. Sample preparation

  • Before analyzing protein structure, make sure the protein sample is in a purified form.
  • Dissolve the protein in 0.5 mL of water and adjust the pH and ionic strength of the solution. (pH range 3-5)[1].
  • The protein concentration of the sample should be between 1 and 6 mM (ideally between 3 and 6 mM). This is to ensure that a 15-30 mg protein sample is available for NMR spectroscopy.[1].
  • If the molecular weight of the protein is around 12,000, isotopic labeling should be added to the preparationfifteenN bzw13C[1].

Some points must be considered before sample preparation. Helps remove contamination and reduces background noise during experimentation.

(Video) Introduction to Biomolecular NMR Spectroscopy - Trevor Rutherford

  • Carefully avoid/remove paramagnetic contaminants by minimizing sample contact with metal surfaces and equipment. These impurities degrade the spectrum.
  • Solution components such as buffer and salt must be prepared using high quality reagents.
  • Avoid vigorously shaking the sample as this can lead to protein denaturation.

An Overview of Protein NMR Spectroscopy - Doing Science (2)

Figure:NMR sample protein preparation in a thin wall tube[13]

2. NMR measurements

To determine the structure of the protein in which thousands of resonances will be present,1The H NMR spectrum overlaps and is crowded. To avoid this confusion, a2-D or 3-D NMR experimentIt is preferable to collect the necessary information.

The 2D and 3D NMR experiments distribute the spectra along two and three frequency axes. The spectra represent "cross peaks" where the spectrum signal is equal on both sides of a diagonal.

The cross peaks arise from magnetization transfer and show that the two nuclei are coupled and have different chemical shifts. The change is so small that it is reported in parts per million (ppm). (You can consult the article1H NMR chemical shiftfor more information on chemical changes during NMR experiments)

The frequency of the detected signal is proportional to the externally applied magnetic field. However, external magnetization is also disturbed and neutralized by the reaction of external electrons. This change in the effective magnetic field causes the spin frequency of the nucleus to change. This is called a "chemical transformation".[10].

Thus, the effective magnetic field rotating the core is calculated using the formula:

BEffective= secondapplied-Blocal

BEffective= the magnetic field acting on the nuclei.

Bapplied= the externally applied magnetic field by NMR.

Blocal= the local magnetic field applied by electrons around atomic nuclei.

The most important information is collected byNuclear Overhauser Enhancement (NOE) - Spectroscopyor NOESY. Helps determine the orientation of atoms in a molecule. When the distance between the two protons is about 5.0 ÅÖthen a cross peak between two hydrogen atoms is observed.

Therefore, the NOESY experiment depends on the distance in space. In several 2-D NMR experiments that support this1H NMR assignment, cross peak means interproton binding ratio. This means that the protons are not separated by more than three covalent bonds and are part of the same amino acid.

An Overview of Protein NMR Spectroscopy - Doing Science (3)

Figure: 1H NMR spectrum of lysozyme[11].

3. Resonance Attributions

In this step, the observed peaks (chemical shifts) in the spectrum are assigned to specific atoms. Resonance mapping helps characterize protein structure and dynamics by specifying the atomic identity of unique frequencies in the spectrum.[3]🇧🇷 But a protein contains many amino acid residues and this creates thousands of peaks in the spectrum.

This confusion is resolved usingsequential allocation strategy[3]. Este método é baseado no conhecimento prévio da sequência de aminoácidos e envolve o uso de (homonucleares)1H NMR experiments. Conventional methods include the heteronuclear or triple resonance approach.

Los1The H NMR procedure follows three steps[9]for the resonance assignment:

  • Identify the amino acid spin side chain:COZY (correlation spectroscopy) or TOCSY (total correlation spectroscopy) is used for this.[5]🇧🇷 These experiments generate the spectra of individual amino acids in the protein. Identify the specific pattern of cross peaks to specify the amino acid.
    For example, consider the cross peak patterns of the amino acids aspartate and valine.[9].

An Overview of Protein NMR Spectroscopy - Doing Science (4)

  • Gather the identified amino acids from the protein: This step requires NOESY data. A strong NOE indicates the adjacent amino acid and this is due to the presence of a short interproton distance between adjacent amino acid residues. The less intense peaks, defined byme, me+2, jI, i+3,are seen in the secondary structure[9].
  • Combine the results of steps a and b: Combining the above two steps leads to specific and precise resonance assignments that help generate an accurate protein structure.[9].

Structure determination from NMR data

To deduce the structure of the protein, it is necessary to determine all three boundary conditions. containsDistance constraints, angle constraints, and orientation constraints🇧🇷 The distance constraint is determined by the NOESY experiment and various software such as PASD, XPLOR-NIH, CYANA and UNIO are used to read the cross peaks.

Resonance assignments can be a cumbersome process when done manually. The use of software algorithms makes the process fast and smooth and also ensures efficient NOESY spectral analysis.

Angular constraints, such as psi () and phi (𝝓) angles, are determined by the Karplus equation or using chemical shift spectra. The twist angle of the molecule can be determined by calculating the coupling constant and the chemical shift.

After all structural constraints, chemical changes and resonance assignment are determined, the structure of the protein is determined using the data. The data obtained helps researchers identify local helical structures, beta sheets and tight turns in the amino acid sequence. The secondary structure obtained is used as a model or computer methods are used to interpret the tertiary structure of the protein.

Current methods for calculating structure from NMR data include:Initial metric matrix spacing geometry followed by molecular dynamics calculations and a variable objective function algorithm, complemented by molecular mechanical energy minimization[1].

An Overview of Protein NMR Spectroscopy - Doing Science (5)

Figure:The first structure of a globular protein called Bull Seminal Proteinase Inhibitor IIA (BUSI IIA) is determined using solution NMR spectroscopy.

Source:Wuthrich Kurt (1990). Determination of the structure of proteins in solution by NMR spectroscopy.Das Journal of Biological Chemistry, 265(36),22059-22062

large protein spectroscopy

The process of determining the structure of large proteins weighing around 25 kDa is complex, and an efficient structure cannot be obtained by NMR spectroscopy alone.[6].

A large number of resonances, an increase in linewidth and a low signal-to-noise ratio lead to clustering and overlapping of spectra. Therefore, advanced isotope labeling and multidimensional experiments proved useful in solving the problem.[12].

Recent developments have introduced a number of techniques that help weaken magnetization relaxation and refine protein structure.[11]🇧🇷 These techniques are optimized transverse relaxation spectroscopy (TROSY) and deuteration.

Application of protein NMR spectroscopy

  1. In vivo NMR experiments are used to study specific enzyme reaction kinetics in situ and to understand metabolic pathways.[2].
  2. It is a powerful tool for determining solution structure, molecular dynamics and protein folding. It is also used in drug detection and design, and chemical and metabolite analysis.[fifteen].
  3. It is used to identify the structure of proteins, amino acids, organic compounds, carotenoids and the mobility of water in food. It also helps to characterize the geographic origin and ripening time of fruits and vegetables.[7].
  4. It is used by chemists and biochemists to study the properties of organic molecules.[14].
  5. Can be used to infer the structure of an unknown chemical compound.[14].


Nuclear magnetic resonance (NMR) spectroscopy is a powerful technique that is widely used in various chemical and biochemical laboratories.

The limitation of the method is that it can only determine the structure of proteins weighing around 12,000. NMR spectroscopy does not produce efficient readable spectra for larger proteins above about 13000-15000.

Therefore, advances in multidimensional spectroscopy and isotopic labeling experiments may pave the way for a better understanding of protein structure and function.

In addition, improvements in software algorithms will help smooth out the complicated process of resonance assignment and molecular structure design.


(Video) Simulating a practice set of protein NMR spectra by POKY (Abigail Chiu)
  1. Wuthrich Kurt (1990). Determination of the structure of proteins in solution by NMR spectroscopy.Das Journal of Biological Chemistry, 265(36),22059-22062.
  2. Fan, T.W.-M. e Lane, A. N. (2016).Applications of NMR spectroscopy in systems biochemistry. Advances in Nuclear Magnetic Resonance Spectroscopy, 92-93, 18-53.DOI:10.1016/j.pnmrs.2016.01.005
  3. Uversky, VN and Dunker, AK (2012).3.9 Intrinsically disordered proteins. Integral Biophysics, 170-211.DOI:10.1016/b978-0-12-374920-8.00312-x
  4. Hinds, M.G. e Norton, R.S. (1997).NMR spectroscopy of peptides and proteins. Molecular Biotechnology, 7(3), 315-331.DOI:10.1007/bf02740822
  5. Wüthrich, K. (2001).Structural Biology of Nature, 8(11), 923–925.DOI:10.1038/nsb1101-923
  6. Keniry, MA & Carver, JA (2002). NMR spectroscopy of large proteins.Annual reports on NMR spectroscopy, 31–69. DOI:10.1016/s0066-4103(02)48003-9.
  7. Parlak Y, Güzeler N (2016). Applications of nuclear magnetic resonance spectroscopy in food.Recent research in the journal Nutrition and Food Science;4. DOI:
  10. http://hiperfí
(Video) Protein NMR - using 1D, 2D and 3D experiments to solve structure
anjali singh

Anjali Singh is a freelance writer. Following his passion for science and research, he completed his Masters in Plant Biology and Biotechnology at the University of Hyderabad, India. He has a strong research background in plant sciences with expertise in molecular engineering, tissue culture, and biochemical assays. In her free time outside of work, she enjoys reading fiction, drawing and writing poetry. In the future, she intends to pursue a doctorate in cancer biology while continuing her excellence as a science writer.

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(Video) NMR Spectroscopy


What is the overview of NMR spectroscopy? ›

NMR spectroscopy can be defined as an indispensable tool which applies a magnetic field to an atomic nucleus (e.g., the most common stable isotopes 1H, 13C, 15N) and radio frequency pulses to characterize the resonant frequency of that atomic nucleus according to its chemical or environmental surroundings.

What is NMR spectroscopy of protein? ›

Nuclear magnetic resonance (NMR) spectroscopy is a routine method for the structural determination of proteins and protein complexes at atomic resolution and can also provide rich information regarding both conformational and interactional dynamics occurring on time scales ranging from picoseconds to seconds or even ...

What is the conclusion of NMR spectroscopy? ›

Conclusion. NMR spectroscopy is, arguably, the most powerful analytical technique in terms of the range of systems that can be studied and the nature of information that can be obtained regarding the system of interest.

What is NMR explained simply? ›

NMR is an abbreviation for Nuclear Magnetic Resonance. An NMR instrument allows the molecular structure of a material to be analyzed by observing and measuring the interaction of nuclear spins when placed in a powerful magnetic field.

How does NMR work in simple terms? ›

NMR uses a large magnet (Magnetic) to probe the intrinsic spin properties of atomic nuclei. Like all spectroscopies, NMR uses a component of electromagnetic radiation (radio frequency waves) to promote transitions between nuclear energy levels (Resonance).

How is NMR spectroscopy used to determine protein structure? ›

Protein NMR Spectroscopy

This method measures the short distances and angles between different protons and then computationally the protein structure is derived. The modern spectroscopy of proteins requires multidimensional experiments that involve 1H, 13C, and 15N nuclei in isotopically labeled proteins.

How NMR is used on protein structure? ›

NMR spectroscopy plays a major role in the determination of the structures and dynamics of proteins and other biological macromolecules. Chemical shifts are the most readily and accurately measurable NMR parameters, and they reflect with great specificity the conformations of native and nonnative states of proteins.

What is NMR analysis of proteins best for? ›

NMR spectroscopy is the only method that allows the determination of three-dimensional structures of proteins molecules in the solution phase. In addition NMR spectroscopy is a very useful method for the study of kinetic reactions and properties of proteins at the atomic level.

How does NMR determine structure of data? ›

Solving NMR Structures Step by Step.
  1. Solving NMR Structures Step by Step. ...
  2. °unsaturation = pi−bonds +rings= C+1−
  3. H + X −N. ...
  4.  ...
  5. hint: four or more °unsaturation often implies the presence of an aromatic ring. ...
  6. ≈ δ 7.0- 8.0 ppm => aromatic. ...
  7. Look at the integration and determine the number of hydogens associated with each.

How do you predict the number of signals in NMR? ›

The number of signals these molecule's produce in a 1H NMR spectrum can be determined just by counting the number of distinct hydrogens on one side of the plane of symmetry.

What are the 2 common solvents used in NMR spectroscopy? ›

Common solvents include chloroform-D, acetone-D6, benzene-D6, deuterium oxide (D2O), DMSO-D6, ethanol-D6, and methanol-D4. Other, less common deuterated solvents can be ordered through Chemistry Stores from Cambridge Isotope Laboratories or Sigma-Aldrich/Isotec.

What is important condition of NMR spectroscopy? ›

Chemical shielding

The most important perturbation of the NMR frequency for applications of NMR is the "shielding" effect of the surrounding shells of electrons. Electrons, similar to the nucleus, are also charged and rotate with a spin to produce a magnetic field opposite to the applied magnetic field.

How do you interpret NMR data Expalin with examples? ›

It is important to understand trend of chemical shift in terms of NMR interpretation. The proton NMR chemical shift is affect by nearness to electronegative atoms (O, N, halogen.) and unsaturated groups (C=C,C=O, aromatic). Electronegative groups move to the down field (left; increase in ppm).

What are the basic components of NMR? ›

Magnetic resonance spectrometers have three basic parts: (1) a large magnet, which is responsible for the static magnetic field H0, (2) a transmitter, which provides the alternating field H1, and (3) a receiver, which amplifies and detects the magnetic resonance signal.

What is the most important application of NMR spectroscopy? ›

But the most widely known application came in the medical field with the development of magnetic resonance imaging (MRI). The A-60 was the workhorse NMR instrument for decades as it allowed chemists to determine molecular structures easily and quickly and to follow the progress of chemical reactions.

Which technique is used to determine the protein structure? ›

The main technique that has been used to discover the three-dimensional structure of molecules, including proteins, at atomic resolution is x-ray crystallography.

What are the main techniques used to determine protein structure? ›

Currently, the main techniques used to determine protein 3D structure are X-ray crystallography and nuclear magnetic resonance (NMR). In X-ray crystallography the protein is crystallized and then using X-ray diffraction the structure of protein is determined.

Why is NMR used in protein dynamics? ›

Dynamic properties of proteins are essential for describing the structural bases of their biological functions including catalysis, binding, regulation and cellular structure. Nuclear magnetic resonance (NMR) spectroscopy represents a powerful technique for measuring these essential features of proteins.

What is NMR studies of protein structure and dynamics? ›

NMR studies of protein dynamics, in principle, give insight into the relation between motion and function. A description of deuterium-based spin relaxation methods for the investigation of side chain dynamics is provided.

Can NMR be used for protein protein interactions? ›

Nuclear magnetic resonance (NMR) is a powerful technique to study protein-protein interactions in solution. Various methods have been developed and applied successfully for locating binding sites on proteins.

What is the limitation of protein NMR? ›

The current size limit of protein NMR is ≈35 kDa, but recent advances in both hardware and experimental design promise to allow the study of much larger proteins (2). The future is even brighter with the development of novel strategies for isotopic labeling of proteins that are synergistic with the new NMR techniques.

How does NMR manipulate data? ›

The procedure is as follows: Expand the region that contains the most downfield or most upfield signal(s). Click integrate and position the cursor on the left-hand side of a peak to be integrated. Click with the left mouse button. Click with middle mouse button Page 2 once: A white arrow (pointing downward) appears.

What frequency is used for NMR? ›


Spectrometers are typically named by frequency: 400 MHz, 300 MHz etc. This is a generic name for the radio frequency to 'flip' a proton under the applied magnetic field of Page 5 that NMR magnet. The higher the frequency the spectrometer means the higher the magnetic field applied to the nuclei.

What frequency is used in NMR? ›

In the NMR experiment, photons with frequencies in the radio frequency (RF) range are used. In NMR spectroscopy, f lies between 60 and 800 MHz for hydrogen nuclei. In clinical MRI, f is typically between 15 and 80 MHz for hydrogen imaging.

What is the most common NMR reference? ›

The 1H sensitivity standard (0.1% ethylbenzene / 0.01% TMS / CDCl3) is widely used by the NMR community to evaluate the signal-to-noise ratio (SNR) in the 3 to 7 ppm range for a variety of NMR instruments (see Figure 1).

Which compounds gives 3 signals in NMR spectroscopy? ›

Three signals total in 1H NMR spectrum. 1,3-dimethylbenzene: Hb is situated between two methyl groups, the two Hc protons are one carbon away from a methyl group, and Hd is two carbons away from a methyl group. Therefore, the four aromatic protons can be divided to three sets.

How many types of NMR are there? ›

There are two types of NMR spectrometers, continuous-wave (cw) and pulsed or Fourier-Transform (FT-NMR).

How do you know what solvent to use in NMR? ›

  1. Chloroform is the standard solvent to try first. ...
  2. If your compound is not soluble in chloroform, try benzene (nonpolar or average polarity compounds), acetone (dissolves almost anything) or methanol (polar compounds).

What is NMR spectroscopy principle and working? ›

Principle of NMR Spectroscopy

The transfer of energy occurs at a wavelength that matches with radio frequencies. Also, when the energy returns to the ground state from an excited state, it is known to emit the radio wave of the same frequency. This emitted radio frequency gives the NMR spectrum.

How many signals are there in NMR spectroscopy? ›

Nuclear Magnetic Resonance (NMR) Spectroscopy

The spectrum has five signals which indicates five types of different protons.

What is the principle and working of NMR spectroscopy? ›

Principle of NMR Spectroscopy

The transfer of energy occurs at a wavelength that matches with radio frequencies. Also, when the energy returns to the ground state from an excited state, it is known to emit the radio wave of the same frequency. This emitted radio frequency gives the NMR spectrum.

What is the principle and application of NMR spectroscopy? ›

Principle of Nuclear Magnetic Resonance (NMR) Spectroscopy

The principle behind NMR is that many nuclei have spin and all nuclei are electrically charged. If an external magnetic field is applied, an energy transfer is possible between the base energy to a higher energy level (generally a single energy gap).

What are the basic components of NMR spectroscopy? ›

Magnetic resonance spectrometers have three basic parts: (1) a large magnet, which is responsible for the static magnetic field H0, (2) a transmitter, which provides the alternating field H1, and (3) a receiver, which amplifies and detects the magnetic resonance signal.

How is NMR used to study proteins? ›

NMR spectroscopy plays a major role in the determination of the structures and dynamics of proteins and other biological macromolecules. Chemical shifts are the most readily and accurately measurable NMR parameters, and they reflect with great specificity the conformations of native and nonnative states of proteins.

Why is it important in NMR? ›

Nuclear magnetic resonance (NMR) spectroscopy today is a powerful tool in analytical chemistry and condensed matter science as well as for the elucidation of structure and dynamics of macromolecules.

What are the two types of NMR spectroscopy? ›

There are two types of NMR spectrometers, continuous-wave (cw) and pulsed or Fourier-Transform (FT-NMR).

What is NMR used for in biology? ›

In biology, NMR is fundamental for determining and exploring the structure of proteins, e.g. enzymes, receptors. It has been used to elucidate the structure and function of numerous biological components.


1. Basic Introduction to NMR Spectroscopy
(The Organic Chemistry Tutor)
2. NMR spectroscopy visualized
3. Globular and Filamentous Proteins Interactions Analysis by NMR and MST | Protocol Preview
(JoVE (Journal of Visualized Experiments))
4. Lecture 9.3: How can NMR be used to determine protein structures?
(Ben McFarland)
5. NMR Nuclear Overhauser Effect for Protein Structure Determination
(Vincent Stevenson)
6. 3D Protein Characterisation Using NMR
(Patrick Pivato)
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