Individual assignments of the methyl resonances in the 1H nuclear magnetic resonance spectrum of the basic pancreatic trypsin inhibitor

AssignSLP_GUI, a software tool exploiting AI for NMR resonance assignment of sparsely labeled proteins

Not all proteins are amenable to uniform isotopic labeling with 13C and 15N, something needed for the widely used, and largely deductive, triple resonance assignment process. Among them are proteins expressed in mammalian cell culture where native glycosylation can be maintained, and proper formation of disulfide bonds facilitated. Uniform labeling in mammalian cells is prohibitively expensive, but sparse labeling with one or a few isotopically enriched amino acid types is an option for these proteins. However, assignment then relies on accessing the best match between a variety of measured NMR parameters and predictions based on 3D structure, often from X-ray crystallography. Finding this match is a challenging process that has benefitted from many computational tools, including trained neural nets for chemical shift prediction, genetic algorithms for searches through a myriad of assignment possibilities, and now AI-based prediction of high-quality structures for protein targets. AssignSLP_GUI, a new version of a software package for assignment of resonances from sparsely-labeled proteins, uses many of these tools. These tools and new additions to the package are highlighted in an application to a sparsely-labeled domain from a glycoprotein, CEACAM1.

CEST-FISP: a novel technique for rapid chemical exchange saturation transfer MRI at 7 T

Chemical exchange saturation transfer (CEST) and magnetization transfer techniques provide unique and potentially quantitative contrast mechanisms in multiple MRI applications. However, the in vivo implementation of these techniques has been limited by the relatively slow MRI acquisition techniques, especially on high-field MRI scanners. A new, rapid CEST-fast imaging with steady-state free precession technique was developed to provide sensitive CEST contrast in ∼20 sec. In this study at 7 T with in vitro bovine glycogen samples and initial in vivo results in a rat liver, the CEST-fast imaging with steady-state free precession technique was shown to provide equivalent CEST sensitivity in comparison to a conventional CEST-spin echo acquisition with a 50-fold reduction in acquisition time. The sensitivity of the CEST-fast imaging with steady-state free precession technique was also shown to be dependent on k-space encoding with centric k-space encoding providing a 30-40% increase in CEST sensitivity relative to linear encoding for 256 or more k-space lines. Overall, the CEST-fast imaging with steady-state free precession acquisition technique provides a rapid and sensitive imaging platform with the potential to provide quantitative CEST and magnetization transfer imaging data.

NMR analysis of carbohydrate-protein interactions

Carbohydrate-protein interactions are frequently characterized by dissociation constants in the microM to mM range. This is normally associated with fast dissociation rates of the corresponding complexes, in turn leading to fast exchange on the nuclear magnetic resonance (NMR) chemical shift time scale and on the NMR relaxation time scale. Therefore, NMR experiments that take advantage of fast exchange are well suited to study carbohydrate-protein interactions. In general, it is possible to analyze ligand binding by observing either protein signals or ligand resonances. Because most receptor proteins to which carbohydrates bind are rather large with molecular weights significantly exceeding 30 kDa, the analysis of the corresponding protein spectra is not trivial, and only very few studies have been addressing this issue so far. We, therefore, focus on NMR experiments that employ observation of free ligand, that is, carbohydrate signals to analyze the bound state. Two types of NMR experiments have been extremely valuable to analyze carbohydrate-protein interactions at atomic resolution. Whereas transferred nuclear Overhauser effect (NOE) experiments deliver bioactive conformations of carbohydrates binding to proteins, saturation transfer difference (STD) NMR spectra provide binding epitopes and valuable information about the binding thermodynamics and kinetics. We demonstrate the power of a combined transfer NOE/STD NMR approach for the analysis of carbohydrate-protein complexes using selected examples.

Electronic effects on the fluorescence of tyrosine in small peptides

It is shown for a series of tyrosine-derivatives and tyrosine-containing peptides that the amide group in combination with electron-withdrawing substituents quenches the fluorescence of the phenol moiety. The ammonium group has the strongest electron-withdrawing effect and thus the largest influence on the quenching rate. The peptide group itself does not quench the fluorescence. In a series of peptides with an increasing number of alanines the decreasing quenching efficiency of the peptide group due to the greater distance of the ammonium group is demonstrated. In tyrosine-containing di- and tripeptides a linear correlation between the 13C-NMR chemical shift delta of the C alpha atom of various aliphatic amino acids and the fluorescence-quenching constant confirms the hypothesis that electron-withdrawing and -donating groups are modulating the fluorescence-quenching efficiency of the peptide group. In small peptides the fluorescence lifetime of tyrosine is characteristic for the neighboring amino acids. Using model substances the redox properties of a peptide group and the phenol ring were studied electrochemically. The highest occupied molecular orbital of the tyrosine (1.4 V vs saturated calomel electrode [SCE]) and the lowest unoccupied molecular orbital of the peptide group (-3.12 V vs SCE) have appropriate energies for a photoinduced electron transfer reaction. For solute-quenching experiments quencher molecules can be systematically selected.

Complete 15N and 1H NMR assignments for the amino-terminal domain of the phage 434 repressor in the urea-unfolded form

The amino-terminal domain of the phage 434 repressor consisting of residues 1-69 forms a globular structure of five tightly packed helices, with nearly identical molecular architectures in crystals and in solution. Upon addition of urea to an aqueous solution of this protein, the NMR spectrum of a second form of the protein appears in addition to the native form, and at a urea concentration of 7 M, this urea-unfolded form is the only species observed. At intermediate urea concentrations, the two forms of the protein inter-convert at a rate that allows the observation of the exchange process by NMR. Starting from the previous assignments for the native protein, we obtained nearly complete sequence-specific (1)H and (15)N NMR assignments for the unfolded form of the protein. For most amino acid residues, the (1)H chemical shifts of the urea-unfolded protein are very similar to the random coil values, but some discrete regions of the polypeptide chain were identified that are likely to retain residual nonrandom spatial structure as evidenced by deviations of (1)H chemical shifts and amide proton exchange rates from the expected random coil values.

A new two-disulphide intermediate in the refolding of reduced bovine pancreatic trypsin inhibitor

The apparently complete refolding of reduced bovine pancreatic trypsin inhibitor (BPTI) is shown to produce a mixture of two species. One of these is native BPTI, but the other lacks the disulphide bond between cysteines 30 and 51. The latter species has a folded conformation very like that of native BPTI, and is oxidized by air to native BPTI on warming in aqueous solution. The two unreactive cysteine thiol groups appear to be buried in the interior of the molecule, which restricts access by reagents that can alkylate them or oxidize them to form the disulphide bond. The implications of this intermediate and its conformation for the understanding of protein folding are discussed.

Proton NMR studies of denatured lysozyme

Evidence is presented from 1H NMR studies for non-random conformational behaviour in denatured lysozyme in aqueous solution. A method is presented which permits the assignment of resonances in the 1H NMR spectrum of the denatured protein by observing magnetisation transfer from resonances of the native state. The use of these experiments in characterising the denatured state and the significance of these studies for the investigation of protein folding are discussed.

The mobility of calcium-trigger proteins and its function

Trigger activity implies the transfer of the energy of a signal to some amplified (energy) response. Actions in cells, from calcium concentration changes to major protein reorganization are discussed here. The changes must be fast, so mobile polymers must be involved. The first step is the calcium on/off binding to its receptor, calmodulin, troponin C or a comparable protein. Calcium binding is to a loop, EF-hand, between helices. The structures and internal mobilities of these proteins are described using nuclear magnetic resonance and the temperature dependence of NMR shifts. It is suggested that these proteins illustrate a general working hypothesis that proteins made from interacting helices as opposed to beta-sheet proteins will have relatively easy internal main chain motions. Loops connecting the helices then provide particularly obvious read-out points, for example of the initial message of calcium binding. These and other regions of loose structure appear to be associated with highly charged sequences. The further transfer of the trigger message is to highly mobile sequences in troponin I, troponin T and tropomyosin.

Right-handed and left-handed DNA: studies of B- and Z-DNA by using proton nuclear Overhauser effect and P NMR

We have differentiated between syn and anti glycosidic torsion angles in nucleic acid duplexes by measuring the transient nuclear Overhauser effect (NOE) between the sugar H-1' protons and the purine H-8 and pyrimidine H-6 base protons. The transient NOE measurements demonstrate a syn glycosidic torsion angle at guanosine and an anti glycosidic torsion angle at cytidine in poly(dG-dC) in 4 M NaCl and in poly(dG-m5dC) in 1.5 M NaCl solution. These features have been observed previously in the left-handed Z-DNA conformation of (dC-dG)3 in the crystalline state. By contrast, transient NOE studies demonstrate that both guanosine and cytidine residues adopt the anti conformation about the glycosidic bond for the right-handed poly(dG-dC) and poly(dG-m5dC) conformation in a low-salt solution. We have used P NMR to monitor the equilibrium between B- and Z-DNA forms of poly(dG-dC) in LiCl solutions; at high temperatures, the equilibrium shifts from B- to Z-DNA.

Solution properties of synthetic chlorophyllide--and bacteriochlorophyllide--apomyoglobin complexes

Well-defined 1:1 complexes have been formed between apomyoglobin (apoMb) and a number of chlorophyllide derivatives. The chlorophyllides substitute for heme in the pocket of myoglobin. These include magnesium chlorophyllide a, magnesium and zinc pyrochlorophyllide a, zinc pyrochlorophyllide b, zinc pyrochlorophyllide d, zinc pyromesochlorophyllide a, zinc 2-acetyl-2-devinylpyrochlorophyllide a, zinc protopyrochlorophyllide a, and zinc bacteriopyrochlorophyllide a. The effects of the protein on the electronic absorption, circular dichroism (CD), magnetic circular dichroism, and triplet state electron spin resonance spectra and fluorescence lifetimes in solution are compared with appropriate models in organic solvents. With the exception of the CD spectra, the protein causes shifts and intensity changes which are within the range observed for solvent effects. The CD spectra change substantially: the signs of several transitions are entirely reversed in the chlorins, and 3-6-fold intensity increases are observed with zinc bacteriochlorophyllide a. High-field 1H NMR spectra of ring current shifted Val-E11 methyl protons for the series porphyrin-, chlorin-, and bacteriochlorin-apoMb are used to establish the probable absolute orientation of the chromophore in the heme pocket. Doubled peaks in the NMR spectra of certain complexes are shown to arise from interconvertible species. The temperature dependence of the peak intensities and saturation transfer studies show that the species giving rise to the doubled peaks exchange on the time scale of about 1-60 s. Arguments are presented against inversion of the macrocycle in the heme pocket by either an inter- or an intramolecular mechanism as the origin of doubled peaks, and simple two-site exchange is ruled out by the NMR data. We suggest that the data are consistent with the idea that at least two slowly interconverting conformational substrates of the protein are populated, depending sensitively on small changes in rings I and II of the macrocycle and temperature.

Systematic application of two-dimensional 1H nuclear-magnetic-resonance techniques for studies of proteins. 1. Combined use of spin-echo-correlated spectroscopy and J-resolved spectroscopy for the identification of complete spin systems of non-labile protons in amino-acid residues

This and the following paper describe the practical application of recently developed, two-dimensional nuclear magnetic resonance techniques for studies of proteins. In the present report spin-echo-correlated spectroscopy and two-dimensional J-resolved spectroscopy are used to identify complete spin systems of non-labile, aliphatic protons in the basic pancreatic trypsin inhibitor. Overall, 41 out of the 58 aliphatic spin systems in this protein were identified; for the first time the spin systems of all the glycyl residues in a protein have been identified in the 1H NMR spectrum. Combined with the following paper, the present data yield new individual assignments for numerous amino acid residues and provide a new avenue, based on accurate measurements of spin-spin coupling constants in the two-dimensional J-resolved spectra, for studying changes of static and dynamic aspects of protein conformation between single crystals and solution, or between different conditions of solvent and temperature.

Use of nuclear Overhauser effect in the study of peptides and proteins

The nuclear Overhauser effect (NOE) leads to changes in the intensity of signal(s) of a set of nuclei as a function of their respective distances. The use of NOE allows to obtain structural informations on peptides and proteins in solution as well as the study of interactions between small ligands and biomolecules. In this review, aspects of the basic theory of the NOE will be presented and the more recent applications of homonuclear and heteronuclear NOE's in biomolecules will be surveyed. Typical examples will be illustrated and limitations of the method will be discussed.

Hydrogen isotope exchange kinetics of single protons in bovine pancreatic trypsin inhibitor

The exchange kinetics of the slowest exchanging BPTI beta-sheet protons are complex compared to model peptides; the activation energy, E alpha, and the pH dependence are temperature dependent. We have measured the exchange kinetics in the range pH 1--11, 33--71 degrees C, particularly the temperature dependence. The data are fit to a model in which exchange of each proton is determined by two discrete dynamical processes, one with E alpha approximately 65 kcal/mol and less than first order dependence on catalyst ion, and one with E alpha 20--30 kcal/mol and approaching first order in catalyst ion. The low activation energy process is the mechanism of interest in the native conformation of globular proteins and involves low energy, small amplitude fluctuations; the high activation energy process involves major unfolding. The model is simple, has a precedent in the hydrogen exchange literature, and explains quantitatively the complex feature of the exchange kinetics of single protons in BPTI, including the following. For the slowest exchanging protons, in the range 36 degrees--68 degrees C, E alpha is approximately 65 kcal/mol at pH approximately 4, 20--30 kcal/mol at pH greater than 10, and rises to approximately 65 kcal/mol with increasing temperature at pH 6--10; the Arrhenius plots converge around 70 degrees C; the pH of minimum rate, pHmin, is greater than 1 pH unit higher at 68 degrees C than for model compounds; and at high pH, the pH-rate profiles shift to steeper slope; the exchange rates around pHmin are correlated to the thermal unfolding temperature in BPTI derivatives (Wagner and Wüthrich, 1979, J. Mol. Biol. 130:31). For the more rapidly exchanging protons in BPTI the model accounts for the observation of normal pHmin and E alpha of 20--30 kcal/mol at all pH's. The important results of our analysis are (a) rates for exchange from the folded state of proteins are not correlated to thermal lability, as proposed by Wuthrich et al. (1979, J. Mol. Biol. 134:75); (b) the unfolding rate for the BPTI cooperative thermal transition is equal to the observed exchange rates of the slowest exchanging protons between pH 8.4--9.6, 51 degrees C; (c) the rates for exchange of single protons from folded BPTI are consistent with our previous hydrogen-tritium exchange results and with a penetration model of the dynamic processes limiting hydrogen exchange.

A conformational isomer of bovine pancreatic trypsin inhibitor protein produced by refolding

Refolding of the bovine pancreatic trypsin inhibitor protein (BPTI) after reduction of its three cysteine disulphide linkages can occur when the reduced protein is placed in a suitable oxidizing medium (ref. 1 and refs therein). The refolding process has been studied by trapping chemically intermediates which contain only one or two disulphide bonds (ref. 1 and refs therein). We report here that during structural studies of these intermediates by NMR, we have found that complete re-oxidation of the protein results in substantial quantities of a metastable folded species which is identical to native BPTI in its covalent bonding (including the disulphide bonds) but possesses a somewhat different conformation. The existence of such a species is supported by circular dichroism measurements on refolded BPTI. This novel form of BPTI is of considerable interest because it can be used to provide information about the folding mechanism and conformational stability of the protein.

Structural characterization by nuclear magnetic resonance of a reactive-site 13carbon-labelled basic pancreatic trypsin inhibitor with the peptide bond Arg-39--Ala-40 cleaved and Arg-39 removed

With the use of an enzymatic replacement method, 90%-enriched [1-13C]lysine was introduced into the reactive site of the basic pancreatic trypsin inhibitor. Characterization of the labelled inhibitor with 13C nuclear magnetic resonance (NMR), 1H NMR and chemical methods showed that while the reactive-site peptide bond Lys-15--Ala-16 was properly resynthesized, the polypeptide chain was cleaved at the peptide bond Arg-39--Ala-40 and Arg-39 was removed. Detailed 1H NMR studies showed further that, with the exception of the immediate environment of the modification site, the average spatial structure of the native inhibitor was preserved in the modified protein. Compared to the native inhibitor, the thermal stability of the globular conformation was found to be reduced, interior amide protons exchanged at a faster rate and the internal mobility of aromatic rings located outside the immediate environment of the cleaved peptide bond was essentially unchanged. These observations coincide closely with previous reports on different modifications of the inhibitor and can be explained by a recently proposed dynamic multi-state model for globular proteins. Since the fundamental structural properties of the native inhibitor and full inhibitory activity are preserved after resynthesis, the [1-13C]lys-15-labelled inhibitor with the peptide bond Arg-39--Ala-40 cleaved and Arg-39 removed should be suitable for 13C NMR studies of mechanistic aspects of proteinase-inhibitor interactions.

Individual assignments of amide proton resonances in the proton NMR spectrum of the basic pancreatic trypsin inhibitor

Studies of proton-proton nuclear Overhauser effects were used to obtain individual assignments of 17 amide proton resonances in the 360 MHz proton nuclear magnetic resonance spectrum of the basic pancreatic trypsin inhibitor. First, optimizing the conditions for obtaining selective nuclear Overhauser effects in the presence of spin diffusion in macromolecules is discussed. Truncated driven nuclear Overhauser experiments were used to assing the amide proton resonances of the beta-sheet in the inhibitor. It is suggested that these techniques could serve quite generally to obtain individual resonance assignments in beta-sheet secondary structures of proteins. Combination of nuclear Overhauser studies with spin decoupling further resulted in individual assignments of the gamma-methyl resonances of the two isoleucines and numerous Calpha and Cbeta protons.

Ring current effects in the conformation dependent NMR chemical shifts of aliphatic protons in the basic pancreatic trypsin inhibitor

Previously, a highly refined crystal structure and energy refined atomic coordinates were obtained for the basic pancreatic trypsin inhibitor, as well as numerous individual resonance assignments in the 1H NMR spectrum. These data were now used to investigate the contributions from the local ring current fields of the aromatic rings to the overall conformation dependent chemical shifts in this globular protein. A program was written which allowed the consideration of certain aspects of internal mobility of the protein, and the different commonly used ring current equa tions were compared. These studies indicate that ring current shifts are the dominant contribution to the observed conformation dependent chemical shifts of the peripheral aliphatic side chain protons. On the other hand, it appears that ring current shifts do not make dominant contributions to the conformation dependent shifts of the backbone alpha- and amide protons or the aromatic protons in the inhibitor. On the basis of the empirical calibration with the peripheral aliphatic side chain protons, the Johnson-Bovey ring current equation was selected for an analysis of the ring geometries of two prolines in the inhibitor.

Structural interpretation of lanthanide binding to the basic pancreatic trypsin inhibitor by 1H NMR at 360 MHz

The weak binding of lanthanides to the five carboxyl groups of the basic pancreatic trypsin inhibitor (hereafter termed "the inhibitor"), has been investigated in detail using high resolution 1H NMR at 360 MHz. Lanthanides bind to the C-terminus with an apparent binding constant of 30 M-1, and thus competitively inhibit the formation of a salt-bridge between the C-terminus and the N-terminus, Lanthanides bind also to the side chain carboxyl groups of Asp 3, Glu 7, Glu 49 and Asp 50, with binding constants of 10--30 M-1. With the use of lanthanides individual resonance assignments for Phe 4 and Phe 45 were obtained in the 1H NMR spectrum of the inhibitor, and for several spin systems previous identifications were independently confirmed. The present experiments also provide a nice illustration for the use of shift reagents to improve the resolution in 1H NMR spectra of proteins. The exchange broadening for Tyr 35 and Phe 45 over the temperature range 4--72 degrees C could thus be observed for almost all the components of these aromatic spin systems and new details on the dynamic properties were obtained also for other aromatic residues.