Strategies for the uses of lanthanide NMR shift probes in the determination of protein structure in solutio. Application to the EF calcium binding site of carp parvalbumin

Lanthanides as Calcium Mimetic Species in Calcium-Signaling/Buffering Proteins: The Effect of Lanthanide Type on the Ca2+/Ln3+ Competition

Lanthanides, the 14 4f-block elements plus Lanthanum, have been extensively used to study the structure and biochemical properties of metalloproteins. The characteristics of lanthanides within the lanthanide series are similar, but not identical. The present research offers a systematic investigation of the ability of the entire Ln3+ series to substitute for Ca2+ in biological systems. A well-calibrated DFT/PCM protocol is employed in studying the factors that control the metal selectivity in biological systems by modeling typical calcium signaling/buffering binding sites and elucidating the thermodynamic outcome of the competition between the “alien” La3+/Ln3+ and “native” Ca2+, and La3+ − Ln3+ within the lanthanide series. The calculations performed reveal that the major determinant of the Ca2+/Ln3+ selectivity in calcium proteins is the net charge of the calcium binding pocket; the more negative the charge, the higher the competitiveness of the trivalent Ln3+ with respect to its Ca2+ contender. Solvent exposure of the binding site also influences the process; buried active centers with net charge of −4 or −3 are characterized by higher Ln3+ over Ca2+ selectivity, whereas it is the opposite for sites with overall charge of −1. Within the series, the competition between La3+ and its fellow lanthanides is determined by the balance between two competing effects: electronic (favoring heavier lanthanides) and solvation (generally favoring the lighter lanthanides).

Pseudocontact Shifts in Biomolecular NMR Spectroscopy

Paramagnetic centers in biomolecules, such as specific metal ions that are bound to a protein, affect the nuclei in their surrounding in various ways. One of these effects is the pseudocontact shift (PCS), which leads to strong chemical shift perturbations of nuclear spins, with a remarkably long range of 50 Å and beyond. The PCS in solution NMR is an effect originating from the anisotropic part of the dipole-dipole interaction between the magnetic momentum of unpaired electrons and nuclear spins. The PCS contains spatial information that can be exploited in multiple ways to characterize structure, function, and dynamics of biomacromolecules. It can be used to refine structures, magnify effects of dynamics, help resonance assignments, allows for an intermolecular positioning system, and gives structural information in sensitivity-limited situations where all other methods fail. Here, we review applications of the PCS in biomolecular solution NMR spectroscopy, starting from early works on natural metalloproteins, following the development of non-natural tags to chelate and attach lanthanoid ions to any biomolecular target to advanced applications on large biomolecular complexes and inside living cells. We thus hope to not only highlight past applications but also shed light on the tremendous potential the PCS has in structural biology.

Synthesis and Characterization of Divalent Samarium and Thulium N,N-Dimethylaminodiboranates

The syntheses and molecular structures of new Sm^II and Tm^II N,N-dimethylaminodiboranate (DMADB) complexes are described. Treating SmI₂(THF)₂ with Na(H₃BNMe₂BH₃) in THF results in the formation of Sm(H₃BNMe₂BH₃)₂(THF)₃ (1), which can be readily converted to Sm(H₃BNMe₂BH₃)₂(DME)₂ (DME = 1,2-dimethoxyethane) or Sm(H₃BNMe₂BH₃)₂(diglyme) by exchange with the corresponding ether. We also show that Sm(H₃BNMe₂BH₃)₂(THF)₃ can be prepared by reduction of the Sm^III compound Sm(H₃BNMe₂BH₃)₃(THF) with KC₈ and that addition of 18-crown-6 to this reaction mixture results in the formation of the Sm^II compound Sm(H₃BNMe₂BH₃)₂(18-crown-6). In a similar fashion, two new Tm^II complexes have been synthesized: treatment of TmI₂ in THF with Na(H₃BNMe₂BH₃) results in the formation of Tm(H₃BNMe₂BH₃)₂(THF)₂ and Tm(H₃BNMe₂BH₃)₂(THF)₃, which form a cocrystal. IR data and elemental analyses are reported for all the new compounds, as are their crystal structures. ¹H and ¹¹B NMR data are provided where available.

Compact, hydrophilic, lanthanide-binding tags for paramagnetic NMR spectroscopy

The design, synthesis and evaluation of four novel lanthanide-binding tags for paramagnetic NMR spectroscopy are reported.

The design, synthesis and evaluation of four novel lanthanide-binding tags for paramagnetic NMR spectroscopy are reported. Each tag is based on the ((2S,2′S,2′′S,2′′′S)-1,1′,1′′,1′′′-(1,4,7,10-tetraazacyclododecane-1,4,7,10-tetrayl)tetrakis(propan-2-ol)) scaffold, featuring small chiral alcohol coordinating pendants to minimise the size and hydrophobic character of each tag. The tags feature different linkers of variable length for conjugation to protein via a single cysteine residue. Each tag's ability to induce pseudocontact shifts (PCS) was assessed on a ubiquitin A28C mutant. Two enantiomeric tags of particular note, C7 and C8, produced significantly larger Δχ-tensors compared to a previously developed tag, C1, attributed to the extremely short linker utilised, limiting the mobility of the bound lanthanide ion. The C7 and C8 tags' capacity to induce PCSs was further demonstrated on GB1 Q32C and 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) S112C/C80A mutants. Whilst factors such as the choice of lanthanide ion, pH and site of conjugation influence the size of the PCSs obtained, the tags represent a significant advance in the field.

Bringing dynamic molecular machines into focus by methyl-TROSY NMR

Large macromolecular assemblies, so-called molecular machines, are critical to ensuring proper cellular function. Understanding how proper function is achieved at the atomic level is crucial to advancing multiple avenues of biomedical research. Biophysical studies often include X-ray diffraction and cryo-electron microscopy, providing detailed structural descriptions of these machines. However, their inherent flexibility has complicated an understanding of the relation between structure and function. Solution NMR spectroscopy is well suited to the study of such dynamic complexes, and continued developments have increased size boundaries; insights into function have been obtained for complexes with masses as large as 1 MDa. We highlight methyl-TROSY (transverse relaxation optimized spectroscopy) NMR, which enables the study of such large systems, and include examples of applications to several cellular machines. We show how this emerging technique contributes to an understanding of cellular function and the role of molecular plasticity in regulating an array of biochemical activities.

Cell-free expression and stable isotope labelling strategies for membrane proteins

Membrane proteins are highly underrepresented in the structural data-base and remain one of the most challenging targets for functional and structural elucidation. Their roles in transport and cellular communication, furthermore, often make over-expression toxic to their host, and their hydrophobicity and structural complexity make isolation and reconstitution a complicated task, especially in cases where proteins are targeted to inclusion bodies. The development of cell-free expression systems provides a very interesting alternative to cell-based systems, since it circumvents many problems such as toxicity or necessity for the transportation of the synthesized protein to the membrane, and constitutes the only system that allows for direct production of membrane proteins in membrane-mimetic environments which may be suitable for liquid state NMR measurements. The unique advantages of the cell-free expression system, including strong expression yields as well as the direct incorporation of almost any combination of amino acids with very little metabolic scrambling, has allowed for the development of a wide-array of isotope labelling techniques which facilitate structural investigations of proteins whose spectral congestion and broad line-widths may have earlier rendered them beyond the scope of NMR. Here we explore various labelling strategies in conjunction with cell-free developments, with a particular focus on alpha-helical transmembrane proteins which benefit most from such methods.

Structure determination of a Galectin-3-carbohydrate complex using paramagnetism-based NMR constraints

The determination of the location and conformation of a natural ligand bound to a protein receptor is often a first step in the rational design of molecules that can modulate receptor function. NMR observables, including NOEs, often provide the basis for these determinations. However, when ligands are carbohydrates, interactions mediated by extensive hydrogen-bonding networks often reduce or eliminate NOEs between ligand and protein protons. In these cases, it is useful to look to other distance- and orientation-dependent observables that can constrain the geometry of ligand-protein complexes. Here we illustrate the use of paramagnetism-based NMR constraints, including pseudo-contact shifts (PCS) and field-induced residual dipolar couplings (RDCs). When a paramagnetic center can be attached to the protein, field-induced RDCs and PCS reflect only bound-state properties of the ligand, even when averages over small fractions of bound states and large fractions of free states are observed. The effects can also be observed over a long range, making it possible to attach a paramagnetic center to a remote part of the protein. The system studied here is a Galectin-3-lactose complex. A lanthanide-binding peptide showing minimal flexibility with respect to the protein was integrated into the C terminus of an expression construct for the Galectin-3-carbohydrate-binding domain. Dysprosium ion, which has a large magnetic susceptibility anisotropy, was complexed to the peptide, making it possible to observe both PCSs and field-induced RDCs for the protein and the ligand. The structure determined from these constraints shows agreement with a crystal structure of a Galectin-3-N-acetyllactosamine complex.

EF-hand protein dynamics and evolution of calcium signal transduction: an NMR view

Calcium signaling, one of the most widespread signaling mechanisms in cells, is generally carried out by EF-hand proteins, characterized by a helix-loop-helix motif paired in functional domains. EF-hand proteins may be viewed as molecular switches activated by calcium concentration transients. The EF-hand structural database has grown to a point where meaningful inferences on the functional conformational rearrangements upon calcium binding can be made by comparing a fair number of pairs of end points, i.e., the structures of the apo and calcium-bound forms. More compact descriptors of the movement associated with calcium binding, in terms of principal component analysis of the six interhelical angles, have also become available. Dynamic information obtained by NMR, also with the aid of calcium substitution with paramagnetic lanthanides, is shedding light on the intrinsic amplitude of the conformational degrees of freedom sampled by the various members of the EF-hand superfamily, as well as on the time scales of the motions. Particularly, NMR of lanthanide derivatives helps in capturing long time scale motions. Both static and dynamic pictures reveal a large variety of behaviors. It is increasingly recognized that the EF-hand machinery has differentiated its behavior during evolution in several ways, e.g., by modifying one of the loops, by undergoing a further duplication after the initial motif duplication that originated the functional domain, or by acquiring the ability to dimerize.

Solution structure of the bacterial frataxin ortholog, CyaY: mapping the iron binding sites

CyaY is the bacterial ortholog of frataxin, a small mitochondrial iron binding protein thought to be involved in iron sulphur cluster formation. Loss of frataxin function leads to the neurodegenerative disorder Friedreich's ataxia. We have solved the solution structure of CyaY and used the structural information to map iron binding onto the protein surface. Comparison of the behavior of wild-type CyaY with that of a mutant indicates that specific binding with a defined stoichiometry does not require aggregation and that the main binding site, which hosts both Fe(2+) and Fe(3+), occupies a highly anionic surface of the molecule. This function is conserved across species since the corresponding region of human frataxin is also able to bind iron, albeit with weaker affinity. The presence of secondary binding sites on CyaY, but not on frataxin, hints at a possible polymerization mechanism. We suggest mutations that may provide further insights into the frataxin function.

A powerful combinatorial screen to identify high-affinity terbium(III)-binding peptides

Lanthanide-binding tags (LBTs) are protein fusion partners consisting of encoded amino acids that bind lanthanide ions with high affinity. Herein, we present a new screening methodology for the identification of new LBT sequences with high affinity for Tb(3+) ions and intense luminescence properties. This methodology utilizes solid-phase split-and-pool combinatorial peptide synthesis. Orthogonally cleavable linkers allow an efficient two-step screening procedure. The initial screen avoids the interference caused by on-bead screening by photochemically releasing a portion of the peptides into an agarose matrix for evaluation. The secondary screen further characterizes each winning sequence in a defined aqueous solution. Employment of this methodology on a series of focused combinatorial libraries yielded a linear peptide sequence of 17 encoded amino acids that demonstrated a 140-fold increase in affinity (57 nM dissociation constant, K(D)) over previously reported lanthanide-binding peptides. This linear sequence was macrocyclized by introducing a disulfide bond between flanking cysteine residues to produce a peptide with a 2-nM apparent dissociation constant for Tb(3+) ions.Supporting information for this article is available on the WWW under http://www.chemphyschem.org or from the author.

13C and 113Cd NMR studies of the chelation of metal ions by the calcium binding protein parvalbumin

13C NMR spectra are presented for the calcium binding protein parvalbumin (pI 4.25) from carp muscle in several different metal bound forms: with Ca2+ in both the CD and EF calcium binding sites, with Cd2+ in both sites, with 113Cd2+ in both sites, and with 113Cd2+ in the CD site and Lu3+ in the EF site. The different metals differentially shift the 13C NMR resonances of the protein ligands involved in chelation of the metal ion. In addition, direct 13C-113Cd spin-spin coupling is observed which allows the assignment of protein carbonyl and carboxyl 13C NMR resonances to ligands directly interacting with the metal ions in the CD and EF binding sites. The displacement of 113Cd2+ from the EF site by Lu3+ further allows these resonances to be assigned to the CD or EF site. The occupancy of the two sites in the two cadmium species and in the mixed Cd2+/Lu3+ species is verified by 113Cd NMR. The resolution in these 113Cd NMR spectra is sufficient to demonstrate direct interaction between the two metal binding sites.

Structural studies of calcium-binding proteins using nuclear magnetic resonance

Lanthanide-shifted 1H nuclear magnetic resonance (NMR) spectroscopy has been used to compare the structure in solution of the EF-hand calcium-binding domains of four parvalbumins (isoelectric pH[pI] 3.95, 4.25, and 4.37 from carp, and pI from buffalo fish). These four parvalbumins are shown by NMR to have very similar structures at the level of resolution typical of x-ray structures. At the higher resolution possible by the lanthanide NMR technique, specific differences are noted between the pI 3.95 isoprotein from carp and the other two carp isoproteins, and the buffalo fish parvalbumin is shown to be different from all three carp isoproteins. The differences are estimated to correspond to changes of the order of 0.2 A in the positions of some of the nuclei surrounding the EF calcium site.

Use of lanthanide-induced nuclear magnetic resonance shifts for determination of protein structure in solution: EF calcium binding site of carp parvalbumin

The binding of the paramagnetic lanthanide ion ytterbium to the calcium binding protein carp parvalbumin results in a series of 1H NMR resonances which are shifted far outside the envelope of the 1H NMR spectrum of the diamagnetic form of the protein; bound Yb3+ also induces shifts in the 13C NMR spectrum of parvalbumin and in the 113Cd NMR spectrum of cadmium-substituted parvalbumin. The interpretation of these lanthanide-shifted resonances in terms of the structure of the protein surrounding the metal binding site requires the determination of the orientation and principal elements of the magnetic susceptibility tensor of the protein-bound Yb3+ ion. A previous comparison [Lee, L., & Sykes, B. D. (1982) Biomolecular Structure Determination by NMR (Bothner-By, A. A., Glickson, J. D., & Sykes, B. D., Eds.) pp 169-188, Marcel Dekker, New York] of the observed Yb3+-shifted 1H NMR spectrum of parvalbumin with a calculated spectrum, based upon the X-ray structure and an initial determination of the magnetic susceptibility tensor, led to the conclusion that there were significant differences between the solution and X-ray structures. In this paper, the magnetic susceptibility tensor has been reevaluated with the aid of newly assigned 13C and 113Cd NMR resonances. The agreement between the calculated and observed spectra is now close overall.

Lanthanide-induced peptide folding: variations in lanthanide affinity and induced peptide conformation

The present work has demonstrated the utility of the diamagnetic lanthanides lutetium and lanthanum as metal binding probes for a synthetic 13-residue fragment representing calcium binding site 3 of rabbit skeletal troponin C (residues 103-115). The peptide conformation induced by these metals was monitored by the proton magnetic resonance at 270 MHz. The peptide affinity for these rare earths is 50-400 times higher than that for calcium (KLu3+, 1.3 X 10(4) M-1; KLa3+, 1.1 X 10(5) M-1; KCa2+, 3 X 10(2) M-1) which is related to the change in cation charge from 2+ to 3+. The peptide conformation induced by the presence of La3+ generates a different 1H NMR spectrum than the one observed for the lutetium-saturated peptide. Thus, it appears that these metals do not fold the peptide into exactly the same conformation. The resonance shifts observed during the Lu3+ titration are much smaller than those seen in the case of La3+ addition. The fact that lutetium binds less tightly than lanthanum to the peptide may be linked directly or indirectly to the difference in ionic radius between these metals (Lu3+, 0.86 A; La3+, 1.03 A). This may in turn indicate that the peptide primary sequence encodes for some aspects of metal ion specificity. The 1H NMR results also demonstrate that glycine-108 adopts a restricted geometry in the absence of metal such that its two alpha-carbon protons are in different environments which are further affected by the addition of either metal. These observations support the concept that geometric constraints arising from the particular peptide folding pattern near this residue correlate with the highly conserved nature of this site of the EF hand. This position remains occupied by glycine in most EF hand domains with the exception of known distorted calcium binding sites present in intestine calcium binding proteins and S-100.