Backbone assignments, and effect of Asn deamidation, of the N-terminal region of the partitioning protein IncC1 from the plasmid RK2

IncC from the low-copy number plasmid RK2, is a member of the ParA family of proteins required for partitioning DNA in many bacteria and plasmids. It is an ATPase that binds DNA and its ParB protein partner, KorB. Together, the proteins move replicated DNA to appropriate cellular positions, so that each daughter cell inherits a copy on cell division. IncC from RK2 is expressed in two forms. IncC2 is homologous to bacterial ParA proteins, while IncC1 has an N-terminal extension of 105 amino acids and is similar in length to ParA homologues in other plasmids. We have been examining the role of this extension, here called IncC NTD. We present its backbone NMR chemical shift assignments and show that it is entirely intrinsically disordered. The assignments were achieved using C-detected, CON-based spectra, complemented by HNN spectra to obtain connectivities from three adjacent amino acids. We also observed evidence of deamidation of the protein at a GNGG sequence, to give isoAsp, giving 2 sets of peaks for residues up to 5 amino acids on either side of the modification. We have assigned resonances from around the position of modification for this form of the protein.

E. coli NfsA: an alternative nitroreductase for prodrug activation gene therapy in combination with CB1954

Prodrug activation gene therapy is a developing approach to cancer treatment, whereby prodrug-activating enzymes are expressed in tumour cells. After administration of a non-toxic prodrug, its conversion to cytotoxic metabolites directly kills tumour cells expressing the activating enzyme, whereas the local spread of activated metabolites can kill nearby cells lacking the enzyme (bystander cell killing). One promising combination that has entered clinical trials uses the nitroreductase NfsB from Escherichia coli to activate the prodrug, CB1954, to a potent bifunctional alkylating agent. NfsA, the major E. coli nitroreductase, has greater activity with nitrofuran antibiotics, but it has not been compared in the past with NfsB for the activation of CB1954. We show superior in vitro kinetics of CB1954 activation by NfsA using the NADPH cofactor, and show that the expression of NfsA in bacterial or human cells results in a 3.5- to 8-fold greater sensitivity to CB1954, relative to NfsB. Although NfsB reduces either the 2-NO₂ or 4-NO₂ positions of CB1954 in an equimolar ratio, we show that NfsA preferentially reduces the 2-NO₂ group, which leads to a greater bystander effect with cells expressing NfsA than with NfsB. NfsA is also more effective than NfsB for cell sensitisation to nitrofurans and to a selection of alternative, dinitrobenzamide mustard (DNBM) prodrugs.

Direct positive selection for improved nitroreductase variants using SOS triggering of bacteriophage lambda lytic cycle

Expression of prodrug-activating enzymes that convert non-toxic substrates to cytotoxic derivatives is a promising strategy for cancer gene therapy. However, their catalytic activity with unnatural, prodrug substrates is often suboptimal. Efforts to improve these enzymes have been limited by the inability to select directly for increased prodrug activation. We have focussed on developing variants of Escherichia coli (E. coli) nitroreductase (NTR) with improved ability to activate the prodrug 5-(aziridin-1-yl)-2,4-dinitrobenzamide (CB1954), and describe here a novel, direct, positive selection for improved enzymes that exploits the alternative life cycles of bacteriophage lambda. In lambda lysogens of E. coli, the activation of the prodrug CB1954 by NTR triggers the SOS response to DNA damage, switching integrated lambda prophages into lytic cycle. This provides a direct, positive selection for phages encoding improved NTR variants, as, upon limiting exposure of lysogenized E. coli to CB1954, only those encoding the most active enzyme variants are triggered into lytic cycle, allowing their selective recovery. We exemplify the selection by isolating highly improved 'turbo-NTR' variants from a library of 6.8 x 10(5) clones, conferring up to 50-fold greater sensitivity to CB1954 than the wild type. Carcinoma cells infected with adenovirus expressing T41Q/N71S/F124T-NTR were sensitized to CB1954 concentrations 40- to 80-fold lower than required with WT-NTR.

The structure of Escherichia coli nitroreductase complexed with nicotinic acid: three crystal forms at 1.7 A, 1.8 A and 2.4 A resolution

Escherichia coli nitroreductase is a flavoprotein that reduces a variety of quinone and nitroaromatic substrates. Its ability to convert relatively non-toxic prodrugs such as CB1954 (5-[aziridin-1-yl]-2,4-dinitrobenzamide) into highly cytotoxic derivatives has led to interest in its potential for cancer gene therapy. We have determined the structure of the enzyme bound to a substrate analogue, nicotinic acid, from three crystal forms at resolutions of 1.7 A, 1.8 A and 2.4 A, representing ten non-crystallographically related monomers. The enzyme is dimeric, and has a large hydrophobic core; each half of the molecule consists of a five-stranded beta-sheet surrounded by alpha-helices. Helices F and F protrude from the core region of each monomer. There is an extensive dimer interface, and the 15 C-terminal residues extend around the opposing monomer, contributing the fifth beta-strand. The active sites lie on opposite sides of the molecule, in solvent-exposed clefts at the dimer interface. The FMN forms hydrogen bonds to one monomer and hydrophobic contacts to both; its si face is buried. The nicotinic acid stacks between the re face of the FMN and Phe124 in helix F, with only one hydrogen bond to the protein. If the nicotinamide ring of the coenzyme NAD(P)H were in the same position as that of the nicotinic acid ligand, its C4 atom would be optimally positioned for direct hydride transfer to flavin N5. Comparison of the structure with unliganded flavin reductase and NTR suggests reduced mobility of helices E and F upon ligand binding. Analysis of the structure explains the broad substrate specificity of the enzyme, and provides the basis for rational design of novel prodrugs and for site-directed mutagenesis for improved enzyme activity.

Transcription activation at the Escherichia coli melAB promoter: the role of MelR and the cyclic AMP receptor protein

MelR is a melibiose-triggered transcription activator that belongs to the AraC family of transcription factors. Using purified Escherichia coli RNA polymerase and a cloned DNA fragment carrying the entire melibiose operon intergenic region, we have demonstrated in vitro open complex formation and activation of transcription initiation at the melAB promoter. This activation is dependent on MelR and melibiose. These studies also show that the cyclic AMP receptor protein (CRP) interacts with the melAB promoter and increases MelR-dependent transcription activation. DNAase I footprinting has been exploited to investigate the location of MelR-and CRP-binding sites at the melAB promoter. We showed previously that MelR binds to two identical 18 bp target sequences centred at position -100.5 (Site 1) and position -62.5 (Site 2). In this work, we show that MelR additionally binds to two other related 18 bp sequences: Site 1', centred at position -120.5, located immediately upstream of Site 1, and Site R, at position -238.5, which overlaps the transcription start site of the divergent melR promoter. MelR can bind to Site 1', Site 1, Site 2 and Site R, in both the absence and the presence of melibiose. However, in the presence of melibiose, MelR also binds to a fifth site (Site 2', centred at position -42.5) located immediately downstream of Site 2, and overlapping the -35 region of the melAB promoter. Additionally, although CRP is unable to bind to the melAB promoter in the absence of MelR, in the presence of MelR, it binds to a site located between MelR binding Site 1 and Site 2. Thus, tandem-bound MelR recruits CRP to the MelR. We propose that expression from the melAB promoter has an absolute requirement for MelR binding to Site 2'. Optimal expression of the melAB promoter requires Sites 1', Site 1, Site 2 and Site 2'; CRP acts as a 'bridge' between MelR bound at Sites 1' and 1 and at Sites 2 and 2', increasing expression from the melAB promoter. In support of this model, we show that improvement of the base sequence of Site 2' removes the requirement for Site 1' and Site 1, and short circuits the effects of CRP.

Repression of the Escherichia coli melR promoter by MelR: evidence that efficient repression requires the formation of a repression loop

The Escherichia coli MelR protein is a transcription activator that, in the presence of melibiose, activates expression of the melAB operon by binding to four sites located just upstream of the melAB promoter. MelR is encoded by the melR gene, which is expressed from a divergent transcript that starts 237 bp upstream of the melAB promoter transcript start point. In a recent study, we have identified a fifth DNA site for MelR that overlaps the melR promoter transcript start and -10 region. Here we show that MelR binding to this site can downregulate expression from the melR promoter; thus, MelR autoregulates its own expression. Optimal repression of the melR promoter is observed in the absence of melibiose and requires one of the four other DNA sites for MelR at the melAB promoter. The two MelR binding sites required for this optimal repression are separated by 177 bp. We suggest that, in the absence of melibiose, MelR forms a loop between these two sites. We argue that, in the presence of melibiose, this loop is broken as the melAB promoter is activated. However, in the presence of melibiose, the melR promoter can still be partially repressed by MelR binding to the site that overlaps the transcript start and -10 region. Parallels with the Escherichia coli araC-araBAD regulatory region are discussed.

Studies of the Escherichia coli Trp repressor binding to its five operators and to variant operator sequences

The Escherichia coli Trp repressor binds to promoters of very different sequence and intrinsic activity. Its mode of binding to trp operator DNA has been studied extensively yet remains highly controversial. In order to examine the selectivity of the protein for DNA, we have used electromobility shift assays (EMSAs) to study its binding to synthetic DNA containing the core sequences of each of its five operators and of operator variants. Our results for DNA containing sequences of two of the operators, trpEDCBA and aroH are similar to those of previous studies. Up to three bands of lower mobility than the free DNA are obtained which are assigned to complexes of stoichiometry 1 : 1, 2 : 1 and 3 : 1 Trp repressor dimer to DNA. The mtr and aroL operators have not been studied previously in vitro. For DNA containing these sequences, we observe predominantly one retarded band in EMSA with mobility corresponding to 2 : 1 complexes. We have also obtained retardation of DNA containing the trpR operator sequence, which has only been previously obtained with super-repressor Trp mutants. This gives bands with mobilities corresponding to 1 : 1 and 2 : 1 complexes. In contrast, DNA containing containing a symmetrized trpR operator sequence, trpRs, gives a single retarded band with mobility corresponding solely to a 1 : 1 protein dimer-DNA complex. Using trpR operator variants, we show that a change in a single base pair in the core 20 base pairs can alter the number of retarded DNA bands in EMSA and the length of the DNase I footprint observed. This shows that the binding of the second dimer is sequence selective. We propose that the broad selectivity of Trp repressor coupled to tandem 2 : 1 binding, which we have observed with all five operator sequences, enables the Trp repressor to bind to a limited number of sites with diverse sequences. This allows it to co-ordinately control promoters of different intrinsic strength. This mechanism may be of importance in a number of promoters that bind multiple effector molecules.

Secondary structure of the C-terminal DNA-binding domain of the transcriptional activator NifA from Klebsiella pneumoniae: spectroscopic analyses

The conformation of the C-terminal DNA-binding domain of the transcriptional activator NifA from Klebsiella pneumoniae has been probed by circular dichroism (CD), Fourier-transformed infrared (FT-IR), and nuclear magnetic resonance (NMR) spectroscopy in combination. Secondary structure prediction suggests that the C-terminal half of the domain contains three alpha-helices. The spectra show that the domain is folded in the absence of DNA and of the N-terminal and central domains of NifA. The three spectroscopic techniques suggest slightly different proportions of secondary structural elements but all suggest that it contains about 33% alpha-helix. These results are in agreement with a previous prediction suggesting that NifA contains a helix-turn-helix motif and with the amount of alpha-helix predicted. The environment of the aromatic residues was examined by CD and NMR spectroscopy, which suggest that one or both of the tryptophan residues are involved in the tertiary structure of the protein but that the tyrosine residue in the helix-turn-helix motif is solvent exposed and so available to bind to DNA. The thermal melting profiles and pH-dependent structural changes were also examined by CD spectroscopy. This technique indicates that at low pH there is an increase in the secondary structure and interactions contributing to the tertiary structure. Many of the acidic residues are predicted to be on a single helix, before the helix-turn-helix motif, which may therefore be important for maintaining the structure and function of the C-terminal peptide; alternatively, the N-terminal half of the domain may become more folded at low pH.

DNA binding and DNA bending by the MelR transcription activator protein from Escherichia coli

The Escherichia coli melR gene encodes MelR protein which is a member of the AraC/XylS family of bacterial transcription activators. The function of MelR was investigated by making a targeted deletion in the melR gene of the Escherichia coli chromosome. MelR is a transcription activator essential for melibiose- dependent expression of the melAB operon which is needed for bacterial growth with melibiose as a carbon source. To investigate the interactions of MelR at the melAB promoter, both full length MelR and a shortened derivative, MelR173, containing the C-terminal DNA-binding domain, were purified as fusions to glutathione- S -transferase. Circular permutation studies show that both full-length MelR and MelR173 induce an apparent bend upon binding to target sites at the melAB promoter. Bound full-length MelR, but not MelR173, can oligomerise to form larger complexes that are likely to be involved in transcription activation.

NMR studies of the Escherichia coli Trp repressor.trpRs operator complex

To understand the specificity of the Escherichia coli Trp repressor for its operators, we have begun to study complexes of the protein with alternative DNA sequences, using 1H-NMR spectroscopy. We report here the 1H-NMR chemical shifts of a 20-bp oligodeoxynucleotide containing the sequence of a symmetrised form of the trpR operator in the presence and absence of the holorepressor. Deuterated protein was used to assign the spectrum of the oligodeoxynucleotide in a 37-kDa complex with the Trp holorepressor. Many of the resonances of the DNA shift on binding to the protein, which suggests changes in conformation throughout the sequence. The largest changes in shifts for the aromatic protons in the major groove are for A15 and G16, which are thought to hydrogen bond to the protein, possibly via water molecules. We have also examined the effect of DNA binding on the corepressor, tryptophan, in this complex. The indole proton resonance of the tryptophan undergoes a downfield shift of 1.2 ppm upon binding of DNA. This large shift is consistent with hydrogen bonding of the tryptophan to the phosphate backbone of the trpR operator DNA, as in the crystal structure of the holoprotein with the trp operator.

Three-dimensional structure of the RGD-containing snake toxin albolabrin in solution, based on 1H NMR spectroscopy and simulated annealing calculations

Albolabrin is a snake toxin that contains a RGD-(Arg-Gly-Asp) sequence motif and competes with fibrinogen to bind to the integrin alpha IIb beta 3 (GpIIb-IIIa) on platelets. It thus inhibits platelet aggregation and cell-cell adhesion. It shows a high sequence similarity to other disintegrins, yet the reported disulfide bonding pattern for this peptide differs from that of others in this family. Recently we reported the assignment of the 1H-NMR spectrum of albolabrin and a preliminary description of its secondary structure [Jaseja, M., Smith, K.J., Lu, X. Williams, J.A., Trayer, H., Trayer, I.P. & Hyde, E.I. (1993) Eur. J. Biochem. 218, 853-860]. Here we present a more detailed description of the secondary and the tertiary structure, based on the 1H NMR results and simulated annealing methods. The structure of albolabrin in solution was calculated using 318 distance and 18 dihedral angle restraints. The average atomic RMS deviation between 12 refined structures and the mean structure was 3.1 A for the backbone. The protein appears to be highly mobile. Its structure is dominated by a series of turns and by three hairpins, each with a short region of distorted antiparallel beta-pleated sheet, held together by six disulfide bridges. The most well defined area is the hydrophobic core, residues 21-47 and 57-67, which is clustered around F40 and has a backbone atomic RMS deviation of only 1.3 A from the mean structure. The RGD adhesion sequence is found at the highly mobile tip of one of the beta-hairpins, protruding from the body of the protein. Many of these structural features are similar to those of other disintegrins, and differences in the disulfide bonding pattern of the disintegrins can be accomodated without significant energy penalty. Comparison of this structure with other proteins of similar function suggests that it is the RGD-loop, rather than the precise technology of the proteins, that is important to antagonist activity.

The Escherichia coli MelR transcription activator: production of a stable fragment containing the DNA-binding domain

A set of nested deletions has been made in the Escherichia coli melR gene, encoding the MelR transcription activator protein. Expression of the resulting melR derivatives led to the production of nine MelR proteins with N-terminal deletions of different lengths. The properties of the shortened proteins have been studied both in vivo and in vitro. None of the truncated proteins activate transcription from the E.coli melAB promoter but three; MelR220, MelR183 and MelR173, inhibit activation of the melAB promoter by chromosomally-encoded full-length MelR. In gel retardation assays, both MelR183 and MelR173 clearly retard DNA fragments carrying the melAB promoter. MelR173 has been overproduced in a T7 expression system and shown to be stable in vivo for up to 2 h. DNAase I footprinting assays of partially purified protein show that it binds to the melAB promoter, protecting the same sites as the full-length protein. This fragment may be suitable for further structure/function studies of this class of transcription activator.

1H-NMR assignments and secondary structure of dendroaspin, an RGD-containing glycoprotein IIb-IIIa (alpha IIb-beta 3) antagonist with a neurotoxin fold

Dendroaspin, also referred to as mambin, was originally isolated from the venom of the Elapidae snake Dendroaspis jamesoni kaimose. It shares a high level of sequence similarity with the short-chain neurotoxins found in other Elapidae but displays approximately 1000-fold lower neurotoxin activity than the closely related protein erabutoxin b. However, unlike neurotoxins, it contains an RGD (Arg-Gly-Asp) motif and functions as an antagonist of platelet aggregation and cell-cell adhesion of comparable potency to the disintegrins from the venoms of Viperidae. We have determined the secondary structure of dendroaspin using 1H-NMR spectroscopy. Its structure resembles that of the short-chain neurotoxins, with three loops extending from a disulphide-bridged core; however, the strands of the triple-stranded beta-sheet are shorter and the loop containing the RGD sequence is moved away from this sheet. The structure bears little resemblance to that of the disintegrins, except in the RGD-containing loop, suggesting that this loop may be of prime importance in its inhibitory function. Comparison of this preliminary structure with that of the neurotoxins and disintegrins furthers our understanding of the mechanism of integrin antagonists and shows how the neurotoxin fold can be manipulated to give a variety of inhibitors.

Three-dimensional structure of the RGD-containing neurotoxin homologue dendroaspin

Dendroaspin is a short chain neurotoxin homologue from the venom of Elapidae snakes, which lacks neurotoxicity. Unlike neurotoxins, it contains an Arg-Gly-Asp-(RGD)-motif and functions as an inhibitor of platelet aggregation and platelet adhesion with comparable potency to the disintegrins from the venoms of Viperidae. We have determined the structure of dendroaspin in solution using NMR spectroscopy. The structure contains a core similar to that of short chain neurotoxins, but with a novel arrangement of loops and a solvent-exposed RGD-motif. Dendroaspin is thus an integrin antagonist with a well defined fold different from that of the disintegrins, based on the neurotoxin scaffold.

1H-NMR studies and secondary structure of the RGD-containing snake toxin, albolabrin

Albolabrin is a naturally occurring peptide from snake venom containing the sequence Arg-Gly-Asp (RGD). It inhibits platelet aggregation by blocking the binding of fibrinogen to the glycoprotein Gp IIb-IIIa, on the surface of activated platelets. Albolabrin consists of 73 residues with six intramolecular disulphide bonds. The 1H-NMR spectrum of albolabrin has been assigned using homonuclear two-dimensional techniques and its secondary structure determined. Like kistrin and echistatin, two related peptides from snake venom, albolabrin appears to have little regular secondary structure in solution. Several bends and two short distorted beta sheets are observed. The RGD sequence, important for binding to the receptor, lies in a mobile loop joining two strands of one of these beta sheets. This loop undergoes a pH-dependent conformational change.

NMR studies of the activation of the Escherichia coli trp repressor

The Escherichia coli trp repressor binds to the trp operator in the presence of tryptophan, thereby inhibiting tryptophan biosynthesis. Tryptophan analogues lacking the alpha-amino group act as inducers of trp operon expression. We have used one- and two-dimensional 1H-NMR spectroscopy to compare the binding to the repressor of the corepressors L-tryptophan, D-tryptophan and 5-methyl-DL-tryptophan with that of the inducer indole-3-propionic acid. We have determined the chemical shifts of the indole ring protons of the ligands when bound to the protein, principally by magnetization-transfer experiments. The chemical shifts of the indole NH and C4 protons differ between corepressors and inducer. At the same time, the pattern of intermolecular NOE between protons of the protein and those of the ligand also differ between the two classes of ligand. These two lines of evidence indicate that corepressors and inducers bind differently in the binding site, and the evidence suggests that the orientation of the indole ring in the binding site differs by approximately 180 degrees between the two kinds of ligand. This is in contrast to a previous solution study [Lane, A.N. (1986) Eur. J. Biochem. 157, 405-413], but consistent with recent X-ray crystallographic work [Lawson, C.L. & Sigler, P.B. (1988) Nature 333, 869-871]. D-Tryptophan and 5-methyltryptophan, which are more effective corepressors than L-tryptophan, bind similarly to L-tryptophan. The indole ring of D-tryptophan appears to bind in essentially the same orientation as that of the L isomer. There are, however, some differences in chemical shifts and NOE for 5-methyltryptophan, which indicate that there are significant differences between the two corepressors L-tryptophan and 5-methyltryptophan in the orientation of the indole ring within the binding site.

1H NMR studies of the glucocorticoid receptor DNA-binding domain: sequential assignments and identification of secondary structure elements

Two protein fragments containing the DNA-binding domain (DBD) of the glucocorticoid receptor (GR) have been studied by two-dimensional 1H NMR spectroscopy. The two peptides (93 and 115 residues, respectively) contain a common segment corresponding to residues C440-I519 of the rat GR or residues C421-I500 of the human GR and include two Zn-binding "finger" domains. The structures of this segment are almost identical in the two protein fragments, as judged from chemical shifts and sequential NOE connectivities. More than 90% of all observable 1H resonances within a 71-residue segment encompassing C440-R510 (rat GR) could be sequentially assigned by standard techniques, and stereospecific assignments could be made for the methyl groups in four valine residues within this segment. Sequential NOE connectivities indicate several elements of secondary structure including two alpha-helical segments consisting of residues S459-E469 and P493-G504, a type I reverse turn between residues R479 and C482, a type II reverse turn between residues L475 and G478, and several regions of extended peptide conformation. No evidence for alpha-helical conformation was found within the two putative zinc-finger domains, indicating that the structures of these domains differ from that of TFIIIA-type zinc fingers. The observation of some very slowly exchanging amide protons in the N-terminal (CI) domain of the DBD in combination with slow rotation of the Y452 aromatic ring indicates that this domain has a restricted conformational flexibility compared to the C-terminal (CII) domain. We also observe several long-range NOE connectivities within C440-R510, suggesting that the sequential assignments presented here will provide a basis for a complete structure determination of this segment of the GR.

NMR studies of the Escherichia coli trp aporepressor. Sequence-specific assignment of the aromatic proton resonances

The resonances in the aromatic region of the 1H-NMR spectrum of the Escherichia coli trp aporepressor have been assigned to amino acid type by two-dimensional correlated spectroscopy (COSY), homonuclear Hartmann-Hahn (HOHAHA) spectroscopy and nuclear Overhauser enhancement spectroscopy (NOESY) techniques and studies of the pH dependence of the chemical shifts, in combination with selective deuteration of the protein. Complete sequence-specific assignments of the aromatic resonances have been made by comparing the observed inter-residue NOEs with those expected on the basis of the crystal structure of the protein [Zhang, R.-G., Joachimiak, A., Lawson, C.L., Shevitz, R.W., Otwinowski, Z. & Sigler, P.B. (1987) Nature 327, 591-597]. The latter experiments have also permitted the sequence-specific assignment of some of the high-field methyl resonances. The complete assignment of the aromatic region of the spectrum, in particular of resonances from residues at the dimer interface, opens the way to detailed studies of the conformational effects of corepressor and operator binding.

Interactions of Bacillus subtilis RNA polymerase with subunits determining the specificity of initiation. Sigma and delta peptides can bind simultaneously to core

The Bacillus subtilis RNA polymerase sigma 43 subunit and the phage SP82 encoded 28-kDa peptide are responsible for the binding of RNA polymerase to early and middle SP82 promoters, respectively. The delta peptide enhances the specificity of the interaction of B. subtilis RNA polymerase with these promoters. We have used sedimentation experiments to determine the effect of each of the three specificity factors, delta, sigma, and the 28-kDa peptide, on the binding of the other two factors to RNA polymerase core and the effect of NaCl on these binding equilibria. We show that sigma 43 and the 28-kDa peptide can each bind to RNA polymerase core at the same time as delta. Sigma 43 and the 28-kDa peptide have similar affinities to core at 0.1 M NaCl, but the 28-kDa peptide binds to core-delta more strongly than sigma 43. The implications of these findings with respect to the replacement of sigma 43 by the 28-kDa peptide and the mechanism of promoter search by B. subtilis RNA polymerase are discussed.

Imino proton NMR assignments and ion-binding studies on Escherichia coli tRNA3Gly

The imino region of the proton NMR spectrum of Escherichia coli tRNA3Gly has been assigned mainly by sequential nuclear Overhauser effects between neighbouring base pairs and by comparison of assignments of other tRNAs. The effects of magnesium, spermine and temperature on the 1H and 31P NMR spectra of this tRNA were studied. Both ions affect resonances close to the G15 . C48 tertiary base pair and in the ribosylthymine loop. The magnesium studies indicate the presence of an altered tRNA conformer at low magnesium concentrations in equilibrium with the high magnesium form. The temperature studies show that the A7 . U66 imino proton (from a secondary base pair) melts before some of the tertiary hydrogen bonds and that the anticodon stem does not melt sequentially from the ends. Correlation of the ion effects in the 1H and 31P NMR spectra has led to the tentative assignment of two 31P resonances not assigned in the comparable 31P NMR spectrum of yeast tRNAPhe. 31P NMR spectra of E. coli tRNA3Gly lack resolved peaks corresponding to peaks C and F in the spectra of E. coli tRNAPhe and yeast tRNAPhe. In the latter tRNAs these peaks have been assigned to phosphate groups in the anticodon loop. Ion binding E. coli tRNA3Gly and E. coli tRNAPhe had different effects on their 1H NMR spectra which may reflect further differences in their charge distribution and conformation.

NMR studies of ion binding to Escherichia coli tRNAPhe

The effects of magnesium, spermine, and temperature on the conformation of Escherichia coli tRNAPhe have been examined by proton and phosphorus nuclear magnetic resonance spectroscopy. In the low-field proton NMR spectra we have characterized two slowly interconverting conformations of this tRNA at low magnesium ion concentrations. The relative proportion of the conformers is ion dependent but not ion specific. Magnesium affects protons in all the stems of tRNA while spermine effects are localized near the s4U-8-A-14 and G-15-C-48 tertiary bonds. The effects seen in the proton NMR spectra are compared and correlated with those observed in the phosphorus spectra to give assignments of some of the resolved signals from the phosphate groups. The phosphorus spectra are compared with those of yeast tRNAPhe [Gorenstein, D. G., Goldfield, E. M., Chen, R., Kovar, K., & Luxon, B. A. (1981) Biochemistry 20, 2141; Salemink, P. J. M., Reijerse, E. J., Mollevanger, L., & Hilbers, C. W. (1981) Eur. J. Biochem. 115, 635], and the ion effects are discussed with reference to the magnesium and spermine sites found in the crystal structures of yeast tRNAPhe [Holbrook, S. R., Sussman, J. L., Warrant, R. W., Church, G. M., & Kim, S.-H. (1977) Nucleic Acids Res. 4, 2811; Quigley, G. J., Teeter, M. M., & Rich, A. (1978) Proc. Natl. Acad. Sci. U.S.A. 75, 64; Jack, A., Ladner, J. E., Rhodes, D., Brown, R. S., & Klug, A. (1977) J. Mol. Biol. 111, 315].

Assignment of the low-field 1H NMR spectrum of Escherichia coli tRNAPhe using nuclear Overhauser effects

The imino region of the proton NMR spectrum of Escherichia coli tRNAPhe has been largely assigned from the nuclear Overhauser effects between neighboring bases. These have led to the unambiguous assignment of the imino protons of the ribothymidine stem and of most of the dihydrouridine stem of this tRNA and given several other sets of connectivities. These connectivities are discussed in reference to the previously reported temperature studies of the spectrum [Hurd, R. E., & Reid, B. R. (1980) J. Mol. Biol. 142, 1981] and compared with assignments of other tRNAs resulting in tentative assignments of the rest of the spectrum.

Hydrogen-1, carbon-13, and phosphorus-31 nuclear magnetic resonance studies of the dihydrofolate reductase-nicotinamide adenine dinucleotide phosphate-folate complex: characterization of three coexisting conformational states

The Lactobacillus casei dihydrofolate reductase-folate-NADP+ complex is shown by 1H and 13C NMR to exist in three interconverting conformational states, I, IIa, and IIb. The proportions of the three states, as estimated from the intensities of the three separate 13C resonances observed in the complex containing [3-carboxamido-13C]NADP+, are pH dependent. State I predominates at low pH and states IIa and IIb predominate at high pH; the ratio IIa:IIb is pH independent. The pH dependence of the interconversion of states I and IIa + IIb can be explained by a model in which a group on the enzyme has a pK of less than 5 in state IIa + IIb and greater than 7 in state I. 1H, 13C, and 31P NMR has been used to characterize the structural differences between the three states of the complex. As judged by the 1H and 13C chemical shifts of the bound coenzyme, states I and IIa are similar to one another but quite different from state IIb. This difference appears to be a localized one, since only the nicotinamide 2 and 4 protons, nicotinamide 3-carboxamide 13C, and pteridine 7 proton show differences in chemical shift between these states. These differences are, however, large--up to 1.4 ppm for 1H and 2 ppm for 13C. The remaining coenzyme protons, as well as the three 31P nuclei, are unaffected. Studies of the C2 proton resonances of the seven histidine residues show that the ionizable group responsible for the interconversion of states I and IIa + IIb is not a histidine (although two histidines show slight differences in environment between states IIa and IIb); the possible identity of this ionizable group and the nature of the conformational differences between the states are discussed.

Negative cooperativity between folinic acid and coenzyme in their binding to Lactobacillus casei dihydrofolate reductase

The binding of folinic acid (5-formyl-5,6,7,8-tetrahydrofolate) to Lactobacillus casei dihydrofolate reductase has been measured. The natural 6S, alpha S diastereoisomer has a binding constant of 1.3 (+/- 0.6) X 10(8) M-1 at pH 6.0, 25 degrees C; the 6R, alpha S diastereoisomer binds approximately 10(4)-fold more weakly. The natural diastereoisomer of folinic acid binds negatively cooperatively with the coenzymes NADP+ and NADPH, binding 3 times more weakly in the presence of NADP+ and 600 times more weakly in the presence of NADPH than to the enzyme alone. Negative cooperativity has been unequivocally distinguished from competition by measurements of coenzyme binding as a function of folinic acid concentration, of the effects of folinic acid on the 1H and 31P chemical shifts of the bound coenzyme, and of the effects of folinic acid on the coenzyme dissociation rate constant. The latter experiments also give evidence for the coexistence of two slowly interconverting conformational forms of the ternary enzyme-coenzyme-folinic acid complex. Small changes in structure of the oxidized coenzymes have substantial effects on the cooperativity with folinic acid, with the thionicotinamide analogue showing positive rather than negative cooperativity. The changes in environment of the bound coenzyme produced by folinic acid, as revealed by 1H and 31P NMR, demonstrate clearly that the negative cooperativity shown by NADP+ and NADPH, respectively, arises by two structurally distinct mechanisms.

Effects of coenzyme binding on histidine residues of Lactobacillus casei dihydrofolate reductase

The effects of coenzyme binding on the seven histidine C2 proton resonances of Lactobacillus casei dihydrofolate reductase have been determined. Binary complexes containing NADP+, NADPH, and their hypoxanthine, thionicotinamide, and acetylpyridine analogues, together with ternary complexes containing the inhibitors trimethoprim or methotrexate, have been examined. Four of the histidine residues are affected by coenzyme binding. The largest effect-a marked upfield shift (0.85 ppm) of the C2 proton resonance-is seen for His-64. The hypoxanthine analogue of the coenzyme was found to produce a smaller upfield shift and, in addition, a decrease in the pK of His-64. The effects on this reductase are discussed in the light of the crystal structure [Matthews, D. A., Alden, R. A., Bolin, J. T., Filman, D. J., Freer, S. T., Hamlin, R., Hol, W. G. J., Kisliuk, R. L., Pastore, E. J., Plante, L. T., Xuong, N., & Kraut, J. (1978) J. Biol. Chem. 253, 6946], and it is concluded that His-64 is close to a carboxyl group in the free enzyme and that the hypoxanthine ring binds in a somewhat different orientation to the adenine ring. The effects on histidine resonances A, E, and G are significantly different for oxidized and reduced coenzymes. The changes in pK of the histidines giving rise to resonances A and E (probably His-22 and His-18) are discussed in terms of ligand-induced conformational changes, which differ for NADP+ and NADPH.

Proton nuclear magnetic resonance saturation transfer studies of coenzyme binding to Lactobacillus casei dihydrofolate reductase

The chemical shifts of all the aromatic proton and anomeric proton resonances of NADP+, NADPH, and several structural analogues have been determined in their complexes with Lactobacillus casei dihydrofolate reductase by double-resonance (saturation transfer) experiments. The binding of NADP+ to the enzyme leads to large (0.9-1.6 ppm) downfield shifts of all the nicotinamide proton resonances and somewhat smaller upfield shifts of the adenine proton resonance. The latter signals show very similar chemical shifts in the binary and ternary complexes of NADP+ and the binary complexes of several other coenzymes, suggesting that the environment of the adenine ring is similar in all cases. In contrast, the nicotinamide proton resonances show much greater variability in position from one complex to another. The data show that the environments of the nicotinamide rings of NADP+, NADPH, and the thionicotinamide and acetylpyridine analogues of NADP+ in their binary complexes with the enzyme are quite markedly different from one another. Addition of folate or methotrexate to the binary complex has only modest effects on the nicotinamide ring of NADP+, but trimethoprim produces a substantial change in its environment. The dissociation rate constant of NADP+ from a number of complexes was also determined by saturation transfer.

Phosphorus-31 nuclear magnetic resonance studies of the binding of oxidized coenzymes to Lactobacillus casei dihydrofolate reductase

The 31P NMR spectra of NADP+ and a number of its structural analogues have been obtained from their binary and ternary complexes with Lactobacillus casei dihydrofolate reductase. The 2'-phosphate resonance is shifted downfield 2.7-2.9 ppm in all cases. Line-shape analysis of this resonance as a function of coenzyme concentration gave values for the dissociation rate constant of the coenzyme from many of the complexes. The values obtained are discussed in terms of the kinetic mechanism of coenzyme binding. The chemical shifts of the pyrophosphate resonances vary from one complex to another over a range of 3.8 ppm. The assignment of these signals to the individuals pyrophosphate 31P nuclei and the structural origins of the chemical shift changes are discussed. From these data, and the 1H NMR experiments describedin the preceding paper [Hyde, E. I., Birdsall, B., Roberts, G. C. K., Feeney, J., & Burgen, A. S. V. (1980) Biochemistry (third paper of four in this issue)], it is concluded that the "nicotinamide" end of the thionicotinamide and acetylpyridine coenzyme analogue binds to the enzyme quite differently from that of the natural coenzyme NADP+.