Nuclear magnetic resonance structures of the zinc finger domain of human DNA polymerase-alpha

The carboxy terminus of the human DNA polymerase-alpha contains a zinc finger motif. Three-dimensional structures of this motif containing 38 amino acid residues, W L I C E E P T C R N R T R H L P L Q F S R T G P L C P A C M K A T L Q P E, were determined by nuclear magnetic resonance (NMR) spectroscopy. The structures reveal an alpha-helix-like domain at the amino terminus, extending 13 residues from L2 through H15 with an interruption at the sixth residue. The helix region is followed by three turns (H15-L18, T23-L26 and L26-A29), all of which involve proline. The first turn appears to be type III, judging by the dihedral angles. The second and third turns appear to be atypical. A second, shorter helix is formed at the carboxy terminus extending from C30 through L35. A fourth type III turn starting at L35 was also observed in the structure. Proline serves as the third residue of all the turns. Four cysteine residues, two located at the beginning of the helix at the N-terminus and two at the carboxy end, are coordinated to Zn(II), facilitating the formation of a loop. One of the cysteines at the carboxy terminus is part of the atypical turn, while the other is the part of the short helix. These structural features are consistent with the circular dichroism (CD) measurements which indicate the presence of 45% helix, 11% beta turns and 19% non-ordered secondary structures. The zinc finger motif described here is different from those observed for C(4), C(2)H(2), and C(2)HC modules reported in the literature. In particular, polymerase-alpha structures exhibit helix-turn-helix motif while most zinc finger proteins show anti-parallel sheet and helix. Several residues capable of binding DNA, T, R, N, and H are located in the helical region. These structural features imply that the zinc finger motif is most likely involved in binding DNA prior to replication, presumably through the helical region. These results are discussed in the context of other eukaryotic and prokaryotic DNA polymerases belonging to the polymerase B family.     

The Reaction of Pt-Antitumor Drugs with Selected Nucleophiles.: II. Preparation and Characterization of Coordination Compounds of Pt(II) andl-Histidine

Various His-Pt(II) coordination compounds were prepared by reaction of K₂PtCl₄ or cis-[Pt(NH₃)₂Cl₂](cis-DDP) with His and analyzed by ¹H and ¹³C NMR spectroscopy, electrophoresis, and ion-exchange chromatography. His may be coordinated to Pt by the imidazol iminogroup and/or the α-aminogroup; the carboxy group remains always free. Both bidentate as well as monodentate ligands were identified. Cis-DDP reacts with His to give a mixture of compounds where all these possibilities are present: cis-diamine-(histidine-N,N-)Pt(II) and three different types of cis-diammine-bis(histidine). HCl trans cleavage of compounds with bidentate His ligands leads to a mixture of two compounds having His ligated to Pt by an amino or imin group. The methods applied are suitable for analyzing reactions of His with cis-DDP under model conditions similar to physiological conditions.     

The differential effects produced by cis- and trans-DDP on DNA in calf thymus nucleosomes

Calf thymus nucleosomes containing H1 were treated with dichlorodiammineplatinum (DDP) at low binding ratios (r = 0.05–0.15). Change in the electrophoretic mobility of the extracted nucleosomal DNA was observed following treatment with cis-DDP and little change with trans-DDP. There was a decrease in the electrophoretic mobility of the nucleosomal DNA as well as obliteration of the nucleosomal repeat distance. The fluorescence intensity of terbium binding to the extracted DNA showed minimal change following drug treatment. However, the thermal melting behavior of the nucleosomal DNA was altered to a greater extent following cis-DDP treatment at 280 rather than 260 nm and a destabilization of the DNA helix was observed. These data suggest that in the whole nucleosome, cis-DDP produces greater structural effects on the packaged DNA than trans-DDP, although similar amounts of drug are bound with both isomers.     

DNA crosslinking induced by 1,2-diaminocyclohexanedichloroplatinum(II) in murine leukemia L1210 cells and comparison with other platinum analogues

1,2-Diaminocyclohexanedichloroplatinum(II) (DCDP) is an analogue of the clinically efficacious cancer chemotherapeutic drug cis-diamminedichloroplatinum(II) (cis-DDP). DCDP is presently undergoing clinical trials at least in part because a cis-DDP-resistant murine leukemia L1210 cell line is sensitive to its action. The alkaline elution technique was used to measure DNA-protein and DNA-interstrand crosslinks induced by DCDP in sensitive and resistant L1210 cells. This was compared to the action of cis-DDP and its clinically ineffective isomer trans-DDP. The action of DCDP was similar to that for cis-DDP with maximum crosslinking occurring between 6 and 12 h after a 1 h treatment. Both cis-DDP and DCDP exhibited proportionately higher levels of interstrand crosslinking than trans-DDP. Near complete removal of both classes of DCDP-induced crosslinks was seen by 72 h. While the extent of crosslinking was different for each compound, little difference between the two cell lines was noted with respect to crosslinking by either DCDP or trans-DDP. These cell lines exhibit a 2-fold resistance to both DCDP and trans-DDP and at equitoxic doses of both drugs the resistant cells demonstrated twice the interstrand crosslinks that were seen in the sensitive cells. The extent of crosslinking related directly to the concentration of drug. When treated with equitoxic doses of DCDP, cis-DDP or trans-DDP, the resistant cells consistently exhibited more interstrand crosslinks than sensitive cells, suggesting the existence of a more critical cytotoxic lesion which was not detectable by the alkaline elution technique. These lesions could be either intrastrand crosslinks or monofunctional platination. Resistance must be due to a differential sensitivity to the lesions that form, which may be due to an altered capacity to repair the lesions.     

Molecular mechanics modeling of oligonucleotide adducts of the antitumor drug cis-diamminedichloroplatinum(II)

In order to assess the geometric changes caused when the antitumor drug cis-diammine-dichloroplatinum(II) (cis-DDP) binds to DNA, molecular mechanics calculations were performed on two double-stranded and two single-stranded oligonucleotides and their adducts with cis-{Pt(NH₃)₂}²⁺. For the platinated duplexes, three model structures have been derived, one involving only local disruption of base pairing with retention of the helix directionality, and two models showing pronounced kinking of the double helix. One of the kinked models is stabilized by bridging sodium ions. The other kinked duplex model shows retention of all Watson–Crick base pairing, including that of the coordinated guanines. All models exhibit hydrogen bonds connecting one ammine ligand of platinum with one or two phosphate groups located at the 5′ side of the platinated strand.     

Neither helix in the coiled coil region of the axle of F1-ATPase plays a significant role in torque production

F₁-ATPase is an ATP-driven rotary molecular motor in which the central γ-subunit rotates inside the cylinder made of α₃β₃ subunits. The amino and carboxy termini of the γ-subunit form the axle, an α-helical coiled coil that deeply penetrates the stator cylinder. We previously truncated the axle step by step, starting with the longer carboxy terminus and then cutting both termini at the same levels, resulting in a slower yet considerably powerful rotation. Here we examine the role of each helix by truncating only the carboxy terminus by 25-40 amino-acid residues. Longer truncation impaired the stability of the motor complex severely: 40 deletions failed to yield rotating the complex. Up to 36 deletions, however, the mutants produced an apparent torque at nearly half of the wild-type torque, independent of truncation length. Time-averaged rotary speeds were low because of load-dependent stumbling at 120° intervals, even with saturating ATP. Comparison with our previous work indicates that half the normal torque is produced at the orifice of the stator. The very tip of the carboxy terminus adds the other half, whereas neither helix in the middle of the axle contributes much to torque generation and the rapid progress of catalysis. None of the residues of the entire axle played a specific decisive role in rotation.     

Elimination of a cis-Proline-Containing Loop and Turn Optimization Stabilizes a Protein and Accelerates Its Folding

In the N2 domain of the gene-3-protein of phage fd, two consecutive β-strands are connected by a mobile loop of seven residues (157-163). The stability of this loop is low, and the Asp160-Pro161 bond at its tip shows conformational heterogeneity with 90% being in the cis and 10% in the trans form. The refolding kinetics of N2 are complex because the molecules with cis or trans isomers at Pro161 both fold to native-like conformations, albeit with different rates. We employed consensus design to shorten the seven-residue irregular loop around Pro161 to a four-residue type I′ turn without a proline. This increased the conformational stability of N2 by almost 10 kJ mol^− 1 and abolished the complexity of the folding kinetics. Turn sequences obtained from in vitro selections for increased stability strongly resembled those derived from the consensus design. Two other type I′ turns of N2 could also be stabilized by consensus design. For all three turns, the gain in stability originates from an increase in the rate of refolding. The turns form native-like structures early during refolding and thus stabilize the folding transition state. The crystal structure of the variant with all three stabilized turns confirms that the 157-163 loop was in fact shortened to a type I′ turn and that the other turns maintained their type I′ conformation after sequence optimization.     

Further characterization of an E. coli strain resistant to the toxic and mutagenic action of cis-diamminedichloroplatinum(II)

An increased resistance to the toxic and mutagenic activity of the antitumor drug cis-diamminedichloroplatinum(II) (cis-DDP) in the E. coli strain BS21 compared to its wild-type parent, F26, has been reported. This resistance was neither due to different binding of cis-DDP to DNA nor to adaptive DNA repair (Germanier et al., 1984) In the present work, we found that mutation of the uvrA, recA and polA genes did not abolish the resistance of BS21 to the toxic action of cis-DDP. The lower mutability of BS21 was not influenced by the polA mutation, while uvrA greatly reduced and recA eliminated the mutagenic activity of cis-DDP in both strains. Treatment of BS21 and F26 with equal doses of cis-DDP produced the same initial number of platinum-DNA lesions. Little excision repair was detected in vivo in either strain during 6-h post-treatment incubation, the F26 strain being the most efficient of the two for this process. In contrast, F26 and BS21 were transformed identically by pBR322 DNA which had been treated with cis-DDP in vitro. Analysis of the platinum-DNA adducts which were formed between cis-DDP and salmon sperm DNA in the buffer conditions of this experiment suggests that plasmid DNA contains 80% monofunctional adducts and 20% bifunctional bis-guanine adducts.These data indicate that the selective toxicity and mutagenicity of these two strains in vivo are neither a result of different numbers of Pt-DNA lesions nor of their repair. The selectivity disappeared when the two bacterial strains were transformed by pBR322 DNA containing identical platinum-DNA lesions, suggesting that the biochemical events which process platinum-DNA lesions are the same in both strains. Hence, it appears that cis-DDP may form qualitatively different platinum-DNA adducts in the BS21 and F26 strains which are responsible for the different toxicity and mutagenicity.     

Sparsely populated residue conformations in protein structures: Revisiting “experimental” Ramachandran maps

The Ramachandran map clearly delineates the regions of accessible conformational (φ–ψ) space for amino acid residues in proteins. Experimental distributions of φ, ψ values in high‐resolution protein structures, reveal sparsely populated zones within fully allowed regions and distinct clusters in apparently disallowed regions. Conformational space has been divided into 14 distinct bins. Residues adopting these relatively rare conformations are presented and amino acid propensities for these regions are estimated. Inspection of specific examples in a completely “arid”, fully allowed region in the top left quadrant establishes that side‐chain and backbone interactions may provide the energetic compensation necessary for populating this region of φ–ψ space. Asn, Asp, and His residues showed the highest propensities in this region. The two distinct clusters in the bottom right quadrant which are formally disallowed on strict steric considerations correspond to the gamma turn (C7 axial) conformation (Bin 12 ) and the i + 1 position of Type II′ β turns (Bin 13) . Of the 516 non‐Gly residues in Bin 13 , 384 occupied the i + 1 position of Type II′ β turns. Further examination of these turn segments revealed a high propensity to occur at the N‐terminus of helices and as a tight turn in β hairpins. The β strand–helix motif with the Type II′ β turn as a connecting element was also found in as many as 57 examples. Proteins 2014; 82:1101–1112. © 2013 Wiley Periodicals, Inc.     

Micelle-bound conformations of a bombesin/gastrin releasing peptide receptor agonist and an antagonist by two-dimensional NMR and restrained molecular dynamics.

Two nonapeptide analogs of the carboxyl termini of bombesin (Bn) and gastrin releasing peptide (GRP) have been synthesized. Despite the small difference in chemical composition between these peptides, one was a potent agonist and the other a potent antagonist of the Bn/GRP receptor in murine pancreas. All protons of both peptides, in dodecylphosphocholine micelles, were assigned by two-dimensional nuclear magnetic resonance spectroscopy. Interproton distance were derived from cross-peak volumes in nuclear Overhauser enhancement spectra. Conformations of both peptides were derived by distance-restrained molecular dynamics simulations using the interproton distances as constrains. The agonist conformation resembled a relaxed helix formed by three connected turns. The two N-terminal turns were similar for both peptides. The third turn of the agonist, at the carboxyl terminus, was absent in the antagonist. One interproton distance at the carboxyl terminus of the antagonist indicates that the chemical group connecting the last two residues of this peptide mimics a cis peptide bond geometry.     

Binding study of the drug cis-dichlorodiammineplatinum(II)to G p5′ and dGp5′ by high resolution proton and carbon-13 NMR spectroscopy

The molecular mode of action leading to the anticancer activity of the drug cis-diamminedichloroplatinum(II), cis-DDP or cis-platinum is still the subject of speculation. In the present high field (400 MHz) ¹H NMR study the results on coupling constants for cis- and trans-diammine bis(guanosine- 5′-monophosphate) and (d-guanosine-5′-monophosphate)platinum(II) complexes are presented and discussed. The ¹H and ¹³C NMR chemical shifts obtained are consistent with the drug binding to N7 of each guanine. It has been found that the drug induces different conformational changes in the nucleotide from the trans-DDP isomer.     

Structural Basis of the Induced-Fit Mechanism of 1,4-Dihydroxy-2-Naphthoyl Coenzyme A Synthase from the Crotonase Fold Superfamily

1, 4-Dihydroxy-2-naphthoyl coenzyme A (DHNA-CoA) synthase is a typical crotonase fold enzyme with an implicated role of conformational changes in catalysis. We have identified these conformational changes by determining the structures of its Escherichia coli and Synechocystis sp. PCC6803 orthologues in complex with a product analog. The structural changes include the folding of an active-site loop into a β-hairpin and significant reorientation of a helix at the carboxy terminus. Interestingly, a new interface is formed between the ordered loop and the reoriented helix, both of which also form additional interactions with the coenzyme A moiety of the ligand. Site-directed mutation of the amino acid residues involved in these ligand-induced interactions significantly diminishes the enzyme activity. These results suggest a catalytically essential induced-fit that is likely initiated by the enzyme-ligand interactions at the active site.     

Disruption of the alpha5 helix of transducin impairs rhodopsin-catalyzed nucleotide exchange

Photoactivated rhodopsin (R) catalyzes nucleotide exchange by transducin, the heterotrimeric G protein of the rod cell. Recently, we showed that certain alanine replacement mutants of the alpha5 helix of the alpha subunit of transducin (Galpha(t)) displayed very rapid nucleotide exchange rates even in the absence of R [Marin, E. P., Krishna, A. G., and Sakmar, T. P. (2001) J. Biol. Chem. 276, 27400-27405]. We suggested that R catalyzes nucleotide exchange by perturbing residues on the alpha5 helix. Here, we characterize deletion, insertion, and proline replacement mutants of amino acid residues in alpha5. In general, the proline mutants exhibited rates of uncatalyzed nucleotide exchange that were 4-8-fold greater than wild type. The proline mutants also generally displayed decreased rates of R-catalyzed activation. The degree of reduction of the activation rate correlated with the position of the residue replaced with proline. Mutants with replacement of residues at the amino terminus of alpha5 exhibited mild (<2-fold) decreases, whereas mutants with replacement of residues at the carboxyl terminus of alpha5 were completely resistant to R-catalyzed activation. In addition, insertion of a single helical turn in the form of four alanine residues following Ile339 at the carboxyl terminus of alpha5 prevented R-catalyzed activation. Together, the results provide evidence that alpha5 serves an important function in mediating R-catalyzed nucleotide exchange. In particular, the data suggest the importance of the connection between the alpha5 helix and the adjacent carboxyl-terminal region of Galpha(t).     

Repair of plasmid DNA damaged in vitro with cis- or trans-diamminedichloroplatinum(II) in Escherichia coli

Plasmid pBR322 was modified in vitro with the antitumor compound cis-diamminedichloroplatimum(II) (cis-DDP) or the isomeric trans-DDP. The numbers of platinum adducts were determined by atomic absorption spectrophotetry. DNA-repair-proficient and various DNA-repair-deficient (uvrB, uvrD, recB and recA) strains of Escherichia coli were transformed by the damaged plasmids and the ratios of the transformation frequencies of cells by damaged plasmids relative to those by untreated plasmids were determined. Results of transformation assays indicated that the uvrB gene function was essential for repair of plasmid DNA damaged with cis-DDP. A functional recA gene product seemed to be of minor importance for repair of plasmids damaged with cis-DDP. trans-DDP had a different effect on plasmid DNA. trans-DDP-modified DNA was better able to transform cells than cis-DDP-modified DNA, and the DNAs appeared to be repaired differently. Prior induction of SOS functions increased the survival of plasmids treated with cis-DDP in wild-type and uvrD mutants, but did not increase the survival of plasmids damaged with trans-DDP in these strains. In in vitro repair experiments, plasmid DNA modified with cis-DDP was more readily incised by the UVRABC excinuclease than that modified with trans-DDP.     

In Vivo and in Vitro binding of platinum to metallothionein

The in vivo binding of platinum to metallothionein (MT) has been observed in rat tissues following injections of the cis and trans isomers of DDP (dichlorodiammine-platinum(II)). Platinum in either cis-DDP or trans-DDP does not directly induce MT; platinum-MT is produced by the replacement of previously bound zinc in the protein. The binding of Pt(II) to MT depends on the availability of SH groups in MT. Preinjection with CdCl₂ significantly enhances the association of Pt(II) with MT fractions compared to the degree of association resulting from injections with either cis-DDP or trans-DDP without CdCl₂ pretreatment. In vitro experiments in which tissue extracts including a known (Cd,Zn)-MT were incubated with either cis-DDP or trans-DDP show that these isomers differ with respect to the transfer of Pt to MT; the equilibrium in both cases was reached when approximately 40% of the available Pt is bound to MT but with this equilibrium value attained in 2 h in the case of trans-DDP and only after 72 h in the case of cis-DDP. Pt-MTs were also formed by a series of incubation steps in which a native MT was used to prepare the apoprotein which was subsequently incubated with either cis-DDP or trans-DDP. Spectrophotometry established that a shoulder occurs at 285 nm for the Pt-MTs resulting from the incubation with either isomer. A competitive double-antibody radioimmunoassay for MT demonstrated that these Pt-MTs had complete cross-reactivity with a native (Cd,Zn)-MT. Gel filtration of tissue extracts after either in vivo or in vitro treatment with DDP showed that Pt was bound to a molecular species with properties characteristic of MT. These results were verified by atomic absorption spectrophotometry and polyacrylamide gel electrophoresis assays.     

Deletion and substitution analysis of the Escherichia coli TonB Q160 region

The active transport of iron siderophores and vitamin B(12) across the outer membrane (OM) of Escherichia coli requires OM transporters and the potential energy of the cytoplasmic membrane (CM) proton gradient and CM proteins TonB, ExbB, and ExbD. A region at the amino terminus of the transporter, called the TonB box, directly interacts with TonB Q160 region residues. R158 and R166 in the TonB Q160 region were proposed to play important roles in cocrystal structures of the TonB carboxy terminus with OM transporters BtuB and FhuA. In contrast to predictions based on the crystal structures, none of the single, double, or triple alanyl substitutions at arginyl residues significantly decreased TonB activity. Even the quadruple R154A R158A R166A R171A mutant TonB still retained 30% of wild-type activity. Up to five residues centered on TonB Q160 could be deleted without inactivating TonB or preventing its association with the OM. TonB mutant proteins with nested deletions of 7, 9, or 11 residues centered on TonB Q160 were inactive and appeared never to have associated with the OM. Because the 7-residue-deletion mutant protein (TonBDelta7, lacking residues S157 to Y163) could still form disulfide-linked dimers when combined with W213C or F202C in the TonB carboxy terminus, the TonBDelta7 deletion did not prevent necessary energy-dependent conformational changes that occur in the CM. Thus, it appeared that initial contact with the OM is made through TonB residues S157 to Y163. It is hypothesized that the TonB Q160 region may be part of a large disordered region required to span the periplasm and contact an OM transporter.     

Comparison by 1H-nmr spectroscopy of the conformation of the 2600 dalton antifreeze glycopeptide of polar cod with that of the high molecular weight antifreeze glycoprotein

The antifreeze glycopeptide (AFGP-8) from polar cod, B. saida, is a 14-amino acid polypeptide having alternating glycotripeptide sequences of Ala-[Gal(β1 → 3)GalNAc(β1 → O)]-Thr-Pro and Ala-[Gal(β1 → 3)GalNAc(β1 → O)]-Thr-Ala, with alanyl residues at amino and carboxy terminals. Conformational studies of AFGP-8 have been carried out by ¹H-nmr and empirical energy calculations to investigate the difference in its antifreeze behavior from that of the more active high-molecular weight AFGP 1-4 of P. borchgrevinki. The ¹H-nmr spectra, including the resonances of the exchangeable amide protons, were assigned by two-dimensional correlated spectroscopy (COSY), one-dimensional difference decoupling, and nuclear Overhauser effect (NOE) measurements. For the four threonyl residues, the amide proton coupling constants and the small coupling constants between H^α and H^β indicate similar conformations, despite significant chemical shift differences. The strong NOE between the α protons and the amide protons of the residue following together with large temperature coefficients of chemical shifts, indicate an extended conformation not consisting of α-helix, turns or bends. Energy computations indicate several low-energy conformations consistent with the observed coupling constants for ?. Among these, a left-handed helical conformation with three repeating residues per turn has been proposed, which is in accordance with the observed NOE between the methyl group of the α-GalNAc and Ala H^βs. While the observed Overhauser effects in the threonyl side chain suggest a certain amount of conformational averaging, the effect involving the acetmido methyl of α-GalNAc and H^βs of Ala indicate that it as is a major conformer. In view of the close similarity between the conformations of AFGP-8 and the more active antifreeze polymer, AFGP 1-4, we propose that the difference in their activities is due to the length of the regular repeating structure with glycosylation at every third amino acid residue, and not due to any fundamental difference in their conformations.     

Cardiac Muscle Activation Blunted by a Mutation to the Regulatory Component,Troponin T

The striated muscle thin filament comprises actin, tropomyosin, and troponin. The Tn complex consists of three subunits, troponin C (TnC), troponin I (TnI), and troponin T (TnT). TnT may serve as a bridge between the Ca²⁺ sensor (TnC) and the actin filament. In the short helix preceding the IT-arm region, H1(T2), there are known dilated cardiomyopathy-linked mutations (among them R205L). Thus we hypothesized that there is an element in this short helix that plays an important role in regulating the muscle contraction, especially in Ca²⁺ activation. We mutated Arg-205 and several other amino acid residues within and near the H1(T2) helix. Utilizing an alanine replacement method to compare the effects of the mutations, the biochemical and mechanical impact on the actomyosin interaction was assessed by solution ATPase activity assay, an in vitro motility assay, and Ca²⁺ binding measurements. Ca²⁺ activation was markedly impaired by a point mutation of the highly conserved basic residue R205A, residing in the short helix H1(T2) of cTnT, whereas the mutations to nearby residues exhibited little effect on function. Interestingly, rigor activation was unchanged between the wild type and R205A TnT. In addition to the reduction in Ca²⁺ sensitivity observed in Ca²⁺ binding to the thin filament, myosin S1-ADP binding to the thin filament was significantly affected by the same mutation, which was also supported by a series of S1 concentration-dependent ATPase assays. These suggest that the R205A mutation alters function through reduction in the nature of cooperative binding of S1.