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Near-infrared photoimmunotherapy (NIR-PIT) employs molecularly targeted antibodies conjugated with a photoabsorbing silicon-phthalocyanine dye derivative which binds to cancer cells. Application of NIR light following binding of the antibody-photoabsorber conjugates (APCs) results in ligand release on the dye, dramatic changes in solubility of the APC-antigen complex, and rapid, irreversible cell membrane damage of cancer cells in a highly selective manner, resulting in a highly immunogenic cell death. Clinically, this process results in edema after treatment mediated by reactive oxygen species (ROS). Based on the chemical and biological mechanism of NIR-PIT cytotoxicity and edema formation, in order to minimize acute inflammatory edema without compromising therapeutic effects, l-sodium ascorbate (l-NaAA) was administered to quench harmful ROS and accelerate the ligand release reaction. l-NaAA suppressed acute edema by reducing ROS after NIR-PIT yet did not alter the therapeutic effects. NIR-PIT could be performed safely under existence of l-NaAA without side effects caused by unnecessary ROS production., Competing Interests: The authors declare no competing financial interest., (© 2021 American Chemical Society.)

Fluorogenic probes in the near-infrared (NIR) region have the potential to provide stimuli-dependent information in living organisms. Here, we describe a new class of fluorogenic probes based on the heptamethine cyanine scaffold, the most broadly used NIR chromophore. These compounds result from modification of heptamethine norcyanines with stimuli-responsive carbamate linkers. The resulting cyanine carbamates (CyBams) exhibit exceptional turn-ON ratios (∼170×) due to dual requirements for NIR emission: carbamate cleavage through 1,6-elimination and chromophore protonation. Illustrating their utility in complex in vivo settings, a γ-glutamate substituted CyBam was applied to imaging γ-glutamyl transpeptidase (GGT) activity in a metastatic model of ovarian cancer. Overall, CyBams have significant potential to extend the reach of fluorogenic strategies to intact tissue and live animal imaging applications.

Near-infrared photoimmunotherapy (NIR-PIT), a newly developed cancer-cell-specific therapy, relies on a monoclonal antibody-photoabsorber conjugate (APC) and is based on a photoinduced ligand release reaction. Local exposure of the tumor to NIR light induces rapid immunogenic necrotic cell death. The molecular properties of APCs, including their stability and aggregation properties, have important implications for the long-term stability and shelf life. In this study, panitumumab was conjugated with IRDye700DX (IR700) as a model for other NIR-PIT agents. Higher IR700-to-mAb conjugation ratios correlated with increased in vitro cell death up to a ratio of 2.5 dye molecules per antibody. Conjugation ratios higher than 2.5 did not improve cell killing activity. APC aggregation was induced in a light-dose-dependent manner. A near-room-level light dose was sufficient to induce aggregation of APCs. Solvent pH lower than 4 induced aggregation, but higher pH did not induce aggregation. The IR700-to-mAb conjugation ratio, light irradiation dose, and solvent pH affect the APC stability and efficacy., Competing Interests: The authors declare no competing financial interest., (Copyright © 2020 U.S. Government.)

Regulatory T (Treg) cells play a major role in immune suppression permitting tumors to evade immune surveillance. Depletion of intratumoral Treg cells can result in tumor regression. However, systemic depletion of Tregs may also induce autoimmune adverse events. Near-infrared photoimmunotherapy (NIR-PIT) is a newly developed cell-specific cancer therapy that locally kills specific cells in the tumor. Antibody-photoabsorber (IRDye700DX) conjugates (APC) are injected and bind to the tumor, and subsequent administration of NIR light to the tumor results in rapid cell death only in targeted cells. CD25-targeted NIR-PIT has been shown to induce spatially selective depletion of tumor-associated Treg cells. In this study, we compared the efficacy of an antibody fragment, anti-CD25-F(ab') 2 , and a full antibody, anti-CD25-IgG, as agents for NIR-PIT. Tumor-bearing mice were divided into four groups: (1) no treatment; (2) anti-CD25-IgG-IR700 i.v. only; (3) anti-CD25-F(ab') 2 -IR700 i.v. with NIR light exposure; and (4) anti-CD25-IgG-IR700 i.v. with NIR light exposure. Although both CD25-targeted NIR-PITs resulted in significant tumor growth inhibition, the anti-CD25-F(ab') 2 -IR700 based NIR-PIT was superior to the anti-CD25-IgG-IR700 NIR-PIT. The anti-CD25-F(ab') 2 -IR700 demonstrated faster clearance from the body than the anti-CD25-IgG-IR700. Sustained circulation of anti-CD25-IgG-IR700 may block IL-2 binding on the activated effector T-cells decreasing immune response. In conclusion, anti-CD25-F(ab') 2 based NIR-PIT was more effective in reducing tumor growth than anti-CD25-IgG based NIR-PIT. Absence of the Fc portion of the APC leads to faster clearance and therefore promotes a superior activated T cell response in tumors.

Near infrared (NIR) fluorescent probes are attractive tools for biomedical in vivo imaging due to the relatively deeper tissue penetration and lower background autofluorescence. Activatable probes are turned on only after binding to their target, further improving target to background ratios. However, the number of available activatable NIR probes is limited. In this study, we introduce two types of activatable NIR fluorophores derived from bacteriochlorin: chlorin-bacteriochlorin energy-transfer dyads and boron-dipyrromethene (BODIPY)-bacteriochlorin energy-transfer dyads. These fluorophores are characterized by multiple narrow excitation bands with relatively strong emission in the NIR. Targeted bacteriochlorin-based antibody or peptide probes have been previously limited by aggregation after conjugation. Polyethylene glycol (PEG) chains were added to improve the hydrophilicity without altering pharmacokinetics of the targeting moieties. These PEGylated bacteriochlorin-based activatable fluorophores have potential as targeted activatable, multicolor NIR fluorescent probes for in vivo applications.

The previously unexplored metal-catalyzed [5 + 2] cycloadditions of vinylcyclopropanes (VCPs) and electron-rich alkynes (ynol ethers) have been found to provide a highly efficient, direct route to dioxygenated seven-membered rings, a common feature of numerous natural and non-natural targets and building blocks for synthesis. The reactions proceed in high yield at room temperature and tolerate a broad range of functionalities. Substituted VCPs were found to react with high regioselectivity.

Emission gas and air contain not only CO 2 but also plentiful moisture, making it difficult to achieve selective CO 2 absorption without hydration. To generate absorbed CO 2 (wet CO 2 ) under heating, the need for external energy to release the absorbed water has been among the most serious problems in the fields of carbon dioxide capture and storage (CCS) and direct air capture (DAC). We found that the introduction of the hydrophobic phenyl group into alkylamines of CO 2 absorbents improved the absorption selectivity between CO 2 and water. Furthermore, ortho-, meta-, and para-xylylenediamines (OXDA, MXDA, PXDA, respectively) absorbed only CO 2 in air without any hydration. Notably, MXDA·CO 2 was formed as an anhydrous carbamic acid even in water, presumably because it was covered with hydrophobic phenyl groups, which induces a reverse lipid bilayer structure. Dry CO 2 was obtained from heating MXDA·CO 2 at 103-120 °C, which was revealed to involve chemically the Grignard reaction to form the resulting carboxylic acids in high yields.

Conventional allenes have not been effective π-reactive 2-carbon components in many intermolecular cycloadditions including metal-catalyzed [5 + 2] cycloadditions. We report herein that rhodium-catalyzed [5 + 2] cycloadditions of propargyltrimethylsilanes and vinylcyclopropanes provide, after in situ protodesilylation, a highly efficient route to formal allene cycloadducts. Propargyltrimethylsilanes function as safe, easily handled synthetic equivalents of gaseous allenes and hard-to-access monosubstituted allenes. In this one-flask procedure, they provide cycloadducts of what is formally addition to the more sterically encumbered allene double bond.

Like most Ras superfamily proteins, the GTPase domain of Ras homologue enriched in brain (Rheb) is tethered to cellular membranes through a prenylated cysteine in a flexible C-terminal region; however, little is known about how Rheb or other GTPases interact with the membrane or how this environment may affect their GTPase functions. We used NMR methods to characterize Rheb tethered to nanodiscs, monodisperse protein-encapsulated lipid bilayers with a diameter of 10 nm. Membrane conjugation markedly reduced the rate of intrinsic nucleotide exchange, while GTP hydrolysis was unchanged. NMR measurements revealed that the GTPase domain interacts transiently with the surface of the bilayer in two distinct preferred orientations, which are determined by the bound nucleotide. We propose models of membrane-dependent signal regulation by Rheb that shed light on previously unexplained in vivo properties of this GTPase. The study presented provides a general approach for direct experimental investigation of membrane-dependent properties of other Ras-superfamily GTPases.

The unprecedented C(sp(3))-C(sp(3)) bond cleavage of unactivated cyclopentane has been achieved. Rh(I)-catalyzed cycloaddition of allenylcyclopentane-alkynes produced in situ the 9-cyclopentyl-8-rhodabicyclo[4.3.0]nona-1,6-diene intermediates, which subsequently underwent [7+2] cycloaddition via β-C elimination, affording bicyclo[7.4.0]tridecatriene derivatives in good yields. Changing the Rh(I) catalyst effected the Cγ-H bond activation of the common 9-cyclopentyl-8-rhodabicyclo[4.3.0]nona-1,6-diene intermediate to produce the novel spiro[2.4]heptane skeleton in a site-selective manner.

Protein N-glycosylation occurs in the three domains of life. Oligosaccharyltransferase (OST) transfers glycan to asparagine in the N-glycosylation sequon. The catalytic subunit of OST is called STT3 in eukaryotes, AglB in archaea, and PglB in eubacteria. The genome of a hyperthermophilic archaeon, Archaeoglobus fulgidus, encodes three AglB paralogs. Two of them are the shortest AglBs across all domains of life. We determined the crystal structure of the C-terminal globular domain of the smallest AglB to identify the minimal structural unit. The Archaeoglobus AglB lacked a β-barrel-like structure, which had been found in other AglB and PglB structures. In agreement, the deletion in a larger Pyrococcus AglB confirmed its dispensability for the activity. By contrast, the Archaeoglobus AglB contains a kinked helix bearing a conserved motif, called DK/MI motif. The lysine and isoleucine residues in the motif participate in the Ser/Thr recognition in the sequon. The Archaeoglobus AglB structure revealed that the kinked helix contained an unexpected insertion. A revised sequence alignment based on this finding identified a variant type of the DK motif with the insertion. A mutagenesis study of the Archaeoglobus AglB confirmed the contribution of this particular type of the DK motif to the activity. When taken together with our previous results, this study defined the classification of OST: one group consisting of eukaryotes and most archaea possesses the DK-type Ser/Thr pocket, and the other group consisting of eubacteria and the remaining archaea possesses the MI-type Ser/Thr pocket. This classification provides a useful framework for OST studies.

The total synthesis of (±)-meloscine was completed in a highly stereoselective manner starting from the known 4-(2-aminophenyl)-2,3-dihydro-N-methoxycarbonylpyrrole. The crucial step in this total synthesis involves the efficient construction of the tetracyclic framework of the target natural product by the intramolecular Pauson-Khand reaction.

The Stille coupling reaction of 3-(benzyloxymethyl)-1-(tert-butyldiphenylsiloxy)ethyl-1-(tributylstannyl)allene with N-(tert-butoxycarbonyl)-2-iodoaniline directly produced the corresponding 2-vinylindole derivative, which was independently transformed into natural (-)-goniomitine and unnatural (+)-goniomitine via the cross-metathesis with chiral oxazolopiperidone lactams. The antiproliferative activity of the synthesized natural (-)-goniomitine in Mock and MDCK/MDR1 cells showed them to be more potent to retard cell growth than unnatural (+)-goniomitine.

The total synthesis of (+)-fawcettimine was completed in a highly stereoselective manner starting from the oxatricyclo[7.3.0.0(1,5)]dodecanedione derivative. The crucial step in this total synthesis involves the efficient construction of the azonane framework by the intramolecular Mitsunobu reaction. Furthermore, the first total synthesis of (+)-lycoposerramine-B was also accomplished via the common synthetic intermediate.

The formal synthesis of (+)-nakadomarin A was completed. The significant points of this synthesis are the highly stereoselective formation of the diazatricyclo[6.4.0.0(1,5)]dodecane skeleton (A, B, and D rings) based on the Pauson-Khand reaction and novel furan ring (C ring) formation, using the vinyl residue of the Pauson-Khand product.

The two conditions for the preparation of the reactive N-(tert-butoxycarbonyl)indolo-2,3-quinodimethane intermediate were developed by the reaction of the N-(tert-butoxycarbonyl)-2-(1-ethoxycarbonyloxymethylallenyl)aniline with K(2)CO(3) or Pd(2)(dba)(3) in refluxing toluene. The resulting N-(tert-butoxycarbonyl)indolo-2,3-quinodimethane was captured by several alkenyl and alkynyl dienophiles to provide the corresponding tetrahydro- and dihydrocarbazole derivatives.

Treatment of 3-(2-ethynylphenyl)prop-2-ynyl benzenesulfinate with 2.5 mol % of [RhCl(CO)(2)](2) at 40 degrees C under an atmosphere of CO effected the successive 2,3-sigmatropic rearrangement and carbonylative [2 + 2 + 1] ring-closing reaction to afford the 8-(phenylsulfonyl)-1H-cyclopent[a]-inden-2-one in a high yield. Chemical modification of the ring-closed product via lipase-mediated optical resolution produced the optically active 3-acetoxy-3a-cyclohexyloxy-3,3a-dihydrocyclopent-[a]indene skeleton, the core carbon framework of cyanosporasides A and B.

Cholangiocarcinoma is an intractable cancer for which there is no effective therapy other than surgical resection, and many patients are not candidates for this treatment. Even for patients who undergo surgical resection, the 5-year survival rate is low. One reason for this is that the disease is often detected in late stages. Thus, there is a clear need for better biomarkers to facilitate early diagnosis and prognostication. During the biomarker discovery phase of our study, we used LC-MS-based proteomics with spectral counting, a semiquantitative approach to differential expression profiling, in paired cancerous and normal bile duct tissue samples from two cases. In total, 38 proteins up-regulated in the cancer samples were identified. These were verified using a SILAC method for MS-based validation. The results led to the identification of well-characterized proteins and proteins of unknown function that are up-regulated in cholangiocarcinoma. We used immunoblot analysis to validate four candidate biomarkers, actinin-1, actinin-4, protein DJ-1 and cathepsin B, with the test case samples and four additional cholangiocarcinoma case samples. Each of the four candidate proteins was overexpressed in a subset of five of the six cases tested. By immunohistochemistry, we further confirmed that expression of these proteins was elevated in cancer cells as compared with normal bile duct cells. Thus, we successfully identified several proteins up-regulated in cholangiocarcinoma. These proteins are candidate biomarkers and may also help to provide new insights into our understanding of the disease.

The simple refluxing of allenynes, having a phenylsulfonyl functionality on the allenyl group, in xylene (or mesitylene) without microwave irradiation resulted in the efficient formation of bicyclo[5.2.0]nona-1,7-dienes and bicyclo[4.2.0]octa-1,6-dienes in high yields. This method was shown to be successfully applicable to the first construction of bicyclo[6.2.0]deca-1,8-dienes. Construction of the corresponding oxa- and azabicyclo[m.2.0] frameworks could also be attained. This thermal ring-closing reaction involves the formal [2+2] cycloaddition in which the distal double bond of an allenyl moiety exclusively served as one of the pi-components regardless of the position of the phenysulfonyl functionality on the allenyl moiety.

[reaction: see text] The novel [RhCl(CO)(2)](2)-catalyzed [2 + 2 + 1] cycloaddition of allenenes leading to the bicyclo[4.3.0]non-1(9)-en-8-one as well as the bicyclo[5.3.0]dec-1(10)-en-9-one skeletons has been developed. This method also provides a new procedure for the construction of the bicyclo[4.3.0]non-1(9)-en-8-one skeleton having an alkyl appendage at the ring juncture, which was hardly attained in a satisfactory yield by the Pauson-Khand reaction of the corresponding enynes.

[reaction: see text] Rhodium(I)-catalyzed PKR of allenynes was found to be applicable for constructing azabicyclo[5.3.0]decadienone as well as oxabicyclo[5.3.0]decadienone frameworks. In addition, a reliable procedure for constructing a 10-monosubstituted bicyclo[5.3.0]deca-1,7-dien-9-one ring system by the rhodium(I)-catalyzed PKR of allenynes was developed under the condition of 10 atm of CO. Investigation of the rhodium(I)-catalyzed cycloisomerization of 4-phenylsulfonylnona-2,3-dien-8-ynes under nitrogen atmosphere gave the corresponding cyclohexene derivatives, whereas the C1-homologated allenynes produced cycloheptene derivatives and/or bicyclo[5.2.0]nonene skeletons depending on the substitution pattern at the allenic terminus. Thus, proper choice of the starting allenynes and reaction conditions led to the selective formation of 2-phenylsulfonylbicyclo[5.3.0]deca-1,7-dien-9-ones (Pauson-Khand-type product), 3-alkylidene-1-phenylsulfonyl-2-vinylcycloheptene derivatives, and bicyclo[5.2.0]nonene frameworks.

The solution structure of a human cystatin A variant, cystatin A2-98 M65L, which maintains the full inhibitory activity of the wild-type protein, was determined at pH 3.8 by sD/3D heteronuclear double- and triple-resonance NMR spectroscopy. The structure is based on a total of 1343 experimental restraints, comprising 1139 distance, 154 phi and chi 1 torsion angle restraints, and 50 distance constraints for 25 backbone hydrogen bonds. A total of 15 structures was calculated using the YASAP protocol with X-PLOR, and the atomic rms distribution about the mean coordinate positions for residues 8-93 was 0.55 +/- 0.10 A for the backbone atoms and 1.05 +/- 0.11 A for all heavy atoms. The structure consists of five antiparallel beta-sheets and two short alpha-helices. Comparison with the X-ray structure of cystatin B in the papain complex shows that the conformation of the first binding loop is quite similar to that of cystatin A, with an rms deviation of 0.78 A for the backbone atoms in the 43-53 region (cystatin A numbering). The second binding loop, however, is significantly different in the two structures, with an rms deviation greater than 2 A. There are some other significant differences, especially for the N-terminal and alpha-helix regions. The overall structure of cystatin A is also compared with the recently reported NMR structure of the wild-type cystatin A (stefin A) at pH 5.5 (Martin et al., 1995) and reveals the following features. that differ in our structure from the previous one: (1) the N-terminal segment, which was unstructured in the previous report, folds over in close vicinity to the C-terminus, as revealed by the distinctive NOEs between those segments; (2) two discrete short alpha-helices linked by a type II reverse turn were found, instead of the continuous single alpha-helix with a slight kink shown in the previous structure; (3) the second binding loop, which was not well converged in the previous study at pH 5.5, is determined very well in our structure. The effect of the N-terminal truncation on the cystatin A structure was examined by comparing the 1H-15N HSQC spectrum of cystatin A2-98 with that of the cystatin A5-98 variant, which lacks the anti-papain activity, revealing significant chemical shift differences in the residual N-terminal segment and the first binding loop, together with small shifts in the other parts.(ABSTRACT TRUNCATED AT 400 WORDS)

A synthetic replacement study of the amino acid residues of mu-conotoxin GIIIA, a peptide blocker for muscle sodium channels, has recently shown that the conformation formed by three disulfide bridges and the molecular basicity, especially the one around the Arg13 residue, are important for blocking activity. In the present study, we determined the three-dimensional structure of an inactive analog, [Ala13]mu-conotoxin GIIIA, and refined that of the native toxin by NMR spectroscopy combined with simulated annealing calculations. The atomic root-mean-square difference of the mutant from the native conotoxin was 0.62 A for the backbone atoms (N, C alpha, C') of all residues except for the two terminal residues. The observation that the replacement of Arg13 by Ala13 does not significantly change the molecular conformation suggests that the loss of activity is not due to the conformational change but to the direct interaction of the essential Arg13 residue with the sodium channel molecules. In the determined structure, important residues for the activity, Arg13, Lys16, Hyp(hydroxyproline)17, and Arg19, are clustered on one side of the molecule, an observation which suggests that this face of the molecule associates with the receptor site of sodium channels. The hydroxyl group of Hyp17 is suggested to interact with the channel site with which the essential hydroxyl groups of tetrodotoxin and saxitoxin interact.

The three-dimensional structures of epidermal growth factors (EGF) previously reported were all in acidic solutions (pH 2.0-3.2), at which pHs EGF cannot bind to the receptor. Here we studied the structure of mouse EGF at pH 6.8, where EGF is physiologically active, and compared it with the structure at pH 2.0 by CD and NMR. From pH dependence of CD spectra and a comparison between the chemical shifts of the proton resonances at pH 6.8 and 2.0, the conformations at two pHs were found to be nearly identical except for the C-terminal tail region. The three-dimensional structures at pH 6.8 and 2.0 were determined independently by a combination of two-dimensional 1H NMR and stimulated annealing calculations using the program XPLOR. The calculations were based on 261 distance constraints at pH 6.8 and 355 distance and 24 torsion angle constraints at pH 2.0. The conformational difference of the C-terminal domain (residues 33-50) was detected between the two structures, which were supported by CD and the chemical shift comparison. The positions of the side chains of Leu47, Arg48, Trp49, and Trp50 are changed probably by the effect of the deprotonation of Asp46. Considering the fact that Leu47 is essential in EGF binding to the receptor, this conformational difference may be important in receptor recognition.

Resonance assignments for interleukin 1 beta at neutral pH were made by using three-dimensional NMR in combination with specific labeling and double-labeling methods with stable isotopes. On the basis of the present assignments, 15N single-quantum coherence spectra of N-terminal truncated and fusion mutants were compared with that of the wild-type. Although these mutants have reduced biological activity, they showed 15N-SQC spectra similar to that of the wild-type. However, small but significant chemical shift changes were observed for amino acid residues within a loop 86-99, in spite of the modification at the N-terminus, supporting the idea that this loop forms a biologically active part of interleukin 1 beta. Receptor-binding activity was studied for mutants (Asp-93)-, (Leu-93)- and des-(Arg-98)interleukin 1 beta's. The results show significant loss of the receptor-binding activity. The N-terminus, the C-terminus, and the loop 86-99 form a part of the open end of a beta-barrel [Finzel, B. C., Clancy, L. L., Holland, D. R., Muchmore, S. W., Watenpaugh, K. D., & Einspahr, H. M. (1989) J. Mol. Biol. 209, 779-791; Clore, G. M., Wingfield, P. T., & Gronenborn, A. M. (1991) Biochemistry 30, 2315-2323], which forms the receptor-binding site of IL-1 beta.

The interaction of mouse epidermal growth factor (mEGF) with micelles of a phospholipid analogue, perdeuterated dodecylphosphocholine (DPC), was investigated by two-dimensional 1H NMR. Sequence-specific resonance assignments of the micelle-bound mEGF have been made, and the chemical shifts were compared with those in the absence of DPC. DPC induced large chemical shift changes of the resonances from the residues in the C-terminal tail (residues 46-53) but little perturbation on the residues in the main core (residues 1-45). Starting from the three-dimensional structure in the absence of DPC, micelle-bound structures were calculated using the program XPLOR with interproton distance data obtained from NOESY spectra recorded in the presence of DPC. The C-terminal tail of mEGF was found to change conformation to form an amphiphilic structure when bound to the micelles. It is possible that induced fit in the C-terminal tail of mEGF occurs upon binding to a putative hydrophobic pocket of the EGF receptor.

The three-dimensional structure of conotoxin GIIIA, an important constituent of the venom from the marine hunting snail Conus geographus L., was determined in aqueous solution by two-dimensional proton nuclear magnetic resonance and simulated annealing based methods. On the basis of 162 assigned nuclear Overhauser effect (NOE) connectivities obtained at the medium field strength frequency of 400 MHz, 74 final distance constraints of sequential and tertiary ones were derived and used together with 18 torsion angle (phi, chi 1) constraints and 9 distance constraints derived from disulfide bridges. A total of 32 converged structures were obtained from 200 runs of calculations. The atomic root-mean-square (RMS) difference about the mean coordinate positions (excluding the terminal residues 1 and 22) is 0.8 A for backbone atoms (N, C alpha, C). Conotoxin GIIIA is characterized by a particular folding of the 22 amino acid peptidic chain, which is stabilized by three disulfide bridges arranged in cage at the center of a discoidal structure of approximately 20-A diameter. The seven cationic side chains of lysine and arginine residues project radially into the solvent and form potential sites of interaction with the skeletal muscle sodium channel for which the toxin is a strong inhibitor. The present results provide a molecular basis to elucidate the remarkable physiological properties of this neurotoxin.

The pH titration shifts for all the nonlabile proton resonances in a 53-residue protein (mouse epidermal growth factor) were measured in the p2H range 1.5-9 with two-dimensional (2D) 1H NMR. The 2D NMR pH titration experiment made it possible to determine the pK values for all the ionizable groups which were titrated in the pH range 1.5-9 in the protein. The pK values of the nine ionizable groups (alpha-amino group, four Asp, two Glu, one His, and alpha-carboxyl group) were found to be near their normal values. The 2D titration experiment also provided a detailed description of the pH-dependent behavior of the proton chemical shifts and enabled us to characterize the pH-dependent changes of protein conformation. Analysis of the pH-dependent shifts of ca. 200 proton resonances offered evidence of conformational changes in slightly basic pH solution: The deprotonation of the N-terminal alpha-amino group induced a widespread conformational change over the beta-sheet structure in the protein, while the effects of deprotonation of the His22 imidazole group were relatively localized. We found that the 2D NMR pH titration experiment is a powerful tool for investigating the structural and dynamic properties of proteins.

We have isolated four novel oligosaccharides with the sialyl-Lea structure from human milk using a monoclonal antibody, MSW 113. These oligosaccharides were purified by affinity chromatography on a column of the immobilized monoclonal antibody and by high-performance liquid chromatography. The results of structural analyses, i.e., 500-MHz 1H NMR spectroscopy, fast atom bombardment mass spectrometry, and binding to specific anticarbohydrate antibodies, are consistent with the following structures. (formula; see text)

Aromatic proton and high field shifted methyl proton resonances of RNase T1 complexed with Guo, 2'GMP, 3'GMP, or 5'GMP were assigned to specific amino acid residues by analyses of the two-dimensional NMR spectra in comparison with the crystal structure of the RNase T1-2'GMP complex. These assignments were subsequently correlated to those of free RNase T1 [Hoffmann & Rüterjans (1988) Eur. J. Biochem. 177, 539-560]. The spatial proximities of amino acid residues as elucidated by NOESY spectra were found to be quite similar among free RNase T1 and the inhibitor complexes, showing that large conformational changes did not occur upon complex formation. However, small but appreciable conformational changes were induced, which were reflected by the systematic chemical shift changes of some amino acid residues in the active site. Furthermore, we confirmed that RNase T1 contains two specific binding sites, one for the guanine base and the other for the phosphate moiety. The inhibitors are forced to adapt their conformations to fit the guanine base and the phosphate moiety to each binding site on the enzyme. This is consistent with our previous studies that 2'GMP and 3'GMP take the syn form as a bound conformation, while 5'GMP takes the anti conformation around glycosidic bonds [Inagaki et al. (1985) Biochemistry 24, 1013-1020]. The slow-exchange process between free and bound forms involving Tyr42 and Tyr45 was found to be specific to the recognition of the guanine base.

The 1H NMR spectrum of human transforming growth factor alpha (TGF-alpha) was analyzed almost completely by the sequential assignment method using two-dimensional NMR techniques. On the basis of the nearly complete sequence-specific resonance assignment, secondary and tertiary structures of human TGF-alpha in solution (pH 4.9, 28 degrees C) were determined to satisfy the upper limits of proton-proton distances derived from nuclear Overhauser effect experiments. Although human TGF-alpha and mouse epidermal growth factor (EGF) share 27% homology in amino acid sequence, the backbone chain folds in the two growth factors are quite similar. The structure and function of TGF-alpha is well characterized by the "mitten model" previously proposed for mouse EGF. The gross shape of the TGF-alpha molecule resembles a mitten. TGF-alpha interacts with the receptor as a mitten would grasp an object. However, there is an appreciable structural difference between the two growth factors in the back of the mitten that is formed by the N-terminal polypeptide segment. This is consistent with the evidence that the backs of these molecules are not involved in the receptor binding.

An advanced method was developed for lanthanide-probe analyses of the conformations of flexible biomolecules such as nucleotides. The new method is to determine structure parameters (such as internal-rotation angles) and population parameters for local conformational equilibria of flexible sites, together with standard deviations of these parameters. As the prominent advantage of this method, the interrelations among local conformations of flexible sites may be quantitatively elucidated from the experimental data of lanthanide-induced shifts and relaxations and vicinal coupling constants. As a structural unit of ribonucleic acids, the molecular conformations and conformational equilibria of uridine 3'-monophosphate in aqueous solution were analyzed. The stable local conformers about the C3'-O3' bond are the G+ (phi' = 281 +/- 11 degrees) and G- (phi' = 211 +/- 8 degrees) forms. The internal rotation about the C3'-O3' bond and the ribose-ring puckering are interrelated; 97 +/- 5% of the C3'-endo ribose ring is associated with the G- form while 70 +/- 22% o the C2'-endo ribose ring is associated with the G+ form. An interdependency also exists between the internal rotation about the C4'-C5' bond and the ribose-ring puckering. These short-range conformational interrelations are probably important in controlling the dynamic aspects of ribonucleic acid structures.

The binding modes of inhibitors to ribonuclease T1 (RNase T1) were studied by the analyses of 270-MHz proton NMR spectra. The chemical shift changes upon binding of phosphate, guanosine, 2'-GMP, 3'-GMP, 5'-GMP, and guanosine 3',5'-bis(phosphate) were observed as high field shifted methyl proton resonances of RNase T1. One methyl resonance was shifted upon binding of phosphate and guanosine nucleotides but not upon binding of guanosine. Four other methyl resonances were shifted upon binding of guanosine and guanosine nucleotides but not upon binding of phosphate. From the analyses of nuclear Overhauser effects for the pair of H8 and H1' protons, together with the vicinal coupling constants for the pair of H1' and H2' protons, the conformation of the guanosine moiety as bound to RNase T1 is found to be C3'-endo-syn for 2'-GMP and 3'-GMP and C3'-endo-anti for 5'-GMP and guanosine 3',5'-bis(phosphate). These observations suggest that RNase T1 probably has specific binding sites for the guanine base and 3'-phosphate group (P1 site) but not for the 5'-phosphate group (PO site) or the ribose ring. The weak binding of guanosine 3',5'-bis(phosphate) and 5'-GMP to RNase T1 is achieved by taking the anti form about the glycosyl bond. The productive binding to RNase T1 probably requires the syn form of the guanosine moiety of RNA substrates.