Search

In non-specific lac headpiece-DNA complexes selective NMR line broadening is observed that strongly depends on length and composition of the DNA fragments. This broadening involves amide protons found in the non-specific lac-DNA structure to be interacting with the DNA phosphate backbone, and can be ascribed to DNA sliding of the protein along the DNA. This NMR exchange broadening has been used to estimate the 1D diffusion constant for sliding along non-specific DNA. The observed 1D diffusion constant of 4×10 cm/s is two orders of magnitude smaller than derived from previous kinetic experiments, but falls in the range of values determined more recently using single molecule methods. This strongly supports the notion that sliding could play at most a minor role in the association kinetics of binding of lac repressor to lac operator and that other processes such as hopping and intersegment transfer contribute to facilitate the DNA recognition process. [ABSTRACT FROM AUTHOR]

The photophysics and photochemistry of kynurenic acid (KNA) and kynurenine yellow (KNY) in neutral aqueous solutions were investigated using time-resolved optical spectroscopy. Both molecules have similar quinoline-like structures, the only difference being the absence of conjugation in the nitrogen containing cycle in KNY. The main channel of S1 excited state decay in the case of partially-unconjugated KNY is the solvent assisted S1→ S0 radiationless transition via intermolecular hydrogen bonds (ΦIC = 0.96), whereas, in the case of fully-conjugated KNA, it is intersystem crossing to the triplet state (ΦT = 0.82). The major intermediate products of the singlet excited KNY deactivation are the triplet state (ΦT = 0.022) and, most probably, the enol form (Φenol = 0.012), which decay with the formation of 2,3-dihydro-4-hydroxyquinoline and 4-hydroxyquinoline, respectively. The results obtained show that KNA and KNY, which are products of the decomposition of the UV filter kynurenine, are significantly more photoactive and less photostable than the parent molecule. [ABSTRACT FROM AUTHOR]

A theoretical study was made of magnetic field-dependent dipolar relaxation in two- and three-spin systems. The results for the nuclear magnetic relaxation dispersion (NMRD) curves were compared with those for the simpler model of fluctuating local fields. For both models it was found that at low fields spins tend to relax with a common T-relaxation time. Sharp features in the NMRD curves coming from nuclear spin level anti-crossings are also predicted by both models. However, the simple model fails to describe the behavior of so-called long-lived spin states (LLS). We have studied the LLS as function of magnetic field and molecular geometry and simulated experimental results for the LLS in histidine amino acid obtained at the laboratory of Prof. H.-M. Vieth (Free University Berlin, Germany). In addition, we described polarization transfer in a three-spin system where two spins are protons, which are initially hyperpolarized by para-hydrogen induced polarization (PHIP), while the third spin is a spin ½ hetero-nucleus, which acquires polarization in the course of cross-relaxation. [ABSTRACT FROM AUTHOR]

In this work we have compared manifestations of degenerate electron exchange (DEE) and dimerization reactions in MARY (magnetically affected reaction yield) spectroscopy and time-resolved magnetic field effects (TR-MFE) of radical ion pairs (RIPs). It is shown that dimerization results in phase and frequency changes of the quantum beats in TR-MFE traces, whereas DEE leads to relaxation-type changes in the spin dynamics of RIPs. Dimerization does not change the width of MARY lines considerably, but leads to new lines corresponding to dimer radical ions. In contrast, DEE substantially changes the MARY line widths. Our treatment provides ways to discriminate between both processes from experimental MARY spectra and TR-MFE kinetics. An experimental example dealing with concentration-dependent broadening of the MARY lines is also discussed. [ABSTRACT FROM AUTHOR]

Parahydrogen-induced polarization has been successfully used for a kinetic study of propylene hydrogenation over a Pt/AlO catalyst. It was shown that the reaction orders with respect to hydrogen are different for the pairwise and the non-pairwise hydrogen addition and are equal to 0.7 and 0.1, respectively. This observation of different reaction orders confirms the coexistence of different types of active sites which are responsible for the overall and the pairwise hydrogen addition to the propylene C=C double bond. Moreover, 0.7 reaction order with respect to H for pairwise hydrogen addition indicates that the contribution of pairwise addition depends on the concentration of molecular hydrogen. Therefore, this observation can be developed into a practical tool for producing fluids with highly polarized nuclear spins by changing the hydrogen concentration. [ABSTRACT FROM AUTHOR]

Immobilized iridium complexes synthesized using [Ir(COD)Cl] by anchoring on hydrous and anhydrous silica gels were studied in terms of generating parahydrogen-induced polarization (PHIP) in the gas-phase hydrogenation of propylene and propyne. Distinguishing differences in the hydrogenations of carbon-carbon double and triple bonds were found. It has been shown that in the double bond hydrogenation both catalysts are very active even at 25 °C. The reaction yield in continuous flow experiments is more than 70 %, whereas the obtained PHIP degrees are very low. In the case of the triple bond hydrogenation, a more or less active hydrogenation reaction was observed at relatively high temperatures (≈70-80 °C) for the catalyst immobilized on anhydrous silica, while the catalyst immobilized on hydrous silica was inactive at these temperatures. Contrary to the double bond hydrogenation, the triple bond hydrogenation provided significant signal enhancements observed in H nuclear magnetic resonance spectra for the signals corresponding to protons of vinyl fragments of product propylene in both PASADENA and ALTADENA experiments. The catalyst, however, is not stable under the triple bond hydrogenation reaction conditions, and deactivates within several minutes. It was also found that at higher temperatures (100-120 °C), this catalyst demonstrates a reactivation most likely associated with the reduction of Ir(I) that results in the formation of Ir(0) surface metal nanoparticles. [ABSTRACT FROM AUTHOR]

Pulsed-field-gradient nuclear magnetic resonance (NMR) combined with time-resolved chemically induced dynamic nuclear polarization (TR-CIDNP) was applied to study the reduction of guanosyl radicals in reactions with the proteins hen egg white lysozyme (HEWL) and bovine α-lactalbumin (BLA) in their native state. Guanosyl radicals were generated photochemically in the reaction of guanosine-5′-monophosphate with photosensitizer, triplet-excited 2,2′-dipyridyl. In this reaction, at pH 5 guanosyl cation radical is formed, which deprotonates to yield the neutral guanosyl radical. To minimize the contribution of the cation radical, phosphate buffer was added, which accelerates the deprotonation of guanosyl cation radical. From model simulations of CIDNP kinetics the rate constants of the reduction were found to be (3.1 ± 0.5) × 10 Ms for HEWL and (1.6 ± 0.4) × 10 Ms for BLA. Also, experiments were carried out at the conditions for denatured HEWL, i.e., at 50 °C in the presence of 10 M urea-d. The rate constant of the reduction of guanosyl radical in this case was (3.6 ± 0.5) × 10 Ms. [ABSTRACT FROM AUTHOR]

The modeling of biomolecular complexes by computational docking using the known structures of their constituents is developing rapidly to become a powerful tool in structural biology. It is especially useful in combination with even limited experimental information describing the interface. Here we demonstrate for the first time the use of diffusion anisotropy in combination with chemical shift perturbation data to drive protein–protein docking. For validation purposes we make use of simulated diffusion anisotropy data. Inclusion of this information, which can be derived from NMR relaxation rates and reports on the orientation of the components of a complex with respect to the rotational diffusion tensor, substantially improves the docking results. [ABSTRACT FROM AUTHOR]

In many NMR experiments, only polarisation of a limited sub-set of all protons is converted into observable coherence. As recently shown by the “longitudinal” TROSY implementation (Pervushin et al. (2002) J. Am. Chem. Soc., 124, 12898–12902) and SOFAST-HMQC (Schanda and Brutscher (2005) J. Am. Chem. Soc., 127, 8014–8015), recovery of unused polarisation can be used indirectly and unspecifically to cool the proton lattice and, thus, accelerate re-equilibration for the selected proton subset. Here we illustrate transfer of this principle to HSQC-based multi-dimensional out-and-back experiments that exploit only polarisation of 15N-bound protons. The presented modifications to the pulse sequences can be implemented broadly and easily, extending standard flip-back of water polarisation to a much larger pool of protons that may comprise all non−15N-bound protons. The underlying orthogonal separation of HN polarisation (selected by the main transfer path) from unused Hu polarisation (flipped-back on the recovery path) is thereby achieved through positive or negative selection by J-coupling, or using band-selective pulses. In practice, Hu polarisation recovery degrades mostly through cumulative pulse imperfections and transverse relaxation; we present, however, strategies to substantially minimise such losses particularly during interim proton decoupling. Depending on the protein’s relaxation properties and the extended flip-back scheme employed, we recovered up to 60% Hu equilibrium polarisation. The concomitant cooling of the proton lattice afforded substantial gains of more than 40%, relative to the water-only flip-back version, in the fast pulsing regime with re-equilibration delays τ much shorter than optimal (τopt = 1.25 · T 1(HN)). These would be typically employed if resolution requirements dominate the total measurement time. Contrarily, if sensitivity is limiting and optimal interscan delays τopt can be set ( optimal pulsing regime), the best of the presented flip-back schemes may still afford up to ca. 10% absolute sensitivity enhancement. [ABSTRACT FROM AUTHOR]

Proteins involved in signal transduction can usually be present in two states: an inactive and an active (signaling) state. In the case of photoreceptors such as PYP, it has been shown that the signaling state has a large degree of structural and dynamic disorder. Conventional structural NMR approaches present difficulties in describing such partially unfolded states. Owing to the disordered dynamical and transient nature of such states classical NOE-based information, when present, is sparse. Chemical shift changes upon partial unfolding can, however, be easily monitored from HSQC spectra. We show here that such states can be modeled by defining native-like inter-residue contacts for those residues that do not shift significantly upon partial unfolding. The feasibility of this approach is demonstrated using lysozyme as a test case and applied to model the partially unfolded signaling state (pB) of a truncated form of the photoactive yellow protein for which a “classical” NOE-based structure is available for validation. This approach should be generally applicable to systems in which part of the structure remains in a well-defined native-like conformation. [ABSTRACT FROM AUTHOR]

We present two new databases of NMR-derived distance and dihedral angle restraints: the Database Of Converted Restraints (DOCR) and the Filtered Restraints Database (FRED). These databases currently correspond to 545 proteins with NMR structures deposited in the Protein Databank (PDB). The criteria for inclusion were that these should be unique, monomeric proteins with author-provided experimental NMR data and coordinates available from the PDB capable of being parsed and prepared in a consistent manner. The Wattos program was used to parse the files, and the CcpNmr FormatConverter program was used to prepare them semi-automatically. New modules, including a new implementation of Aqua in the BioMagResBank (BMRB) software Wattos were used to analyze the sets of distance restraints (DRs) for inconsistencies, redundancies, NOE completeness, classification and violations with respect to the original coordinates. Restraints that could not be associated with a known nomenclature were flagged. The coordinates of hydrogen atoms were recalculated from the positions of heavy atoms to allow for a full restraint analysis. The DOCR database contains restraint and coordinate data that is made consistent with each other and with IUPAC conventions. The FRED database is based on the DOCR data but is filtered for use by test calculation protocols and longitudinal analyses and validations. These two databases are available from websites of the BMRB and the Macromolecular Structure Database (MSD) in various formats: NMR-STAR, CCPN XML, and in formats suitable for direct use in the software packages CNS and CYANA. [ABSTRACT FROM AUTHOR]

The emerging antibiotics-resistance problem has underlined the urgent need for novel antimicrobial agents. Lantibiotics (lanthionine-containing antibiotics) are promising candidates to alleviate this problem. Nisin, a member of this family, has a unique pore-forming activity against bacteria. It binds to lipid II, the essential precursor of cell wall synthesis. As a result, the membrane permeabilization activity of nisin is increased by three orders of magnitude. Here we report the solution structure of the complex of nisin and lipid II. The structure shows a novel lipid II-binding motif in which the pyrophosphate moiety of lipid II is primarily coordinated by the N-terminal backbone amides of nisin via intermolecular hydrogen bonds. This cage structure provides a rationale for the conservation of the lanthionine rings among several lipid II-binding lantibiotics. The structure of the pyrophosphate cage offers a template for structure-based design of novel antibiotics. [ABSTRACT FROM AUTHOR]

Signal propagation in biological systems occurs through a series of inter- and intramolecular events, the precise pathways of which remain elusive in most cases. With respect to protein?DNA interactions in particular, little is known about the association and dissociation reaction pathways. Here we show that the exchange of amide protons detected by NMR can be used to characterize, at residue level, the mechanism, kinetics and thermodynamics of Lac headpiece (HP) interaction with DNA operators. Specific protein?DNA contacts responsible for the direct readout of the sequence are formed and broken at distinct time scales. Unfolding of the hinge helices triggers protein?DNA dissociation by progressive destabilization of distinct structural units, which is facilitated by the low stability of the protein in the uncomplexed state. Upon DNA binding, a dramatic alteration in the dynamics of the protein is observed, which may be used advantageously by the biological system to switch between functional states. Hydrogen-deuterium exchange can provide an unusually detailed view of the interaction mechanism of a protein?DNA complex and the associated energetics of DNA recognition with residue-level specificity. [ABSTRACT FROM AUTHOR]

The possibility of generating protein folds at the stage of backbone assignment using structural restraints derived from experimentally measured cross-hydrogen bond scalar couplings and secondary chemical shift information is investigated using as a test case the small α/β protein chymotrypsin inhibitor 2. Dihedral angle restraints for the φ and ψ angles of 32 out of 64 residues could be obtained from secondary chemical shift analysis with the TALOS program (Corneliscu et al., 1999a). This information was supplemented by 18 hydrogen-bond restraints derived from experimentally measured cross-hydrogen bond 3hbJNC′ coupling constants. These experimental data were sufficient to generate structures that are as close as 1.0 Å backbone rmsd from the crystal structure. The fold is, however, not uniquely defined and several solutions are generated that cannot be distinguished on the basis of violations or energetic considerations. Correct folds could be identified by combining clustering methods with knowledge-based potentials derived from structural databases. [ABSTRACT FROM AUTHOR]

Joint refinement, i.e., the simultaneous refinement of a structure against both nuclear magnetic resonance (NMR) spectroscopic and X-ray crystallographic data, was performed on the HU protein from Bacillus stearothermophilus (HUBst). The procedure was aimed at investigating the compatibility of the two data sets and at identifying conflicting information. Wherever important differences were found, such as peptide flips in the main-chain conformation, the data were further analyzed to find the cause. The NMR data showed some errors arising either from the manual interpretation of the spectra or from the incorrect account for spin diffusion. The most important artefact inherent to the X-ray data is the crystal packing of the molecules: the effects range from the limitation of the freedom of the flexible parts of the HUBst molecule to possibly one of the peptide flips. [ABSTRACT FROM AUTHOR]

The solution structure of the dimeric N-terminal domain of HIV-2 integrase (residues 1–55, named IN1-55) has been determined using NMR spectroscopy. The structure of the monomer, which was already reported previously [Eijkelenboom et al. (1997) Curr. Biol., 7, 739–746], consists of four α-helices and is well defined. Helices α1, α2 and α3 form a three-helix bundle that is stabilized by zinc binding to His12, His16, Cys40 and Cys43. The dimer interface is formed by the N-terminal tail and the first half of helix α3. The orientation of the two monomeric units with respect to each other shows considerable variation. 15N relaxation studies have been used to characterize the nature of the intermonomeric disorder. Comparison of the dimer interface with that of the well-defined dimer interface of HIV-1 IN1-55 shows that the latter is stabilized by additional hydrophobic interactions and a potential salt bridge. Similar interactions cannot be formed in HIV-2 IN1-55 [Cai et al. (1997) Nat. Struct. Biol., 4, 567–577], where the corresponding residues are positively charged and neutral ones. [ABSTRACT FROM AUTHOR]

15N-1H 1J couplings were measured at 500 MHz and 800 MHz for 15N enriched oxidized cytochrome b562 from E. coli. The magnetic field dependence of 70 1J values, which could be measured without signal overlap, shows that there is a molecular magnetic anisotropy which provides partial molecular orientation in the magnetic field and, consequently, residual dipolar couplings (rdc). The rdc were used as further constraints to improve the existing structure [Arnesano et al. (1999) Biochemistry, 38, 8657–8670] with a protocol which uses the rhombic anisotropy [Banci et al. (1998) J. Am. Chem. Soc., 120, 12903–12909]. The overall large molecular magnetic anisotropy has been found to be determined by both the low spin iron (III) and the four helix bundle structure magnetic susceptibility anisotropy contributions. [ABSTRACT FROM AUTHOR]

The tetrameric Mnt repressor is involved in the genetic switch between the lysogenic and lytic growth of Salmonella bacteriophage P22. The solution structure of its C-terminal tetramerization domain, which holds together the two dimeric DNA-binding domains, has been determined by NMR spectroscopy. This structure reveals an assembly of four α-helical subunits, consisting of a dimer of two antiparallel coiled coils with a unique right-handed twist. The superhelical winding is considerably stronger and the interhelical separation closer than those found in the well-known left-handed coiled coils in fibrous proteins and leucine zippers. An unusual asymmetry arises between the two monomers that comprise one right-handed coiled coil. A difference in the packing to the adjacent monomer of the other coiled coil occurs with an offset of two helical turns. The two asymmetric monomers within each coiled coil interconvert on a time scale of seconds. Both with respect to symmetry and handedness of helical packing, the C2 symmetric four-helix bundle of Mnt differs from other oligomerization domains that assemble DNA-binding modules, such as that in the tumor suppressor p53 and the E. coli lac repressor. [ABSTRACT FROM AUTHOR]

A pulse sequence is proposed to select water magnetization with enhanced specificity through a synergetic combination of several filtering principles. This approach relies on a constant-time evolution period implemented without quadrature detection, which results in a √2 increase in signal-to-noise ratios as compared to traditional non-selective methods for water filtration. In addition, the quadrature-free constant-time block facilitates the implementation of the water flip-back strategy, which leads to further gains in sensitivity. The proposed experiment was applied to unlabeled HEW lysozyme and to 15 N-labeled chymotrypsin inhibitor 2 which was partially or non 13C-enriched. Water molecules belonging to a spine of hydration between two pseudo β-sheet strands were identified, solving previously reported discrepancies between the X-ray and the refined NMR structure of CI2. The proposed experiment is particularly suitable for hydration studies of mixtures of labeled and unlabeled components, such as ligand–macromolecule complexes. [ABSTRACT FROM AUTHOR]

The structure and dynamics of the chymotryptic tetramerization domain of the Mnt repressor of Salmonella bacteriophage P22 have been studied by NMR spectroscopy. Two sets of resonances (A and B) were found, representing the asymmetry within the homotetramer. Triple-resonance techniques were used to obtain unambiguous assignments of the A and B resonances. Intra-monomeric NOEs, which were distinguished from the inter-monomeric NOEs by exploiting 13C/15N-filtered NOE experiments, demonstrated a continuous α-helix of approximately seven turns for both the A and B monomers. The asymmetry facilitated the interpretation of inter-subunit NOEs, whereas the antiparallel alignment of the subunits allowed further discrimination of inter-monomeric NOEs. The three-dimensional structure revealed an unusual asymmetric packing of a dimer of two antiparallel right-handed intertwined coiled α-helices. The A and B forms exchange on a timescale of seconds by a mechanism that probably involves a relative sliding of the two coiled coils. The amide proton solvent exchange rates demonstrate a stable tetrameric structure. The essential role of Tyr 78 in oligomerization of Mnt, found by previous mutagenesis studies, can be explained by the many hydrophobic and hydrogen bonding interactions that this residue participates in with adjacent monomers. [ABSTRACT FROM AUTHOR]

The completeness of experimentally observed NOE restraints of a set of 97 NMR protein structures deposited in the PDB has been assessed. Completeness is defined as the ratio of the number of experimentally observed NOEs and the number of 'expected NOEs'. A practical definition of 'expected NOEs' based on inter-proton distances in the structures up to a given cut-off distance is proposed. The average completeness for the set of 97 structures is 68, 48, and 26% up to 3, 4, and 5 Å cut-off distances, respectively. For recent state-of-the-art structures these numbers are approximately 90, 75, and 45%. Almost 20% of the observed NOEs are between atoms that are further than 5 Å apart in the final structures. The completeness is independent of the relative surface accessibility and does not depend strongly on residue type, secondary structure or local precision, although the number of observed NOEs in these classes varies considerably. The completeness of NOE restraints is a useful quality criterion in the course of structure refinement. The completeness per residue is more informative than the number of NOEs per residue, which makes it a useful tool to assess the quality of the NMR data set in relation to the resulting structures. [ABSTRACT FROM AUTHOR]

Slow protein dynamics can be studied by 15N spin-echo (CPMG) and off-resonance rotating frame relaxation through the effective field dependence of the exchange-mediated relaxation contribution. It is shown that, by a combination of these complementary techniques, a more extended sampling of the microsecond time scale processes is achieved than by either method alone. 15N R2 and improved off-resonance R1ρ experiments [Mulder et al. (1998) J. Magn. Reson., 131, 351–357] were applied to the 9- cis-retinoic acid receptor DNA-binding domain and allowed the identification of 14 residues exhibiting microsecond time scale dynamics. Assuming exchange between two conformational substates, average lifetimes ranging from 37 to 416 μs, and chemical shift differences of up to 3 ppm were obtained. The largest perturbation of tertiary structure was observed for the second zinc finger region, which was found to be disordered in the solution structure [Holmbeck et al. (1998) J. Mol. Biol., 281, 271–284]. Since this zinc-coordinating domain comprises the principal dimerization interface for RXR in a wide repertoire of complexes with different hormone receptors to their cognate response elements, this finding has important implications for our understanding of nuclear receptor assembly on DNA direct repeats. The flexibility observed for the dimerization domain may explain how RXR, through the ability to adaptively interact with a wide variety of highly homologous partner molecules, demonstrates such a versatile DNA-binding repertoire. [ABSTRACT FROM AUTHOR]

A pulse sequence is proposed which uses a train of band-selective pulses for the editing of slow chemical exchange-relay effects in experiments designed to study water-macromolecule interactions. Compared to previous methods, this experiment does not require knowledge of the exact chemical shift of the relaying labile protons and needs only the recording of a single experiment to edit the relay through different exchanging groups resonating at different frequencies. The pulse sequence has been implemented using Gaussian cascades and was applied to the study of the hydration of HEW lysozyme. [ABSTRACT FROM AUTHOR]

The human pentraxin serum amyloid P component (SAP) exhibits no microheterogeneity in its complex di-antennary glycan. To elucidate whether the removal of sialic acids from this glycoprotein might affect the accessibility of certain amino acid residues of the protein we employed the laser photo CIDNP approach as a sensitive tool. The CIDNP effect is generated by the interaction of a photoexcited dye with reactive amino acids and results in enhanced absorption- or emission-signals which can be observed for the three aromatic amino acids histidine, tryptophan, and tyrosine if they are accessible to the dye. Therefore, this technique can be applied to explore surface exposure of these amino acid residues. The respective spectra of SAP and enzymatically desialylated SAP were determined. Six tryptophan/histidine signals and one tyrosine signal are present in the aromatic part of the CIDNP difference spectrum of SAP. The corresponding spectrum of desialylated SAP shows remarkable alterations. The chemical shift of one Trp/His-characteristic signal is decreased by 0.1 ppm. One Trp/His-signal disappeared and a new one was formed in the CIDNP difference spectrum of desialylated SAP, while the other signals were unaffected. The Tyr signal has a clearly enhanced intensity in desialylated SAP. Therefore, the removal of sialic acid moieties from the single N-glycan of each monomer apparently affects surface presentation of distinct CIDNP-reactive amino acids of SAP [1]. A conformational change of the protein part of SAP in relation with a different orientation of the desialylated oligosaccharide chain in comparison to the complete one is a possible explanation of our CIDNP results. [ABSTRACT FROM AUTHOR]

The side chains of tyrosine, tryptophan and histidine are able to produce CIDNP (Chemically Induced Dynamic Nuclear Polarization) signals after laser irradiation in the presence of a suitable radical pair-generating dye. Elicitation of such a response in proteins implies surface accessibility of the respective groups to the light-absorbing dye. In principle, this technique allows the monitoring of the effect of ligand binding to a receptor and of site-directed mutagenesis on conformational aspects of any protein if CIDNP-reactive amino acids are involved. The application of this method in glycosciences can provide insights into the protein-carbohydrate interaction process, as illustrated in this initial model study for several N-acetyl-glucosamine-binding lectins of increasing structural complexity as well as for a wild type bacterial sialidase and its mutants. Experimentally, the shape and intensity of CIDNP signals are determined in the absence and in the presence of specific glycoligands. When the carbohydrate is bound, CIDNP signals of side chain protons of tyrosine, tryptophan or histidine residues can be broadened and of reduced intensity. This is the case for hevein, pseudo-hevein, the four hevein domains-containing lectin wheat germ agglutinin (WGA) and the cloned B-domain of WGA 1 (domB) representing one hevein domain. This response indicates either a spatial protection by the ligand or a ligand-induced positioning of formerly surface-exposed side chains into the protein’s interior part, thereby precluding interaction with the photo-activated dye. Some signals of protons from the reactive side chains can even disappear when the lectin-ligand complexes are monitored. The ligand binding, however, can apparently also induce a conformational change in a related lectin that causes the appearance of a new signal, as seen for Urtica dioica agglutinin (UDA) which consists of two hevein domains. Additionally, the three CIDNP-reactive amino acids are used as sensors for the detection of conformational changes caused by pH variations or by deliberate amino acid exchanges, as determined for the isolectins hevein and pseudo-hevein as well as for the cloned small sialidase of Clostridium perfringens and two of its mutants. Therefore, CIDNP has proven to be an excellent tool for protein-carbohydrate binding studies and can be established in glycosciences as a third biophysical method beside X-ray-crystallography and high-resolution multidimensional NMR studies which provides reliable information of certain structural aspects of carbohydrate-binding proteins in solution. [ABSTRACT FROM AUTHOR]

Galectins (Galactose binding lectins) from bacteria, plants and animals have been shown to possess tyrosine or tryptophan residues that form hydrophobic contacts with their ligands in the binding sites. At the present time, the X-ray structures of only two galectins from human and bovine tissues are known. In the present study we applied X-ray data of bovine heart galectin-1 as a template for homology modelling of a number of galectins from mammalian and avian tissues. The conservation of one tryptophan and at least one histidine in binding pocket can be observed from the comparison of the model structures. We also show that it is possible to obtain information of the architecture of the binding pocket of several galectins in solution using CIDNP (Chemically Induced Dynamic Nuclear Polarisation) techniques. The CIDNP approach offers a possibility to analyse these lectins in solution thereby providing supplementary information to the available X-ray data. All studied galectins show comparable alterations when they are recorded by CIDNP-technique in the absence and in the presence of their specific carbohydrate ligands. [ABSTRACT FROM AUTHOR]

The success of knowledge-based homology modelling is critically dependent on the predictive potency of the program structure-based calculations, which attempt to translate homologous sequences into three-dimensional structures, and on the actual relevance of the crystal structure for the protein topology. As quality control, experimental data for selected parameters of the protein′s conformation are required. Using the crystal structure of the sialidase of Salmonella typhimurium as framework for model building of the homologous enzyme from Clostridium perfringens, a set of energy-minimised conformers is derived. These proteins present e.g. Tyr, Trp and His residues with an assessable area on the surface, since the side chains of these amino acid residues are responsive to chemically induced dynamic nuclear polarization (CIDNP), monitored by NMR. Hence, as first lesson, a comparative analysis for model-derived and experimentally determined values can be performed. The second lesson of this study concerns the notable impact of single amino acid substitutions (Tyr/Phe, Cys/Ser) on the surface accessibility of the CIDNP-reactive amino acid side chains in mutant forms of the sialidase. Corroborating the predictions from the theoretical calculations, the spectra of the engineered mutants reveal marked and non-uniform alterations. Thus, the effect of apparently rather conservative amino acid substitutions on a distinct conformational aspect of this protein, even at distant sites, should not be underestimated. [ABSTRACT FROM AUTHOR]

The recommendations presented here are designed to support easier communication of NMR data and NMR structures of proteins and nucleic acids through unified nomenclature and reporting standards. Much of this document pertains to the reporting of data in journal articles; however, in the interest of the future development of structural biology, it is desirable that the bulk of the reported information be stored in computer-accessible form and be freely accessible to the scientific community in standardized formats for data exchange. These recommendations stem from an IUPAC-IUBMB-IUPAB inter-union venture with the direct involvement of ICSU and CODATA. The Task Group has reviewed previous formal recommendations and has extended them in the light of more recent developments in the field of biomolecular NMR spectroscopy. Drafts of the recommendations presented here have been examined critically by more than 50 specialists in the field and have gone through two rounds of extensive modification to incorporate suggestions and criticisms. [ABSTRACT FROM AUTHOR]

The dynamics of the backbone NH bonds of protein HU from Bacillus stearothermophilus (HUBst) have been characterized using measurements of cross-relaxation, longitudinal and transverse relaxation rates $$({\text{R}}_{\text{N}} ({\text{H}}_{\text{z}} \leftrightarrow {\text{N}}_{\text{z}} ),{\text{R}}_{\text{N}} {\text{(N}}_{\text{z}} ){\text{ and R}}_{\text{N}} ({\text{N}}_{{\text{x,y}}} ))$$ at 11.7, 14.1 and 17.6 T. Linear regression of the values $$2{\text{R}}_{\text{N}} ({\text{N}}_{{\text{x,y}}} ) - {\text{R}}_{\text{N}} ({\text{N}}_{\text{Z}} )$$ with the squared Larmor frequency ω has revealed global exchange processes, which contributed on the order of 0.5–5.0 s-1to the transverse relaxation rate. Subsequently, the experimental values $${\text{R}}_{\text{N}} ({\text{N}}_{{\text{x,y}}} )$$ were corrected for these exchange contributions. A reduced spectral density mapping procedure has been employed with the experimental relaxation rates and seven values of the spectral density function J(ω) have been extracted. These spectral densities have been fitted within the framework of the model-free approach. The densities agree well with an axially symmetric rotational diffusion tensor with a diffusion anisotropy D_∥/D_⊥ of 1.15, indicating that the flexible arms of HUBst do not significantly contribute to the rotational diffusion. The overall correlation time is 8.9 ± 0.6 ns/rad. The fast internal motions of most of the NH bonds in the core display order parameters ranging between 0.74 and 0.83 and internal correlation times between 1 and 20 ps. For the residues in the DNA-binding β-arms, an extended version of the model function has been used. The slow internal motions show correlation times of 1–2 ns. The concomitant order parameters (0.3–0.6) are lower than those observed on the fast time scale, indicating that the flexibility of the β-arms is mainly determined by the slower internal motions. A substantial decrease of the generalized order parameters in the β-arms starting at residues Arg55 and Ser74, opposite on both strands of the β-ribbon arms, has been explained as a ‘hinge’ motion. A comparison of the order parameters for free and DNA-bound protein has demonstrated that the slow hinge motions largely disappear when HU binds DNA. [ABSTRACT FROM AUTHOR]

A modified HNHB experiment is presented that allows thedetermination of J(NH) coupling constants directly from the ratio ofcross-peak to diagonal-peak intensities. The experiment was applied to thephotoactive yellow protein (PYP) and yielded the magnitude of 1173J(NHβ) coupling constants. In addition, 293J(NHα(i−1)) coupling constantscould be measured, providing information about the backbone angle ψ.These data, in conjunction with the magnitudes of the3J(HNHα) coupling constantsobtained from the HNHA spectrum, effectively discriminate the twopossibilities for the stereospecific assignment of theHα resonances in glycine residues. For all eight glycineresidues in PYP that were not subject to conformational averaging and hadnon-degenerate Hα resonance frequencies, the J-couplingdata, together with limited NOE data, yielded the stereospecific assignmentof the Hα resonances for these residues. In addition,reliable and precise φ,ψ dihedral constraints were also derived forthese residues from the J-coupling data. [ABSTRACT FROM AUTHOR]

A new method to selectively detect the ring resonances of the aromatic residues in 15N-labelled proteins is presented. The experiment consists of a 2D 1H TOCSY sequence withremoval of the amide signals via 15N-filtering. Experiments are acquired in the absence andpresence of water inversion; combining the two spectra allows selective observation of thetyrosine ring resonances and enables the identification of their δ andε ring protons. The experiment is demonstrated on a 15N-labelled sample of Photoactive Yellow Protein and isshown to give good selectivity for tyrosine ring resonances under a wide range oftemperatures and pH values. [ABSTRACT FROM AUTHOR]

Light irradiation of photoactive yellow protein (PYP) induces a photocycle, in which red-shifted (pR) and blue-shifted (pB) intermediates have been characterized. An NMR study of the long-lived pB intermediate now reveals that it exhibits a large degree of disorder and exists as a family of multiple conformers that exchange on a millisecond time scale. This shows that the behavior of PYP in solution is different from what has been observed in the crystalline state. Furthermore, differential refolding to ground state pG is observed, whereby the central β-sheet and parts of the helical structure are formed first and the region around the chromophore at a later stage. [ABSTRACT FROM AUTHOR]