Zα Domain of ADAR1 Binds to an A-Form-like Nucleic Acid Duplex with Low Micromolar Affinity

The left-handed Z-conformation of nucleic acids can be adopted by both DNA and RNA when bound by Zα domains found within a variety of viral and innate immune response proteins. While Z-form adoption is preferred by certain sequences, such as the commonly studied (CpG)n repeats, Zα has been reported to bind to a wide range of sequence contexts. Studying how Zα interacts with B-/A-form helices prior to their conversion to the Z-conformation is challenging as binding coincides with Z-form adoption. Here, we studied the binding of Zα fromHomo sapiens ADAR1 to a locked "A-type" version of the (CpG)3 construct (LNA (CpG)3) where the sugar pucker is locked into the C3'-endo/C2'-exo conformation, which prevents the duplex from adopting the alternating C2'/C3'-endo sugar puckers found in the Z-conformation. Using NMR and other biophysical techniques, we find that ZαADAR1 binds to the LNA (CpG)3 using a similar interface as for Z-form binding, with a dissociation constant (KD) of ∼4 μM. In contrast to Z-DNA/Z-RNA, where two ZαADAR1 bind to every 6 bp stretch, our data suggests that ZαADAR1 binds to multiple LNA molecules, indicating a completely different binding mode. Because ZαADAR1 binds relatively tightly to a non-Z-form model, its binding to B/A-form helices may need to be considered when experiments are carried out which attempt to identify the Z-form targets of Zα domains. The use of LNA constructs may be beneficial in experiments where negative controls for Z-form adoption are needed.

Z-Form Adoption of Nucleic Acid is a Multi-Step Process Which Proceeds through a Melted Intermediate

The left-handed Z-conformation of nucleic acids can be adopted by both DNA and RNA when bound by Zα domains found within a variety of innate immune response proteins. Zα domains stabilize this higher-energy conformation by making specific interactions with the unique geometry of Z-DNA/Z-RNA. However, the mechanism by which a right-handed helix contorts to become left-handed in the presence of proteins, including the intermediate steps involved, is poorly understood. Through a combination of nuclear magnetic resonance (NMR) and other biophysical measurements, we have determined that in the absence of Zα, under low salt conditions at room temperature, d(CpG) and r(CpG) constructs show no observable evidence of transient Z-conformations greater than 0.5% on either the intermediate or slow NMR time scales. At higher temperatures, we observed a transient unfolded intermediate. The ease of melting a nucleic acid duplex correlates with Z-form adoption rates in the presence of Zα. The largest contributing factor to the activation energies of Z-form adoption as calculated by Arrhenius plots is the ease of flipping the sugar pucker, as required for Z-DNA and Z-RNA. Together, these data validate the previously proposed "zipper model" for Z-form adoption in the presence of Zα. Overall, Z-conformations are more likely to be adopted by double-stranded DNA and RNA regions flanked by less stable regions and by RNAs experiencing torsional/mechanical stress.

Differential Structural Features of Two Mutant ADAR1p150 Zα Domains Associated with Aicardi-Goutières Syndrome

The Zα domain of ADARp150 is critical for proper Z-RNA substrate binding and is a key factor in the type-I interferon response pathway. Two point-mutations in this domain (N173S and P193A), which cause neurodegenerative disorders, are linked to decreased A-to-I editing in disease models. To understand this phenomenon at the molecular level, we biophysically and structurally characterized these two mutated domains, revealing that they bind Z-RNA with a decreased affinity. Less efficient binding to Z-RNA can be explained by structural changes in beta-wing, part of the Z-RNA-protein interface, and alteration of conformational dynamics of the proteins.

Z-RNA biology: a central role in the innate immune response?

Z-RNA is a higher-energy, left-handed conformation of RNA, whose function has remained elusive. A growing body of work alludes to regulatory roles for Z-RNA in the immune response. Here, we review how Z-RNA features present in cellular RNAs-especially containing retroelements-could be recognized by a family of winged helix proteins, with an impact on host defense. We also discuss how mutations to specific Z-contacting amino acids disrupt their ability to stabilize Z-RNA, resulting in functional losses. We end by highlighting knowledge gaps in the field, which, if addressed, would significantly advance this active area of research.

Structure and Formation of Z-DNA and Z-RNA

Despite structural differences between the right-handed conformations of A-RNA and B-DNA, both nucleic acids adopt very similar, left-handed Z-conformations. In contrast to their structural similarities and sequence preferences, RNA and DNA exhibit differences in their ability to adopt the Z-conformation regarding their hydration shells, the chemical modifications that promote the Z-conformation, and the structure of junctions connecting them to right-handed segments. In this review, we highlight the structural and chemical properties of both Z-DNA and Z-RNA and delve into the potential factors that contribute to both their similarities and differences. While Z-DNA has been extensively studied, there is a gap of knowledge when it comes to Z-RNA. Where such information is lacking, we try and extend the principles of Z-DNA stability and formation to Z-RNA, considering the inherent differences of the nucleic acids.

Adoption of A-Z Junctions in RNAs by Binding of Zα Domains

While DNA and RNA helices often adopt the canonical B- or A-conformation, the fluid conformational landscape of nucleic acids allows for many higher energy states to be sampled. One such state is the Z-conformation of nucleic acids, which is unique in that it is left-handed and has a "zigzag" backbone. The Z-conformation is recognized and stabilized by Z-DNA/RNA binding domains called Zα domains. We recently demonstrated that a wide range of RNAs can adopt partial Z-conformations termed "A-Z junctions" upon binding to Zα and that the formation of such conformations may be dependent upon both sequence and context. In this chapter, we present general protocols for characterizing the binding of Zα domains to A-Z junction-forming RNAs for the purpose of determining the affinity and stoichiometry of interactions as well as the extent and location of Z-RNA formation.

Slow methyl axes motions in perdeuterated villin headpiece subdomain probed by cross-correlated NMR relaxation measurements

Protein methyl groups can participate in multiple motional modes on different time scales. Sub-nanosecond to nano-second time scale motions of methyl axes are particularly challenging to detect for small proteins in solutions. In this work we employ NMR relaxation interference between the methyl H-H/H-C dipole-dipole interactions [Sun&Tugarinov, J. Magn. Reason. 2012] to characterize methyl axes motions as a function of temperature in a small model protein villin headpiece subdomain (HP36), in which all non-exchangeable protons are deuterated with the exception of methyl groups of leucine and valine residues. The data points to the existence of slow motional modes of methyl axes on sub-nanosecond to nanosecond time scales. Further, at high temperatures for which the overall tumbling of the protein is on the order of 2 ns, we observe a coupling between the slow internal motion and the overall molecular tumbling, based on the anomalous order parameters and their temperature-dependent trends. The addition of 28%(w/w) glycerol-d8 increases the viscosity of the solvent and separates the timescales of internal and overall tumbling, thus permitting for another view of the necessity of the coupling assumption for these sites at high temperatures.

On the use of residual dipolar couplings in multi-state structure calculation of two-domain proteins

Residual dipolar couplings (RDCs) are powerful nuclear magnetic resonance (NMR) probes for the structure calculation of biomacromolecules. Typically, an alignment tensor that defines the orientation of the entire molecule relative to the magnetic field is determined either before refinement of individual bond vectors or simultaneously with this refinement. For single-domain proteins this approach works well since all bond vectors can be described within the same coordinate frame, which is given by the alignment tensor. However, novel approaches are sought after for systems where no universal alignment tensor can be used. Here, we present an approach that can be applied to two-domain proteins that enables the calculation of multiple states within each domain as well as with respect to the relative positions of the two domains.

Reconstruction of Coupled Intra- and Interdomain Protein Motion from Nuclear and Electron Magnetic Resonance

Proteins composed of multiple domains allow for structural heterogeneity and interdomain dynamics that may be vital for function. Intradomain structures and dynamics can influence interdomain conformations and vice versa. However, no established structure determination method is currently available that can probe the coupling of these motions. The protein Pin1 contains separate regulatory and catalytic domains that sample "extended" and "compact" states, and ligand binding changes this equilibrium. Ligand binding and interdomain distance have been shown to impact the activity of Pin1, suggesting interdomain allostery. In order to characterize the conformational equilibrium of Pin1, we describe a novel method to model the coupling between intra- and interdomain dynamics at atomic resolution using multistate ensembles. The method uses time-averaged nuclear magnetic resonance (NMR) restraints and double electron-electron resonance (DEER) data that resolve distance distributions. While the intradomain calculation is primarily driven by exact nuclear Overhauser enhancements (eNOEs), J couplings, and residual dipolar couplings (RDCs), the relative domain distribution is driven by paramagnetic relaxation enhancement (PREs), RDCs, interdomain NOEs, and DEER. Our data support a 70:30 population of the compact and extended states in apo Pin1. A multistate ensemble describes these conformations simultaneously, with distinct conformational differences located in the interdomain interface stabilizing the compact or extended states. We also describe correlated conformations between the catalytic site and interdomain interface that may explain allostery driven by interdomain contact.

Solution NMR backbone assignments of the N-terminal Zα-linker-Zβ segment from Homo sapiens ADAR1p150

Adenosine-to-inosine (A-to-I) editing of a subset of RNAs in a eukaryotic cell is required in order to avoid triggering the innate immune system. Editing is carried out by ADAR1, which exists as short (p110) and long (p150) isoforms. ADAR1p150 is mostly cytoplasmic, possesses a Z-RNA binding domain (Zα), and is only expressed during the innate immune response. A structurally homologous domain to Zα, the Zβ domain, is separated by a long linker from Zα on the N-terminus of ADAR1 but its function remains unknown. Zβ does not bind to RNA in isolation, yet the binding kinetics of the segment encompassing Zα, Zβ and the 95-residue linker between the two domains (Zα-Zβ) are markedly different compared to Zα alone. Here we present the solution NMR backbone assignment of Zα-Zβ from H. Sapiens ADAR1. The predicted secondary structure of Zα-Zβ based on chemical shifts is in agreement with previously determined structures of Zα and Zβ in isolation, and indicates that the linker is intrinsically disordered. Comparison of the chemical shifts between the individual Zα and Zβ domains to the full Zα-Zβ construct suggests that Zβ may interact with the linker, the function of which is currently unknown.

The Inherent Dynamics and Interaction Sites of the SARS-CoV-2 Nucleocapsid N-Terminal Region

The nucleocapsid protein is one of four structural proteins encoded by SARS-CoV-2 and plays a central role in packaging viral RNA and manipulating the host cell machinery, yet its dynamic behavior and promiscuity in nucleotide binding has made standard structural methods to address its atomic-resolution details difficult. To begin addressing the SARS-CoV-2 nucleocapsid protein interactions with both RNA and the host cell along with its dynamic behavior, we have specifically focused on the folded N-terminal domain (NTD) and its flanking regions using nuclear magnetic resonance solution studies. Studies performed here reveal a large repertoire of interactions, which includes a temperature-dependent self-association mediated by the disordered flanking regions that also serve as binding sites for host cell cyclophilin-A while nucleotide binding is largely mediated by the central NTD core. NMR studies that include relaxation experiments have revealed the complicated dynamic nature of this viral protein. Specifically, while much of the N-terminal core domain exhibits micro-millisecond motions, a central β-hairpin shows elevated inherent flexibility on the pico-nanosecond timescale and the serine/arginine-rich region of residues 176-209 undergoes multiple exchange phenomena. Collectively, these studies have begun to reveal the complexities of the nucleocapsid protein dynamics and its preferred interaction sites with its biological targets.

Reducing the measurement time of exact NOEs by non-uniform sampling

We have previously reported on the measurement of exact NOEs (eNOEs), which yield a wealth of additional information in comparison to conventional NOEs. We have used these eNOEs in a variety of applications, including calculating high-resolution structures of proteins and RNA molecules. The collection of eNOEs is challenging, however, due to the need to measure a NOESY buildup series consisting of typically four NOESY spectra with varying mixing times in a single measurement session. While the 2D version can be completed in a few days, a fully sampled 3D-NOESY buildup series can take 10 days or more to acquire. This can be both expensive as well as problematic in the case of samples that are not stable over such a long period of time. One potential method to significantly decrease the required measurement time of eNOEs is to use non-uniform sampling (NUS) to decrease the number of points measured in the indirect dimensions. The effect of NUS on the extremely tight distance restraints extracted from eNOEs may be very pronounced. Therefore, we investigated the fidelity of eNOEs measured from three test cases at decreasing NUS densities: the 18.4 kDa protein human Pin1, the 4.1 kDa WW domain of Pin1 (both in 3D), and a 4.6 kDa 14mer RNA UUCG tetraloop (2D). Our results show that NUS imparted negligible error on the eNOE distances derived from good quality data down to 10% sampling for all three cases, but there is a noticeable decrease in the eNOE yield that is dependent upon the underlying sparsity, and thus complexity, of the sample. For Pin1, this transition occurred at roughly 40% while for the WW domain and the UUCG tetraloop it occurred at lower NUS densities of 20% and 10%, respectively. We rationalized these numbers through reconstruction simulations under various conditions. The extent of this loss depends upon the number of scans taken as well as the number of peaks to be reconstructed. Based on these findings, we have created guidelines for choosing an optimal NUS density depending on the number of peaks needed to be reconstructed in the densest region of a 2D or 3D NOESY spectrum.

A New Subclass of Exoribonuclease-Resistant RNA Found in Multiple Genera of Flaviviridae

Viruses have developed innovative strategies to exploit the cellular machinery and overcome the antiviral defenses of the host, often using specifically structured RNA elements. Examples are found in the Flavivirus genus (in the family Flaviviridae), where during flaviviral infection, pathogenic subgenomic flaviviral RNAs (sfRNAs) accumulate in the cell. These sfRNAs are formed when a host cell 5' to 3' exoribonuclease degrades the viral genomic RNA but is blocked by an exoribonuclease-resistant RNA structure (xrRNA) located in the viral genome's 3' untranslated region (UTR). Although known to exist in several Flaviviridae genera, the full distribution and diversity of xrRNAs in this family were unknown. Using the recently solved high-resolution structure of an xrRNA from the divergent flavivirus Tamana bat virus (TABV) as a reference, we used bioinformatic searches to identify xrRNAs in the remaining three genera of Flaviviridae: Pegivirus, Pestivirus, and Hepacivirus We biochemically and structurally characterized several examples, determining that they are genuine xrRNAs with a conserved fold. These new xrRNAs look superficially similar to the previously described xrRNAs but possess structural differences making them distinct from previous classes of xrRNAs. Overall, we have identified the presence of xrRNA in all four genera of Flaviviridae, but not in all species. Our findings thus require adjustments of previous xrRNA classification schemes and expand the previously known distribution of xrRNA in Flaviviridae.IMPORTANCE The members of the Flaviviridae comprise one of the largest families of positive-sense single-stranded RNA (+ssRNA) and are divided into the Flavivirus, Pestivirus, Pegivirus, and Hepacivirus genera. The genus Flavivirus contains many medically relevant viruses such as Zika virus, dengue virus, and Powassan virus. In these, a part of the RNA of the virus twists up into a distinct three-dimensional shape called an exoribonuclease-resistant RNA (xrRNA) that blocks the ability of the cell to "chew up" the viral RNA. Hence, part of the RNA of the virus remains intact, and this protected part is important for viral infection. These xrRNAs were known to occur in flaviviruses, but whether they existed in the other members of the family was not known. In this study, we identified a new subclass of xrRNA found not only in flaviviruses but also in the remaining three genera. The fact that these structured viral RNAs exist throughout the Flaviviridae family suggests they are important parts of the infection strategy of diverse pathogens, which could lead to new avenues of research.

Integrating NMR and simulations reveals motions in the UUCG tetraloop

We provide an atomic-level description of the structure and dynamics of the UUCG RNA stem-loop by combining molecular dynamics simulations with experimental data. The integration of simulations with exact nuclear Overhauser enhancements data allowed us to characterize two distinct states of this molecule. The most stable conformation corresponds to the consensus three-dimensional structure. The second state is characterized by the absence of the peculiar non-Watson-Crick interactions in the loop region. By using machine learning techniques we identify a set of experimental measurements that are most sensitive to the presence of non-native states. We find that although our MD ensemble, as well as the consensus UUCG tetraloop structures, are in good agreement with experiments, there are remaining discrepancies. Together, our results show that (i) the MD simulation overstabilize a non-native loop conformation, (ii) eNOE data support its presence with a population of ≈10% and (iii) the structural interpretation of experimental data for dynamic RNAs is highly complex, even for a simple model system such as the UUCG tetraloop.

NWChem: Past, present, and future

Specialized computational chemistry packages have permanently reshaped the landscape of chemical and materials science by providing tools to support and guide experimental efforts and for the prediction of atomistic and electronic properties. In this regard, electronic structure packages have played a special role by using first-principle-driven methodologies to model complex chemical and materials processes. Over the past few decades, the rapid development of computing technologies and the tremendous increase in computational power have offered a unique chance to study complex transformations using sophisticated and predictive many-body techniques that describe correlated behavior of electrons in molecular and condensed phase systems at different levels of theory. In enabling these simulations, novel parallel algorithms have been able to take advantage of computational resources to address the polynomial scaling of electronic structure methods. In this paper, we briefly review the NWChem computational chemistry suite, including its history, design principles, parallel tools, current capabilities, outreach, and outlook.

Deuteration of nonexchangeable protons on proteins affects their thermal stability, side-chain dynamics, and hydrophobicity

We have investigated the effect of deuteration of non-exchangeable protons on protein global thermal stability, hydrophobicity, and local flexibility using well-known thermostable model systems such as the villin headpiece subdomain (HP36) and the third immunoglobulin G-binding domain of protein G (GB3). Reversed-phase high-performance liquid chromatography (RP-HPLC) measurements as a function of temperature probe global thermal stability in the presence of acetonitrile, while differential scanning calorimetry determines thermal stability in solution. Both indicate small but measurable changes in the order of several degrees. RP-HPLC also permitted quantification of the effect of deuteration of just three core phenylalanine side chains of HP36. NMR dynamics investigation has focused on methyl axes motions using cross-correlated relaxation measurements. The analysis of order parameters provided a complex picture indicating that deuteration generally increases motional amplitudes of sub-nanosecond motion in GB3 but decreases those in HP36. Combined with earlier dynamics measurements at C_α -C_β sites and backbone sites of GB3, which probed slower time scales, the results point to the need to probe multiple atoms in the protein and variety of time scales to the discern the full complexity of the effects of deuteration on dynamics.

Solution NMR backbone assignment reveals interaction-free tumbling of human lineage-specific Olduvai protein domains

Olduvai protein domains, encoded primarily by NBPF genes, have been linked to both human brain evolution and cognitive diseases such as autism and schizophrenia. There are six primary domains that comprise the Olduvai family: three conserved domains (CON1-3) and three human lineage-specific domains (HLS1-3), which typically occur as a triplet (HLS1, HLS2 and HLS3). Herein, we present the solution NMR assignment of the backbone chemical shifts of the separate HLS1, 2 and 3 domains of NBPF15. Our data suggest that there is no change in the structure of the separate domains when compared to the full-length triplet (HLS1-HLS2-HLS3). We also demonstrate that there is no direct interaction between the three domains.

Backbone and side-chain chemical shift assignments of full-length, apo, human Pin1, a phosphoprotein regulator with interdomain allostery

Pin1 is a human peptidyl-prolyl cis-trans isomerase important for the regulation of phosphoproteins that are implicated in many diseases including cancer and Alzheimer's. Further biophysical study of Pin1 will elucidate the importance of the two-domain system to regulate its own activity. Here, we report near-complete backbone and side-chain ¹H, ¹³C and ¹⁵N NMR chemical shift assignments of full-length, apo Pin1 for the purpose of studying interdomain allostery and dynamics.

A transient helix in the disordered region of dynein light intermediate chain links the motor to structurally diverse adaptors for cargo transport

All animal cells use the motor cytoplasmic dynein 1 (dynein) to transport diverse cargo toward microtubule minus ends and to organize and position microtubule arrays such as the mitotic spindle. Cargo-specific adaptors engage with dynein to recruit and activate the motor, but the molecular mechanisms remain incompletely understood. Here, we use structural and dynamic nuclear magnetic resonance (NMR) analysis to demonstrate that the C-terminal region of human dynein light intermediate chain 1 (LIC1) is intrinsically disordered and contains two short conserved segments with helical propensity. NMR titration experiments reveal that the first helical segment (helix 1) constitutes the main interaction site for the adaptors Spindly (SPDL1), bicaudal D homolog 2 (BICD2), and Hook homolog 3 (HOOK3). In vitro binding assays show that helix 1, but not helix 2, is essential in both LIC1 and LIC2 for binding to SPDL1, BICD2, HOOK3, RAB-interacting lysosomal protein (RILP), RAB11 family-interacting protein 3 (RAB11FIP3), ninein (NIN), and trafficking kinesin-binding protein 1 (TRAK1). Helix 1 is sufficient to bind RILP, whereas other adaptors require additional segments preceding helix 1 for efficient binding. Point mutations in the C-terminal helix 1 of Caenorhabditis elegans LIC, introduced by genome editing, severely affect development, locomotion, and life span of the animal and disrupt the distribution and transport kinetics of membrane cargo in axons of mechanosensory neurons, identical to what is observed when the entire LIC C-terminal region is deleted. Deletion of the C-terminal helix 2 delays dynein-dependent spindle positioning in the one-cell embryo but overall does not significantly perturb dynein function. We conclude that helix 1 in the intrinsically disordered region of LIC provides a conserved link between dynein and structurally diverse cargo adaptor families that is critical for dynein function in vivo.

A highly conserved mechanism links the microtubule minus end–directed motor dynein to structurally diverse cargo adaptors through its light intermediate chain; this interaction is crucial for dynein function in vivo.

The large size and complex organization of animal cells make the correct and efficient distribution of intracellular content a challenge. The solution is to use motor proteins, which harness energy from ATP hydrolysis to walk along actin filaments or microtubules, for directional transport of cargo. The multi-subunit motor cytoplasmic dynein 1 (dynein) is responsible for transport directed toward the minus ends of microtubules. An important question is how dynein is recruited to its diverse cargo, which includes organelles such as endosomes and mitochondria, proteins, and mRNA. In this study, we use nuclear magnetic resonance spectroscopy to show that the light intermediate chain (LIC) subunit of human dynein uses a short helix in its disordered C-terminal region to bind structurally distinct adaptor proteins that connect the motor to specific cargo. We then use genome editing in the animal model C. elegans to demonstrate the functional relevance of the C-terminal LIC helix for dynein-dependent cargo transport in neurons. Thus, dynein recruitment to cargo involves a highly conserved interaction between LIC and adaptor proteins.

Correlated motions of C'-N and Cα-Cβ pairs in protonated and per-deuterated GB3

We investigated correlated µs-ms time scale motions of neighboring ¹³C'-¹⁵N and ¹³C_α-¹³C_β nuclei in both protonated and perdeuterated samples of GB3. The techniques employed, NMR relaxation due to cross-correlated chemical shift modulations, specifically target concerted changes in the isotropic chemical shifts of the two nuclei associated with spatial fluctuations. Field-dependence of the relaxation rates permits identification of the parameters defining the chemical exchange rate constant under the assumption of a two-site exchange. The time scale of motions falls into the intermediate to fast regime (with respect to the chemical shift time scale, 100-400 s^-1 range) for the ¹³C'-¹⁵N pairs and into the slow to intermediate regime for the ¹³C_α-¹³C_β pairs (about 150 s^-1). Comparison of the results obtained for protonated and deuterated GB3 suggests that deuteration has a tendency to reduce these slow scale correlated motions, especially for the ¹³C_α-¹³C_β pairs.

Extending the Applicability of Exact Nuclear Overhauser Enhancements to Large Proteins and RNA

Distance-dependent nuclear Overhauser enhancements (NOEs) are one of the most popular and important experimental restraints for calculating NMR structures. Despite this, they are mostly employed as semiquantitative upper distance bounds, and this discards the wealth of information that is encoded in the cross-relaxation rate constant. Information that is lost includes exact distances between protons and dynamics that occur on the sub-millisecond timescale. Our recently introduced exact measurement of the NOE (eNOE) requires little additional experimental effort relative to other NMR observables. So far, we have used eNOEs to calculate multistate ensembles of proteins up to approximately 150 residues. Here, we briefly revisit eNOE methodology and present two new directions for the use of eNOEs: applications to large proteins and RNA.

High-resolution small RNA structures from exact nuclear Overhauser enhancement measurements without additional restraints

RNA not only translates the genetic code into proteins, but also carries out important cellular functions. Understanding such functions requires knowledge of the structure and dynamics at atomic resolution. Almost half of the published RNA structures have been solved by nuclear magnetic resonance (NMR). However, as a result of severe resonance overlap and low proton density, high-resolution RNA structures are rarely obtained from nuclear Overhauser enhancement (NOE) data alone. Instead, additional semi-empirical restraints and labor-intensive techniques are required for structural averages, while there are only a few experimentally derived ensembles representing dynamics. Here we show that our exact NOE (eNOE) based structure determination protocol is able to define a 14-mer UUCG tetraloop structure at high resolution without other restraints. Additionally, we use eNOEs to calculate a two-state structure, which samples its conformational space. The protocol may open an avenue to obtain high-resolution structures of small RNA of unprecedented accuracy with moderate experimental efforts.

An Efficient Synthesis of the Taxane-Derived Anticancer Agent ABT-271

ABT-271, 1, has been identified as a promising anticancer agent. ABT-271 is a novel taxane possessing a C9-(R)-hydroxyl group as opposed to a C9-ketone which is present in Taxol and Taxotere. To further evaluate ABT-271 as a potential anticancer agent, an efficient synthesis was developed which allows the large scale synthesis of ABT-271. Ketalization of the 7,9-diol of 9-DHAB-III, 2, allows selective removal of the C13-acetate with phenyllithium. The resulting C13-hydroxyl group is then acylated using LiHMDS and beta-lactam 22 to give ABT-271 in protected form. The protecting groups were removed first by acidic hydrolysis followed by basic hydrolysis to provide ABT-271. Application of this synthetic sequence provided over 600 g of ABT-271, 1.

Synthesis of the C-13 side chain precursors of the 9-dihydrotaxane analogue ABT-271

N-Boc-L-Leucinol was converted to two C-13 side chain precursors of the 9-dihydrotaxane analogue ABT-271. The trans-oxazolidine acid 4 and the cis-Boc-lactam 2b were prepared in 44% and 40% overall yield, respectively, and with excellent (>98%) stereochemical purity.

Metastatic malignant melanoma: an unusual case presentation

Secondary involvement of the genitourinary tract with malignant melanoma is a common autopsy finding, but rarely evident clinically. We report a rare case involving a previously asymptomatic patient presenting with gross hematuria and a large renal mass, which was found to be metastatic melanoma. We propose that metastatic melanoma to the kidney, although rare, be considered in the differential diagnosis of disease processes causing hematuria.

Heterobinuclear Oxo-Bridged Complexes. II. Interactions of CrIIIOFeIII Complexes With Lewis Bases, Mössbauer Spectra and Magnetic Susceptibilities

Equilibrium constants are reported for reaction of Lewis bases, including H2O, with ( thf )( tpp ) CrOFe ( salmah ) in tetrahydrofuran and toluene solutions [ tpp = dianion of 5,10,15,20- tetraphenylporphyrin ; salmah = dianion of N,N?-(4-methyl-4-azaheptane-1,7-diyl) bis ( salicyli - deneimine )]. Mossbauer spectra of several ( tpp ) CrOFe (L) compounds have also been measured in order to define the spin states of the FeIII centres (L= salmah , other tetradentate salicylideneimines, or anions of dithiocarbamates ). The variation of magnetic susceptibility with temperature for several complexes has been studied to 4.2 K, and shows evidence of antiferromagnetic coupling between chromium and iron centres . The interaction can be fitted to an isotropic coupling model for several (B)( tpp ) CrOFe ( salmah ) complexes (B is H2O or 1-methylimidazole).

The Oxidation of Dithiocarbamate Anion by Substitution Inert Metal Complexes

The kinetics of oxidation of dithiocarbamate anions to thiuram disulfides in aqueous acetone by {Fe(CN)6}3- and 11 other substitution inert metal complexes have been investigated. Outer-sphere electron transfer, resulting in the formation of dithiocarbamate thio radicals, is the rate determining step. A Marcus cross reaction treatment allows an estimate for the redox potential for the dithiocarbamate radical/anion couple. For diethyldithiocarbamate, E �(edtc/edtc-) = 425 � 33 mV v.s.c.e. and the outer-sphere electron self-exchange rate constant is log kex = 7.0 � 0.3. A comparison with thiophenolate oxidation is also given.

Physiotherapy exercises for low back pain: process and clinical outcome

This study was designed to assess whether physiotherapy exercises administered for low back pain have the physiological effects that they purport to have (increase spinal mobility and muscle strength) and whether these effects are of clinical relevance (related to changes in pain and function). Thirty-six patients were allocated to three treatment conditions, mobilizing exercises, isometric exercises or an attention-placebo control procedure. The results did not support the hypotheses concerning the effects of physiotherapy exercises, and hence challenge widely held views concerning the mechanism by which some patients suffering from low back pain improve whilst undergoing physiotherapy exercises.

Synthesis of Heterobinuclear Oxo-Bridged Compounds of Chromium, Iron, Manganese and Molybdenum

The synthesis of a series of heterobinuclear oxo -bridged compounds has been accomplished by redox reactions between FeII or MnII complexes of pentadentate and tetradentate salicylideneimines and thiosalicylideneimines and bidentate dithiocarbamates and either CrIVO ( tpp )( tpp ≡ dianion of 5,10,15,20-tetraphenylporphyrin) or MoVI (O)2( dtc )2 ( dtc ≡ diethyldithiocarbamato anion). The compounds are stable in solution in the absence of air but yield various homonuclear derivatives of the metals in its presence, these results indicating a degree of disproportionation of the oxo complexes. The compounds show reduced magnetic moments in line with magnetic coupling between the metal centres.

Thermal dissociation of thiuram disulfides in solution; an electron spin resonance and kinetic study

Tetraisopropylthiuram disulfide dissociates reversibly in solution to form dithiocarbamate thioradicals which can be detected by e.s.r. (g 2.015). The thermodynamics of the dissociation has been examined in decalin by quantitative e.s.r. and a dissociation enthalpy of 104 � 2 kJ mol-1 and anentropy of dissociation of 57 � 5 JK-1 mol-1 has been obtained. Replacing the isopropyl group by other alkyl groups significantly affects the extent of dissociation which decreases in the sequence isopropyl ≈ cyclohexyl > ethyl ≈ methyl > benzyl as the alkyl group is changed. Studies of the kinetics of dissociation of the thiuram disulfides are consistent with the e.s.r, observations and indicate that thio radical recombination occurs at a near diffusion-controlled rate.

Reduction potentials of thiuram disulfide/dithiocarbamate couples in acetone/water

Reduction potentials relative to the saturated calomel electrode, E�, of a series of thiuram disulfide/ dithiocarbamate couples have been measured in 30% v/v water in acetone and at ,μ 0.2 moll-1 (NaNO3) by a combination of potentiometric measurements and equilibrium constant determinations for thiolate/disulfide interchange reactions. E� values lie in the range -250 to -340 mV which place dithiocarbamates as intermediate between thiophenolate (E� - 540 mV) and ethylxanthate (E� -206 mV) in reducing properties. The significant effect on EO of varying the substituents on the nitrogen in the dithiocarbamates correlates with the substituent effects on the acid dissociation constants of the parent dithiocarbamic acid and with trends in the half-wave potentials for metal-based oxidation and reduction of transition metal dithiocarbamate complexes.

Hoists in the home: their recommendation and use

The number of hoists recommended from Mary Marlborough Lodge has increased considerably between 1970 and 1976. This paper reports on the recommendation of hoists and slings for 233 severely disabled patients and the use made of them at follow-up by 146 patients. Electric hoists accounted for 42% of all recommendations and were more frequently used by patients in their homes than manual ones. Manual hosts were more reliable than electric ones but generated a greater number of complaints. The selection of hoists and the type of training given are considered.

A comparison of follow-up regimes in rheumatoid arthritis

One hundred and thirty-two patients discharged from a rheumatology unit were randomly allocated to general practitioner care, attendance at hospital outpatient clinics, or follow-up by a senior occupational therapist attached to the hospital treatment team. At the end of 1 and 2 years a number of clinical and functional tests were applied, and information was gathered about the provision and use of aids and the provision of domestic support. In addition the standard of overall care was judged by an independent assessor. Although no significant intergroup differences in disease activity or function emerged, it is clear that patients prefer continuing contact with the hospital team, and this may lead to differences appearing in the future. The financial advantages of therapist follow-up are discussed.

Out-patient physiotherapy: patterns of provision

A total of 1014 physiotherapy out-patients and their therapists were interviewed at 10 hospitals in Oxfordshire and Devonshire, including a District General Hospital, a Geriatric, and a sample of associated Community Hospitals in each of the two regions. Over 70% of these patients were suffering from long-term disabilities. The proportion of this type of patient varied between the hospital types, and this variation was similar in the two regions. The overall frequencies with which the different physiotherapy treatments were employed were, for the most part, similar in all departments regardless of hospital type or regions involved. Exercises and heat were the predominant treatments everywhere. The standard frequency of attendance was twice or three times a week. One third of the patients used hospital transport; most patients attended a hospital reasonably close to their homes.

The Kinetics and Mechanism of a Reaction in Which Ligand Substitution is Accompanied by a Spin-State Change: Observation of the Elusive Monodithiocarbamatonickel(II) Complex in Dimethyl Sulfoxide

In solutions in Me2SO containing low concentrations of diethyldithiocarbamate ion (dtc-) and very high concentrations of Ni(Me2SO)62+ ion, the hitherto undetected Ni(dtc)+ complex is kinetically stabilized and its electronic spectrum can be recorded. The mono complex is thermodynamically unstable and is converted into Ni(dtc)2 by two independent pathways, one involving direct reaction between Ni(dtc)+ and dtc-, the other being a dimerization reaction, 2Ni(dtc)+ → Ni2+ + Ni(dtc)2. Analysis of the mechanistic scheme Ni2+ + dtc ↔ Ni(dtc)2 Ni(dtc)+ + dtc- → Ni(dtc)2 2Ni(dtc)+ → Ni2+ + Ni(dtc)2 gives k1 = 3 × 103 l, mol-1 s-1, k-1 ≈ 0.01 s-1, k2 ≈ 4 × 105 l, mol-1 s-1 and k3 ≈ 1 × 103 l. mol-1 s-1. Coordinated dtc- exerts a significant labilizing effect on coordinated Me2SO molecules in Ni(dtc)+.

Mobile arm supports: an evaluation

The results of a follow-up survey of 124 patients fitted with mobile arm supports at Mary Marlborough Lodge between 1970 and 1976 are presented. Of the patients fitted with mobile arm supports 33% are known to have used them for over one year, and 47% of those who were contacted were still using them. The reasons for non-use and the implications of the necessity for readjustments are discussed.

The value of flexor hinge hand splints

Functional hand splints have been in use in a number of spinal injury units in the USA since the early 1950s. The splints are designed to provide a pinch-grip either by harnessing wrist dorsiflexion or by external power. Such devices are little used in the United Kingdom. This paper describes the results of late provision of 62 such splints in a Disabled Living Unit. A proportion of tetraplegic patients found such splints of considerable functional value. It is estimated that some 30--60 patients each year would benefit from them if appropriate facilities for early fitting were available.

The kinetics and mechanism of the reaction between nickel(II) and dithiocarbamate ions in dimethyl sulfoxide. Evidence for the ID mechanism for a bidentate uninegative ligand

13C Fourier-transform N.M.R. has been used to measure the rate of exchange of dimethyl sulfoxide with hexakis(dimethyl sulfoxide)nickel(II) cation. The parameters obtained, kex(25°C)(9.8�4.6) × 103 s-1, ΔH‡ 50�2 kJ mol-1 and ΔS‡ 0�4 J K-1 mol-1, are in excellent agreement with those of the most recent 1H N.M.R. study. The reaction between Ni(Me2SO)62+ and diethyldithiocarbamate (dtc-) gives only Ni(dtc)2. When dtc- is in excess, the rate of formation of Ni(dtc)2 is first order in Ni2+ and dtc-. The ionic-strength and temperature dependences of the second-order rate constants are consistent with the rate-determining formation of an unstable Ni(dtc)+ complex by an ID mechanism.

The spinal abnormalities in thalidomide embryopathy

In 1968 a study was made of the spinal changes in 32 children with multiple congenital abnormalities due to thalidomide. Twenty-eight of these children have been traced and their spinal changes reviewed. Only four patients had normal spines on radiography. In eight children, scoliosis was present and had progressed though it was still of mild degree. Disc and end-plate abnormalities were seen in 14 children, and in some appeared to be progressive, leading to intervertebral fusion.