The SKMT Algorithm: A method for assessing and comparing underlying protein entanglement.

We present fast and simple-to-implement measures of the entanglement of protein tertiary structures which are appropriate for highly flexible structure comparison. These are performed using the SKMT algorithm, a novel method of smoothing the Cα backbone to achieve a minimal complexity curve representation of the manner in which the protein's secondary structure elements fold to form its tertiary structure. Its subsequent complexity is characterised using measures based on the writhe and crossing number quantities heavily utilised in DNA topology studies, and which have shown promising results when applied to proteins recently. The SKMT smoothing is used to derive empirical bounds on a protein's entanglement relative to its number of secondary structure elements. We show that large scale helical geometries dominantly account for the maximum growth in entanglement of protein monomers, and further that this large scale helical geometry is present in a large array of proteins, consistent across a number of different protein structure types and sequences. We also show how these bounds can be used to constrain the search space of protein structure prediction from small angle x-ray scattering experiments, a method highly suited to determining the likely structure of proteins in solution where crystal structure or machine learning based predictions often fail to match experimental data. Finally we develop a structural comparison metric based on the SKMT smoothing which is used in one specific case to demonstrate significant structural similarity between Rossmann fold and TIM Barrel proteins, a link which is potentially significant as attempts to engineer the latter have in the past produced the former. We provide the SWRITHE interactive python notebook to calculate these metrics.

DEER and RIDME Measurements of the Nitroxide-Spin Labelled Copper-Bound Amine Oxidase Homodimer from Arthrobacter Globiformis.

In the study of biological structures, pulse dipolar spectroscopy (PDS) is used to elucidate spin-spin distances at nanometre-scale by measuring dipole-dipole interactions between paramagnetic centres. The PDS methods of Double Electron Electron Resonance (DEER) and Relaxation Induced Dipolar Modulation Enhancement (RIDME) are employed, and their results compared, for the measurement of the dipolar coupling between nitroxide spin labels and copper-II (Cu(II)) paramagnetic centres within the copper amine oxidase from Arthrobacter globiformis (AGAO). The distance distribution results obtained indicate that two distinct distances can be measured, with the longer of these at c.a. 5 nm. Conditions for optimising the RIDME experiment such that it may outperform DEER for these long distances are discussed. Modelling methods are used to show that the distances obtained after data analysis are consistent with the structure of AGAO. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00723-021-01321-6.

Distal tibial triplane fracture with ipsilateral tibial shaft fracture: A case series.

BACKGROUND & PURPOSE: Distal tibial Triplane fracture with ipsilateral tibial shaft fracture is a rare but important problem. This rarely reported combination of injuries if not recognised may lead to deleterious consequences. METHODS/PATIENTS: The local database of all emergency admissions was scrutinised to identify subjects before interrogation of the clinical notes and relevant radiographic imaging. FINDINGS: This paper reports a series of five children who were found to have triplane fracture of the distal tibia with concomitant ipsilateral fracture of the tibial shaft. CONCLUSIONS: We suggest that a high index of suspicion for concomitant fractures should be maintained in the presence of either triplane fracture of the distal tibia or tibial shaft fractures in the peri-adolescent child. Minimum appropriate imaging should include orthogonal full length plain radiographs of the tibia as well as formal ankle radiographs.

Prediction of EPR Spectra of Lyotropic Liquid Crystals using a Combination of Molecular Dynamics Simulations and the Model-Free Approach.

We report the first application of fully atomistic molecular dynamics (MD) simulations to the prediction of the motional electron paramagnetic resonance (EPR) spectra of lyotropic liquid crystals in different aggregation states doped with a paramagnetic spin probe. The purpose of this study is twofold. First, given that EPR spectra are highly sensitive to the motions and order of the spin probes doped within lyotropic aggregates, simulation of EPR line shapes from the results of MD modelling provides an ultimate test bed for the force fields currently employed to model such systems. Second, the EPR line shapes are simulated using the motional parameters extracted from MD trajectories using the Model-Free (MF) approach. Thus a combined MD-EPR methodology allowed us to test directly the validity of the application of the MF approach to systems with multi-component molecular motions. All-atom MD simulations using the General AMBER Force Field (GAFF) have been performed on sodium dodecyl sulfate (SDS) and dodecyltrimethylammonium chloride (DTAC) liquid crystals. The resulting MD trajectories were used to predict and interpret the EPR spectra of pre-micellar, micellar, rod and lamellar aggregates. The predicted EPR spectra demonstrate good agreement with most of experimental line shapes thus confirming the validity of both the force fields employed and the MF approach for the studied systems. At the same time simulation results confirm that GAFF tends to overestimate the packing and the order of the carbonyl chains of the surfactant molecules.

A simplified, validated protocol for measuring fibular reduction on ankle CT.

BACKGROUND: Inadequate ankle syndesmotic reduction is a common and important cause of poor outcome after surgery. It is not clear what magnitude or planes of displacement impact most. Many computerised tomography (CT) measurement techniques rely on landmarks that are difficult to reproduce, and none measure all types of mal-positioning in a single protocol. The purpose of this study was to design and validate a protocol for measuring the distal tibio-fibular relationship. METHODS: We devised a method for measuring fibular diastasis, antero-posterior translation (APT) and fibular length on CT images. CTs of sixteen un-injured ankles were examined using our protocol and that of an established alternative method for comparison. The measurements were recorded by two independent observers and repeated for inter- and intra-observer agreement scores. RESULTS: Our method showed inter- and intra-observer agreement of r=0.994 and r=0.999, demonstrating strong agreement. This compared to r=0.218 and r=0.820 respectively for the comparative protocol. CONCLUSION: This ankle CT measurement protocol is accurate, reproducible and simple to use. Its aim is to be a useful tool for clinicians to quantify post-operative mal-positioning of the distal fibula in comparison to the un-injured ankle. We believe that routine, bilateral, post-operative CT imaging will lead to improvements in the understanding and outcomes of the treatment of complex ankle fractures. To our knowledge no other validated measurement of fibular length on CT images exists in the literature.

Enantiopure Ferrocene-Based Planar-Chiral Iridacycles: Stereospecific Control of Iridium-Centred Chirality.

Reaction of [IrCp*Cl2 ]2 with ferrocenylimines (Fc=NAr, Ar=Ph, p-MeOC6 H4 ) results in ferrocene C-H activation and the diastereoselective synthesis of half-sandwich iridacycles of relative configuration Sp *,RIr *. Extension to (S)-2-ferrocenyl-4-(1-methylethyl)oxazoline gave highly diastereoselective control over the new elements of planar chirality and metal-based pseudo-tetrahedral chirality, to give both neutral and cationic half-sandwich iridacycles of absolute configuration Sc ,Sp ,RIr . Substitution reactions proceed with retention of configuration, with the planar chirality controlling the metal-centred chirality through an iron-iridium interaction in the coordinatively unsaturated cationic intermediate.

Nitrosylation of Nitric-Oxide-Sensing Regulatory Proteins Containing [4Fe-4S] Clusters Gives Rise to Multiple Iron-Nitrosyl Complexes.

The reaction of protein-bound iron-sulfur (Fe-S) clusters with nitric oxide (NO) plays key roles in NO-mediated toxicity and signaling. Elucidation of the mechanism of the reaction of NO with DNA regulatory proteins that contain Fe-S clusters has been hampered by a lack of information about the nature of the iron-nitrosyl products formed. Herein, we report nuclear resonance vibrational spectroscopy (NRVS) and density functional theory (DFT) calculations that identify NO reaction products in WhiD and NsrR, regulatory proteins that use a [4Fe-4S] cluster to sense NO. This work reveals that nitrosylation yields multiple products structurally related to Roussin's Red Ester (RRE, [Fe2 (NO)4 (Cys)2 ]) and Roussin's Black Salt (RBS, [Fe4 (NO)7 S3 ]. In the latter case, the absence of 32 S/34 S shifts in the Fe-S region of the NRVS spectra suggest that a new species, Roussin's Black Ester (RBE), may be formed, in which one or more of the sulfide ligands is replaced by Cys thiolates.

Distal tibial osteotomy compared to proximal osteotomy for limb lengthening in children.

AIMS: The aim of this retrospective cohort study was to assess and investigate the safety and efficacy of using a distal tibial osteotomy compared to proximal osteotomy for limb lengthening in children. METHODS: In this study, there were 59 consecutive tibial lengthening and deformity corrections in 57 children using a circular frame. All were performed or supervised by the senior author between January 2013 and June 2019. A total of 25 who underwent a distal tibial osteotomy were analyzed and compared to a group of 34 who had a standard proximal tibial osteotomy. For each patient, the primary diagnosis, time in frame, complications, and lengthening achieved were recorded. From these data, the frame index was calculated (days/cm) and analyzed. RESULTS: All patients ended their treatment with successful lengthening and deformity correction. The frame index for proximal versus distal osteotomies showed no significant difference, with a mean 48.5 days/cm (30 to 85) and 48.9 days/cm (28 to 81), respectively (p = 0.896). In the proximal osteotomy group, two patients suffered complications (one refracture after frame removal and one failure of regenerate maturation with subsequent valgus deformity) compared to zero in the distal osteotomy group. Two patients in each group sustained obstacles that required intervention (one necessitated guided growth, one fibula lengthening, and two required change of wires). There was a similar number of problems (pin-site infections) in each group. CONCLUSION: Our data show that distal tibial osteotomies can be safely employed in limb lengthening for children using a circular frame, which has implications in planning a surgical strategy; for example, when treating a tibia with shortening and distal deformity, a second osteotomy for proximal lengthening is not required.Cite this article: Bone Joint J 2022;104-B(11):1273-1278.

Ilizarov Method for Acute Paediatric Tibial Fractures.

AIM AND BACKGROUND: A systemic method for the application of Ilizarov fixators and on-table fracture reduction is described in this instructional article. This technique has been developed from the unit's practice in adult patients. The indications, underlying principles and rationale for the method are also discussed. TECHNIQUE: The basic concept involves the construction of a series of concentric, colinear rings aligned with the mechanical axis of the limb. An orthogonal ring block is initially placed on the proximal segment and extended distally. Wire to ring reduction techniques are used resulting in the contact, alignment and stability required for early full weight-bearing, free movement of knee and ankle, and subsequent healing. CONCLUSION AND CLINICAL SIGNIFICANCE: Our step-by-step guide takes the reader through a systematic approach to surgery along with tips and tricks on how to achieve reduction and avoid the common pitfalls. With this method, it is possible to achieve an on-table reduction and correction of a multiplanar deformity without the use of expensive hexapod technology. This may allow less experienced users reproduce the technique with a shorter learning curve. HOW TO CITE THIS ARTICLE: Messner J, Prior CP, Pincher B et al. Ilizarov Method for Acute Paediatric Tibial Fractures. Strategies Trauma Limb Reconstr 2021;16(1):46-52.

Correction of the Neglected Clubfoot in the Adolescent and Adult Patient.

Clubfoot is a complex 4-dimensional deformity involving the hindfoot, midfoot, and forefoot. The fourth dimension is time. Treatment aims at achieving a pain-free, plantigrade, and mobile foot but, over time, flexible deformities become fixed and more difficult to manage. The Ponseti method of serial manipulation and casting can be used successfully in older children and may reduce the need for extensive open surgery. Alternatively, gradual correction of by an external device enables simultaneous correction of all components of the deformity without shortening the foot. Combining gradual soft tissue distraction with open releases and/or bony procedures may achieve a pain-free and plantigrade foot.

Obtaining Tertiary Protein Structures by the ab Initio Interpretation of Small Angle X-ray Scattering Data.

Small angle X-ray scattering (SAXS) is an important tool for investigating the structure of proteins in solution. We present a novel ab initio method representing polypeptide chains as discrete curves used to derive a meaningful three-dimensional model from only the primary sequence and SAXS data. High resolution structures were used to generate probability density functions for each common secondary structural element found in proteins, which are used to place realistic restraints on the model curve's geometry. This is coupled with a novel explicit hydration shell model in order to derive physically meaningful three-dimensional models by optimizing against experimental SAXS data. The efficacy of this model is verified on an established benchmark protein set, and then it is used to predict the lysozyme structure using only its primary sequence and SAXS data. The method is used to generate a biologically plausible model of the coiled-coil component of the human synaptonemal complex central element protein.

Regioisomeric Family of Novel Fluorescent Substrates for SHIP2.

SHIP2 (SH2-domain containing inositol 5-phosphatase type 2) is a canonical 5-phosphatase, which, through its catalytic action on PtdInsP3, regulates the PI3K/Akt pathway and metabolic action of insulin. It is a drug target, but there is limited evidence of inhibition of SHIP2 by small molecules in the literature. With the goal to investigate inhibition, we report a homologous family of synthetic, chromophoric benzene phosphate substrates of SHIP2 that display the headgroup regiochemical hallmarks of the physiological inositide substrates that have proved difficult to crystallize with 5-phosphatases. Using time-dependent density functional theory (TD-DFT), we explore the intrinsic fluorescence of these novel substrates and show how fluorescence can be used to assay enzyme activity. The TD-DFT approach promises to inform rational design of enhanced active site probes for the broadest family of inositide-binding/metabolizing proteins, while maintaining the regiochemical properties of bona fide inositide substrates.

Cobalt-based molecular electrocatalysis of nitrile reduction: evolving sustainability beyond hydrogen.

Two new cobalt bis-iminopyridines, [Co(DDP)(H2O)2](NO3)2 (1, DDP = cis-[1,3-bis(2-pyridinylenamine)] cyclohexane) and [Co(cis-DDOP)(NO3)](NO3) (2, cis-DDOP = cis-3,5-bis[(2-Pyridinyleneamin]-trans-hydroxycyclohexane) electrocatalyse the 4-proton, 4-electron reduction of acetonitrile to ethylamine. For 1, this reduction occurs in preference to reduction of protons to H2. A coordinating hydroxyl proton relay in 2 reduces the yield of ethylamine and biases the catalytic system back towards H2.

Quantifying reconnective activity in braided vector fields.

We introduce a technique for evaluating the changing connectivity of a vector field whose integral curves (field lines) form tangled tubular bundles. Applications of such fields include magnetic flux ropes, relativistic plasma jets, stirred two-dimensional fluids, superfluid vortices, and polymer networks. The technique is based on maps of the field line winding-the average entanglement of a given field line with all other field lines. Previously this had been developed for divergence-free vector fields. By extending some previous theoretical results, we show how it can be applied to any vector field that forms a tubular bundle. We demonstrate the efficacy of this technique on data from laboratory plasma experiments with two interacting magnetic flux ropes. Performed in the UCLA Large Plasma Device, the plasma's magnetic field structure is too complex to identify a single dominant current sheet as an expected site of magnetic reconnection. Previously, this complex structure had restricted the ability to analyze the evolving magnetic connectivity, but this is no such restriction to our method. We demonstrate that the plasma establishes a periodically oscillating cycle of magnetic field structure variation which, while triggered by an ideal instability, is dominated by magnetic reconnection. This reconnection leads to periodically varying coherence of a merged central flux rope, a conclusion supported by analysis of the writhing structure of the magnetic field.

Correction: EPR detection and characterisation of a paramagnetic Mo(iii) dihydride intermediate involved in electrocatalytic hydrogen evolution.

Correction for 'EPR detection and characterisation of a paramagnetic Mo(iii) dihydride intermediate involved in electrocatalytic hydrogen evolution' by Christopher Prior, et al., Dalton Trans., 2016, 45, 2399-2403.

EPR detection and characterisation of a paramagnetic Mo(iii) dihydride intermediate involved in electrocatalytic hydrogen evolution.

EPR spectroscopy and theoretical data show that the slow heterogeneous electron-transfer kinetics associated with the reduction of an 18-electron Mo(IV) acetato dihydride are a consequence of an η(2)-η(1) rearrangement of the carboxylate ligand which gives a unique paramagnetic 17-electron Mo(III) dihydride.