Autosomal recessive hypotrichosis with loose anagen hairs associated with TKFC mutations.

BACKGROUND: Loose anagen hair is a rare form of impaired hair anchorage in which anagen hairs that lack inner and outer root sheaths can be gently and painlessly plucked from the scalp. This condition usually occurs in children and is often self-limiting. A genetic basis for the disorder has been suggested but not proven. A better understanding the aetiology of loose anagen hair may improve prevention and treatment strategies. OBJECTIVES: To identify a possible genetic basis of loose anagen hair using next-generation DNA sequencing and functional analysis of variants identified. METHODS: In this case study, whole-exome sequencing analysis of a pedigree with one affected individual with features of loose anagen hair was performed. RESULTS: The patient was found to be compound heterozygous for two single-nucleotide substitutions in TKFC resulting in the following missense mutations: c.574G> C (p.Gly192Arg) and c.682C> T (p.Arg228Trp). Structural analysis of human TKFC showed that both mutations are located near the active site cavity. Kinetic assays of recombinant proteins bearing either of these amino acid substitutions showed almost no dihydroxyacetone kinase or D-glyceraldehyde kinase activity, and FMN cyclase activity reduced to just 10% of wildtype catalytic activity. CONCLUSIONS: TKFC missense mutations may predispose to the development of loose anagen hairs. Identification of this new biochemical pathobiology expands the metabolic and genetic basis of hypotrichosis.

SARS-CoV-2 spike protein predicted to form complexes with host receptor protein orthologues from a broad range of mammals.

SARS-CoV-2 has a zoonotic origin and was transmitted to humans via an undetermined intermediate host, leading to infections in humans and other mammals. To enter host cells, the viral spike protein (S-protein) binds to its receptor, ACE2, and is then processed by TMPRSS2. Whilst receptor binding contributes to the viral host range, S-protein:ACE2 complexes from other animals have not been investigated widely. To predict infection risks, we modelled S-protein:ACE2 complexes from 215 vertebrate species, calculated changes in the energy of the complex caused by mutations in each species, relative to human ACE2, and correlated these changes with COVID-19 infection data. We also analysed structural interactions to better understand the key residues contributing to affinity. We predict that mutations are more detrimental in ACE2 than TMPRSS2. Finally, we demonstrate phylogenetically that human SARS-CoV-2 strains have been isolated in animals. Our results suggest that SARS-CoV-2 can infect a broad range of mammals, but few fish, birds or reptiles. Susceptible animals could serve as reservoirs of the virus, necessitating careful ongoing animal management and surveillance.

Publisher Correction: A dynamically cold disk galaxy in the early Universe.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

A dynamically cold disk galaxy in the early Universe.

The extreme astrophysical processes and conditions that characterize the early Universe are expected to result in young galaxies that are dynamically different from those observed today1-5. This is because the strong effects associated with galaxy mergers and supernova explosions would lead to most young star-forming galaxies being dynamically hot, chaotic and strongly unstable1,2. Here we report the presence of a dynamically cold, but highly star-forming, rotating disk in a galaxy at redshift6 z = 4.2, when the Universe was just 1.4 billion years old. Galaxy SPT-S J041839-4751.9 is strongly gravitationally lensed by a foreground galaxy at z = 0.263, and it is a typical dusty starburst, with global star-forming7 and dust properties8 that are in agreement with current numerical simulations9 and observations10. Interferometric imaging at a spatial resolution of about 60 parsecs reveals a ratio of rotational to random motions of 9.7 ± 0.4, which is at least four times larger than that expected from any galaxy evolution model at this epoch1-5 but similar to the ratios of spiral galaxies in the local Universe11. We derive a rotation curve with the typical shape of nearby massive spiral galaxies, which demonstrates that at least some young galaxies are dynamically akin to those observed in the local Universe, and only weakly affected by extreme physical processes.

Understanding the structural details of APOBEC3-DNA interactions using graph-based representations.

Human APOBEC3 (A3; apolipoprotein B mRNA editing catalytic polypeptide-like 3) is a family of seven enzymes involved in generating mutations in nascent reverse transcripts of many retroviruses, as well as the human genome in a range of cancer types. The structural details of the interaction between A3 proteins and DNA molecules are only available for a few family members. Here we use homology modelling techniques to address the difference in structural coverage of human A3 enzymes interacting with different DNA substrates. A3-DNA interfaces are represented as residue networks ("graphs"), based on which features at these interfaces are compared and quantified. We demonstrate that graph-based representations are effective in highlighting structural features of A3-DNA interfaces. By large-scale in silico mutagenesis of the bound DNA chain, we predicted the preference of substrate DNA sequence for multiple A3 domains. These data suggested that computational modelling approaches could contribute in the exploration of the structural basis for sequence specificity in A3 substrate selection, and demonstrated the utility of graph-based approaches in evaluating a large number of structural models generated in silico.

Rate-independent dissipation and loading direction effects in compressed carbon nanotube arrays.

Arrays of nominally-aligned carbon nanotubes (CNTs) under compression deform locally via buckling, exhibit a foam-like, dissipative response, and can often recover most of their original height. We synthesize millimeter-scale CNT arrays and report the results of compression experiments at different strain rates, from 10(-4) to 10(-1) s(-1), and for multiple compressive cycles to different strains. We observe that the stress-strain response proceeds independently of the strain rate for all tests, but that it is highly dependent on loading history. Additionally, we examine the effect of loading direction on the mechanical response of the system. The mechanical behavior is modeled using a multiscale series of bistable springs. This model captures the rate independence of the constitutive response, the local deformation, and the history-dependent effects. We develop here a macroscopic formulation of the model to represent a continuum limit of the mesoscale elements developed previously. Utilizing the model and our experimental observations we discuss various possible physical mechanisms contributing to the system's dissipative response.

Highly nonlinear solitary wave propagation in Y-shaped granular crystals with variable branch angles.

We study the propagation of highly nonlinear waves in a branched (Y-shaped) granular crystal composed of chains of spherical particles of different materials, arranged at variable branch angles. We experimentally test the dynamic behavior of a solitary pulse, or of a train of solitary waves, crossing the Y-junction interface, and splitting between the two branches. We describe the dependence of the split pulses' speed and amplitude on the branch angles. Analytic predictions based on the quasiparticle model and numerical simulations based on Hertzian interactions between the particles are found to be in excellent agreement with the experimental data.

A multiscale approach to the elastic moduli of biomembrane networks.

We develop equilibrium fluctuation formulae for the isothermal elastic moduli of discrete biomembrane models at different scales. We account for the coupling of large stretching and bending strains of triangulated network models endowed with harmonic and dihedral angle potentials, on the basis of the discrete-continuum approach presented in Schmidt and Fraternali (J Mech Phys Solids 60:172-180, 2012). We test the proposed equilibrium fluctuation formulae with reference to a coarse-grained molecular dynamics model of the red blood cell (RBC) membrane (Marcelli et al. in Biophys J 89:2473-2480, 2005; Hale et al. in Soft Matter 5:3603-3606, 2009), employing a local maximum-entropy regularization of the fluctuating configurations (Fraternali et al. in J Comput Phys 231:528-540, 2012). We obtain information about membrane stiffening/softening due to stretching, curvature, and microscopic undulations of the RBC model. We detect local dependence of the elastic moduli over the RBC membrane, establishing comparisons between the present theory and different approaches available in the literature.

Highly nonlinear pulse splitting and recombination in a two-dimensional granular network.

The propagation of highly nonlinear signals in a branched two-dimensional granular system was investigated experimentally and numerically for a system composed of chains of spherical beads of different materials. The system studied consists of a double Y-shaped guide in which high- and low-modulus/mass chains of spheres are arranged in various geometries. We observed the transformation of a single or a train of solitary pulses crossing the interface between branches. We report fast splitting of the initial pulse, rapid chaotization of the signal and impulse redirection and bending. Pulse and energy trapping was also observed in the branches. Numerical analysis based on Hertzian interaction between the particles and the side walls of the guide was found in agreement with the experimental data, except for nonsymmetric arrangements of particles excited by a large mass striker.

Tailored graph ensembles as proxies or null models for real networks I: tools for quantifying structure.

We study the tailoring of structured random graph ensembles to real networks, with the objective of generating precise and practical mathematical tools for quantifying and comparing network topologies macroscopically, beyond the level of degree statistics. Our family of ensembles can produce graphs with any prescribed degree distribution and any degree-degree correlation function, its control parameters can be calculated fully analytically, and as a result we can calculate (asymptotically) formulae for entropies and complexities, and for information-theoretic distances between networks, expressed directly and explicitly in terms of their measured degree distribution and degree correlations.

Anisotropic constitutive equations and experimental tensile behavior of brain tissue.

The present study deals with the experimental analysis and mechanical modeling of tensile behavior of brain soft tissue. A transversely isotropic hyperelastic model recently proposed by Meaney (2003) is adopted and mathematically studied under uniaxial loading conditions. Material parameter estimates are obtained through tensile tests on porcine brain materials accounting for regional and directional differences. Attention is focused on the short-term response. An extrapolation of tensile test data to the compression range is performed theoretically, to study the effect of the heterogeneity in the tensile/compressive response on the material parameters. Experimental and numerical results highlight the sensitivity of the adopted model to the test direction.

Modularity and homology: modelling of the titin type I modules and their interfaces.

Titin is a giant muscle protein with a highly modular architecture consisting of multiple repeats of two sequence motifs, named type I and type II. Type I motifs are homologous to members of the fibronectin type 3 (Fn3) superfamily, one of the motifs most widespread in modular proteins. Fn3 domains are thought to mediate protein-protein interactions and to act as spacers. In titin, Fn3 modules are present in two different super-repeated patterns, likely to be involved in sarcomere assembly through interactions with A-band proteins. Here, we discuss results from homology modelling the whole family of Fn3 domains in titin. Homology modelling is a powerful tool that will play an increasingly important role in the post-genomic era. It is particularly useful for extending experimental structure determinations of parts of multidomain proteins that contain multiple copies of the same motif. The 3D structures of a representative titin type I domain and of other extracellular Fn3 modules were used as a template to model the structures of the 132 copies in titin. The resulting models suggest residues that contribute to the fold stability and allow us to distinguish these from residues likely to have functional importance. In particular, analysis of the models and mapping of the consensus sequence onto the 3D structure suggest putative surfaces of interaction with other proteins. From the structures of isolated modules and the pattern of conservation in the multiple alignment of the whole titin Ig and Fn3 families, it is possible to address the question of how tandem modules are assembled. Our predictions can be validated experimentally.

Leap-dynamics: efficient sampling of conformational space of proteins and peptides in solution.

A molecular simulation scheme, called Leap-dynamics, that provides efficient sampling of protein conformational space in solution is presented. The scheme is a combined approach using a fast sampling method, imposing conformational 'leaps' to force the system over energy barriers, and molecular dynamics (MD) for refinement. The presence of solvent is approximated by a potential of mean force depending on the solvent accessible surface area. The method has been successfully applied to N-acetyl-L-alanine-N-methylamide (alanine dipeptide), sampling experimentally observed conformations inaccessible to MD alone under the chosen conditions. The method predicts correctly the increased partial flexibility of the mutant Y35G compared to native bovine pancreatic trypsin inhibitor. In particular, the improvement over MD consists of the detection of conformational flexibility that corresponds closely to slow motions identified by nuclear magnetic resonance techniques.

An immunoglobulin-like fold in a major plant allergen: the solution structure of Phl p 2 from timothy grass pollen.

BACKGROUND: Grass pollen allergens are the most important and widespread elicitors of pollen allergy. One of the major plant allergens which millions of people worldwide are sensitized to is Phl p 2, a small protein from timothy grass pollen. Phl p 2 is representative of the large family of cross-reacting plant allergens classified as group 2/3. Recombinant Phl p 2 has been demonstrated by immunological cross-reactivity studies to be immunologically equivalent to the natural protein. RESULTS: We have solved the solution structure of recombinant Phl p 2 by means of nuclear magnetic resonance techniques. The three-dimensional structure of Phl p 2 consists of an all-beta fold with nine antiparallel beta strands that form a beta sandwich. The topology is that of an immunoglobulin-like fold with the addition of a C-terminal strand, as found in the C2 domain superfamily. Lack of functional and sequence similarity with these two families, however, suggests an independent evolution of Phl p 2 and other homologous plant allergens. CONCLUSIONS: Because of the high homology with other plant allergens of groups 1 and 2/3, the structure of Phl p 2 can be used to rationalize some of the immunological properties of the whole family. On the basis of the structure, we suggest possible sites of interaction with IgE antibodies. Knowledge of the Phl p 2 structure may assist the rational structure-based design of synthetic vaccines against grass pollen allergy.

Novel RNA-binding motif: the KH module.

The KH motif has recently been identified in single or multiple copies in a number of RNA associated proteins. Here we review the current knowledge accumulated about the sequence, structure, and functions of the KH. The multidomain architecture of most of the KH-containing proteins inspired an approach based on the production of peptides spanning the sequence of an isolated KH motif. Correct identification of the minimal length necessary for producing a folded peptide has had a number of important consequences for interpreting functional data. The presence of the KH motifs in fmr1, the protein responsible for the fragile X syndrome, and their possible role in the fmr1 functions are also discussed.

Modularity and homology: modelling of the type II module family from titin.

We report the homology modelling of the structures of the 162 type II modules from the giant multi-domain protein titin (also known as connectin). The package MODELLER was used and implemented in an automated fashion using four experimentally determined structures as templates. Validation of the models was assessed in terms of divergence from the templates and consensus of the alignments. The homology within the whole family of type II modules as well as with the templates is relatively high (20-35% identity and ca 50% similarity). Comparison between the models of domains for which an NMR structure has been solved and the experimental solution gives an estimate of the quality of the modelling. Our results allow us to distinguish between a set of structurally relevant residues, which are conserved throughout the whole family and buried in the hydrophobic core, from the residues that are conserved and exposed. These latter residues are potentially functionally important. Comparison of exposed conserved patches for modules in different regions of the titin molecule suggests potential interaction surfaces. Our results may be tested directly for those modules whose binding partner is known.

Neurologically active plant compounds and peptide hormones: a chirality connection.

The most dramatic, but seldom mentioned, difference between alkaloid and peptide opioids is the change of chirality of the alpha carbon of the tyramine moiety. We propose that the presence of Gly2 or D-Ala2 in the two most common message domains compensates this change by allowing the attainment of unusual conformations. A thorough conformational search of Tyr-D-Ala-Phe-NH-CH3 and of its isomer Tyr-L-Ala-Phe-NH-CH3 backs this view and establishes a solid link between alkaloid and peptide opioids. This finding supports the notion that morphine, like other neurologically active plant compounds, may bind to endogenous receptors in plants to regulate cell-to-cell signaling systems.

Exploring protein interiors: the role of a buried histidine in the KH module fold.

The K-homology (KH) module is a novel RNA-binding motif. The structures of a representative KH motif from vigilin (vig-KH6) and of the first KH domain of fmr1 have been recently solved by nuclear magnetic resonance (NMR) and automated assignment-refinement techniques (ARIA). While a hydrophobic residue is found at position 21 in most of the KH modules, a buried His is conserved in all the 15 KH repeats of vigilin. This position must therefore have a key structural role in stabilizing the hydrophobic core. In the present work, we have addressed the following questions in order to obtain a detailed description of the role of His 21: i) what is the exact role of the histidine in the hydrophobic core of vig-KH6? ii) can we define the interactions that allow a conserved buried position to be occupied by a histidine both in vig-KH6 and in the whole vigilin KH sub-family? iii) how is the structure and stability of vig-KH6 influenced by the state of protonation of this histidine? To answer these questions, we have carried out an extensive refinement of the vig-KH6 structure using both an improved ARIA protocol starting from different initial structures and successively running restrained and unrestrained trajectories in water. An analysis of the stability of secondary structural elements, solvent accessibility, and hydrogen bonding patterns allows hypothesis on the structural role of residue His 21 and on the interactions that this residue forms with the environment. The importance of the protonation state of His 21 on the stability of the KH fold was addressed and validated by experimental results.

A conformational study in solution of pro-somatostatin fragments by NMR and computational methods.

The results of a conformational study by nuclear magnetic spectroscopy and computational methods on a series of point-mutated synthetic peptides, containing 14 amino acid residues and mimicking the region containing the Arg-Lys dibasic cleavage site of pro-somatostatin, have confirmed the possible role of a well defined secondary structure in the recognition phenomenon by processing enzymes. The importance of the residues located near the Arg-Lys dibasic site in the C-terminal region of the pro-hormone for the cleavage of the precursor into somatostatin-14 has been confirmed. The present structural analysis indicates the occurrence of two beta-turns in the 4-7 and 11-14 regions, flanking the cleavage site, for all the peptides recognized as substrates by the processing enzyme. Interestingly, in the point-mutated analogue not processed by the enzyme and containing the replacement of proline by alanine in position 5 the first -turn is displaced by one residue and involves the Ala5-Arg8 segment. This observation may explain the lack of recognition by the maturation enzyme.

Mapping the active site of factor Xa by selective inhibitors: an NMR and MD study.

The structure of two selective inhibitors, Ac-Tyr-Ile-Arg-Ile-Pro-NH2 and Ac-(4-Amino-Phe)-(Cyclohexyl-Gly)-Arg-NH2, in the active site of the blood clotting enzyme factor Xa was determined by using transferred nuclear Overhauser effect nuclear magnetic resonance (NMR) spectroscopy. They represent a family of peptidic inhibitors obtained by the screening of a vast combinatorial library. Each structure was first calculated by using standard computational procedures (distance geometry, simulated annealing, energy minimization) and then further refined by systematic search of the conformation of the inhibitor docked in the active site and repeating the simulated annealing and energy minimization. The final structure was optimized by molecular dynamics simulations of the inhibitor-complex in water. The NMR restraints were kept throughout the refinement. The inhibitors assume a compact, very well defined conformation, embedded into the substrate binding site not in the same way as a substrate, blocking thus the catalysis. The model allows to explain the mode of action, affinity, and specificity of the peptides and to map the active site.