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The RUNT‐related transcription factor RUNX2 plays a critical role in osteoblast differentiation, and alterations to gene dosage cause distinct craniofacial anomalies. Uniquely amongst the RUNT‐related family, vertebrate RUNX2 encodes a polyglutamine/polyalanine repeat (Gln23‐Glu‐Ala17 in humans), with the length of the polyalanine component completely conserved in great apes. Surprisingly, a frequent 6‐amino acid deletion polymorphism, p.(Ala84_Ala89)del, occurs in humans (termed 11A allele), and a previous association study (Cuellar et al. Bone137:115395;2020) reported that the 11A variant was significantly more frequent in non‐syndromic sagittal craniosynostosis (nsSag; allele frequency [AF] = 0.156; 95% confidence interval [CI] 0.126–0.189) compared to non‐syndromic metopic craniosynostosis (nsMet; AF = 0.068; 95% CI 0.045–0.098). However, the gnomAD v.2.1.1 control population used by Cuellar et al. did not display Hardy–Weinberg equilibrium, hampering interpretation. To re‐examine this association, we genotyped the RUNX2 11A polymorphism in 225 individuals with sporadic nsSag as parent–child trios and 164 singletons with sporadic nsMet, restricting our analysis to individuals of European ancestry. We compared observed allele frequencies to the non‐transmitted alleles in the parent–child trios, and to the genome sequencing data from gnomAD v.4, which display Hardy–Weinberg equilibrium. Observed AFs (and 95% CI) were 0.076 (0.053–0.104) in nsSag and 0.082 (0.055–0.118) in nsMet, compared with 0.062 (0.042–0.089) in non‐transmitted parental alleles and 0.065 (0.063–0.067) in gnomAD v.4.0.0 non‐Finnish European control genomes. In summary, we observed a non‐significant excess, compared to gnomAD data, of 11A alleles in both nsSag (relative risk 1.18, 95% CI 0.83–1.67) and nsMet (relative risk 1.29, 95% CI 0.87–1.92), but we did not replicate the much higher excess of RUNX2 11A alleles in nsSag previously reported (p = 0.0001). [ABSTRACT FROM AUTHOR]

Congenital central hypoventilation syndrome (CCHS) is a rare genetic disorder of the autonomic nervous system resulting in decreased brain sensitivity to hypercapnia and hypoxia characterized by a genetic abnormality in the pair-like homeobox 2B (PHOX2B) gene. Most patients have a heterozygous expansion of the polyalanine repeat in exon 3 (PARM), while 10 % of patients have non-PARM (NPARM) mutations that can span the entire gene. The majority of pathogenic variants are de novo, but variants with incomplete penetrance can be identified in the heterozygous state. In the present report, CCHS was diagnosed in a symptomatic 3-month-old infant with neonatal respiratory distress. Genetic analysis revealed a new mutation in exon 1 of the PHOX2B gene – p.Ser28* (c.83C>G) – which was further identified in two family members, one minimally symptomatic and one asymptomatic. The identification of this new mutation supports the importance of sequencing the entire gene even when the classic PARM mutation is not found and highlights the phenotypic variability of CCHS. [ABSTRACT FROM AUTHOR]

Unstable DNA repeat expansions and insertions have been found to cause more than 50 neurodevelopmental, neurodegenerative, and neuromuscular disorders. One of the main hallmarks of repeat expansion diseases is the formation of abnormal RNA or protein aggregates in the neuronal cells of affected individuals. Recent evidence indicates that alterations of the dynamic or material properties of biomolecular condensates assembled by liquid/liquid phase separation are critical for the formation of these aggregates. This is a thermodynamically-driven and reversible local phenomenon that condenses macromolecules into liquid-like compartments responsible for compartmentalizing molecules required for vital cellular processes. Disease-associated repeat expansions modulate the phase separation properties of RNAs and proteins, interfering with the composition and/or the material properties of biomolecular condensates and resulting in the formation of abnormal aggregates. Since several repeat expansions have arisen in genes encoding crucial players in transcription, this raises the hypothesis that wide gene expression dysregulation is common to multiple repeat expansion diseases. This review will cover the impact of these mutations in the formation of aberrant aggregates and how they modify gene transcription. [ABSTRACT FROM AUTHOR]

Using extensive molecular dynamics simulations of a single eight-residue alanine polypeptide in explicit water, we investigate the influence of a-helix formation on the dielectric spectrum. For this, we project long equilibrium trajectories into folded and unfolded states and thereby obtain dielectric spectra representative for disordered as well a-helical conformations without the need to change any other system parameter such as pH or temperature. The absorption spectrum in the a-helical state exhibits a feature in the sub-GHz range that is significantly stronger than in the unfolded state. As we show by an additional decomposition into peptide and water contributions, this slow dielectric mode, the relaxation time of which matches the independently determined peptide rotational relaxation time, is mostly caused by peptide polarization correlations, but also contains considerable contributions from peptide-water correlations. In contrast, the peptide spectral contribution shows no features in the GHz range where bulk water absorbs, not even in the peptide-water correlation part, we conclude that hydration water around Ala8 is more influenced by peptide polarization relaxation effects than the other way around. A further decomposition into water-self and water-collective polarization correlations shows that the dielectric response of hydration water is, in contrast to electrolyte solutions, retarded and that this retardation is mostly due to collective effects, the self relaxation of hydration water molecules is only slightly slowed down compared to bulk water. We find the dynamic peptide-water polarization cross correlations to be rather long-ranged and to extend more than one nanometer away from the peptide-water interface into the water hydration shell, in qualitative agreement with previous simulation studies and recent THz absorption experiments. [ABSTRACT FROM AUTHOR]

Runt-related transcription factor 2 (RUNX2) is critical for the development of the vertebrate bony skeleton. Unlike other RUNX family members, RUNX2 possesses a variable poly-glutamine, poly-alanine (QA) repeat domain. Natural variation within this repeat is able to alter the transactivation potential of RUNX2, acting as an evolutionary 'tuning knob' suggested to influence mammalian skull shape. However, the broader role of the RUNX2 QA repeat throughout vertebrate evolution is unknown. In this perspective, we examine the role of the RUNX2 QA repeat during skeletal development and discuss how its emergence and expansion may have facilitated the evolution of morphological novelty in vertebrates. In this Perspective, Axel Newton and Andrew Pask examine the role of the Runt-related transcription factor 2 (RUNX2) QA repeat during skeletal development and discuss how its emergence and expansion may have facilitated the evolution of morphological novelty in vertebrates. [ABSTRACT FROM AUTHOR]

We analyze free energy estimators from simulation trials mimicking single-molecule pulling experiments on a neck linker of a kinesin motor. For that purpose, we have performed a version of steered molecular dynamics (SMD) calculations. The sample trajectories have been analyzed to derive distribution of work done on the system. In order to induce stretching of the linker, we have applied a constant pulling force to the molecule and allowed for a subsequent relaxation of its structure. The use of fluctuation relations (FR) relevant to non-equilibrium systems subject to thermal fluctuations allows us to assess the difference in free energy between stretched and relaxed conformations. To further understand effects of potential mutations on elastic properties of the linker, we have performed similar in silico studies on a structure formed of a polyalanine sequence (Ala-only) and on three other structures, created by substituting selected types of amino acid residues in the linker's sequence with alanine (Ala) ones. The results of SMD simulations indicate a crucial role played by the Asparagine (Asn) and Lysine (Lys) residues in controlling stretching and relaxation properties of the linker domain of the motor. [ABSTRACT FROM AUTHOR]

Homopolymeric amino acid repeats (AARs) like polyalanine (polyA) and polyglutamine (polyQ) in some developmental proteins (DPs) regulate certain aspects of organismal morphology and behavior, suggesting an evolutionary role for AARs as developmental "tuning knobs." It is still unclear, however, whether these are occasional protein-specific phenomena or hints at the existence of a whole AAR-based regulatory system in DPs. Using novel approaches to trace their functional and evolutionary history, we find quantitative evidence supporting a generalized, combinatorial role of AARs in developmental processes with evolutionary implications. We observe nonrandom AAR distributions and combinations in HOX and other DPs, as well as in their interactomes, defining elements of a proteome-wide combinatorial functional code whereby different AARs and their combinations appear preferentially in proteins involved in the development of specific organs/systems. Such functional associations can be either static or display detectable evolutionary dynamics. These findings suggest that progressive changes in AAR occurrence/combination, by altering embryonic development, may have contributed to taxonomic divergence, leaving detectable traces in the evolutionary history of proteomes. Consistent with this hypothesis, we find that the evolutionary trajectories of the 20 AARs in eukaryotic proteomes are highly interrelated and their individual or compound dynamics can sharply mark taxonomic boundaries, or display clock-like trends, carrying overall a strong phylogenetic signal. These findings provide quantitative evidence and an interpretive framework outlining a combinatorial system of AARs whose compound dynamics mark at the same time DP functions and evolutionary transitions. [ABSTRACT FROM AUTHOR]

Graphical abstract Highlights • The interaction of Pd(II)/Ni(II) with polyalanine and the effects on fragmentation. • A globular conformation of the Pd(II)/Ni(II)-polyalanine complexes. • A characteristic fragmentation pattern for Pd(II)/Ni(II)-polyalanine complexes. • Pd(II) and Ni(II) preferred to coordinating to the N atoms of the four residues at the N-terminus. Abstract The interaction between metal ions and peptides have attracted interests because of the important roles of metal ions in many biological processes and the potential application in different fields. The binding patterns of Pd(II)/Ni(II) with polyalanine and the consequent conformational changes as well as the effects on fragmentation have been studied by electrospray ionization ion mobility mass spectrometry (ESI-IM-MS) experiments and density functional theory (DFT). The collision cross section (CCS) values that were measured showed that such complexes tend to adopt compact globular conformations in the case of polyalanines with more than 6 residues, while conformational change was detected in shorter polyalanines with 4 or 5 residues. Collision induced dissociation (CID) experiments revealed a characteristic fragmentation pattern for Pd(II)/Ni(II)-polyalanine complexes of length n in which neutral part Ala 4 –H 2 O + M–2H (M = Pd or Ni) and fragment ions [b 4 +M–2 H]+, [a 4 +M–2 H]+ were formed in much higher abundance than any other product ions. Density functional theory (DFT) calculations indicated that Pd(II) and Ni(II) preferred to coordinating to the N atoms of the four residues at the N-terminus. Such a binding pattern accelerates fragmentation involving a structure moiety containing four residues and a metal. This analysis suggested a strong structural correlation between Pd(II) and Ni(II) and the four residues located at the N-terminus of polyalanines. [ABSTRACT FROM AUTHOR]

Abstract Recent computational simulations on protein-ligand binding/unbinding have precisely been uncovering the ligand-binding process at the atomic level. In the process, the non-specific binding of ligands to the target site is suggested to occur before binding to the target. We in this study analyzed the conformations of ligands under the non-specific binding on a protein surface to figure out the differences in the conformational characteristics in aqueous solution using the 55-ns molecular dynamic simulation. As for the protein surface, we constructed an artificial β-sheet, composed of poly-alanine residues (Ala-sheet). For the ligands, the four α-thrombin inhibitors possessing two scaffolds with distinct hydrophobicity profiles were used. During the simulation, all the inhibitors kept interaction with Ala-sheet and had the limited conformational fluctuations compared with in aqueous solution. The representative conformations obtained from the cluster analysis showed that two of hydrophobic inhibitors adopted the extended conformations in aqueous solution and also on Ala-sheet. For the other two hydrophilic inhibitors, the conformations in aqueous solution adopted the bent conformation with two terminal hydrophobic rings closely packed. On Ala-sheet, contrarily, the two hydrophobic rings were open and took the extended conformations, which were placed on the sheet as a foothold. The charged moieties in the hydrophilic inhibitors were protruded into aqueous environment with the extended conformation. The conformational characteristics of the inhibitors in aqueous solution and Ala-sheet varied likely by chemical features or structures of the inhibitors, but each was considered to be physicochemically reasonable. Graphical abstract Image 1 Highlights • Hydrophobic inhibitors were extended in aqueous, on sheet and in target-complexes. • Hydrophilic inhibitors were bent in aqueous and complexes, but extended on sheet. • Each inhibitor was varied conformations with chemical features. • However, they were considered to be physicochemically reasonable. [ABSTRACT FROM AUTHOR]

Abstract Short polyserine (polyS) repeats are frequently found in proteins and longer ones are produced in neurological disorders such as Huntington disease (HD) owing to translational frameshifting or non-ATG-dependent translation, together with polyglutamine (polyQ) and polyalanine (polyA) repeats, forming intracellular aggregates. However, the physiological and pathological structures of polyS repeats are not clearly understood. Early studies highlighted their structural versatility, similar to other homopolymers whose conformation is influenced by the surrounding protein context. As polyS stretches are frequently near polyQ and polyA repeats, which can be part of coiled coil (CC) structures, and the frameshift-derived polyS repeats in HD directly flank CC heptads important for aggregation, we investigate here the structural and aggregation properties of polyS in the context of CC structures. We have taken advantage of peptide models, previously used to study polyQ and polyA in CCs, in which we inserted polyS repeats of variable length and studied them in comparison with polyQ and polyA peptides. We found that polyS repeats promote CC-mediated polymerization and fibrillization as revealed by circular dichroism, chemical crosslinking, and atomic force microscopy. Furthermore, they promote CC-based, length-dependent intracellular aggregation, which is negligible with 7 and widespread with 49 serines. These findings show that polyS repeats can participate in the formation of CCs, as previously found for polyQ and polyA, conferring to peptides distinctive structural properties with aggregation kinetics that are intermediate between those of polyA and polyQ CCs, and contribute to an overall structural definition of the pathophysiogical roles of homopolymeric repeats in CC structures. [ABSTRACT FROM AUTHOR]

Summary: Background: Midface toddler excoriation syndrome (MiTES) is a condition recently reported in three unrelated children. Habitual scratching from the first year of life inflicted deep, chronic, scarring wounds around the nose and eyes. One child had a mild neurological deficit but there was no other evidence of insensitivity to pain. Bilateral distribution and localization to the midface distinguish MiTES from other causes of self‐inflicted skin damage such as trigeminal trophic syndrome. An earlier study of five siblings from a consanguineous Irish family, with lesions corresponding to MiTES plus other sensory deficits, showed homozygous mutations in a gene for hereditary sensory and autonomic neuropathy type VIII (HSAN8), PRDM12. Objectives: To study further cases of MiTES, including analysis of PRDM12. Methods: We describe five further children, from four families, with facial lesions typical of MiTES, in whom mutation analysis of PRDM12 was carried out. Results: Homozygous or compound heterozygous pathogenic expansions of the PRDM12 polyalanine tract were found in four of five affected individuals, in three families. Conclusions: Our finding of autosomal recessive mutations in PRDM12 in four of five patients with MiTES extends the phenotypic spectrum of PRDM12 mutations, which usually cause HSAN8, characterized by mutilating self‐inflicted wounds of the extremities, lips and tongue. By contrast, MiTES shows severe midfacial lesions with little if any evidence of generalized pain insensitivity. The condition is probably genetically heterogeneous, and other congenital insensitivity to pain and HSAN genes such as SCN11A may be implicated. This new understanding of the nature of MiTES, which can masquerade as factitious disease, will facilitate appropriate management. What's already known about this topic? Midface toddler excoriation syndrome (MiTES) is a newly recognized condition, described in three children, characterized by severe, chronic, scarring, self‐inflicted midface excoriations, commencing in infancy.MiTES resembles fabricated and induced illness.The gene PRDM12 is responsible for an autosomal recessive disorder, hereditary sensory and autonomic neuropathy type VIII (HSAN8), characterized by congenital insensitivity to pain with ulceration to the extremities.A family with mild manifestations of HSAN8 and MiTES lesions had homozygous mutations in PRDM12. What does this study add? We report a further five children with MiTES, in four families.Mutation analysis revealed biallelic mutations in PRDM12 in four children in three families. No mutations were found in the fifth child.This confirms MiTES as a recessive disorder of pain sensation, which is probably genetically heterogeneous.This new finding will improve our understanding of children presenting with this condition. Linked Comment:Greenblatt and Mellerio. Br J Dermatol 2018; 179:1029. Respond to this article Plain language summary available online [ABSTRACT FROM AUTHOR]

Nanostructure of polyaniline (n-PANI) is assembled to form a polymer solar cell on fluorine-doped tin oxide (FTO) and aluminum electrodes. The characterization and doping process of n-PANI are verified by ultraviolet–visible (UV–Vis) and Fourier transform infrared spectroscopies. The n-PANI conductivity is in the semiconductive range, and its contact resistance is determined by circular-TLM. The morphologies of n-PANI, FTO and n-PANI film deposited on FTO surface are investigated using atomic force microscopy, scanning electron microscope and transmission electron microscopy. The energy levels of HOMO and LUMO and band gap energy are obtained by cyclic voltammetry and UV–Vis spectroscopy. The similar results are found for band gap energy. The photovoltaic cell characteristics, i.e., open-circuit voltage (VOC), short-circuit current density (JSC), fill factor and power conversion efficiency (PCE or η), are evaluated by measuring the current density–voltage (J–V) under illumination condition and resistance measurements and are found to be 936 mV, 2.72 mA/cm2, 0.377 and 1.6%, respectively, for FTO│n-PANI│Al structure. The mechanism of photoelectron conduction within the cell is studied by the electrochemical impedance spectroscopy. The results shows that not only FTO│n-PANI│Al cell is completely efficient (in comparison with other similar cells, PCE is relatively high), but also its fabrication is of low cost, simple, oxidation resistant and under the green condition. [ABSTRACT FROM AUTHOR]

We investigate the problem of artifacts caused by the periodic boundary conditions (PBC) used in molecular simulation studies. Despite the long history of simulations with PBCs, the existence of measurable artifacts originating from PBCs applied to inherently nonperiodic physical systems remains controversial. Specifically, these artifacts appear as differences between simulations of the same system but with different simulation-cell sizes. Earlier studies have implied that, even in the simple case of a small model peptide in water, sampling inefficiency is a major obstacle to understanding these artifacts. In this study, we have resolved the sampling issue using the replica exchange molecular dynamics (REMD) enhanced-sampling method to explore PBC artifacts. Explicitly solvated zwitterionic polyalanine octapeptides with three different cubic-cells, having dimensions of L = 30, 40, and 50 Å, were investigated to elucidate the differences with 64 replica × 500 ns REMD simulations using the AMBER parm99SB force field. The differences among them were not large overall, and the results for the L = 30 and 40 Å simulations in the conformational free energy landscape were found to be very similar at room temperature. However, a small but statistically significant difference was seen for L = 50 Å. We observed that extended conformations were slightly overstabilized in the smaller systems. The origin of these artifacts is discussed by comparison to an electrostatic calculation method without PBCs. [ABSTRACT FROM AUTHOR]

ARCIMBOLDO solves the phase problem by combining the location of small model fragments using Phaser with density modification and autotracing using SHELXE. Mainly helical structures constitute favourable cases, which can be solved using polyalanine helical fragments as search models. Nevertheless, the solution of coiled‐coil structures is often complicated by their anisotropic diffraction and apparent translational noncrystallographic symmetry. Long, straight helices have internal translational symmetry and their alignment in preferential directions gives rise to systematic overlap of Patterson vectors. This situation has to be differentiated from the translational symmetry relating different monomers. ARCIMBOLDO_LITE has been run on single workstations on a test pool of 150 coiled‐coil structures with 15–635 amino acids per asymmetric unit and with diffraction data resolutions of between 0.9 and 3.0 Å. The results have been used to identify and address specific issues when solving this class of structures using ARCIMBOLDO. Features from Phaser v.2.7 onwards are essential to correct anisotropy and produce translation solutions that will pass the packing filters. As the resolution becomes worse than 2.3 Å, the helix direction may be reversed in the placed fragments. Differentiation between true solutions and pseudo‐solutions, in which helix fragments were correctly positioned but in a reverse orientation, was found to be problematic at resolutions worse than 2.3 Å. Therefore, after every new fragment‐placement round, complete or sparse combinations of helices in alternative directions are generated and evaluated. The final solution is once again probed by helix reversal, refinement and extension. To conclude, density modification and SHELXE autotracing incorporating helical constraints is also exploited to extend the resolution limit in the case of coiled coils and to enhance the identification of correct solutions. This study resulted in a specialized mode within ARCIMBOLDO for the solution of coiled‐coil structures, which overrides the resolution limit and can be invoked from the command line (keyword coiled_coil) or ARCIMBOLDO_LITE task interface in CCP4i. [ABSTRACT FROM AUTHOR]

For the first time, we determined the relative percentages of "rectangular" and "staggered" packing arrangements in the crystalline polyalanine regions with antiparallel β-sheet structure within spider dragline silk fiber from Nephila clavata (NCF) and recombinant silk protein (RSP). The methods used included X-ray diffraction and 13C NMR coupled with selective 13C isotope labeling of the Ala Cβ carbons. From deconvolution analyses of the Ala Cβ peaks in the 13C CP/MAS NMR spectra, the relative percentages of the rectangular arrangements in [3-13C]Ala-NCF were determined to be 49 ± 8% and 40 ± 7% in the dry and hydrated states, respectively, and in [3-13C]Ala-RSP 62 ± 11% and 81 ± 5% in the dry and hydrated states, respectively. Thus, the packing structure changed significantly between the two spider silks and also between the two physical states. The use of NMR was critical in this analysis; from X-ray diffraction patterns alone it would have been difficult to obtain these quantitative data. [ABSTRACT FROM AUTHOR]

Background/Aims: Blepharophimosis-ptosis-epicanthus inversus syndrome (BPES) is a rare autosomal dominant disease caused by FOXL2 gene mutations, and it is clinically characterized by an eyelid malformation associated (type I) or not (type II) with premature ovarian failure (POF). Functional study of novel mutations is especially critical for female patients, as it may allow the prediction of infertility and early planning of an appropriate therapy. Methods: A clinical and molecular genetic investigation was performed in all members of a Chinese family with BPES. Genomic DNA was extracted, and the FOXL2 coding region was sequenced. Subcellular localization was performed by confocal microscopy. Transactivation studies were performed by real-time PCR, dual luciferase reporter assays and electrophoretic mobility shift assays. Results: A novel deletion mutation (C.634_641 del, CCCATGC) between the forkhead domain and the polyalanine domain was found, resulting in a frameshift mutation and a truncated protein. Functional studies showed a strong cytoplasmic mislocalization and abnormal transactivation activity, implying a type I kind mutation with a large chance of infertility. Conclusion: This study identifies that this mutation indicates the probability of developing into POF and shows the importance and necessity of early recognition of BPES type through mutation testing for female patients. Prompt personalized therapy and follow-up is of great clinical significance for female patients carrying this kind of mutation. [ABSTRACT FROM AUTHOR]

Peptide adsorption occurs across technology, medicine, and nature. The functions of adsorbed peptides are related to their conformation. In the past, molecular simulation methods such as molecular dynamics have been used to determine key conformations of adsorbed peptides. However, the transitions between these conformations often occur too slowly to be modeled reliably by such methods. This means such transitions are less well understood. In the study reported here, discrete path sampling is used for the first time to study the potential energy surface of an adsorbed peptide (polyalanine) and the transition pathways between various stable adsorbed conformations that have been identified in prior work by two of the authors [Mijajlovic, M.; Biggs, M. J. J. Phys. Chem. C 2007, 111, 15839-15847]. Mechanisms for the switching of adsorbed polyalanine between the stable conformations are elucidated along with the energetics of these switches. [ABSTRACT FROM AUTHOR]

Spider silks continue to attract researchers because of their excellent mechanical properties and supercontraction behavior. In this paper, the structure and dynamics of recombinant spider silk protein (RSP) were characterized using 13C CP/MAS, 13C DD/MAS, and 13C refocused-INEPT NMR spectroscopies in the dry and hydrated states. The fractions of several structures of RSP with helical, random coil, and β-sheet polyalanine sequences were determined from the CP/MAS NMR spectra in the dry state. The CP/MAS NMR spectra changed to very simple one with dominant β-sheet Ala peaks by hydration due to a significant loss in CP signals of the other mobile carbons. On the contrary, only sharp mobile peaks, and both mobile and immobile peaks could be observed in the refocused-INEPT and DD/MAS NMR spectra, respectively. The cis/trans proportion of the Gly-Pro bond was also determined. Our measurements provide new insight into understanding the supercontraction phenomenon of spider silks. [ABSTRACT FROM AUTHOR]

Polyalanine chains have been extensively considered in the context of the development of peptides for self-organization of peptide nanostructures. Atomistic molecular dynamics simulations allowed us to analyze the structure and thermodynamics of the hydration of four polyalanines: A 3 , A 6 , A 9 and A 12 . These chains have been considered to interact exactly as lipid in a peptide nanostructure, however our results show that such a view is inaccurate since alanine tails must interact strongly with each other, not only because of the hydrophobic interactions of side chains but also because of their hydrophilic groups. Our results show that the hydration free energy of such chains varies linearly with the length of the polyalanine, is strongly negative and is mostly driven by enthalpy. There is an entropic penalty, however, which is not enough to compensate for the enthalpic gain obtained in the hydration process. [ABSTRACT FROM AUTHOR]

Collision-induced dissociation (or tandem mass spectrometry, MS/MS) of a protonated peptide results in a spectrum of fragment ions that is useful for inferring amino acid sequence. This is now commonplace and a foundation of proteomics. The underlying chemical and physical processes are believed to be those familiar from physical organic chemistry and chemical kinetics. However, first-principles predictions remain intractable because of the conflicting necessities for high accuracy (to achieve qualitatively correct kinetics) and computational speed (to compensate for the high cost of reliable calculations on such large molecules). To make progress, shortcuts are needed. Inspired by the popular mobile proton model, we have previously proposed a simplified theoretical model in which the gas-phase fragmentation pattern of protonated peptides reflects the relative stabilities of N-protonated isomers, thus avoiding the need for transition-state information. For singly protonated Ala ( n = 3-11), the resulting predictions were in qualitative agreement with the results from low-energy MS/MS experiments. Here, the comparison is extended to a model tryptic peptide, doubly protonated AlaArg. This is of interest because doubly protonated tryptic peptides are the most important in proteomics. In comparison with experimental results, our model seriously overpredicts the degree of backbone fragmentation at N. We offer an improved model that corrects this deficiency. The principal change is to include Coulombic barriers, which hinder the separation of the product cations from each other. Coulombic barriers may be equally important in MS/MS of all multiply charged peptide ions. [ABSTRACT FROM AUTHOR]

The Aristaless- related homeobox gene ( ARX ) is a known intellectual disability (ID) gene that frequently presents with X-linked infantile spasm syndrome as a comorbidity. ID with epilepsy in children is a chronic and devastating disorder that has poor treatment options and disease outcomes. To gain a better understanding of the role that mutations in ARX play in ID and epilepsy, we investigate ARX patient mutations modelled in mice. Over half of all ARX mutations result from expansions of the first two polyalanine (PA1 and PA2 respectively) tracts. However, phenotypic data for the mouse modelling the more frequent ARX PA2 dup24 mutation in patients has not been reported and constitutes a barrier to understanding the molecular mechanisms involved. Here we report the first comprehensive analysis of postnatal outcomes for mice modelling disease-causing expansions to both PA1 and PA2 tracts. Both strains were found to have impaired learning and memory, reduced activity, increased anxiety and reduced sociability; with PA1 mice generally displaying greater behavioural deficits in keeping with the more severe phenotype reported in patients. In agreement with previous reports, 70% of PA1 males exhibit myoclonic seizures by two months of age, with the first observed at P18. In this report, we show 80% of PA2 males also display myoclonic seizures, with the first observed at P19. Consistent with patient phenotypes, we observe large variations in seizure progression and severity for both PA1 and PA2 individual mice. The generation of this comprehensive baseline data is a necessary step on the path to the development of therapies to improve patient outcomes. [ABSTRACT FROM AUTHOR]

The Aristaless-related homeobox gene ( ARX ) is indispensable for interneuron development. Patients with ARX polyalanine expansion mutations of the first two tracts (namely PA1 and PA2) suffer from intellectual disability of varying severity, with seizures a frequent comorbidity. The impact of PA1 and PA2 mutations on the brain development is unknown, hindering the search for therapeutic interventions. Here, we characterized the disturbances to cortical interneuron development in mice modeling the two most common ARX polyalanine expansion mutations in human. We found a consistent ∼40–50% reduction of calbindin-positive interneurons, but not Stt+ or Cr+ interneurons, within the cortex of newborn hemizygous mice ( p = 0.024 ) for both mutant strains compared to wildtype ( p = 0.011 ). We demonstrate that this was a consequence of calbindin precursor cells being arrested or delayed at the ventral subpallium en route of tangential migration. Ex-vivo assay validated this migration deficit in PA1 cells ( p = 0.0002 ) suggesting that the defect is contributed by intrinsic loss of Arx function within migrating cells. Both humans and mice with PA1 mutations present with severe clinical features, including intellectual disability and infantile spasms. Our data further demonstrated the pathogenic mechanism was robustly shared between PA1 and PA2 mutations, as previously reported including Arx protein reduction and overlapping transcriptome profiles within the developing mouse brains. Data from our study demonstrated that cortical calbindin interneuron development and migration is negatively affected by ARX polyalanine expansion mutations. Understanding the cellular pathogenesis contributing to disease manifestation is necessary to screen efficacy of potential therapeutic interventions. [ABSTRACT FROM AUTHOR]

HSCR is a congenital disorder of the enteric nervous system, characterized by the absence of neurons along a variable length of the gut resulting from loss-of-function RET mutations. Congenital Central Hypoventilation Syndrome (CCHS) is a rare neurocristopathy characterized by impaired response to hypercapnia and hypoxemia caused by heterozygous mutations of the PHOX2B gene, mostly polyalanine (polyA) expansions but also missense, nonsense, and frameshift mutations, while polyA contractions are common in the population and believed neutral. HSCR associated CCHS can present in patients carrying PHOX2B mutations. Indeed, RET expression is orchestrated by different transcriptional factors among which PHOX2B, thus suggesting its possible role in HSCR pathogenesis. Following the observation of HSCR patients carrying in frame trinucleotide deletions within the polyalanine stretch in exon 3 (polyA contractions), we have verified the hypothesis that these PHOX2B variants do reduce its transcriptional activity, likely resulting in a down-regulation of RET expression and, consequently, favouring the development of the HSCR phenotype. Using proper reporter constructs, we show here that the in vitro transactivation of the RET promoter by different HSCR-associated PHOX2B polyA variants has resulted significantly lower compared to the effect of PHOX2B wild type protein. In particular, polyA contractions do induce a reduced transactivation of the RET promoter, milder compared to the severe polyA expansions associated with CCHS + HSCR, and correlated with the length of the deleted trait, with a more pronounced effect when contractions are larger. [ABSTRACT FROM AUTHOR]

A random poly(L-alanine-co-L-lactic acid) (PAL) with excellent thermo-sensitivity and no cytotoxicity was synthesized by the structure-controlled polycondensation from naturalL-alanine andL-lactic acid. Only those PALs in which the contents ofL-alanine structural unit are rigidly controlled in the smaller range of 53–65% show a reversible lower critical solution temperature of 35–60°C. The change of secondary structure in poly(L-alanine) segments by the introduction ofL-lactic acid structural unit plays a decisive role in regulating the thermo-sensitivity of PAL. The viability of HeLa cells exposed to PAL reaches up to 91–116% after incubation of 24 and 72 h, indicating no cytotoxicity. Furthermore, PAL can easily form curcumin-loaded nano-carriers through its thermo-sensitivity and self-assembly. The curcumin-loaded PAL nano-particles are observed to clearly internalize into the cells by confocal laser-scanning microscopy, and thus can be used as a potential nano-drug-carrier. [ABSTRACT FROM AUTHOR]

Samia cynthia ricini is one of the wild silkworms and its silk fibroin (SF) consists of alternatively repeating poly-l-alanine (PLA) sequences as crystalline domain and glycine-rich sequences as noncrystalline domain; the structure is similar to those of spider silk and other wild silkworm silks. In this paper, we proposed a new staggered model for the packing arrangement of the PLA sequence through the use of the Cambridge Serial Total Energy Package program and a comparison of the observed and calculated chemical shifts of the PLA sequence with the Gauge Including Projector Augmented Wave method. The new model was supported by the interatomic distance information from the cross peaks of Ala Cβ dipolar-assisted rotational resonance (DARR) spectrum of the PLA sequences in S. c. ricini SF fiber. In addition, three 13C NMR peaks observed in the β-sheet region were assigned to the carbons with different environments in the same model, but not assigned to different β-sheet structures. [ABSTRACT FROM AUTHOR]

This study describes a convenient and phosgene ‐ free synthesis of poly(N ‐ methyl L ‐ alanine) with solubility in water using polycondensation of activated urethane derivative of N ‐ methyl L ‐ alanine was described. The polycondensation of activated urethane derivative was heated at 60 °C with n ‐ butylamine as an initiator to give the corresponding poly(N ‐ methyl L ‐ alanine), accompanying the elimination of phenol and CO2. The investigation of SEC and MALDI TOF mass spectrometry characterized the control of molecular weight and terminal structure. [ABSTRACT FROM AUTHOR]

Background: Runt-related transcription factor 2 (RUNX2) is a transcription factor essential for skeletal development. Variation within the RUNX2 polyglutamine / polyalanine (QA) repeat is correlated with facial length within orders of placental mammals and is suggested to be a major driver of craniofacial diversity. However, it is not known if this correlation exists outside of the placental mammals. Results: Here we examined the correlation between the RUNX2 QA repeat ratio and facial length in the naturally evolving sister group to the placental mammals, the marsupials. Marsupials have a diverse range of facial lengths similar to that seen in placental mammals. Despite their diversity there was almost no variation seen in the RUNX2 QA repeat across individuals spanning the entire marsupial infraclass. The extreme conservation of the marsupial RUNX2 QA repeat indicates it is under strong purifying selection. Despite this, we observed an unexpectedly high level of repeat purity. Conclusions: Unlike within orders of placental mammals, RUNX2 repeat variation cannot drive craniofacial diversity in marsupials. We propose conservation of the marsupial RUNX2 QA repeat is driven by the constraint of accelerated ossification of the anterior skeleton to facilitate life in the pouch. Thus, marsupials must utilize alternate pathways to placental mammals to drive craniofacial evolution. [ABSTRACT FROM AUTHOR]

Using precomputed near neighbor or proximal distribution functions (pDFs) that approximate solvent density about atoms in a chemically bonded context one can estimate the solvation structures around complex solutes and the corresponding solute-solvent energetics. In this contribution, we extend this technique to calculate the solvation free energies (ΔG) of a variety of solutes. In particular we use pDFs computed for small peptide molecules to estimate ΔG for larger peptide systems. We separately compute the non polar (ΔGvdW) and electrostatic (ΔGelec) components of the underlying potential model. Here we show how the former can be estimated by thermodynamic integration using pDF-reconstructed solute-solvent interaction energy. The electrostatic component can be approximated with Linear Response theory as half of the electrostatic solute-solvent interaction energy. We test the method by calculating the solvation free energies of butane, propanol, polyalanine, and polyglycine and by comparing with traditional free energy simulations. Results indicate that the pDF-reconstruction algorithm approximately reproduces ΔGvdW calculated by benchmark free energy simulations to within ~ kcal/mol accuracy. The use of transferable pDFs for each solute atom allows for a rapid estimation of ΔG for arbitrary molecular systems. [ABSTRACT FROM AUTHOR]

Polyalanine (poly(A)) diseases are caused by the expansion of translated GCN triplet nucleotide sequences encoding poly(A) tracts in proteins. To date, nine human disorders have been found to be associated with poly(A) tract expansions, including congenital central hypoventilation syndrome and oculopharyngeal muscular dystrophy. Previous studies have demonstrated that unexpanded wild-type poly(A)-containing proteins localize to the cell nucleus, whereas expanded poly(A)-containing proteins primarily localize to the cytoplasm. Because most of these poly(A) disease proteins are transcription factors, this mislocalization causes cellular transcriptional dysregulation leading to cellular dysfunction. Correcting this faulty localization could potentially point to strategies to treat the aforementioned disorders, so there is a pressing need to identify the mechanisms underlying the mislocalization of expanded poly(A) protein. Here, we performed a glutathione S-transferase pulldown assay followed by mass spectrometry and identified eukaryotic translation elongation factor 1+1 (eEF1A1) as an interacting partner with expanded poly(A)-containing proteins. Strikingly, knockdown of eEF1A1 expression partially corrected the mislocalization of the expanded poly(A) proteins in the cytoplasm and restored their functions in the nucleus. We further demonstrated that the expanded poly(A) domain itself can serve as a nuclear export signal. Taken together, this study demonstrates that eEF1A1 regulates the subcellular location of expanded poly(A) proteins and is therefore a potential therapeutic target for combating the pathogenesis of poly(A) diseases. [ABSTRACT FROM AUTHOR]

The three-body fragment molecular orbital (FMO3) method is formulated for density-functional tight-binding (DFTB). The energy, analytic gradient, and Hessian are derived in the gas phase, and the energy and analytic gradient are also derived for polarizable continuum model. The accuracy of FMO3-DFTB is evaluated for five proteins, sodium cation in explicit solvent, and three isomers of polyalanine. It is shown that FMO3-DFTB is considerably more accurate than FMO2-DFTB. Molecular dynamics simulations for sodium cation in water are performed for 100 ps, yielding radial distribution functions and coordination numbers. © 2017 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

An appropriate modification technique for silk materials is needed to effectively improve their physical properties for specific applications. A telechelic-type polyalanine (T-polyA) was synthesized by papain-catalyzed polymerization as a novel reinforcing agent for silk materials. A silk fibroin obtained from Bombyx mori was homogeneously doped with T-polyA, and casting a solution of silk fibroin and T-polyA in 1,1,1,3,3,3-hexafluoro-2-propanol (HFIP) resulted in a robust and transparent film. Tensile deformation studies of the silk composite film containing T-polyA with prestretching revealed that the tensile strength and toughness were enhanced relative to those of a silk-only film. To determine the capability of T-polyA to reinforce the tensile property of silk films, the secondary structure in the silk composite film was characterized by wide-angle X-ray diffraction (WAXD) analysis. Antiparallel β-sheet structures of T-polyA and GAGAGS motifs of silk fibroin formed independently in the prestretched composite film. In addition, measuring the tensile deformation and performing WAXD analysis simultaneously demonstrated that the β-sheet structures of both T-polyA and the silk fibroin were aligned along the stretching direction and that T-polyA had no significant effect on the final morphology of the silk crystal domains. The silk film was toughened by the addition of T-polyA because of the generation of the T-polyA β-sheet in the amorphous region of the composite film. This work provides novel insight into the design and development of tough silk materials with controlled and aligned β-sheet structures. [ABSTRACT FROM AUTHOR]

Background: Several functional single-nucleotide polymorphisms (SNPs) at the FOXE1 locus on chromosome 9q22.33 have been associated with the risk for papillary thyroid carcinoma (PTC). This study set out to elucidate whether their effects are independent, using genotyping results in populations of Asian and European descent. Methods: SNPs rs965513 and rs1867277 and a polymorphic region determining the length of the FOXE1 polyalanine (poly-Ala) tract were genotyped in 501 patients with PTC and 748 healthy individuals from Japan, and in 660 patients and 820 population controls from Belarus. Functional analysis of transactivation activities of FOXE1 isoforms with varying number of alanine repeats was performed by a Dual-Luciferase® Assay. Results: All three polymorphisms were significantly associated with PTC in both populations on univariate analysis. However, conditional analysis revealed independent effects of rs965513 and rs1867277 SNPs but not of the FOXE1 poly-Ala polymorphism. The independent effect of the lead rs965513 SNP was observed in both populations, while that of rs1867277 was only identified in the Japanese population, in which linkage disequilibrium between the three polymorphisms is markedly weaker. Despite the strong decrease in transcriptional activity with increasing FOXE1 poly-Ala tract length, no difference in transactivation potential of the FOXE1 poly-Ala isoforms could be seen after adjustment for the minimal promoter activity in the reporter vectors. Plasmids encoding FOXE1 isoforms of increasing poly-Ala tract length were also found to produce less FOXE1 protein after cell transfection. Conclusions: The functional variants rs965513 and rs1867277 independently contribute to genetic predisposition to PTC, while a contributing role of the FOXE1 poly-Ala polymorphism could not be confirmed. [ABSTRACT FROM AUTHOR]

Objective Polymorphisms in the thyroid transcription factor forkhead factor E1 ( FOXE1) gene have been implicated in the genetic susceptibility to differentiated thyroid cancer, but little is known about their effect on tumour characteristics. The objective of this study was to determine the contribution of the FOXE1 polyalanine repeat region to the susceptibility to thyroid cancer and to its clinical characteristics. Design, patients and measurements A total of 500 patients with sporadic thyroid cancer (440 papillary and 60 follicular thyroid carcinoma) and 502 healthy controls were included in this case-control association study. The number of FOXE1 alanine repeats in each subject was determined by PCR and multiplex fragment analysis by capillary electrophoresis. FOXE1 genotype and allele frequencies among groups were compared by logistic regression and adjusted for sex and age at diagnosis. Data were analysed according to cancer subtype, tumour size and the presence of lymph node or distant metastasis. Results FOXE1 alleles with 16 or more alanine repeats were more frequent in patients with tumour size > 1 cm compared to tumour size ≤ 1 cm (adjusted OR 1·44; 95% CI 1·05-1·88; P = 0·019). Genotypes containing at least one allele with 16 or more alanine repeats were associated with larger tumour size (adjusted OR 1·71; 95% CI 1·15-2·57; P = 0·009). No significant differences were observed between cancer subtypes or the presence/absence of metastasis. Conclusions FOXE1 polyalanine repeat polymorphisms are associated with thyroid cancer, but only for tumours larger than 1 cm, suggesting a role in disease progression. [ABSTRACT FROM AUTHOR]

The structural analysis of alanine oligopeptides is important for understanding the crystalline region in silks from spiders and wild silkworms and also the mechanism of cellular toxicity of human diseases arising from expansion in polyalanine sequences. The atomic-level structures of alanine tripeptide and tetrapeptide with antiparallel β-sheet structures (AP-Ala3 and AP-Ala4, respectively) together with alanine tripeptide with parallel β-sheet structures (P-Ala3) have been determined, but alanine tetrapeptide with a parallel β-sheet structure (P-Ala4) has not been reported yet. In this article, first, we established the preparation protocol of P-Ala4 from more stable AP-Ala4. Second, complete assignments of the 13C, 15N, and ¹H solid-state NMR spectra were performed with 13C- and 15N-labeled Ala4 samples using several solid-state NMR techniques. Then, the structural constraints were obtained, for example, the amide proton peaks of P-Ala4 in the ¹H double-quantum magic-angle spinning NMR spectrum were heavily overlapped and observed at about 7.4 ppm, which was a much higher field than that of 8.7-9.1 ppm observed for AP-Ala4, indicating that the intermolecular hydrogen-bond lengths across strands (N-H···OC) were considerably longer for P-Ala4, that is, 2.21-2.34 Å, than those reported for AP-Ala4, that is, 1.8-1.9 Å. The structural model was proposed for P-Ala4 by NMR results and MD calculations. [ABSTRACT FROM AUTHOR]

Background: Congenital Central Hypoventilation Syndrome (CCHS) is a rare neurocristopathy characterized by severe hypoventilation and autonomic dysregulation, with typical presentation in the neonatal period, and deficient cognitive skills in school-aged patients. We hypothesized that younger (preschool) children with CCHS would also show neurocognitive delay and that CCHS-related physiologic factors would impact neurocognitive test results.Methods: We studied developmental (Bayley) test results collected during routine clinical care in 31 children (mean age 25.0 ± 8.5 months; range, 6-40 months) with PHOX2B mutation-confirmed CCHS by comparing them with the normative reference mean from the Bayley standardization sample; we also examined associations between Bayley scores and CCHS disease-related factors.Results: Preschool patients with CCHS fell significantly below the normative mean of 100 on Bayley indices of mental (mean, 83.35 ± 24.75) and motor (mean, 73.33 ± 20.48) development (P < .001 for both). Significantly lower Bayley mental and motor scores were associated with severe breath-holding spells, prolonged sinus pauses, and need for 24 h/d artificial ventilation. Lower Bayley motor scores were also associated with seizures. Bayley scores differed among children with the three most common polyalanine repeat expansion mutation genotypes (mental, P = .001; motor, P = .006), being essentially normal in children with the 20/25 genotype but significantly lower in the other genotype groups (P < .05).Conclusions: These results confirm neurodevelopmental impairment of CCHS preschoolers, with severity related to physiologic compromise and PHOX2B genotype. These findings suggest that adverse effects begin early in the disease process, supporting the need for neurodevelopmental monitoring and intervention from early infancy. [ABSTRACT FROM AUTHOR]

In recent years chiral molecules were found to act as efficient spin filters. Using a multilayer structure with chiral molecules magnetic memory was realized. Observed rare magnetic phenomena in a chiral-based magnetic memory device was reported by O-Ben Dor et. al in Nature Commun, 4, 2256 (2013). This multi-layered device is built from α-helix l -polyalanine (AHPA-L) adsorbed on gold, Al 2 O 3 (7 nm) and Ni (30 nm) layers. It was shown that certain temperature range the FC branch crosses the magnetic peak (at 55 K) observed in the ZFC curve thus ZFC>FC. We show here that in another similar multi-layered material, at low applied field, the ZFC curve lies above the FC one up to 70 K. The two features have the same origin and the crucial necessary components to exhibit them are: AHPA-L and 30 nm Ni layered thick. Similar effects were also reported in sulfur doped amorphous carbon. A comparison between the two systems and the ingredients for these peculiar observations is discussed. [ABSTRACT FROM AUTHOR]

High-performance, biobased materials can potentially be manufactured from polymerized α-amino acids (α-polypeptides). This paper reports on the synthesis, structure, and properties of both polyalanine enantiomers (PLAla and PDAla). The molecular structure of the polypeptide chains, their molecular weight, and polydispersity were investigated by ¹H NMR, MALDI-TOF, and size-exclusion chromatography. The secondary structure and crystalline order were probed via Fourier transform infrared spectroscopy, circular dichroism, and (synchrotron) wide-angle X-ray diffraction. The phase behavior and thermal stability were assessed by differential scanning calorimetry and thermogravimetric analysis. The kinetically trapped PAla chain conformation in the solid state, after synthesis or solvent treatments, is the α-helical shape. Upon heating, crystals from the α-helices convert into more stable crystals from β-sheets at a temperature higher than 210 °C. This temperature is close to where polymer degradation sets in. The β-sheet crystals combine melting with thermal degradation at temperatures above 330 °C. In the presence of superheated water, the conversion from α-helices to β-sheets happens at lower temperatures, allowing for a conversion without degradation. [ABSTRACT FROM AUTHOR]

Ion mobility mass spectrometry is used to measure the drift-time of an ion. The drift-time of an ion can be used to calculate the collision cross-section (CCS) in travelling wave ion mobility (e.g. Waters Synapt and Vion instruments) or directly determine the experimental CCS (e.g. Agilent 6560 instrument and many drift-tube instruments). A comparison of the experimental CCS and theoretical CCS values obtained from trajectory method He(g) parameterised MOBCAL and N2(g) parameterised MOBCAL software, for a range of 20 ‘small molecules’ is presented. This study utilises density functional theory B3LYP methods and the 6-31G+(d,p) basis set to calculate theoretical CCS values. This study seeks to assess the accuracy of a common procedure using CCS calibration with poly-(d/l)-alanine derived from drift-cell measurements and the original release of MOBCAL software and compare it with recent improvements with a drug-like molecule calibration set and a revision of MOBCAL parameterised for N2(g) drift gas. This study represents one of the first quantitative evaluations of the agreement between theoretical CCS and experimental CCS values for a range of small pharmaceutically relevant molecules using travelling wave ion mobility mass spectrometry. Accurate theoretical CCS may allow optimisation of ion mobility separations in silico, provide CCS databases that can confirm structures without the need for alternative analytical tools such as nuclear magnetic resonance spectroscopy (NMR) and assignment of unknowns and positional isomers without requiring reference materials. [ABSTRACT FROM AUTHOR]

The wild silkworm Samia cynthiariciniproducessilk fibroin containing polyalanine sequences. The structure of atypical tandem repeat sequence YGGDGG(A)12GGAG within S. c. ricinisilk fibroin in liquid silk was determinedby solution NMR. 13C, 15N, and 1Hshifts were assigned from solution NMR spectra for the tandem repeat.TALOS-N was then used to predict the backbone dihedral angles fromthe chemical shifts. Dihedral angles revealed a well-structured α-helixfor the polyalanine region and less stable capping motifs for theN- and C-terminal regions. Consistent with this, the amide protontemperature coefficients of the last glycine in the N-terminal regionand the first two glycines in the C-terminal region show more positivevalues than that of a random coil structure. Thus, the α-helicalstructure of the polyalanine region of S. c. riciniliquid silk is stabilized by capping motifs. [ABSTRACT FROM AUTHOR]

ARCIMBOLDO solves the phase problem at resolutions of around 2 Å or better through massive combination of small fragments and density modification. For complex structures, this imposes a need for a powerful grid where calculations can be distributed, but for structures with up to 200 amino acids in the asymmetric unit a single workstation may suffice. The use and performance of the single-workstation implementation, ARCIMBOLDO_LITE, on a pool of test structures with 40-120 amino acids and resolutions between 0.54 and 2.2 Å is described. Inbuilt polyalanine helices and iron cofactors are used as search fragments. ARCIMBOLDO_BORGES can also run on a single workstation to solve structures in this test set using precomputed libraries of local folds. The results of this study have been incorporated into an automated, resolution- and hardware-dependent parameterization. ARCIMBOLDO has been thoroughly rewritten and three binaries are now available: ARCIMBOLDO_LITE, ARCIMBOLDO_SHREDDER and ARCIMBOLDO_BORGES. The programs and libraries can be downloaded from . [ABSTRACT FROM AUTHOR]

Examine the genotype-phenotype relationship in Japanese congenital central hypoventilation syndrome (CCHS) patients and estimate the incidence of CCHS in Japan. Subjects were 92 Japanese patients with PHOX2B mutations; 19 cases carried 25 polyalanine repeat expansion mutations (PARMs); 67 cases carried 26 or more PARMs; and 6 had non-PARMs (NPARMs). We collected clinical data in all patients and estimated the development or intelligent quotients only in the patients carrying 25 PARM. The estimated incidence of CCHS was greater than one case per 148 000 births. Polyhydramnios was observed in three cases. Twelve infants exhibited depressed respiration at birth. In 19 cases carrying 25 PARM, the male-to-female ratio was ~3, no cases had Hirschsprung disease; 7 cases (37%) developed hypoventilation after the neonatal period, and 8 cases (42%) had mental retardation. In other 73 cases carrying 26 or more PARMs or NPARMs, male-to-female ratio was equal; patients frequently complicated with Hirschsprung disease and constipation, and all patients presented with hypoventilation in the neonatal period. Clinical symptoms were severe in most patients carrying long PARMs and NPARMs. In 25 PARM, additional genetic and/or epigenetic factors were required for CCHS development and male sex is likely a predisposing factor. The patients carrying 25 PARM frequently had mental retardation likely because they were not able to receive appropriate ventilation support following a definitive diagnosis owing to subtle and or irregular hypoventilation. Molecular diagnosis provides a definitive diagnosis and enables to receive appropriate ventilator support. [ABSTRACT FROM AUTHOR]

We developed the energy and its analytic gradient for the self-consistent-charge density-functional tight-binding method with the third-order expansion (DFTB3) combined with the fragment molecular orbital (FMO) method, FMO-DFTB3. FMO-DFTB3 reproduced full DFTB3 relative stabilities and the optimized structures of three polyalanine isomers. FMO-DFTB3 was applied to optimize a nano flake of cellulose I β , consisting of 10 944 atoms, and a good agreement with the experimental structure was obtained. For a cellulose sheet containing 1368 atoms, FMO-DFTB3 was 43.5 times faster than full DFTB3. The binding between sheets and chains in cellulose was elucidated, and two dispersion models were compared. [ABSTRACT FROM AUTHOR]

Oculopharyngeal muscular dystrophy (OPMD), a polyalanine myopathy, occurs due to expansion of homopolyalanine stretch in normal polyadenylating binding protein nuclear 1 (PABPN1) protein from Ala10 to Ala11-17. Therefore, the conformational behavior of polyalanine peptides with n=10–17, with and without terminal protecting groups, have been investigated with different starting geometries in water by molecular dynamics simulation studies. Alanine peptides are shown to give rise to unordered structure irrespective of starting geometry and not more than two residues at a stretch have the same/similar set of φ, ψ values. However, the final structure with terminal protecting groups look like β-strand. Unprotected poly-Ala peptides adopt twisted β-hairpin/multi hairpin like structure with increasing chain length. The number of residues having φ, ψ values in collagen region is found to be less in peptides with unprotected termini as compared to peptides with protected termini of same chain length. The results have been supported by recent synchrotron radiation circular dichroism spectroscopy of polyproline II and unordered secondary structures. Opening of the helical structure in poly-Ala peptides with protecting groups has been shown to take place from C-terminal and in peptides without protecting groups opening of helix starts from both terminals. Further, opening of helix takes more time in poly-Ala peptides without terminal protecting groups. The deviations in amide bond planarity have been discussed and compared with available experimental and computational results. [ABSTRACT FROM AUTHOR]

The Aristaless-related homeobox ( ARX) gene is implicated in intellectual disability with the most frequent pathogenic mutations leading to expansions of the first two polyalanine tracts. Here, we describe analysis of the ARX gene outlining the approaches in the Australian and Portuguese setting, using an integrated clinical and molecular strategy. We report variants in the ARX gene detected in 19 patients belonging to 17 families. Seven pathogenic variants, being expansion mutations in both polyalanine tract 1 and tract 2, were identifyed, including a novel mutation in polyalanine tract 1 that expands the first tract to 20 alanines. This precise number of alanines is sufficient to cause pathogenicity when expanded in polyalanine tract 2. Five cases presented a probably non-pathogenic variant, including the novel HGVS: c.441_455del, classified as unlikely disease causing, consistent with reports that suggest that in frame deletions in polyalanine stretches of ARX rarely cause intellectual disability. In addition, we identified five cases with a variant of unclear pathogenic significance. Owing to the inconsistent ARX variants description, publications were reviewed and ARX variant classifications were standardized and detailed unambiguously according to recommendations of the Human Genome Variation Society. In the absence of a pathognomonic clinical feature, we propose that molecular analysis of the ARX gene should be included in routine diagnostic practice in individuals with either nonsyndromic or syndromic intellectual disability. A definitive diagnosis of ARX-related disorders is crucial for an adequate clinical follow-up and accurate genetic counseling of at-risk family members. [ABSTRACT FROM AUTHOR]

By the forced unfolding of polyglutamineand polyalanine homopeptidesin competing α-helix and β-hairpin secondary structures,we disentangle equilibrium free energetics from nonequilibrium dissipativeeffects. We find that α-helices are characterized by largerfriction or dissipation upon unfolding, regardless of whether theyare free energetically preferred over β-hairpins or not. Ouranalysis, based on MD simulations for atomistic peptide models withexplicit water, suggests that this difference is related to the internalfriction and mostly caused by the different number of intrapeptidehydrogen bonds in the α-helix and β-hairpin states. [ABSTRACT FROM AUTHOR]

We present a web toolkit STructure mapper and Online Coarse-graining Kit for setting up coarse-grained molecular simulations. The kit consists of two tools: structure mapping and Boltzmann inversion tools. The aim of the first tool is to define a molecular mapping from high, for example, all-atom, to low, that is, coarse-grained, resolution. Using a graphical user interface it generates input files, which are compatible with standard coarse-graining packages, for example, Versatile Object-oriented Toolkit for Coarse-graining Applications and DL_CGMAP. Our second tool generates effective potentials for coarse-grained simulations preserving the structural properties, for example, radial distribution functions, of the underlying higher resolution model. The required distribution functions can be provided by any simulation package. Simulations are performed on a local machine and only the distributions are uploaded to the server. The applicability of the toolkit is validated by mapping atomistic pentane and polyalanine molecules to a coarse-grained representation. Effective potentials are derived for systems of TIP3P (transferable intermolecular potential 3 point) water molecules and salt solution. The presented coarse-graining web toolkit is available at . © 2014 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

The role played by side-chain interactions on the formation of a-helices is studied using extensive all-atom molecular dynamics simulations of polyalanine-like peptides in explicit T1P4P water. The peptide is described by the OPLS-AA force field except for the Lennard-Jones interaction between Cß-Cß atoms, which is modified systematically. We identify values of the Lennard-Jones parameter that promote a-helix formation. To rationalize these results, potentials of mean force (PMF) between methane-like molecules that mimic side chains in our polyalanine-like peptides are computed. These PMF exhibit a complex distance dependence where global and local minima are separated by an energy barrier. We show that a-helix propensity correlates with values of these PMF at distances corresponding to Cß-Cß of i - i + 3 and other nearest neighbors in the a-helix. In particular, the set of Lennard-Jones parameters that promote a-helices is characterized by PMF that exhibit a global minimum at distances corresponding to i - i + 3 neighbors in α-helices. Implications of these results are discussed. [ABSTRACT FROM AUTHOR]

Spider silk proteins undergo a complexseries of molecular eventsbefore being converted into an outstanding hierarchically organizedfiber. Recent literature has underlined the crucial role of the C-terminaldomain in silk protein stability and fiber formation. However, theeffect of pH remains to be clarified. We have thus developed an efficientpurification protocol to obtain stable native-like recombinant MaSp1C-terminal domain of Nephila clavipes(NCCTD). Its structure was investigated as a function of pH usingcircular dichroism, fluorescence and solution NMR spectroscopy. Theresults show that the NCCTD structure is very sensitive to pH andsuggest that a molten globule state occurs at pH 5.0 and below. Electronicmicroscopy images also indicate fiber formation at low pH and coarserglobular particles at more basic pH. The results are consistent witha spinning process model where the NCCTD acts as an aggregation nucleusfavoring the β-aggregation of the hydrophobic polyalanine repeatsupon spinning. [ABSTRACT FROM AUTHOR]

Presence of polyalanine (polyA) stretches in some proteins is found to be associated with their aggregation, which causes disorders in various developmental processes. In this work, inherent propensities towards aggregation of some residues, which are not part of the polyA stretches, have been identified by using the primary sequences of seven polyA proteins with the help of Betascan, PASTA and Tango programs and explored unambiguously. This provides a basis for proposing molecular mechanism of this type of aggregation. Reported suppression of aggregation of polyA proteins by chaperones like HSP40 and HSP70 is substantiated through molecular docking. The hydrophobic residues of identified aggregating region are found to be interacting with hydrophobic surface of chaperones. This suggests a crucial clue for possible way to inhibit the aggregation of such proteins. [ABSTRACT FROM AUTHOR]

Ion mobility (IM) is a gas-phase electrophoretic method that separates ions according to charge and ion-neutral collision cross-section (CCS). Herein, we attempt to apply a traveling wave (TW) IM polyalanine calibration method to shotgun proteomics and create a large peptide CCS database. Mass spectrometry methods that utilize IM, such as HDMS, often use high transmission voltages for sensitive analysis. However, polyalanine calibration has only been demonstrated with low voltage transmission used to prevent gas-phase activation. If polyalanine ions change conformation under higher transmission voltages used for HDMS, the calibration may no longer be valid. Thus, we aimed to characterize the accuracy of calibration and CCS measurement under high transmission voltages on a TW IM instrument using the polyalanine calibration method and found that the additional error was not significant. We also evaluated the potential error introduced by liquid chromatography ( LC)-HDMS analysis, and found it to be insignificant as well, validating the calibration method. Finally, we demonstrated the utility of building a large-population peptide CCS database by investigating the effects of terminal lysine position, via LysC or LysN digestion, on the formation of two structural sub-families formed by triply charged ions. [Figure not available: see fulltext.] [ABSTRACT FROM AUTHOR]