Numerical Study of the Structural and Thermal Properties of Vitreous Silica

Abstract

We use classical molecular dynamics simulations to study both the structural modifications through the glass transition and the thermal conductivity k of a model silica glass. The first part is based on the Voronoï tessellation and we show that the structural freezing following upon the glass transition is noticeable in all the geometric characteristics of the Voronoï cells and a possible interpretation in terms of geometrical frustration is proposed.

In the second part we calculate k directly in the simulation box by using the standard equations of heat transport. The calculations have been done between 10 and 1000 Kelvin and the results are in good agreement with the experimental data at temperatures above 20 K. The plateau observed around 10 K can be accounted for by correcting our results taking into account finite size effects in a phenomenological way.     

A pH-dependent Structural Transition in the Homopurine-homopyrimidine Tract in Superhelical DNA

Abstract

We have inserted the 509-bp-long fragment of sea urchin P. miliaris histone gene spacer region into plasmid pUC19. The fragment contains the 60-bp-long homopurine-homopyrimidine tract that is known to be hypersensitive to the S1 endonuclease. Using two-dimensional gel electrophoresis we have observed a sharp structural transition in the insert with increasing DNA superhelicity. As in the cases of cruciform and Z form formation, the observed transition partly relaxes the superhelical stress. In contrast with the other two well documented transitions, the observed transition strongly depends on pH. At pH7 and above the transition occurs at negative superhelicities exceeding the physiological range (σ>0.08). For pH6 the transition occurs at ?σ = 0.055, whereas for pH4.3 it takes place at ?σ = 0.001. A comprehensive analysis of the obtained data has made it possible to define the nature of the observed transition. We conclude that under superhelical stress or/and at low pH homopurine- homopyrimidine tracts adopt a novel spatial structure called the H form.     

Activated breast stromal fibroblasts exhibit myoepithelial and mammary stem cells features

BackgroundActive breast cancer-associated fibroblasts (CAFs) promote tumor growth and spread, and like tumor cells they are also heterogeneous with various molecular sub-types and different pro-tumorigenic capacities.MethodsWe have used immunoblotting as well as quantitative RT-PCR to assess the expression of various epithelial/mesenchymal as well as stemness markers in breast stromal fibroblasts. Immunofluorescence was utilized to assess the level of different myoepithelial and luminal markers at the cellular level. Flow cytometry allowed to determine the proportion of CD44- and ALDH1-positive breast fibroblasts, while sphere formation assay was used to test the ability of these cells to form mammospheres.ResultsWe have shown here that IL-6-dependent activation of breast and skin fibroblasts promotes mesenchymal-to-epithelial transition and stemness in a STAT3- and p16-dependent manner. Interestingly, most primary CAFs isolated from breast cancer patients exhibited such transition and expressed lower levels of the mesenchymal markers N-cadherin and vimentin as compared to their adjacent normal fibroblasts (TCFs) isolated from the same patients. We have also shown that some CAFs and IL-6-activated fibroblasts express high levels of the myoepithelial markers cytokeratin 14 and CD10. Interestingly, 12 CAFs isolated from breast tumors showed higher proportions of CD24^low/CD44^high and ALDH^high cells, compared to their corresponding TCF cells. These CD44^high cells have higher abilities to form mammospheres and to enhance cell proliferation of breast cancer cells in a paracrine manner relative to their corresponding CD44^low cells.ConclusionTogether, the present findings show novel characteristics of active breast stromal fibroblasts, which exhibit additional myoepithelial/progenitor features.     

A Structural Transition in d(AT) n ·d(AT) n Inserts within Superhelical DNA

Abstract

We have constructed plasmids carrying d(AT)_n·d(AT)_n inserts of different lengths. Two- dimensional gel electrophoresis patterns show that an increase in the negative superhelicity of these DNAs brings about a structural transition within the inserts, resulting in a reduction of the superhelical stress. However, this reduction corresponds to the expected values neither for cruciform nor for the Z form. Those DNA topoisomers in which the structural transition had occurred proved to be specifically recognizable by single-strand-specific endonuclease SI, with the cleavage site situated at the centre of the insert. These data, as well as kinetic studies, suggest that the cloned d(AT)_n·d(AT) _n sequences adopt a cruciform rather than the Z-form structure. We discuss plausible reasons of the discrepancy between the observed superhelical stress release and that expected for the transition of the insert to the cruciform state.     

Computational investigation on effect of mutations in PCNA resulting in structural perturbations and inhibition of mismatch repair pathway

Abstract

From bacteria to mammals, DNA mismatch repair (MMR) pathway plays an essential role in eliminating mismatched nucleotides and insertion-deletion mismatches during the process of DNA replication. Among many of the proteins which participate in the mismatch repair process, proliferating cell nuclear antigen (PCNA) remains the principal conductor at the replication fork. The pol30-201 and pol30-204 are the two mutated alleles which encode for C22Y and C81R mutant forms of PCNA proteins. We performed long term molecular dynamics (MD) simulations analysis (0.8 μs) to understand the dynamic behavior and alterations in the structure of wild type and mutated forms of PCNA at the atomic level. We observed changes in the structural characteristics like length, radius, rise per residue of alpha helices in both the mutated forms of PCNA. Apart from it, disfigurement of the charge distribution which effects binding with the dsDNA due to mutant C22Y and other structural perturbations were also seen in regions significant for the formation of a biologically active trimeric form of PCNA due to mutant C81R. Our analysis of native and mutated forms of PCNA provides an insight into the essential structural and functional features required for proper and well-coordinated DNA mismatch repair process and consequences of the mutation leading to an impaired process of MMR. These structural characteristics are fundamental for the MMR process and hence our analysis likely contributes to or presents the novel mechanism involved in the process of MMR.

Communicated by Ramaswamy H. Sarma     

A Model of the Strain-induced B-Z Transition

Abstract

The B-to-Z transition in supercoiled circular DNA is modeled as a strain-induced nonlinear excitation process. Using a model, in which DNA is regarded as a chain of units with a bistable energy function along the twisting coordinate together with a harmonic inter-unit interaction, we show that a Z region and the accompanying two B-Z junctions of finite width appear naturally as a solution of nonlinear equations, when the strain exceeds a critical value. We examine the B-Z transition behaviour as a function of twist under various situations. We also analyse available experimental results on B-Z transition in supercoiled plasmid with G-C insertions by this mechanistic model in order to estimate the magnitude of model parameters. The energy barrier of the B-Z transition is estimated to be of the order of 1 kcal/mole per base pair. The analysis shows that if the length of the insertion is less than a certain value, the entire insertion converts to Z form at a transition point, but if the insertion is much longer, the B-Z transition exhibits a different behavior, in which part of the insertion flips to Z form and the Z region expands linearly upon changing linking number.     

The Formation Of Parallel RNA-RNA Duplexes In Vitro

Abstract

Over the years the structural properties of nucleic acids have been of interest, providing data that may be of importance for DNA and RNA organization and function in the cell. We have attempted to look for the formation of parallel RNA-RNA duplexes in vitro. RNA molecules comprising complementary in the same polarity alternating stretches of A and U of increasing length were enzymatically synthesized and annealed in physiological conditions. The fractionation in the denaturing Polyacrylamide gels revealed the formation of two types of full-length parallel RNase A - stable duplexes established either by A-U or by A-A and U-U self pairs. These results suggest novel structural properties of versatile RNA molecules that potentially may be realized in vivo.     

Conformational Changes in DNA and Soft Modes

Abstract

In this paper we explore the applicability of the soft mode approach to study the conformational transitions of DNA. It is believed that the A-B conformation change is a first order transition. Soft mode theories only apply to the initial stages of a first order transition. However the mode softening in such a case can be the initiating factor which ultimately leads to the transition. The first order transition is, then, a breakdown of what otherwise would have been a true second order transition. The mode softening is causally connected to onset of the transition. We use the eigenvectors obtained from lattice dynamics calculations to identify the softmode. We use the eigenvector projections to form a force constimi matrix that is required to drive a mode soft. We explore the methods by which this force constant matrix can be formed. We suggest that the breaking of specific “water bridges” between phosphate groups in the two single strands can drive the conformation change.     

Structure of (dG)n · (dC)n Under Superhelical Stress and Acid pH

Abstract

We have recently shown that a (GA)_n · (TC)_n tract undergoes a sharp structural transition under superhelical stress (V.I. Lyamichev, S.M. Mirkin and M.D. Frank-Kamenetskii, J. Biomol. Struct. Dyn. 2, 327 (1985)). Unlike the well studied transitions to the cruciform and to the Z form, this novel transition was strongly pH-dependent. We have found the (dG)_n · (dC)_n insert to undergo a pH-dependent structural transition similar to that of the (GA)_n · (TC)_n tract. These new data meet our earlier expectations and disagree with the data of D.E. Pulleyblank, D.B. Haniford and A.R. Morgan, Cell 42, 271 (1985). We conclude that a novel DNA structure (the H-form) is typical of homopurine-homopyrimidine mirror repeats (the H palindromes) under superhelical stress and/or acid pH. In the H-form the homopyrimidine strand forms a hairpin while half of the homopurine strand interacts with the hairpin forming a triplex, the other half of the homopurine strand being unstructured (V.I. Lyamichev, S.M. Mirkin and M.D. Frank-Kamenetskii, J. Biomol. Struct. Dyn. 2, 3,667 (1986)).     

Towards New Thymidine Phosphorylase/PD-ECGF Inhibitors Based on the Transition State of the Enzyme Reaction

Abstract

Computational studies have been conducted to built a closed form of TPase and to characterize the transition state of the phosphorylisis reaction catalyzed by TPase. The results obtained point to a crucial role of His-85 and the O2 of thymine in the catalysis. This modelled transition state forms the basis for the design of new TPase inhibitors.     

Synthesis and evaluation of novel N–H and N-substituted indole-2- and 3-carboxamide derivatives as antioxidants agents

We have previously reported on the synthesis of novel indole derivatives where some compounds showed significant antioxidant activity. Here, we report the synthesis of novel N–H and N-substituted indole-2- and 3-carboxamide derivatives and investigated their antioxidant role in order to identify structural characteristics responsible for activity. Although all compounds showed a strong inhibitory (95–100%) effect on superoxide anion (SOD) only compounds 4, 5 and 6 showed simliar potency for the inhibition of lipid peroxidation (81–94%) which revealed that compounds 4, 5 and 6 possessed highly potent antioxidant properties. Substitution in the 1-position of the indole ring caused the significant differences between the activity results regarding lipid peroxidation inhibition.     

Three-State Diagram for DNA

Abstract

Experimental phase diagrams (A form, B form, Coil) were built in the coordinates (a, alcohol fraction: T, temperature) for the natural DNAs and poly d(A-T). The main parameter of the B-A transition,—cooperativity length, v _o, was estimated by the slopes of the branches A-B, A-Coil, B-Coil in the vicinity of the triple point: v _o +AD0- 10-20 base pairs, which corresponds to the energy for the B/A junction of 1.2–1.8 kcal/mol.

We discovered two new effects which are due to the coexistence of the three different conformations in one polymeric molecule: an increase in the melting temperature above that for the ‘ideal’ triple point (i.e. for the case of the ideal phase transitions); a widening of the melting curve within the B-A transition range.

The physics of these phenomena is discussed.     

Healthcare Transition from Pediatric to Adult Medical Homes

ObjectiveTo review and exemplify the complexities and challenges in healthcare transition from the pediatric medical home to the adult medical home for patients with type 1 and type 2 diabetes mellitus and to highlight the importance of this topic to adult-focused clinical endocrinologists.MethodsWe performed a literature search using PubMed and multiple key words. To set the scene for discussions, we also reviewed landmark publications in the general healthcare transition literature over the last several decades; we provide a brief historical perspective at the beginning of our discussions.ResultsGiven the critical importance of successful healthcare transition, there is little empirical evidence on key aspects of these transitions. The vast majority of the literature focuses on type 1 diabetes because historically, this form has predominantly affected pediatric patients. However, the increasing incidence and prevalence of pediatric patients with type 2 diabetes makes investigations vital for this patient population too. The Treatment Options for Type 2 Diabetes in Adolescents and Youth study has proved informative in this regard.ConclusionCrossing the chasm between pediatric and adult healthcare remains a remarkably flawed transition process. Healthcare transition should be a planned process of discussing and preparing pediatric patients for the transition and then ensuring continued care as an adult; the greater the collaboration of pediatric and adult endocrinologists in this process, the greater the chance of a successful transition. (Endocr Pract. 2014;20:714-720)     

Metal Ion Binding and Conformational Transitions in Concanavalin A: A Structure-Function Study

Abstract

The affinity of the lectin Concanavalin A (Con A) for saccharides, and its requirement for metal ions such as Mn²⁺ and Ca²⁺, have been known for about 50 years. However the relationship between metal ion binding and the saccharide binding activity of Con A has only recently been examined in detail. Brown et al. (Biochemistry 16, 3883 (1977)) showed that Con A exists as a mixture of two conformational states: a “locked” form and an “unlocked” form. The unlocked form of the protein weakly binds metal ions and saccharide, and is the predominate conformation of demetallized Con A (apo-Con A) at equilibrium. The locked form binds two metal ions per monomer with the resulting complex(es) possessing full saccharide binding activity. Brown and coworkers measured the kinetics of the transition of the unlocked form to the fully metallized locked conformation containing Mn²⁺and Ca²⁺. They also demonstrated that Mn²⁺ alone could form a locked ternary complex with Con A, and that rapid removal of the ions resulted in a metastable form of apo-Con A in the locked conformation which slowly (hours at 25°C) reverted back to (predominantly) the unlocked conformation. The ability to form either conformation in the absence or presence of metal ions has thus allowed us to explore the relationship between metal ion binding and conformational transitions in Con A as determinants of the saccharide binding activity of the lectin.

Based on the kinetics of the transition of unlocked apo-Con A to fully metallized locked Con A, and X-ray crystallographic data, it appears that the transition between the two conformations of Con A involves a cis-trans isomerization of an Ala-Asp peptide bond in the backbone of the protein, near one of the two metal ion binding sites. The relatively large activation energy for the transition (～ 22 kcal M^?1) results in relatively slow interconversions between the conformations (from minutes to days), whereas the equilibria with metal ions and saccharide are rapid. Thus, many metastable complexes can be formed and a variety of transition pathways between the two conformations studied.

We have identified and characterized binary, ternary, and quaternary complexes of both conformations of Con A containing Mn²⁺ and saccharide, and have determined both metalion and saccharide dissociation constants for all of them, as well as equilibrium and kinetic values for the conformational transitions between them. The main finding is that saccharide binds very weakly (K_d～2 M) to unlocked apo-Con A and very tightly to the locked ternary Mn²⁺-Con A complex (K_d～ 10^?4 M). Saccharide binding increases along the various pathways connecting these two species in a nonadditive fashion. Thus, both conformation and metal ion binding determine the saccharide affinity of each complex, although the specificity of saccharide binding of the various species is maintained throughout.     

Benchmarking of ONIOM method for the study of NH<Subscript>3</Subscript> dissociation at open ends of BNNTs

The reliability of ONIOM approach have been examined in calculations of adsorption energies, transition structures, change of HOMO-LUMO energy gaps and equilibrium geometries of the interaction between NH₃ and N-enriched (A) or B-enriched (B) open ended boron nitride nanotubes. To these ends, four models of the A or B, with different inner and outer layers have been studied. In addition, various low-levels including, AM1, PM3, MNDO and UFF have been examined, applying B3LYP/6-31 G* in all high-levels. It was shown, that in the case of A, (choosing two atom layers of the tube open-end as inner layer) the results of ONIOM approach are in best agreement with those of the pure density functional theory (DFT) calculations, while their results significantly differ from those of DFT in the case of B in same conditions. All above and population analysis demonstrate that the ONIOM may be a reliable scheme in the study of weak interactions while it is a controversial approach and should be applied cautiously in the case of strong interactions. We also probed the effect of tube length and diameter on the consistency between ONIOM and DFT results, showing that this consistency is independent of the mentioned parameters.     

Left-handed Z Form in Superhelical DNA: A Theoretical Study

Abstract

This is a comprehensive statistical mechanical treatment of the Z form formation in purine- pyrimidine stretches of different length inserted into superhelical DNA. The B-Z transition for short inserts is shown to follow the “all-or-none” principle. Over some critical value of the insert length n, the B-Z transition in the insert proceeds in two stages. The flipping of m base pairs into the Z form is followed by a gradual growth of the Z-form stretch until it occupies the whole insert. By fitting the theoretical transition curves to experimental ones the fundamental thermodynamic parameters of the B-Z transition have been determined: the B-Z junction energy Fj = 4–5kcal?mol^?1 and the free energy change ΔF_B-Z = 0.5–0.7 kcal?mol^?1 under standard salt conditions. Calculations show that the B-Z transition in short purine-pyrimidine inserts may be seriously affected by cruciform formation in the carrier DNA.     

Gene expression signatures of mouse bone marrow-derived mesenchymal stem cells in the cutaneous environment and therapeutic implications for blistering skin disorder

Background aimsMultiple studies have demonstrated that mesenchymal stromal cells (MSC) can be utilized therapeutically for various congenital and acquired disorders. The involvement of MSC in the maintenance of skin homeostasis and their curative application for the treatment of skin wounds have also been documented. However, it is not known whether MSC can commit to cutaneous lineages, produce structural proteins essential for the skin integrity or be used for hereditary skin disordersMethodsTo address these questions, we conducted a comparative expression analysis between MSC and potentially adjacent cutaneous cells, fibroblasts and keratinocytes, with specific emphasis on extracellular matrix encoding and related genesResultsOur data demonstrated that MSC share many features with cutaneous fibroblasts. We also observed that under direct influence of cutaneous fibroblasts in vitro and fibroblast-derived matrix in vivo, MSC acquired a fibroblastic phenotype, suggesting that specific cell–cell interactions play a key regulatory role in the differentiation of MSC. Additionally, the observed fibroblastic transition of MSC was underlined by a significant up-regulation of several cutaneous-specific genes encoding lumican, decorin, type VII collagen, laminin and other structural proteins. As many of the identified genes have considerable therapeutic value for dermatologic afflictions, particularly type VII collagen, we evaluated further the therapeutic potential of congenic MSC in the skin of Col7a1-null mice recapitulating human recessive dystrophic epidermolysis bullosa (RDEB). Remarkably, MSC-derived type VII collagen was sufficient for restoration of the damaged dermal–epidermal junction and partial reversal of the RDEB phenotypeConclusionsCollectively, our results suggest that MSC may offer promising therapeutics for the treatment of RDEB and potentially other genodermatoses.     

Transition states in protein folding kinetics: modeling phi-values of small beta-sheet proteins

Small single-domain proteins often exhibit only a single free-energy barrier, or transition state, between the denatured and the native state. The folding kinetics of these proteins is usually explored via mutational analysis. A central question is which structural information on the transition state can be derived from the mutational data. In this article, we model and structurally interpret mutational Φ-values for two small β-sheet proteins, the PIN and the FBP WW domains. The native structure of these WW domains comprises two β-hairpins that form a three-stranded β-sheet. In our model, we assume that the transition state consists of two conformations in which either one of the hairpins is formed. Such a transition state has been recently observed in molecular dynamics folding-unfolding simulations of a small designed three-stranded β-sheet protein. We obtain good agreement with the experimental data 1), by splitting up the mutation-induced free-energy changes into terms for the two hairpins and for the small hydrophobic core of the proteins; and 2), by fitting a single parameter, the relative degree to which hairpins 1 and 2 are formed in the transition state. The model helps us to understand how mutations affect the folding kinetics of WW domains, and captures also negative Φ-values that have been difficult to interpret.