Sequence Of Subdomains Research Articles

Wind turbine wake computation with the ST-VMS method, isogeometric discretization and multidomain method: I. Computational framework

In this first part of a two-part article, we present a framework for wind turbine wake computation. The framework is made of the Space–Time Variational Multiscale (ST-VMS) method, ST isogeometric discretization, and the Multidomain Method (MDM). The ST context provides higher-order accuracy in general, and the VMS feature of the ST-VMS addresses the computational challenges associated with the multiscale nature of the flow. The ST isogeometric discretization enables increased accuracy in the flow solution. With the MDM, a long wake can be computed over a sequence of subdomains, instead of a single, long domain, thus somewhat reducing the computational cost. Furthermore, with the MDM, the computation over a downstream subdomain can start several turbine rotations after the computation over the upstream subdomain starts, thus reducing the computational cost even more. All these good features of the framework, in combination, enable accurate representation of the turbine long-wake vortex patterns in a computationally efficient way. In the computations we present, the velocity data on the inflow plane comes from a previous wind turbine computation, extracted by projection from a plane located 10 m downstream of the turbine, which has a diameter of 126 m. The results show the effectiveness of the framework in wind turbine long-wake computation.

Engineered Escherichia coli Biofilms Produce Adhesive Nanomaterials Shaped by a Patterned 43 kDa Barnacle Cement Protein.

Barnacles integrate multiple protein components into distinct amyloid-like nanofibers arranged as a bulk material network for their permanent underwater attachment. The design principle for how chemistry is displayed using adhesive nanomaterials, and fragments of proteins that are responsible for their formation, remains a challenge to assess and is yet to be established. Here, we use engineered bacterial biofilms to display a library of amyloid materials outside of the cell using full-length and subdomain sequences from a major component of the barnacle adhesive. A staggered charged pattern is found throughout the full-length sequence of a 43 kDa cement protein (AACP43), establishing a conserved sequence design evolved by barnacles to make adhesive nanomaterials. AACP43 domain deletions vary in their propensity to aggregate and form fibers, as exported extracellular materials are characterized through staining, immunoblotting, scanning electron microscopy, and atomic force microscopy. Full-length AACP43 and its domains have a propensity to aggregate into nanofibers independent of all other barnacle glue components, shedding light on its function in the barnacle adhesive. Curliated Escherichia coli biofilms are a compatible system for heterologous expression and the study of foreign functional amyloid adhesive materials, used here to identify the c-terminal portion of AACP43 as critical in material formation. This approach allows us to establish a common sequence pattern between two otherwise dissimilar families of cement proteins, laying the foundation to elucidate adhesive chemistries by one of the most tenacious marine fouling organisms in the ocean.

A Proof via Finite Elements for Schiffer’s Conjecture on a Regular Pentagon

A modified version of Schiffer’s conjecture on a regular pentagon states that Neumann eigenfunctions of the Laplacian do not change sign on the boundary. In a companion paper by Bartlomiej Siudeja it was shown that eigenfunctions which are strictly positive on the boundary exist on regular polygons with at least 6 sides, while on equilateral triangles and cubes it is not even possible to find an eigenfunction which is nonnegative on the boundary. The case for the regular pentagon is more challenging, and has resisted a completely analytic attack. In this paper, we present a validated numerical method to prove this case, which involves iteratively bounding eigenvalues for a sequence of subdomains of the triangle. We use a learning algorithm to find and optimize this sequence of subdomains, making it straightforward to check our computations with standard software. Our proof has a short proof certificate, is checkable without specialized software and is adaptable to other situations.

Existence of solution to Korteweg–de Vries equation in a non-parabolic domain

In this paper, we study the semilinear Korteweg–de Vries equation with time variable coefficients, subject to boundary conditions in a non-parabolic domain. Some assumptions on the boundary of the domain and on the coefficients of the equation will be imposed. The source term and its derivative with respect to t are taken in L2(Ω). The existence and uniqueness of the solution is obtained by using the parabolic regularization method, the Faedo–Galerkin and a method based on the approximation of the non-parabolic domain by a sequence of subdomains which can be transformed into regular domains. This paper is an extension of the work Benia and Sadallah (2018).

Three-dimensional structure of the 3'X-tail of hepatitis C virus RNA in monomeric and dimeric states.

The 3′X domain is a 98-nt region located at the 3′ end of hepatitis C virus genomic RNA that plays essential functions in the viral life cycle. It contains an absolutely conserved, 16-base palindromic sequence that promotes viral RNA dimerization, overlapped with a 7-nt tract implicated in a distal contact with a nearby functional sequence. Using small angle X-ray scattering measurements combined with model building guided by NMR spectroscopy, we have studied the stoichiometry, structure, and flexibility of domain 3′X and two smaller subdomain sequences as a function of ionic strength, and obtained a three-dimensional view of the full-length domain in its monomeric and dimeric states. In the monomeric form, the 3′X domain adopted an elongated conformation containing two SL1′ and SL2′ double-helical stems stabilized by coaxial stacking. This structure was significantly less flexible than that of isolated subdomain SL2′ monomers. At higher ionic strength, the 3′X scattering envelope nearly doubled its size, reflecting the formation of extended homodimers containing an antiparallel SL2′ duplex flanked by coaxially stacked SL1′ helices. Formation of these dimers could initialize and/or regulate the packaging of viral RNA genomes into virions.

Adaptively refined multi-patch B-splines with enhanced smoothness

A spline space suitable for Isogeometric Analysis (IgA) on multi-patch domains is presented. Our construction is motivated by emerging requirements in isogeometric simulations. In particular, IgA spaces should allow for adaptive mesh refinement and they should guarantee the optimal smoothness of the discretized solution, even across interfaces of adjacent patches.Given a domain manifold M consisting of individual patches (isomorphic to the unit square or cube) that are glued together along interfaces, we present a construction of multi-patch B-splines defined on them. Their smoothness is enhanced by locally modifying or merging basis functions around the boundary of each patch. The resulting multi-patch B-splines with enhanced smoothness (MPBES) possess the property of local linear independence and form a non-negative partition of unity. Moreover, their span can be characterized as the linear space of all piecewise polynomial functions on the domain manifold that possess certain smoothness properties.Subsequently, adaptively refined MPBES are obtained by generalizing the construction of truncated hierarchical (TH) B-splines. More precisely, a nested sequence of spaces spanned by MPBES is considered, corresponding to steps of local enrichment. In addition, an inversely nested sequence of subdomains (which are submanifolds of M) is used to specify the local refinement level of functions in these spaces. Finally, truncated hierarchical MPBES are obtained by means of the selection and truncation mechanism of THB-splines. The desired properties of linear independence and convex partition of unity are maintained.The paper presents several numerical examples which demonstrate potential applications of the new basis in isogeometric analysis.

Studying protein fold evolution with hybrids of differently folded homologs.

To study the sequence determinants governing protein fold evolution, we generated hybrid sequences from two homologous proteins with 40% identity but different folds: Pfl 6 Cro, which has a mixed α + β structure, and Xfaso 1 Cro, which has an all α-helical structure. First, we first examined eight chimeric hybrids in which the more structurally conserved N-terminal half of one protein was fused to the more structurally divergent C-terminal half of the other. None of these chimeras folded, as judged by circular dichroism spectra and thermal melts, suggesting that both halves have strong intrinsic preferences for the native global fold pattern, and/or that the interfaces between the halves are not readily interchangeable. Second, we examined 10 hybrids in which blocks of the structurally divergent C-terminal region were exchanged. These hybrids showed varying levels of thermal stability and suggested that the key residues in the Xfaso 1 C terminus specifying the all-α fold were concentrated near the end of helix 4 in Xfaso 1, which aligns to the end of strand 2 in Pfl 6. Finally, we generated hybrid substitutions for each individual residue in this critical region and measured thermal stabilities. The results suggested that R47 and V48 were the strongest factors that excluded formation of the α + β fold in the C-terminal region of Xfaso 1. In support of this idea, we found that the folding stability of one of the original eight chimeras could be rescued by back-substituting these two residues. Overall, the results show not only that the key factors for Cro fold specificity and evolution are global and multifarious, but also that some all-α Cro proteins have a C-terminal subdomain sequence within a few substitutions of switching to the α + β fold.

On a Fourth Order Parabolic Equation in a Nonregular Domain of $${ \mathbb{R} ^{3}}$$ R 3

In this work, we give new results of existence, uniqueness and maximal regularity of a solution to the following two space linear fourth order parabolic equation $${\partial_{t}u + \partial _{x_{1}}^{4}u + \partial _{x_{2}}^{4}u = f}$$ , set in a domain $${Q = \left\{\left( t, x_{1} \right) \in \mathbb{R}^{2} : 0 < t < T; \varphi _{1}\left( t \right) < x_{1} < \varphi _{2}\left(t \right) \right\}\times \left] 0, b \right[ }$$ of $${\mathbb{R} ^{3}}$$ , with Cauchy-Dirichlet boundary conditions, under some assumptions on the functions ( $${\varphi _{i}}$$ ) i=1, 2. The right-hand side f of the equation is taken in a weighted Lebesgue space. One of the main issues of this work is that the domain Q can possibly be nonregular, for instance, the singular case where $${\varphi_{1} \left( 0 \right) = \varphi _{2}\left( 0 \right) }$$ is allowed. The method used is based on the approximation of the domain Q by a sequence of subdomains $${\left( Q_{n} \right) _{n}}$$ which can be transformed into regular domains. This work is an extension of the one space variable case studied in [1].

Parabolic equations with Cauchy–Dirichlet boundary conditions in a non-regular domain of ℝN+1

Abstract. New results on the existence, uniqueness and maximal regularity of a solution are given for a parabolic equation set in a non-regular domain Q = ( t , x 1 ) ∈ ℝ 2 : 0 &lt; t &lt; T ; ϕ 1 ( t ) &lt; x 1 &lt; ϕ 2 ( t ) × ∏ i = 1 N - 1 ] 0 , b i [ $ Q=\bigl \lbrace (t,x_1) \in \mathbb {R}^{2}:0&amp;lt;t&amp;lt;T;\; \varphi _1(t) &amp;lt;x_1&amp;lt;\varphi _{2}(t) \bigr \rbrace \times \prod _{i=1}^{N-1}{]0,b_i[} $ of ℝN+1, with Cauchy–Dirichlet boundary conditions, under some assumptions on the functions ϕ 1 $\varphi _1$ and ϕ 2 $\varphi _2$ . The right-hand side term of the equation is taken in L 2 ( Q ) $L^{2}(Q)$ . The method used is based on the approximation of the domain Q by a sequence of sub-domains ( Q n ) $(Q_n)$ which can be transformed into regular domains. This work is an extension of the two space variables case studied in [Differ. Equ. Appl. 2 (2010), no. 2, 251–263].

Context-Dependent Folding: Sequence-Encoded Strategies for Stabilizing a Protein Subdomain in Isolation

Many proteins are made up of smaller structural units called subdomains. Dissecting proteins into these small units is important for protein engineering and design. In part, the ability to create novel fusion proteins relies on a subdomain's ability to fold autonomously. Subdomains are usually identified as regions that have high contact density, in other words, they have more residue-residue contacts within a specified region than they do with other areas of the protein. Due to their high contact density, subdomains are often assumed to be able to fold in isolation. We evaluate this hypothesis, by examining the foldability of a subdomain from T4 Lysozyme (T4L). In full-length T4L, the N-terminal subdomain has high contact density yet its sequence does not fold in isolation. This suggests that high contact density is not always enough for subdomain folding. To explore this, we have extended the boundary to the complete the sequence of a helix found in the full-length protein that has no contacts with the rest of the subdomain. We find that even without increasing predicted contacts, the sequence is able to fold autonomously. To determine if the sequence of the helix is important, we created a fusion protein that appends an alanine-based helix, which is able to fold in isolation, to the original N-terminal subdomain sequence. Surprisingly, we find that this structural mimicry allows the sequence to fold. In total, our findings point to the importance of considering not just considering the contact density when choosing boundaries of subdomains. We also demonstrate strategies to stabilize the folding of otherwise unfolded subdomain sequences.

Curve intersection using hybrid clipping

This paper presents a novel approach, called hybrid clipping, for computing all intersections between two polynomial Bézier curves within a given parametric domain in the plane. Like Bézier clipping, we compute a ‘fat line’ (a region along a line) to bound one of the curves. Then we compute a ‘fat curve’ around the optimal low degree approximation curve to the other curve. By clipping the fat curve with the fat line, we obtain a new reduced subdomain enclosing the intersection. The clipping process proceeds iteratively and then a sequence of subdomains that is guaranteed to converge to the corresponding intersection will be obtained. We have proved that the hybrid clipping technique has at least a quadratic convergence rate. Experimental results have been presented to show the performance of the proposed approach with comparison with Bézier clipping.

On the resolution of a parabolic equation in a nonregular domain of ℝ^3

In this work we give new results of existence , uniqueness and maximal regularity of a solution to a parabolic equation set in a nonregular domain Q with Cauchy-Dirichlet boundary conditions, where Q = � (t,x1) ∈ R 2 :0 <t < T;ϕ1(t) < x1 < ϕ2(t) � ×)0,b( ⊆ R 3 with some assumptions on the functions (ϕi)i=1,2. The right-hand side term of the equation is taken in L 2 (Q) . The method used is based on the approximation of the domain Q by a sequence of subdomains (Qn)n which can be transformed into regular domains . This work is an extension of the one space variable case studied in (12).

An Inter-Domain Path Computation Scheme Adaptive to Traffic Load in Domains

The establishment of inter-domain traffic engineered paths is a requisite to accomplishing an end-to-end bandwidth guarantee and end-to-end resource optimization. Though the inter-domain paths must be reliable, it is difficult to compute suitable backup inter-domain paths in advance when the traffic engineering information is not disclosed outside of each domain. This means that the inter-domain path computation must satisfy the severe requirement of path establishment delay, since all inter-domain paths traversing the links in failure need to be computed after the failure occurs. Though several inter-domain path computation schemes have been proposed, their relative characteristics remain unknown. First, this paper classifies the conventional inter-domain path computation schemes into two types, i.e. end-to-end and per-domain schemes, and compares their performances under various traffic loads. Based on results of the comparisons, this paper proposes an adaptive inter-domain path computation scheme that can satisfy the severe requirement of the path establishment delay. In this scheme, the domain sequence from the source node to the destination node is divided into multiple sub-domain sequences according to the traffic load in each domain. The end-to-end path computation scheme is applied to the sub-domain sequences under heavy traffic loads, while the per-domain path computation scheme is applied to those under normal traffic loads. The simulation results show that the proposed scheme can adaptively satisfy the requirement for the path establishment delay while it maintains the optimality of path computation, even if the traffic load applied to each domain changes.

The CBS subdomain of inosine 5′‐monophosphate dehydrogenase regulates purine nucleotide turnover

Inosine 5'-monophosphate dehydrogenase (IMPDH) catalyses the rate-limiting step in guanine nucleotide biosynthesis. IMPDH has an evolutionary conserved CBS subdomain of unknown function. The subdomain can be deleted without impairing the in vitro IMPDH catalytic activity and is the site for mutations associated with human retinitis pigmentosa. A guanine-prototrophic Escherichia coli strain, MP101, was constructed with the subdomain sequence deleted from the chromosomal gene for IMPDH. The ATP content was substantially elevated in MP101 whereas the GTP content was slighty reduced. The activities of IMPDH, adenylosuccinate synthetase and GMP reductase were two to threefold lower in MP101 crude extracts compared with the BW25113 wild-type strain. Guanine induced a threefold reduction in the MP101 ATP pool and a fourfold increase in the GTP pool within 10 min of addition to growing cells; this response does not result from the reduced IMPDH activity or starvation for guanylates. In vivo kinetic analysis using 14-C tracers and 33-P pulse-chasing revealed mutation-associated changes in purine nucleotide fluxes and turnover rates. We conclude that the CBS subdomain of IMPDH may coordinate the activities of the enzymes of purine nucleotide metabolism and is essential for maintaining the normal ATP and GTP pool sizes in E. coli.

Interaction of Paxillin with Poly(A)-Binding Protein 1 and Its Role in Focal Adhesion Turnover and Cell Migration

We have previously identified poly(A)-binding protein 1 (PABP1) as a ligand for paxillin and shown that the paxillin-PABP1 complex undergoes nucleocytoplasmic shuttling. By targeting the paxillin-binding subdomain sequences in PABP1, we have generated mutants of PABP1 that do not bind to cellular paxillin. Here we report that paxillin association is necessary for efficient nuclear export of PABP1 and that RNA interference of paxillin drives the nuclear accumulation of PABP1. Furthermore, ablation of paxillin-PABP1 association impeded a number of indices of cell motility including spreading on fibronectin, cell migration on two-dimensional matrices, and transmigration in Boyden chambers. These data indicate that PABP1 must associate with paxillin in order to be efficiently transported from the nucleus to the cytoplasm and that this event is necessary for cells to remodel their focal adhesions during cell migration.

The Role of Hepatic Nuclear Factor 1α and PDX-1 in Transcriptional Regulation of the pdx-1 Gene

The PDX-1 homeodomain transcription factor regulates pancreatic development and adult islet beta cell function. Expression of the pdx-1 gene is almost exclusively localized to beta cells within the adult endocrine pancreas. Islet beta cell-selective transcription is controlled by evolutionarily conserved subdomain sequences (termed Areas I (-2839 to -2520 base pairs (bp)), II (-2252 to -2023 bp), and III (-1939 to -1664 bp)) found within the 5'-flanking region of the pdx-1 gene. Areas I and II are independently capable of directing beta cell-selective reporter gene activity in transfection assays, with Area I-mediated stimulation dependent upon binding of hepatic nuclear factor 3 beta (HNF3 beta), a key regulator of islet beta cell function. To identify other transactivators of Area I, highly conserved sequence segments within this subdomain were mutagenized, and their effect on activation was determined. Several of the sensitive sites were found by transcription factor data base analysis to potentially bind endodermally expressed transcription factors, including HNF1 alpha (-2758 to -2746 bp, Segment 2), HNF4 (-2742 to -2730 bp, Segment 4; -2683 to -2671 bp, Segment 7-8), and HNF6 (-2727 to -2715 bp, Segment 5). HNF1 alpha, but not HNF4 and HNF6, binds specifically to Area I sequences in vitro. HNF1 alpha was also shown to specifically activate Area I-driven transcription through Segment 2. In addition, PDX-1 itself was found to stimulate Area I activation. The chromatin immunoprecipitation assay performed with PDX-1 antisera also demonstrated that this factor bound to Area I within the endogenous pdx-1 gene in beta cells. Our results indicate that regulatory factors binding to Area I conserved sequences contribute to the selective transcription pattern of the pdx-1 gene and that control is mediated by endodermal regulators like HNF1 alpha, HNF3 beta, and PDX-1.

Self recognition in the Ig superfamily. Identification of precise subdomains in carcinoembryonic antigen required for intercellular adhesion.

The homophilic binding of extracellular domains of membrane-bound immunoglobulin superfamily (IgSF) molecules is often required for intercellular adhesion and signaling. Carcinoembryonic antigen (CEA), a member of the IgSF, is a widely used tumor marker that functions in vitro as a homotypic intercellular adhesion molecule. CEA has also been shown to contribute to tumorigenicity by inhibiting cellular differentiation, an effect that requires the homophilic binding of its extracellular domains. It was of interest, therefore, to identify small subdomain sequences in CEA that could serve as a focus in the design of peptides that disrupt CEA-mediated intercellular adhesion. Three subdomains in the N-terminal domain of CEA, identified by site-directed deletions and point mutations, were shown to be required for intercellular adhesion. Cyclized peptides representing two of these subdomains, (42)NRQII and (80)QNDTG, were found to be effective in blocking CEA-mediated cellular aggregation when added to CEA-expressing transfectants in suspension. Intermolecular binding involving each of these subdomains is therefore essential for intercellular adhesion and cannot be compensated for by known binding contributions of other regions in the CEA molecule. In further support of this assumption, the binding epitope of an anti-CEA monoclonal antibody (monoclonal antibody A20) known to block CEA-mediated adhesion, was shown to bridge two of the three required subdomains: (42)NRQII and (30)GYSWYK.

Sequences within Pr160gag-pol affecting the selective packaging of primer tRNALys3 into HIV-1

The selective packaging of the primer tRNALys3 into HIV-1 particles is dependent upon the viral incorporation of the Pr160gag-pol precursor protein. In order to map a tRNALys3 binding site within this precursor, we have studied the effects of mutations in Pr160gag-pol upon the selective incorporation of tRNALys3. Many of these mutations were placed in a protease-negative HIV-1 proviral DNA to prevent viral protease degradation of the mutant Gag-Pol protein. C-terminal deletions of protease-negative Gag-Pol that removed the entire integrase sequence and the RNase H and connection subdomains of reverse transcriptase did not inhibit the incorporation of either the truncated Gag-Pol or the tRNALys3, indicating that these regions are not required for tRNALys3 binding. On the other hand, larger C-terminal deletions, which also remove the thumb subdomain sequence, did prevent tRNALys3 packaging, without inhibiting viral incorporation of the truncated Gag-Pol, indicating a possible interaction between thumb subdomain sequences and tRNALys3. While point mutations K249E, K249Q, and R307E in the primer grip region of the thumb subdomain have been reported to inhibit the in vitro interaction of mature reverse transcriptase with the anticodon loop of tRNALys3, we find that these mutations do not inhibit tRNALys3 packaging into the virus, which supports other work indicating that the anticodon loop of tRNALys3 is not involved in interactions with Pr160gag-pol during tRNALys3 packaging.

Characterization of an 88-kDa Heat Shock Protein of Neurospora crassa That Interacts with Hsp30

The small heat shock protein of Neurospora crassa, Hsp30, when employed in affinity chromatography, bound two cellular proteins that were identified as Hsp70 and Hsp88. Both Hsp70 and Hsp88 bound to Hsp30 in preference to other proteins, but binding of Hsp88 was more selective for Hsp30, and a direct interaction was observed. Transcripts for Hsp88, a newly characterized protein, are present at normal temperature, but they are strongly induced by heat shock. Its cDNA sequence predicts a protein with homology to mammalian Hsp110 family proteins, which are distantly related to Hsp70. Hsp88 and its homologues show greater similarity to Hsp70 in its N-terminal ATPase domain than in the C-terminal peptide-binding domain, and its ATP-binding motifs are conserved. Nevertheless, the N-terminal domain of Hsp88 (and related proteins) is consistently more hydrophobic and more basic than that of Hsp70 proteins. Within the C-terminal domain, the sequence corresponding to the DnaK alpha subdomain is conserved in the Hsp88/Hsp110 family proteins, whereas the DnaK beta subdomain sequence is not conserved. The interaction between Hsp70 and Hsp30 may reflect their cooperation as cochaperones for denatured proteins, whereas Hsp88 and Hsp30 may form a complex that interacts with potential substrates.

Prediction of substrate-specific pockets in cyclosporin synthetase

Amino acid sequence comparisons between domains of cyclosporin synthetase have been used to identify regions of the sequence which are responsible for the recognition and binding of the individual amino acids. Using a limited set of selection rules it was possible to identify three amino acid positions in the subdomain sequences which are responsible for amino acid specificity. Homology with the firefly luciferase protein shows that these three key residues are close to each other and line the surface of a putative specific substrate binding pocket located on the amino acyl-adenylation subdomain. These results allow us to predict a large number of cyclosporin synthetase mutants which could be used to synthesise alternative cyclosporin-like peptides.