Coil Region Research Articles

Predictive approach for protein aggregation: Correlation of protein surface characteristics and conformational flexibility to protein aggregation propensity.

The aggregation of proteins became one of the major challenges in the development of biopharmaceu-ticals since the formation of aggregates can affect drug quality and immunogenicity. However, aggregation mechanisms are highly complex and the investigation requires cost, time, and material intensive experi-mental effort. In the present work, the predictive power of protein characteristics for the phase behavior of three different proteins which are very similar in size and structure was studied. In particular, the surface hydrophobicity, zeta potential, and conformational flexibility of human lysozyme, lysozyme from chicken egg white, and α-lactalbumin at pH 3, 5, 7, and 9 were assessed and examined for correlation with experimental stability studies focusing on protein phase behavior induced by sodium chloride and ammonium sulfate. The molecular dynamics (MD) simulation based study of the conformational flexibility without precipitants was able to identify highly flexible protein regions which could be associated to the less regular secondary structure elements and random coiled and terminal regions in particular. Conformational flex-ibility of the entire protein structure and protein surface hydrophobicity could be correlated to differing aggregation propensities among the studied proteins and could be identified to be applicable for predic-tion of protein phase behavior in aqueous solution without precipitants. For prediction of protein phase behavior and aggregation propensity in aqueous solution with precipitants, protein flexibility was further studied in dependency of salt concentration and species by means of human lysozyme. Even though the results of the salt dependent MD simulations could not be shown to be sufficient for prediction of salt depending phase behavior, this study revealed a more pronounced destabilizing effect of ammonium sulfate in comparison to sodium chloride and thus, was found to be in good agreement with theoretical considerations along the Hofmeister series as well as experimentally evaluated phase behavior. Biotechnol. Bioeng. 2017;114: 1170-1183. © 2016 Wiley Periodicals, Inc.

Kinetic simulations and photometry measurements of the E-H transition in cylindrical inductively coupled plasmas

Inductively coupled plasmas (ICP) are well known to exhibit two modes of operation: a low density capacitive E-mode and a high density inductive H-mode. In this study we investigate the E-H transition in a cylindrical ICP, and show the effect of an external magnetic cusp field on the transition dynamics. The plasma is simulated by an electro-magnetic particle-in-cell Monte Carlo collision code in order to take into account spatio-temporal variations of the plasma dynamics as well as kinetic effects. Simulations are compared to photometry measurements on the Linac4 H−ion source plasma chamber. We show that the E-H transition is characterized by strong spatial variations of the plasma parameters, with an axial plasma oscillation in E-mode followed by a centring in the coil region in H-mode. The external magnetic cusp field prevents electrons close to the wall to be accelerated and reduces the inductive power deposition in the plasma. This resulted in a ≈50% higher current to achieve E-H transition compared to the configuration without cusp field. The results indicate possible improvements to the magnetic cusp field configuration in order to achieve optimal power transfer.

The coil array method for creating a dynamic imaging volume.

Gradient strength and speed are limited by peripheral nerve stimulation (PNS) thresholds. The coil array method allows the gradient field to be moved across the imaging area. This can help reduce PNS and provide faster imaging for image-guided therapy systems such as the magnetic resonance imaging-guided linear accelerator (MRI-linac). The coil array is designed such that many coils produce magnetic fields, which combine to give the desired gradient profile. The design of the coil array uses two methods: either the singular value decomposition (SVD) of a set of field profiles or the electromagnetic modes of the coil surface. Two whole-body coils and one experimental coil were designed to investigate the method. The field produced by the experimental coil was compared to simulated results. The experimental coil region of uniformity (ROU) was moved along the z axis as shown in simulation. The highest observed field deviation was 16.9% at the edge of the ROU with a shift of 35 mm. The whole-body coils showed a median field deviation across all offsets below 5% with an eight-coil basis when using the SVD design method. Experimental results show the feasibility of a moving imaging region within an MRI with a low number of coils in the array. Magn Reson Med 78:784-793, 2017. © 2016 International Society for Magnetic Resonance in Medicine.

Replica Exchange Molecular Dynamics Study of Dimerization in Prion Protein: Multiple Modes of Interaction and Stabilization.

The pathological forms of prions are known to be a result of misfolding, oligomerization, and aggregation of the cellular prion. While the mechanism of misfolding and aggregation in prions has been widely studied using both experimental and computational tools, the structural and energetic characterization of the dimer form have not garnered as much attention. On one hand dimerization can be the first step toward a nucleation-like pathway to aggregation, whereas on the other hand it may also increase the conformational stability preventing self-aggregation. In this work, we have used extensive all-atom replica exchange molecular dynamics simulations of both monomer and dimer forms of a mouse prion protein to understand the structural, dynamic, and thermodynamic stability of dimeric prion as compared to the monomeric form. We show that prion proteins can dimerize spontaneously being stabilized by hydrophobic interactions as well as intermolecular hydrogen bonding and salt bridge formation. We have computed the conformational free energy landscapes for both monomer and dimer forms to compare the thermodynamic stability and misfolding pathways. We observe large conformational heterogeneity among the various modes of interactions between the monomers and the strong intermolecular interactions may lead to as high as 20% β-content. The hydrophobic regions in helix-2, surrounding coil regions, terminal regions along with the natively present β-sheet region appear to actively participate in prion-prion intermolecular interactions. Dimerization seems to considerably suppress the inherent dynamic instability observed in monomeric prions, particularly because the regions of structural frustration constitute the dimer interface. Further, we demonstrate an interesting reversible coupling between the Q160-G131 interaction (which leads to inhibition of β-sheet extension) and the G131-V161 H-bond formation.

Three novel C1q domain containing proteins from the disk abalone Haliotis discus discus: Genomic organization and analysis of the transcriptional changes in response to bacterial pathogens.

The globular C1q (gC1q) domain containing proteins, commonly referred as C1q domain containing (C1qDC) proteins, are an essential family of proteins involved in various innate immune responses. In this study, three novel C1qDC proteins were identified from the disk abalone (Haliotis discus discus) transcriptome database and designated as AbC1qDC1, AbC1qDC2, and AbC1qDC3. The cDNA sequences of AbC1qDC1, AbC1qDC2, and AbC1qDC3 consisted of 807, 1305, and 660bp open reading frames (ORFs) encoding 269, 435, and 220 amino acids (aa), respectively. Putative signal peptides and the N-terminal gC1q domain were identified in all three AbC1qDC proteins. An additional predicted motif region, known as the coiled coil region (CCR), was identified next to the signal sequence of AbC1qDC2. The genomic organization of the AbC1qDCs was determined using a bacterial artificial chromosome (BAC) library. It was found that the CDS of AbC1qDC1 was distributed among three exons, while the CDSs of AbC1qDC2 and AbC1qDC3 were distributed between two exons. Sequence analysis indicated that the AbC1qDC proteins shared <40% identity with other counterparts from different species. According to the neighbor-joining phylogenetic tree, the proteins were grouped within an invertebrate group with high evolutionary distances, which suggests that they are new members of the C1qDC family. Higher expression of AbC1qDC1 and AbC1qDC2 was detected in hepatopancreas, muscle, and mantle tissues compare to the other tissues analyzed, using reverse transcription, followed by quantitative real-time PCR (qPCR) using SYBR Green, whereas AbC1qDC3 was predominantly expressed in gill tissues, followed by muscles and the hepatopancreas. The temporal expression of AbC1qDC transcripts in gills after bacterial (Vibrio parahaemolyticus and Listeria monocytogenes) and lipopolysaccharide stimulation indicated that AbC1qDCs can be strongly induced by both Gram-negative and Gram-positive bacterial species with different response profiles. The results of this study suggest that AbC1qDCs are involved in immune responses against invading bacterial pathogens.

Molecular insights into DNA binding and anchoring by the Bacillus subtilis sporulation kinetochore-like RacA protein.

During Bacillus subtilis sporulation, segregating sister chromosomes are anchored to cell poles and the chromosome is remodeled into an elongated structure called the axial filament. Data indicate that a developmentally regulated protein called RacA is involved in these functions. To gain insight into how RacA performs these diverse processes we performed a battery of structural and biochemical analyses. These studies show that RacA contains an N-terminal winged-helix-turn-helix module connected by a disordered region to a predicted coiled-coil domain. Structures capture RacA binding the DNA using distinct protein–protein interfaces and employing adjustable DNA docking modes. This unique DNA binding mechanism indicates how RacA can both specifically recognize its GC-rich centromere and also non-specifically bind the DNA. Adjacent RacA molecules within the protein–DNA structure interact leading to DNA compaction, suggesting a mechanism for axial filament formation. We also show that the RacA C-domain coiled coil directly contacts the coiled coil region of the polar protein DivIVA, which anchors RacA and hence the chromosome to the pole. Thus, our combined data reveal unique DNA binding properties by RacA and provide insight into the DNA remodeling and polar anchorage functions of the protein.

Structural and evolutionary relationships among RuBisCOs inferred from their large and small subunits.

Ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is the key enzyme to assimilate CO(2) into the biosphere. The nonredundant structural data sets for three RuBisCO domain superfamilies, i.e. large subunit C-terminal domain (LSC), large subunit N-terminal domain (LSN) and small subunit domain (SS), were selected using QR factorization based on the structural alignment with QH as the similarity measure. The structural phylogenies were then constructed to investigate a possible functional significance of the evolutionary diversification. The LSC could have occurred in both bacteria and archaea, and has evolved towards increased complexity in both bacteria and eukaryotes with a 4-helix-2-helix-2-helix bundle being extended into a 5-helix-3-helix-3-helix one at the LSC carboxyl-terminus. The structural variations of LSN could have originated not only in bacteria with a short coil, but also in eukaryotes with a long one. Meanwhile, the SS dendrogram can be contributed to the structural variations at the βA-βB-loop region. All the structural variations observed in the coil regions have influence on catalytic performance or CO(2)/O(2) selectivities of RuBisCOs from different species. Such findings provide insights on RuBisCO improvements.

The Effects of Trifluoroethanol on the Helical Structure of SIKE

Suppressor of IKKe (SIKE)inhibits TBK1 mediated phosphorylation of interferon regulatory factor 3 (IRF3) and misregulation of TBK1 is involved in both autoimmune disorders and cancer. Our work (Marion et al, J.Biol.Chem 288, 18612–23, 2013) demonstrated that TBK1 can phosphorylate SIKE in up to 6 positions, altering its ability to inhibit TBK1. Little however is known concerning the three dimensional structure of SIKE. SIKE (his tagged) has been expressed and purified using Nickel NTA affinity chromatography and shown to be homogenous by MALDI‐tof mass spectrometry. To examine the structure of SIKE we have performed two dimensional proton NMR experiments and Circular Dichroism spectroscopy and compared the results with both secondary and tertiary structure predictions. 2D NOESY spectra obtained using several mixing times in general revealed little stable structure in the molecule as detected in the NH‐NH cross peak region, suggesting the protein may contain significant disordered regions. CD spectra suggest significant alpha helix content and the possibility of coiled coil regions of structure. Addition of Trifluoroethanol, known to stabilize alpha helical structures, led to increased CD signal at 222nm. Using a range of TFE concentrations optimal stabilization of helical structure in SIKE allowed comparison with helical secondary structure predications.Support or Funding InformationThis work was supported by NIH grant R21A1 107447 to JKB

MKS5 and CEP290 Dependent Assembly Pathway of the Ciliary Transition Zone.

Cilia have a unique diffusion barrier (“gate”) within their proximal region, termed transition zone (TZ), that compartmentalises signalling proteins within the organelle. The TZ is known to harbour two functional modules/complexes (Meckel syndrome [MKS] and Nephronophthisis [NPHP]) defined by genetic interaction, interdependent protein localisation (hierarchy), and proteomic studies. However, the composition and molecular organisation of these modules and their links to human ciliary disease are not completely understood. Here, we reveal Caenorhabditis elegans CEP-290 (mammalian Cep290/Mks4/Nphp6 orthologue) as a central assembly factor that is specific for established MKS module components and depends on the coiled coil region of MKS-5 (Rpgrip1L/Rpgrip1) for TZ localisation. Consistent with a critical role in ciliary gate function, CEP-290 prevents inappropriate entry of membrane-associated proteins into cilia and keeps ARL-13 (Arl13b) from leaking out of cilia via the TZ. We identify a novel MKS module component, TMEM-218 (Tmem218), that requires CEP-290 and other MKS module components for TZ localisation and functions together with the NPHP module to facilitate ciliogenesis. We show that TZ localisation of TMEM-138 (Tmem138) and CDKL-1 (Cdkl1/Cdkl2/Cdkl3/Cdlk4 related), not previously linked to a specific TZ module, similarly depends on CEP-290; surprisingly, neither TMEM-138 or CDKL-1 exhibit interdependent localisation or genetic interactions with core MKS or NPHP module components, suggesting they are part of a distinct, CEP-290-associated module. Lastly, we show that families presenting with Oral-Facial-Digital syndrome type 6 (OFD6) have likely pathogenic mutations in CEP-290-dependent TZ proteins, namely Tmem17, Tmem138, and Tmem231. Notably, patient fibroblasts harbouring mutated Tmem17, a protein not yet ciliopathy-associated, display ciliogenesis defects. Together, our findings expand the repertoire of MKS module-associated proteins—including the previously uncharacterised mammalian Tmem80—and suggest an MKS-5 and CEP-290-dependent assembly pathway for building a functional TZ.

A comparative statement on molecular approach of large HSPs from Macrobrachium rosenbergii

This study reported a comparative account of large heat shock proteins (HSPs) namely HSP60, 70 and 90 from freshwater prawn Marcobrachium rosenbergii (Mr) at molecular level. The MrHSP60, 70 and 90 was 2158, 1998 and 2220 base pairs (bp) long that contain an open reading frame (ORF) of 1722, 1995 and 2157 bp, respectively. These MrHSP60, 70 and 90 ORFs encoded a polypeptide of 574, 665 and 719 amino acids and their respective molecular mass was 60.75, 71.40 and 82.65 kDa. MrHSP60 and 70 are mitochondrial, whereas MrHSP90 is cytoplasmic in nature. The bioinformatics analysis showed that MrHSP60 possess a chaperonin (cpn) 60 domain at 46-547 and a cpn 60 signature motif between 427 and 438. Similarly, MrHSP70 possessed a HSP70 domain at 21-624, whereas MrHSP90 contained a HSP90 domain at 188-719 along with a HSP90 family signature between 30 and 39. MrHSP60 and 70 are rich in hydrophobic (glycine) residues at C-terminal ends, whereas 90 is rich in hydrophilic (aspartate) residues. Homology and evolutionary analysis revealed that these three MrHSP60, 70 and 90 are very close to Macrobrachium nipponense, Cherax cainii and Palaemon carinicauda, respectively. The structural analysis showed that MrHSP60 carried maximum amino acids (52%) in helices and it carries cpn 60 signature in helical and coil regions. In MrHSP70, the nucleotide binding domain was distributed throughout the helices, sheets and coils, whereas in MrHSP90, the HSP90 family signature is present in the helical region. Tissue distribution results revealed that significantly (P<0.05) highest expression of MrHSP60, 70 and 90 was observed in haemocyte, gill and hapatopancreas, respectively. Moreover, their mRNA regulation upon exposure to microbial pathogens significantly (P<0.05) increased their expression. Overall, the study showed the potential involvement of large HSPs against microbial stress in immune function of M. rosenbergii.

General trends of dihedral conformational transitions in a globular protein.

Dihedral conformational transitions are analyzed systematically in a model globular protein, cytochrome P450cam, to examine their structural and chemical dependences through combined conventional molecular dynamics (cMD), accelerated molecular dynamics (aMD) and adaptive biasing force (ABF) simulations. The aMD simulations are performed at two acceleration levels, using dihedral and dual boost, respectively. In comparison with cMD, aMD samples protein dihedral transitions approximately two times faster on average using dihedral boost, and ∼ 3.5 times faster using dual boost. In the protein backbone, significantly higher dihedral transition rates are observed in the bend, coil, and turn flexible regions, followed by the β bridge and β sheet, and then the helices. Moreover, protein side chains of greater length exhibit higher transition rates on average in the aMD-enhanced sampling. Side chains of the same length (particularly Nχ = 2) exhibit decreasing transition rates with residues when going from hydrophobic to polar, then charged and aromatic chemical types. The reduction of dihedral transition rates is found to be correlated with increasing energy barriers as identified through ABF free energy calculations. These general trends of dihedral conformational transitions provide important insights into the hierarchical dynamics and complex free energy landscapes of functional proteins.

Magnesium and manganese binding sites on proteins have the same predominant motif of secondary structure

Manganese ion (Mn2+) can substitute magnesium ion (Mg2+) in active sites of numerous enzymes. Binding sites for these two ions have been studied in two sets of protein 3D structures from the Protein Data Bank with the homology level lower than 25%. The structural motif “beta strand – binder – random coil” is predominant in both Mn2+ and Mg2+ coordination spheres, especially in functionally relevant ones. That predominant motif works as an active binder of those divalent cations which can then attract additional ligands, such as different phosphate-containing compounds. In contrast, such Mg2+ and Mn2+ binding motif as “GK(T/S)T” being the N-terminal part of alpha helices works as an active binder of phosphates which can then attract divalent cations. There are few differences between Mg2+ and Mn2+ coordination spheres responsible of the cation specificity. His residues are underrepresented in certain positions around Asp and Glu residues involved in Mg2+ coordination, while they are overrepresented in certain positions around Asp and Glu residues coordinating Mn2+. The random coil region in the “beta strand – random coil – alpha helix” motif for Mg2+ binding is usually shorter than that in the same motif for Mn2+ coordination. This feature is associated with the lower number of binding amino acids (and lower levels of usage of such “major” binders as Asp and Glu) for Mg2+ (which is a hard Lewis acid) in comparison with those for Mn2+ (an intermediate Lewis acid).

Analytical Solution of the Magnetic Field and EMF Calculation in Ironless BLDC Motor

The ironless brushless DC (BLDC) motors are widely used for flywheel due to their light mass, high efficiency, and high inertia-to-mass ratio. In this paper, a 2-D analytical solution for predicting the magnetic field distribution in an ironless BLDC motor is presented and compared with the 2-D finite-element method (FEM). The results of the proposed 2-D analytical method and the 2-D FEM are in good agreement. It is also found that the intensity and direction of the magnetic field change largely in the coil region, which makes the electromotive force (EMF) of strands in one coil package different from one another. Hence, three different models to calculate the EMF of ironless BLDC motor are proposed and compared. Meanwhile, both the axial end effect and the influence of end winding on EMF are considered, and then, a correction factor is proposed for the ironless BLDC motor. The effectiveness of the proposed method is validated by the experimental results. Due to its accuracy and computational speed, the method can be used in the design and optimization of ironless BLDC motors.

Conformational Change in the Ectodomain of the Amyloid Precursor Protein in Response to Proteolytic Processing: The Random Coil Regions Matter

Proteolytic cleavage of the amyloid precursor protein (APP) by the enzyme BACE1 is the initial step in production of amyloid-β peptide (Aβ), and has been a major target of Alzheimer's drug discovery efforts. A recent study demonstrated that sAPPα, the product of the cleavage of the ectodomain of APP by α-secretase, is a potent direct inhibitor of the BACE1 enzyme. However, sAPPβ, the product of APP by BACE1 is not an inhibitor of BACE1. Since sAPPα differs from sAPPβ (578 residues) only by an additional 16 amino acids at the carboxyl-terminus, both variants were studied with small-angle X-ray scattering (SAXS) in an effort to understand their different behaviour. Surprisingly, sAPPβ turned out to adopt a completely different conformation than sAPPα: a compact conformation in which the N-terminal E1 domain is juxtaposed with the C-terminus of the sAPPβ as opposed to the more linear conformation of sAPPα in which the E1 domain is stacked adjacent to the E2 domain. Studies with intrinsic fluorescence confirmed the conformational change. This observation indicates that the ectodomain of APP can switch between at least two stable conformations as a result of proteolytic processing. Heterodimerization studies of different fragments of APP using surface plasmon resonance indicated that the acidic region, the linker between the two domains, may play an important role in determining the position of the E1 domain relative to the rest of the protein. Combined with the SAXS analysis of the fragments, these studies demonstrate that functional conclusions based on the study of isolated fragments of APP can be misleading and suggest the “flexible” regions of APP may be much more important to its function than has been previously thought.

Structure of the TBC1D7-TSC1 complex reveals that TBC1D7 stabilizes dimerization of the TSC1 C-terminal coiled coil region.

TSC1 and TSC2 mutations account for the majority of tuberous sclerosis complex cases. The TSC1 and TSC2 proteins assemble into a complex that is stabilized by TBC1D7 through its direct interaction with the TSC1 coiled coil (CC) region. Loss of TBC1D7 is associated with intellectual disability and megalencephaly. Here, we determine the crystal structure of the complex between TBC1D7 and the C-terminal part (residues 939-992) of TSC1-CC. The structure reveals that two TSC1-CCs form a parallel homodimer, which results in the formation of two symmetric surfaces for interaction with TBC1D7. TBC1D7 employs its α4 and α5 helices to interact with the α1 helix of one TSC1 (939-992) molecule mainly through hydrophobic interactions, and simultaneously associates with the other TSC1 (939-992) molecule using the C-terminal tip of its α4 helix. Biochemical and cell biological data demonstrate that TBC1D7 indeed substantially stabilizes the homodimerization of TSC1-CC, and mutations to the critical interface residues greatly compromise this effect. Together, our data reveal the molecular mechanism underlying TBC1D7-mediated stabilization of TSC1 dimerization, and its contribution to the structural integrity of the holo-TSC complex.

Coil Winding Losses: Decomposition Strategy

Precise modeling of the magnetic field in the coil wire of an electric machine often becomes a major challenge: with the high number of turns and small penetration depth, the number of degrees of freedom exceeds reasonable limits in any standard approximation method. Precise approximation, however, is critical, e.g., to reliable coil loss estimation. Hence, there is a call for specialized approximative methods. This paper presents a method for time-harmonic coil wire field computations in 2-D problems. We replace the coil by a lattice of polygonal plane fillers and span a low-dimensional function space on the polygon boundaries. The reliability of loss estimates requires accurate computations of the responses to the interface excitations of this space. The responses constitute a Dirichlet-to-Neumann map to efficiently couple plane fillers together and to a standard finite-element method (FEM) outside the coil regions. The outcome is significantly faster than the standard FEM alone. The results are still in good agreement.

Edge position detection of on-line vehicles with segmental wireless power supply

Online charged electrical vehicles (EVs) with segmental wireless power supply obtain energy from power tracks without a physical cable contact while traveling. When a vehicle moves from one segmental track to another, the power supply coils should switch accordingly to provide energy continually at various positions. As the secondary coil fixed in the vehicle moves along the primary coil mounted in the segmental track, the mutual inductance of these two coils changes accordingly, which results in the varying of the phase angle that the current lags the voltage in the resonant circuit at the primary side. The paper presents a method to decide the power switching time through detecting the changing of the phase angle. A higher phase angle varying range (PAVR) is preferred to achieve a better position judgment. Quality factors at the primary and secondary sides, as well as the mutual inductance between two sides for the higher PAVR, are analyzed. The phase angle change can be detected in the circuit at the primary side when an EV leaves the energized coil region. Besides that, a detecting signal is introduced to find the approaching of EVs for those de-energized coils. The system robustness and magnetic saturation are also analyzed. A scaled-down laboratory prototype is set up to test the proposed method. Within parameter drifts of ±4% of the rating inductance or capacitance, the prototype works perfectly under the rated operation frequency and switching threshold angle. Experiments show that the position detection method can detect not only the approaching but the leaving of vehicles as well.

Metastasis-associated S100A4 is a specific amine donor and an activity-independent binding partner of transglutaminase-2.

Transglutaminase-2 (TG2) is best known as a Ca(2+)-dependent cross-linking enzyme; however, some of its extracellular matrix-related functions are independent of its catalytic activity and include matrix remodelling, adhesion and migration. S100A4 belongs to the Ca(2+)-binding EF-hand S100 protein family and acts both intra- and extra-cellularly through binding to various partners. It regulates cell migration and its overexpression is strongly associated with metastasis and poor survival in various cancers. It has recently been suggested that TG2 mediates S100A4-dependent tumour cell migration. In the present study we provide evidence that S100A4 is an interacting partner and also a specific amine donor of TG2. TG2 incorporates a glutamine donor peptide to Lys(100) in the C-terminal random coil region of S100A4. Importantly, the enzyme activity is not necessary for the interaction: S100A4 also binds to TG2 in the presence of a specific inhibitor that keeps the enzyme in an open conformation, or to an enzymatically inactive mutant. We also found that S100A4 considerably enhances TG2-mediated adhesion of A431 epithelial carcinoma cells to the extracellular matrix. This role is independent of enzyme activity and requires the open conformation of TG2. We propose that S100A4 stabilizes the open conformation of TG2, which binds to its cell-surface receptor in this state and increases cell adhesion.

In silico characterization and Molecular modeling of double-strand break repair protein MRE11 from Phoenix dactylifera v deglet nour.

BackgroundDNA double-strand breaks (DSBs) are highly cytotoxic and mutagenic. MRE11 plays an essential role in repairing DNA by cleaving broken ends through its 3′ to 5′ exonuclease and single-stranded DNA endonuclease activities.MethodsThe present study aimed to in silico characterization and molecular modeling of MRE11 from Phoenix dactylifera L cv deglet nour (DnMRE11) by various bioinformatic approaches. To identify DnMRE11 cDNA, assembled contigs from our cDNA libraries were analysed using the Blast2GO2.8 program.ResultsThe DnMRE11 protein length was 726 amino acids. The results of HUMMER show that DnMRE11 is formed by three domains: the N-terminal core domain containing the nuclease and capping domains, the C-terminal half containing the DNA binding and coiled coil region. The structure of DnMRE11 is predicted using the Swiss-Model server, which contains the nuclease and capping domains. The obtained model was verified with the structure validation programs such as ProSA and QMEAN servers for reliability. Ligand binding studies using COACH indicated the interaction of DnMRE11 protein with two Mn2+ ions and dAMP. The ConSurf server predicted that residues of the active site and Nbs binding site have high conservation scores between plant species.ConclusionsA model structure of DnMRE11 was constructed and validated with various bioinformatics programs which suggested the predicted model to be satisfactory. Further validation studies were conducted by COACH analysis for active site ligand prediction, and revealed the presence of six ligands binding sites and two ligands (2 Mn2+ and dAMP).Electronic supplementary materialThe online version of this article (doi:10.1186/s12976-015-0013-2) contains supplementary material, which is available to authorized users.

Conformational Parameters for Amino Acids in Helical, β-Sheet, and Random Coil Regions Calculated from Proteins: After 40 Years

Forty years ago, Peter Y. Chou and Gerald D. Fasman (1974a), relying on the information from fifteen proteins calculated α helix, β-sheet, and coil conformational parameters, Pα,Pβ,and Pc,for the 20 naturally occurring amino acids from the frequency of occurrence of each amino acid residue in the α, β, and coil conformations. Secondary structure of these 15 proteins had been determined by X-ray crystallography. Although the accuracy could not go over to the level of 60% too much, these values utilized for a long time to provide a simple procedure, devoid of complex computer calculations, to predict the secondary structure of proteins from their known amino acid sequences. In the same article of Peter Y. Chou and Gerald D. Fasman, a detailed analysis of the helix and β-sheet boundary residues in proteins provided amino acid frequencies at the N-and C-terminal ends which were used to delineate helical and β regions. Charged residues are found with the greatest frequency at both helical ends, but they were mostly absent in β-sheet regions. In the same article a mechanism of protein folding was proposed, whereby helix nucleation starts at the centers of the helix where the Pα values are highest, and propagates in both directions, until strong helix breakers where Pα values are lowest, terminate the growth at both ends. Similarly, residues with the highest Pβ values will initiate β regions and residues with the lowest Pβ values will terminate β regions. The helical region with the largest Pα was proposed as the site of the first fold during protein renaturation. The mechanism whereby proteins fold into their native conformation, capable of biological activity, has been a long sought after goal. With the elucidation of the three-dimensional structure of many proteins through X-ray crystallography, a new momentum has been given to understanding the factors governing this complex assembly of polypeptide chains. In this paper, using similar statistics from 20 347 proteins, the level of reliability of formerly found results is discussed.