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Predicted Structure (predicted + structure)
Selected AbstractsDiversification in MHC class II invariant chain-like proteins among fishesJOURNAL OF APPLIED ICHTHYOLOGY, Issue 4 2004M. Sakai Summary The major histocompatibility complex (MHC) class II invariant chains are important for an efficient and complete presentation of antigens by MHC class II molecules. Invariant chain-like proteins (Iclp) 1 and 2 were identified by expressed sequence tag analysis from cDNA library of common carp head kidney (HK) stimulated with concanavalin A and lipopolysaccharide. The sequences were 1043 and 1016 bp in length encoding 234 and 198 amino acid proteins, respectively. Based on their predicted structure, the genes harboured transmembrane domain (TMD) and Tg (thyroglobulin) type 1 domains. Expression analysis revealed that both genes were expressed in normal tissues of HK, intestine, brain and gill. By database search, similar homologues were found in Atlantic salmon, fugu and catfish. Phylogenetic and alignment analysis indicate diversity among fish Iclps. [source] Tryptophanyl fluorescence lifetime distribution of hyperthermophilic ,-glycosidase from molecular dynamics simulation: A comparison with the experimental dataPROTEIN SCIENCE, Issue 9 2000Ettore Bismuto Abstract A molecular dynamics simulation approach has been utilized to understand the unusual fluorescence emission decay observed for ,-glycosidase from the hyperthermophilic bacterium Solfolobus sulfataricus (S,gly), a tetrameric enzyme containing 17 tryptophanyl residues for each subunit. The tryptophanyl emission decay of (S,gly) results from a bimodal distribution of fluorescence lifetimes with a short-lived component centered at 2.5 ns and a long-lived one at 7.4 ns Bismuto E, Nucci R, Rossi M, Irace G, 1999, Proteins 27:71,79). From the examination of the trajectories of the side chains capable of causing intramolecular quenching for each tryptophan microenvironment and using a modified Stern,Volmer model for the emission quenching processes, we calculated the fluorescence lifetime for each tryptophanyl residue of S,gly at two different temperatures, i.e., 300 and 365 K. The highest temperature was chosen because in this condition S,lgy evidences a maximum in its catalytic activity and is stable for a very long time. The calculated lifetime distributions overlap those experimentally determined. Moreover, the majority of trytptophanyl residues having longer lifetimes correspond to those originally identified by inspection of the crystallographic structure. The tryptophanyl lifetimes appear to be a complex function of several variables, such as microenvironment viscosity, solvent accessibility, the chemical structure of quencher side chains, and side-chain dynamics. The lifetime calculation by MD simulation can be used to validate a predicted structure by comparing the theoretical data with the experimental fluorescence decay results. [source] Predicted crystal structures of tetramethylsilane and tetramethylgermane and an experimental low-temperature structure of tetramethylsilaneACTA CRYSTALLOGRAPHICA SECTION B, Issue 2 2010Alexandra K. Wolf No crystal structure at ambient pressure is known for tetramethylsilane, Si(CH3)4, which is used as a standard in NMR spectroscopy. Possible crystal structures were predicted by global lattice-energy minimizations using force-field methods. The lowest-energy structure corresponds to the high-pressure room-temperature phase (, Z = 8). Low-temperature crystallization at 100,K resulted in a single crystal, and its crystal structure has been determined. The structure corresponds to the predicted structure with the second lowest energy rank. In X-ray powder analyses this is the only observed phase between 80 and 159,K. For tetramethylgermane, Ge(CH), no experimental crystal structure is known. Global lattice-energy minimizations resulted in 47 possible crystal structures within an energy range of 5,kJ,mol,1. The lowest-energy structure was found in , Z = 8. [source] A complicated quasicrystal approximant ,16 predicted by the strong-reflections approachACTA CRYSTALLOGRAPHICA SECTION B, Issue 1 2010Mingrun Li The structure of a complicated quasicrystal approximant ,16 was predicted from a known and related quasicrystal approximant ,6 by the strong-reflections approach. Electron-diffraction studies show that in reciprocal space, the positions of the strongest reflections and their intensity distributions are similar for both approximants. By applying the strong-reflections approach, the structure factors of ,16 were deduced from those of the known ,6 structure. Owing to the different space groups of the two structures, a shift of the phase origin had to be applied in order to obtain the phases of ,16. An electron-density map of ,16 was calculated by inverse Fourier transformation of the structure factors of the 256 strongest reflections. Similar to that of ,6, the predicted structure of ,16 contains eight layers in each unit cell, stacked along the b axis. Along the b axis, ,16 is built by banana-shaped tiles and pentagonal tiles; this structure is confirmed by high-resolution transmission electron microscopy (HRTEM). The simulated precession electron-diffraction (PED) patterns from the structure model are in good agreement with the experimental ones. ,16 with 153 unique atoms in the unit cell is the most complicated approximant structure ever solved or predicted. [source] K2[HCr2AsO10]: redetermination of phase II and the predicted structure of phase IACTA CRYSTALLOGRAPHICA SECTION C, Issue 12 2004T. J. R. Weakley Our prediction that phase II of dipotassium hydrogen chromatoarsenate, K2[HCr2AsO10], is ferroelectric, based on the analysis of the atomic coordinates by Averbuch-Pouchot, Durif & Guitel [Acta Cryst. (1978), B34, 3725,3727], led to an independent redetermination of the structure using two separate crystals. The resulting improved accuracy allows the inference that the H atom is located in the hydrogen bonds of length 2.555,(5),Å which form between the terminal O atoms of shared AsO3OH tetrahedra in adjacent HCr2AsO102, ions. The largest atomic displacement of 0.586,Å between phase II and the predicted paraelectric phase I is by these two O atoms. The H atoms form helices of radius ,0.60,Å about the 31 or 32 axes. Normal probability analysis reveals systematic error in seven or more of the earlier atomic coordinates. [source] Design of (Gd-DO3A)n -polydiamidopropanoyl-peptide nucleic acid- D(Cys-Ser-Lys-Cys) magnetic resonance contrast agentsBIOPOLYMERS, Issue 12 2008Nariman V. Amirkhanov Abstract We hypothesized that chelating Gd(III) to 1,4,7-tris(carboxymethylaza)cyclododecane-10-azaacetylamide (DO3A) on peptide nucleic acid (PNA) hybridization probes would provide a magnetic resonance genetic imaging agent capable of hybridization to a specific mRNA. Because of the low sensitivity of Gd(III) as an magnetic resonance imaging (MRI) contrast agent, a single Gd-DO3A complex per PNA hybridization agent could not provide enough contrast for detection of cancer gene mRNAs, even at thousands of mRNA copies per cell. To increase the Gd(III) shift intensity of MRI genetic imaging agents, we extended a novel DO3An -polydiamidopropanoyl (PDAPm) dendrimer, up to n = 16, from the N-terminus of KRAS PNA hybridization agents by solid phase synthesis. A C-terminal D(Cys-Ser-Lys-Cys) cyclized peptide analog of insulin-like growth factor 1 (IGF1) was included to enable receptor-mediated cellular uptake. Molecular dynamic simulation of the (Gd-DO3A-AEEA)16 -PDAP4 -AEEA2 - KRAS PNA-AEEA- D(Cys-Ser-Lys-Cys) genetic imaging nanoparticles in explicit water yielded a pair correlation function similar to that of PAMAM dendrimers, and a predicted structure in which the PDAP dendron did not sequester the PNA. Thermal melting measurements indicated that the size of the PDAP dendron included in the (DO3A-AEEA)n -PDAPm -AEEA2 - KRAS PNA-AEEA- D(Cys-Ser-Lys-Cys) probes (up to 16 Gd(III) cations per PNA) did not depress the melting temperatures (Tm) of the complementary PNA/RNA hybrid duplexes. The Gd(III) dendrimer PNA genetic imaging agents in phantom solutions displayed significantly greater T1 relaxivity per probe (r1 = 30.64 ± 2.68 mM,1 s,1 for n = 2, r1 = 153.84 ± 11.28 mM,1 s,1 for n = 8) than Gd-DTPA (r1 = 10.35 ± 0.37 mM,1 s,1), but less than that of (Gd-DO3A)32 -PAMAM dendrimer (r1 = 771.84 ± 20.48 mM,1 s,1) (P < 0.05). Higher generations of PDAP dendrimers with 32 or more Gd-DO3A residues attached to PNA- D(Cys-Ser-Lys-Cys) genetic imaging agents might provide greater contrast for more sensitive detection. © 2008 Wiley Periodicals, Inc. Biopolymers 89: 1061,1076, 2008. This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] PC1/3, PC2 and PC5/6A are targeted to dense core secretory granules by a common mechanismFEBS JOURNAL, Issue 16 2007Jimmy D. Dikeakos There are seven members of the proprotein convertase (PC) family of secreted serine proteases that cleave their substrates at basic amino acids, thereby activating a variety of hormones, growth factors, and viruses. PC1/3, PC2 and PC5/6A are the only members of the PC family that are targeted to dense core secretory granules, where they carry out the processing of proteins that are secreted from the cell in a regulated manner. Previous studies have identified ,-helices in the C-termini of the PC1/3 and PC2 proteases that are required for this subcellular targeting. In the current study, we demonstrate that a predicted ,-helix in the C-terminus of PC5/6A is also critical for the ability of this domain to target a heterologous protein to the regulated secretory pathway of mouse endocrine AtT-20 cells. Analysis of the subcellular distribution of fusion proteins containing the C-terminal domains of PC1/3, PC2 and PC5/6A confirmed that all three domains have the capacity to redirect a constitutively secreted protein to the granule-containing cytoplasmic extensions. Analysis of the predicted structures formed by these three granule-sorting helices shows a correlation between their granule-sorting efficiency and the clustering of hydrophobic amino acids in their granule-targeting helices. [source] Application of statistical potentials to protein structure refinement from low resolution ab initio modelsBIOPOLYMERS, Issue 4 2003Hui Lu Abstract Recently ab initio protein structure prediction methods have advanced sufficiently so that they often assemble the correct low resolution structure of the protein. To enhance the speed of conformational search, many ab initio prediction programs adopt a reduced protein representation. However, for drug design purposes, better quality structures are probably needed. To achieve this refinement, it is natural to use a more detailed heavy atom representation. Here, as opposed to costly implicit or explicit solvent molecular dynamics simulations, knowledge-based heavy atom pair potentials were employed. By way of illustration, we tried to improve the quality of the predicted structures obtained from the ab initio prediction program TOUCHSTONE by three methods: local constraint refinement, reduced predicted tertiary contact refinement, and statistical pair potential guided molecular dynamics. Sixty-seven predicted structures from 30 small proteins (less than 150 residues in length) representing different structural classes (,, ,, ,,/,) were examined. In 33 cases, the root mean square deviation (RMSD) from native structures improved by more than 0.3 Å; in 19 cases, the improvement was more than 0.5 Å, and sometimes as large as 1 Å. In only seven (four) cases did the refinement procedure increase the RMSD by more than 0.3 (0.5) Å. For the remaining structures, the refinement procedures changed the structures by less than 0.3 Å. While modest, the performance of the current refinement methods is better than the published refinement results obtained using standard molecular dynamics. © 2003 Wiley Periodicals, Inc. Biopolymers 70: 575,584, 2003 [source] | |||||||||||||||||||