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Root Mean Square Deviation (root + mean_square_deviation)
Selected AbstractsProbing multiple effects on 15N, 13C,, 13C,, and 13C, chemical shifts in peptides using density functional theoryBIOPOLYMERS, Issue 6 2002Xiao-Ping Xu Abstract We have used density functional calculations on model peptides to study conformational effects on 15N, 13C,, 13C,, and 13C, chemical shifts, associated with hydrogen bonding, backbone conformation, and side-chain orientation. The results show a significant dependence on the backbone torsion angles of the nearest three residues. Contributions to 15N chemical shifts from hydrogen bonding (up to 8 ppm), backbone conformation (up to 13 ppm), side-chain orientation and neighborhood residue effects (up to 22 ppm) are significant, and a unified theory will be required to account for their behavior in proteins. In contrast to this, the dependence on sequence and hydrogen bonding is much less for 13C, and 13C, chemical shifts (<0.5 ppm), and moderate for carbonyl carbon shifts (<2 ppm). The effects of side-chain orientation are mainly limited to the residue itself for both nitrogen and carbon, but the ,1 effect is also significant for the nitrogen shift of the following residue and for the 13C, shift of the preceding residue. The calculated results are used, in conjunction with an additive model of chemical shift contributions, to create an algorithm for prediction of 15N and 13C shifts in proteins from their structure; this includes a model to extrapolate results to regions of torsion angle space that have not been explicitly studied by density functional theory (DFT) calculations. Crystal structures of 20 proteins with measured shifts have been used to test the prediction scheme. Root mean square deviations between calculated and experimental shifts 2.71, 1.22, 1.31, and 1.28 ppm for N, C,, C,, and C,, respectively. This prediction algorithm should be helpful in NMR assignment, crystal and solution structure comparison, and structure refinement. © 2002 Wiley Periodicals, Inc. Biopolymers 65: 408,423, 2002 [source] Nanocrystalline Electroplated Cu,Ni: Metallic Thin Films with Enhanced Mechanical Properties and Tunable Magnetic BehaviorADVANCED FUNCTIONAL MATERIALS, Issue 6 2010Eva Pellicer Abstract Nanocrystalline 3,µm thick Cu1,xNix (0.45,,,x,,,0.87) films are electrodeposited galvanostatically onto Cu/Ti/Si (100) substrates, from a citrate- and sulphate-based bath containing sodium lauryl sulphate and saccharine as additives. The films exhibit large values of reduced Young's modulus (173,<,Er,<,192,GPa) and hardness (6.4,<,H,<,8.2,GPa), both of which can be tailored by varying the alloy composition. The outstanding mechanical properties of these metallic films can be ascribed to their nanocrystalline nature,as evidenced by X-ray diffraction, transmission electron microscopy, and atomic force microscopy,along with the occurrence of stacking faults and the concomitant formation of intragranular nanotwins during film growth. Due to their nanocrystalline character, these films also show very low surface roughness (root mean square deviation of around 2,nm). Furthermore, tunable magnetic properties, including a transition from paramagnetic to ferromagnetic behavior, are observed when the Ni percentage is increased. This combination of properties, together with the simplicity of the fabrication method, makes this system attractive for widespread technological applications, including hard metallic coatings or magnetic micro/nano-electromechanical devices. [source] A self-adaptive genetic algorithm-artificial neural network algorithm with leave-one-out cross validation for descriptor selection in QSAR studyJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 10 2010Jingheng Wu Abstract Based on the quantitative structure-activity relationships (QSARs) models developed by artificial neural networks (ANNs), genetic algorithm (GA) was used in the variable-selection approach with molecule descriptors and helped to improve the back-propagation training algorithm as well. The cross validation techniques of leave-one-out investigated the validity of the generated ANN model and preferable variable combinations derived in the GAs. A self-adaptive GA-ANN model was successfully established by using a new estimate function for avoiding over-fitting phenomenon in ANN training. Compared with the variables selected in two recent QSAR studies that were based on stepwise multiple linear regression (MLR) models, the variables selected in self-adaptive GA-ANN model are superior in constructing ANN model, as they revealed a higher cross validation (CV) coefficient (Q2) and a lower root mean square deviation both in the established model and biological activity prediction. The introduced methods for validation, including leave-multiple-out, Y-randomization, and external validation, proved the superiority of the established GA-ANN models over MLR models in both stability and predictive power. Self-adaptive GA-ANN showed us a prospect of improving QSAR model. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] Improved pKa prediction: Combining empirical and semimicroscopic methodsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 15 2008Gernot Kieseritzky Abstract Using three different methods we tried to compute 171 experimentally known pKa values of ionizable residues from 15 different proteins and compared the accuracies of computed pKa values in terms of the root mean square deviation (RMSD) from experiment. One method is based on a continuum electrostatic model of the protein including conformational flexibility (KBPLUS). The others are empirical approaches with PROPKA deploying physically motivated energy terms with adjustable parameters and PKAcal using an empirical function with no physical basis. PROPKA reproduced the pKa values with highest overall accuracy. Differentiating the data set into weakly and strongly shifted experimental pKa values, however, we found that PROPKA's accuracy is better if the pKa values are weakly shifted but on equal footing with that of KBPLUS for more strongly shifted values. On the other hand, PKAcal reproduces strongly shifted pKa values badly but weakly shifted values with the same accuracy as PROPKA. We tested different consensus approaches combining data from all three methods to find a general procedure for most accurate pKa predictions. In most of the cases we found that the consensus approach reproduced experimental data with better accuracy than any of the individual methods alone. © 2008 Wiley Periodicals, Inc. J Comput Chem 2008 [source] High-resolution stimulated Raman spectroscopy and analysis of the 2,10 overtone symmetric motion of C2H4JOURNAL OF RAMAN SPECTROSCOPY, Issue 8 2009M. Loroño Abstract The high-resolution stimulated Raman spectrum of the 2,10 band located at 1664.16 cm,1 of C2H4 has been reanalyzed, thanks to the tensorial formalism developed in Dijon for X2Y4 asymmetric-top molecules. A total of 191 lines were assigned and fitted as a single band without including perturbations such as Fermi or Coriolis coupling constants. We obtained a global root mean square deviation of 8.5 × 10,3 cm,1. Further investigations are required to include interactions with the ,2 and ,7 + ,10 bands. Copyright © 2009 John Wiley & Sons, Ltd. [source] Solution structure determination of oligoureas using methylene spin state selective NMR at 13C natural abundanceMAGNETIC RESONANCE IN CHEMISTRY, Issue 10 2008Gilles Guichard Abstract Ability of N,N,-linked oligoureas containing proteinogenic side chains to adopt a stable helix conformation in solution has been described recently. NMR as well as circular dichroism (CD) spectroscopies were employed to gain insight into their specific fold. It is herein proposed to extend the structural information available on these peptidomimetics by an advantageous use of a methylene spin state selective NMR experiment. Homodecoupling provided by the pulse scheme made it possible to readily measure conformation-dependent 3JHH constants that are difficult if not impossible to obtain with standard NMR experiments. Adding those couplings to the NMR restraints improved the quality of the structure calculations significantly, as judged by a ca 30% decrease of the root mean square deviation (RMSD) obtained over an ensemble of 20 structures. Moreover, accurate determination of individual 1JCH couplings within each methylene group revealed uniform values throughout the oligourea sequence, with 1JCH systematically slightly larger for the pro-S hydrogen than for the pro-R. As shown in this study, the methylene spin state selective NMR experiment displays a good intrinsic sensitivity and could therefore provide valuable structural information at 13C natural abundance for peptidomimetic molecules and foldamers bearing diastereotopic methylene protons. Copyright © 2008 John Wiley & Sons, Ltd. [source] The Crystal Structure of the L1 Intermediate of Halorhodopsin at 1.9 Å Resolution,PHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 2 2007Walter Gmelin The mutant T203V of the light driven chloride pump halorhodopsin from Halobacterium salinarum was crystallized and the X-ray structure was solved at 1.6 Å resolution. The T203V structure turned out to be nearly identical to the wild type protein with a root mean square deviation of 0.43 Å for the carbon , atoms of the protein backbone. Two chloride binding (CB) sites were demonstrated by a substitution of chloride with bromide and an analysis of anomalous difference Fourier maps. The CB1 site was found at the same position as in the wild type structure. In addition, a second chloride binding site CB2 was identified around Q105 due to higher resolution in the mutant crystal. As T203V showed a 10 times slower decay of its photocycle intermediate L, this intermediate could be trapped with an occupancy of 60% upon illumination at room temperature and subsequent cooling to 120°K. Fourier transform infrared spectroscopy clearly identified the crystal to be trapped in the L1 intermediate state and the X-ray structure was solved to 1.9 Å resolution. In this intermediate, the chloride moved by 0.3 Å within binding site CB1 as indicated by peaks in difference Fourier density maps. The chloride in the second binding site CB2 remained unchanged. Thus, intraproteinous chloride translocation from the extracellular to the cytoplasmic part of the protein must occur in reaction steps following the L1 intermediate in the catalytic cycle of halorhodopsin. [source] All three Ca2+ -binding loops of photoproteins bind calcium ions: The crystal structures of calcium-loaded apo-aequorin and apo-obelinPROTEIN SCIENCE, Issue 3 2005Lu Deng HLH, helix,loop,helix; HSQC, heteronuclear single quantum coherence; RMSD, root mean square deviation; SAD, single wavelength anomalous dispersion Abstract The crystal structures of calcium-loaded apoaequorin and apo-obelin have been determined at resolutions 1.7 Å and 2.2 Å, respectively. A calcium ion is observed in each of the three EF-hand loops that have the canonical calcium-binding sequence, and each is coordinated in the characteristic pentagonal bipyramidal configuration. The calcium-loaded apo-proteins retain the same compact scaffold and overall fold as the unreacted photoproteins containing the bound substrate, 2-hydroperoxycoelenterazine, and also the same as the Ca2+ -discharged obelin bound with the product, coelenteramide. Nevertheless, there are easily discerned shifts in both helix and loop regions, and the shifts are not the same between the two proteins. It is suggested that these subtle shifts are the basis of the ability of these photoproteins to sense Ca2+ concentration transients and to produce their bioluminescence response on the millisecond timescale. A mechanism of intrastructural transmission of the calcium signal is proposed. [source] Structure and stability of the ankyrin domain of the Drosophila Notch receptorPROTEIN SCIENCE, Issue 11 2003Mark E. Zweifel RMSD, root mean square deviation; CD, circular dichroism spectroscopy Abstract The Notch receptor contains a conserved ankyrin repeat domain that is required for Notch-mediated signal transduction. The ankyrin domain of Drosophila Notch contains six ankyrin sequence repeats previously identified as closely matching the ankyrin repeat consensus sequence, and a putative seventh C-terminal sequence repeat that exhibits lower similarity to the consensus sequence. To better understand the role of the Notch ankyrin domain in Notch-mediated signaling and to examine how structure is distributed among the seven ankyrin sequence repeats, we have determined the crystal structure of this domain to 2.0 Å resolution. The seventh, C-terminal, ankyrin sequence repeat adopts a regular ankyrin fold, but the first, N-terminal ankyrin repeat, which contains a 15-residue insertion, appears to be largely disordered. The structure reveals a substantial interface between ankyrin polypeptides, showing a high degree of shape and charge complementarity, which may be related to homotypic interactions suggested from indirect studies. However, the Notch ankyrin domain remains largely monomeric in solution, demonstrating that this interface alone is not sufficient to promote tight association. Using the structure, we have classified reported mutations within the Notch ankyrin domain that are known to disrupt signaling into those that affect buried residues and those restricted to surface residues. We show that the buried substitutions greatly decrease protein stability, whereas the surface substitutions have only a marginal affect on stability. The surface substitutions are thus likely to interfere with Notch signaling by disrupting specific Notch-effector interactions and map the sites of these interactions. [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] Force field-dependant structural divergence revealed during long time simulations of Calbindin d9kJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 9 2010Elad Project Abstract The structural and the dynamic features of the Calbindin (CaB) protein in its holo and apo states are compared using molecular dynamics simulations under nine different force fields (FFs) (G43a1, G53a6, Opls-AA, Amber94, Amber99, Amber99p, AmberGS, AmberGSs, and Amber99sb). The results show that most FFs reproduce reasonably well the majority of the experimentally derived features of the CaB protein. However, in several cases, there are significant differences in secondary structure properties, root mean square deviations (RMSDs), root mean square fluctuations (RMSFs), and S2 order parameters among the various FFs. What is more, in certain cases, these parameters differed from the experimentally derived values. Some of these deviations became noticeable only after 50 ns. A comparison with experimental data indicates that, for CaB, the Amber94 shows overall best agreement with the measured values, whereas several others seem to deviate from both crystal and nuclear magnetic resonance data. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] Side chain substitution benchmark for peptide/MHC interactionPROTEIN SCIENCE, Issue 6 2008Bernhard Knapp Abstract The prediction of T-cell epitopes is an essential part in virtual immunology. Apart from sequence-based techniques, which achieve good results but fail to give insight into the binding behavior of a certain peptide binding to a major histocompatibility complex, structure-based approaches are another important technique. An essential step is the correct placement of the side chains for a given peptide in cases where no experimental data for the structure are available. To our knowledge, no benchmark for side chain substitution in the area of HLA has been reported in the literature. Here, we present a comparison of five different tools (SCWRL, SCATD, SPDBV, SCit, IRECS) applicable for side chain substitution. Each tool is tested on 29 different HLA-A2 structures with experimentally known side chain positions. Parts of the benchmark are correctness, reliability, runtime, and usability. For validation, the root mean square deviations between X-ray structures and predicted structures are used. All tools show different strengths and weaknesses. [source] | ||||||||||