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Root-mean-square Deviation (root-mean-square + deviation)
Selected AbstractsSPICKER: A clustering approach to identify near-native protein foldsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 6 2004Yang Zhang Abstract We have developed SPICKER, a simple and efficient strategy to identify near-native folds by clustering protein structures generated during computer simulations. In general, the most populated clusters tend to be closer to the native conformation than the lowest energy structures. To assess the generality of the approach, we applied SPICKER to 1489 representative benchmark proteins ,200 residues that cover the PDB at the level of 35% sequence identity; each contains up to 280,000 structure decoys generated using the recently developed TASSER (Threading ASSembly Refinement) algorithm. The best of the top five identified folds has a root-mean-square deviation from native (RMSD) in the top 1.4% of all decoys. For 78% of the proteins, the difference in RMSD from native to the identified models and RMSD from native to the absolutely best individual decoy is below 1 Å; the majority belong to the targets with converged conformational distributions. Although native fold identification from divergent decoy structures remains a challenge, our overall results show significant improvement over our previous clustering algorithms. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 865,871, 2004 [source] Soft protein,protein docking in internal coordinatesPROTEIN SCIENCE, Issue 2 2002Juan Fernández-Recio PDB, Protein Data Bank; ICM, Internal Coordinate Mechanics; RMSD, root-mean-square deviation Abstract The association of two biological macromolecules is a fundamental biological phenomenon and an unsolved theoretical problem. Docking methods for ab initio prediction of association of two independently determined protein structures usually fail when they are applied to a large set of complexes, mostly because of inaccuracies in the scoring function and/or difficulties on simulating the rearrangement of the interface residues on binding. In this work we present an efficient pseudo-Brownian rigid-body docking procedure followed by Biased Probability Monte Carlo Minimization of the ligand interacting side-chains. The use of a soft interaction energy function precalculated on a grid, instead of the explicit energy, drastically increased the speed of the procedure. The method was tested on a benchmark of 24 protein,protein complexes in which the three-dimensional structures of their subunits (bound and free) were available. The rank of the near-native conformation in a list of candidate docking solutions was <20 in 85% of complexes with no major backbone motion on binding. Among them, as many as 7 out of 11 (64%) protease-inhibitor complexes can be successfully predicted as the highest rank conformations. The presented method can be further refined to include the binding site predictions and applied to the structures generated by the structural proteomics projects. All scripts are available on the Web. [source] Structural studies of a baboon (Papio sp.) plasma protein inhibitor of cholesteryl ester transferasePROTEIN SCIENCE, Issue 8 2000Garry W. Buchko Abstract A 38-residue protein associated with cholesteryl ester transfer inhibition has been identified in baboons (Papio sp.). The cholesteryl ester transfer inhibitor protein (CETIP) corresponds to the N-terminus of baboon apoC-I. Relative to CETIP, baboon apoC-I is a weak inhibitor of baboon cholesteryl ester transferase (CET). To study the structural features responsible for CET inhibition, CETIP was synthesized by solid-phase methods. Using sodium dodecyl sulfate (SDS) to model the lipoprotein environment, the solution structure of CETIP was probed by optical and 1HNMR spectroscopy. Circular dichroism data show that the protein lacks a well-defined structure in water but, upon the addition of SDS, becomes helical (56%). A small blue shift of 8 nm was observed in the intrinsic tryptophan fluorescence of CETIP in the presence of saturating amounts of SDS, suggesting that tryptophan-23 is not buried deeply in the lipid environment. The helical nature of CETIP in the presence of SDS was confirmed by upfield 1H, secondary shifts and an average solution structure determined by distance geometry/simulated annealing calculations using 476 NOE-based distance restraints. The backbone (N , C, , C, = O ) root-mean-square deviation of an ensemble of 17 out of 25 calculated structures superimposed on the average structure was 1.06 ± 0.30 Å using residues V4-P35 and 0.51 ± 0.17 Å using residues A7-S32. Although the side-chain orientations fit the basic description of a class A amphipathic helix, both intramolecular salt bridge formation and "snorkeling" of basic side chains toward the polar face play minor, if any, roles in stabilizing the lipid-bound amphipathic structure. Conformational features of the calculated structures for CETIP are discussed relative to models of CETIP inhibition of cholesteryl ester transferase. [source] A revised proof of the metric properties of optimally superimposed vector setsACTA CRYSTALLOGRAPHICA SECTION A, Issue 5 2002Boris Steipe A revised proof is given that the root-mean-square deviation between more than two vector sets after optimal superposition induces a metric. This corrects an error in a previous manuscript [Kaindl & Steipe (1997). Acta Cryst. A53, 809]. [source] Metric properties of the root-mean-square deviation of vector sets.ACTA CRYSTALLOGRAPHICA SECTION A, Issue 5 2002Erratum A technical error invalidates the proof that the optimal root-mean-square deviation of vector sets induces a metric given in Kaindl & Steipe [Acta Cryst. (1997), A53, 809]. Nevertheless, the conclusions are correct and a revised proof is given in Steipe [Acta Cryst. (2002), A58, 506]. [source] Dynamics of the Hck-SH3 domain: Comparison of experiment with multiple molecular dynamics simulationsPROTEIN SCIENCE, Issue 1 2000David A. Horita Abstract Molecular dynamics calculations provide a method by which the dynamic properties of molecules can be explored over timescales and at a level of detail that cannot be obtained experimentally from NMR or X-ray analyses. Recent work (Philippopoulos M, Mandel AM, Palmer AG III, Lim C, 1997, Proteins 28:481,493) has indicated that the accuracy of these simulations is high, as measured by the correspondence of parameters extracted from these calculations to those determined through experimental means. Here, we investigate the dynamic behavior of the Src homology 3 (SH3) domain of hematopoietic cell kinase (Hck) via 15N backbone relaxation NMR studies and a set of four independent 4 ns solvated molecular dynamics calculations. We also find that molecular dynamics simulations accurately reproduce fast motion dynamics as estimated from generalized order parameter (S2) analysis for regions of the protein that have experimentally well-defined coordinates (i.e., stable secondary structural elements). However, for regions where the coordinates are not well defined, as indicated by high local root-mean-square deviations among NMR-determined structural family members or high B -factors/low electron density in X-ray crystallography determined structures, the parameters calculated from a short to moderate length (less than 5,10 ns) molecular dynamics trajectory are dependent on the particular coordinates chosen as a starting point for the simulation. [source] Refinement of protein crystal structures using energy restraints derived from linear-scaling quantum mechanicsACTA CRYSTALLOGRAPHICA SECTION D, Issue 3 2005Ning Yu A novel method is proposed in which combined restraints derived from linear-scaling semiempirical quantum-mechanical (QM) calculations and X-ray diffraction data are combined to refine crystal structures of proteins. Its performance has been tested on a small protein molecule, bovine pancreatic trypsin inhibitor (BPTI). The refinement involves minimization of the sum of a geometric energy function and an X-ray target function based on either the least-squares residual or the maximum-likelihood formalism. For comparison, similar refinement runs have also been performed using energy restraints derived from the force field available in the Crystallography & NMR System (CNS) program. The QM refinements were carried out with weights that were varied by several orders of magnitude and the optimal weights were identified by observing the trend in the final free R values, QM heats of formation and coordinate root-mean-square deviations (r.m.s.d.s) from the crystal structure. It is found that the QM weights are typically smaller but generally on the same scale as the molecular-mechanics (MM) weights for the respective X-ray target functions. The crystallographic R, free R, real-space R values and correlation coefficients based on the structures refined with the energy restraints derived from our QM calculations and Engh and Huber parameters are comparable, suggesting that the QM restraints are capable of maintaining reasonable stereochemistry to a similar degree as the force-field parameters. A detailed inspection of the structures refined with the QM and MM energy restraints reveals that one of the common differences between them and the crystal structure is that the strained bond angles in the crystal structure are corrected after energetically restrained refinements. Systematic differences in certain bond lengths between the QM-refined structures and the statistical averages of experimental structures have also been observed and discussed. [source] Structure of human erythrocyte NADH-cytochrome b5 reductaseACTA CRYSTALLOGRAPHICA SECTION D, Issue 11 2004Sachiko Bando Erythrocyte NADH-cytochrome b5 reductase reduces methaemoglobin to functional haemoglobin. In order to examine the function of the enzyme, the structure of NADH-cytochrome b5 reductase from human erythrocytes has been determined and refined by X-ray crystallography. At 1.75,Å resolution, the root-mean-square deviations (r.m.s.d.) from standard bond lengths and angles are 0.006,Å and 1.03°, respectively. The molecular structure was compared with those of rat NADH-cytochrome b5 reductase and corn nitrate reductase. The human reductase resembles the rat reductase in overall structure as well as in many side chains. Nevertheless, there is a large main-chain shift from the human reductase to the rat reductase or the corn reductase caused by a single-residue replacement from proline to threonine. A model of the complex between cytochrome b5 and the human reductase has been built and compared with that of the haem-containing domain of the nitrate reductase molecule. The interaction between cytochrome b5 and the human reductase differs from that of the nitrate reductase because of differences in the amino-acid sequences. The structures around 15 mutation sites of the human reductase have been examined for the influence of residue substitutions using the program ROTAMER. Five mutations in the FAD-binding domain seem to be related to cytochrome b5. [source] Phase transition of triclinic hen egg-white lysozyme crystal associated with sodium bindingACTA CRYSTALLOGRAPHICA SECTION D, Issue 4 2004Kazuaki Harata A triclinic crystal of hen egg-white lysozyme obtained from a D2O solution at 313,K was transformed into a new triclinic crystal by slow release of solvent under a temperature-regulated nitrogen-gas stream. The progress of the transition was monitored by X-ray diffraction. The transition started with the appearance of strong diffuse streaks. The diffraction spots gradually fused and faded with the emergence of diffraction from the new lattice; the scattering power of the crystal fell to a resolution of 1.5,Å from the initial 0.9,Å resolution. At the end of the transition, the diffuse streaks disappeared and the scattering power recovered to 1.1,Å resolution. The transformed crystal contained two independent molecules and the solvent content had decreased to 18% from the 32% solvent content of the native crystal. The structure was determined at 1.1,Å resolution and compared with the native structure refined at the same resolution. The backbone structures of the two molecules in the transformed crystal were superimposed on the native structure with root-mean-square deviations of 0.71 and 0.96,Å. A prominent structural difference was observed in the loop region of residues Ser60,Leu75. In the native crystal, a water molecule located at the centre of this helical loop forms hydrogen bonds to main-chain peptide groups. In the transformed crystal, this water molecule is replaced by a sodium ion with octahedral coordination that involves water molecules and a nitrate ion. The peptide group connecting Arg73 and Asn74 is rotated by 180° so that the CO group of Arg73 can coordinate to the sodium ion. The change in the X-ray diffraction pattern during the phase transition suggests that the transition proceeds at the microcrystal level. A mechanism is proposed for the crystal transformation. [source] Structure of the newly found green turtle egg-white ribonucleaseACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 7 2010Somporn Katekaew Marine green turtle (Chelonia mydas) egg-white ribonuclease (GTRNase) was crystallized from 1.1,M ammonium sulfate pH 5.5 and 30% glycerol using the sitting-drop vapour-diffusion method. The structure of GTRNase has been solved at 1.60,Å resolution by the molecular-replacement technique using a model based on the structure of RNase 5 (murine angiogenin) from Mus musculus (46% identity). The crystal belonged to the monoclinic space group C2, with unit-cell parameters a = 86.271, b = 34.174, c = 39.738,Å, , = 90, , = 102, , = 90°. GTRNase consists of three helices and seven ,-strands and displays the ,+, folding topology typical of a member of the RNase A superfamily. Superposition of the C, coordinates of GTRNase and RNase A superfamily members indicates that the overall structure is highly similar to that of angiogenin or RNase 5 from M. musculus (PDB code 2bwl) and RNase A from Bos taurus (PDB code 2blz), with root-mean-square deviations of 3.9 and 2.0,Å, respectively. The catalytic residues are conserved with respect to the RNase A superfamily. The three disulfide bridges observed in the reptilian enzymes are conserved in GTRNase, while one further disulfide bond is required for the structural stability of mammalian RNases. GTRNase is expressed in egg white and the fact that its sequence has the highest similarity to that of snapping turtle pancreatic RNase suggests that the GTRNase secreted from oviduct cells to form egg white is probably the product of the same gene as activated in pancreatic cells. [source] | ||||||||||