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Atomic Models (atomic + models)
Selected AbstractsA software system for rigid-body modelling of solution scattering dataJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 3-1 2000M.B. Kozin A computer system for rigid body modelling against solution scattering data is described. Fast algorithms to compute scattering from a complex of two arbitrary positioned subunits are implemented and coupled with the graphics program ASSA (Kozin, Volkov & Svergun, 1997, J. Appl. Cryst.30, 811-815). Mutual positions and orientations of the subunits (represented by low-resolution envelopes or by atomic models) can be determined by interactively fitting the experimental scattering curve from the complex. The system runs on the major Unix platforms (SUN, SGI and DEC workstations). [source] Dynamical view of membrane binding and complex formation of human factor VIIa and tissue factorJOURNAL OF THROMBOSIS AND HAEMOSTASIS, Issue 5 2010Y. Z. OHKUBO Summary.,Background:,The molecular mechanism of enhancement of the enzymatic activity of factor VIIa by tissue factor (TF) is not fully understood, primarily because of the lack of atomic models for the membrane-bound form of the TF,FVIIa complex. Objectives:,To construct the first membrane-bound model of the TF,FVIIa complex, and to investigate the dynamics of the complex in solution and on the surface of anionic membranes by using large-scale molecular dynamics (MD) simulations in full atomic detail. Methods:,Membrane-bound models of the TF,FVIIa complex and the individual factors were constructed and subjected to MD simulations, in order to characterize protein,protein and protein,lipid interactions, and to investigate the dynamics of TF and FVIIa. Results:,The MD trajectories reveal that isolated FVIIa undergoes large structural fluctuation, primarily due to the hinge motions between its domains, whereas soluble TF (sTF) is structurally stable. Upon complex formation, sTF restricts the motion of FVIIa significantly. The results also show that, in the membrane-bound form, sTF directly interacts with the lipid headgroups, even in the absence of FVIIa. Conclusion:,The first atomic models of membrane-bound sTF,FVIIa, FVIIa and sTF are presented, revealing that sTF forms direct contacts with the lipids, both in the isolated form and in complex with FVIIa. The main effect of sTF binding to FVIIa is spatial stabilization of the catalytic site of FVIIa, which ensures optimal interaction with the substrate, FX. [source] Inclusion of weak high-resolution X-ray data for improvement of a group II intron structureACTA CRYSTALLOGRAPHICA SECTION D, Issue 9 2010Jimin Wang It is common to report the resolution of a macromolecular structure with the highest resolution shell having an averaged I/,(I) , 2. Data beyond the resolution thus defined are weak and often poorly measured. The exclusion of these weak data may improve the apparent statistics and also leads to claims of lower resolutions that give some leniency in the acceptable quality of refined models. However, the inclusion of these data can provide additional strong constraints on atomic models during structure refinement and thus help to correct errors in the original models, as has recently been demonstrated for a protein structure. Here, an improved group II intron structure is reported arising from the inclusion of these data, which helped to define more accurate solvent models for density modification during experimental phasing steps. With the improved resolution and accuracy of the experimental phases, extensive revisions were made to the original models such that the correct tertiary interactions of the group II intron that are essential for understanding the chemistry of this ribozyme could be described. [source] Features and development of CootACTA CRYSTALLOGRAPHICA SECTION D, Issue 4 2010P. Emsley Coot is a molecular-graphics application for model building and validation of biological macromolecules. The program displays electron-density maps and atomic models and allows model manipulations such as idealization, real-space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers and Ramachandran idealization. Furthermore, tools are provided for model validation as well as interfaces to external programs for refinement, validation and graphics. The software is designed to be easy to learn for novice users, which is achieved by ensuring that tools for common tasks are `discoverable' through familiar user-interface elements (menus and toolbars) or by intuitive behaviour (mouse controls). Recent developments have focused on providing tools for expert users, with customisable key bindings, extensions and an extensive scripting interface. The software is under rapid development, but has already achieved very widespread use within the crystallographic community. The current state of the software is presented, with a description of the facilities available and of some of the underlying methods employed. [source] UROX 2.0: an interactive tool for fitting atomic models into electron-microscopy reconstructionsACTA CRYSTALLOGRAPHICA SECTION D, Issue 7 2009Xavier Siebert Electron microscopy of a macromolecular structure can lead to three-dimensional reconstructions with resolutions that are typically in the 30,10,Å range and sometimes even beyond 10,Å. Fitting atomic models of the individual components of the macromolecular structure (e.g. those obtained by X-ray crystallography or nuclear magnetic resonance) into an electron-microscopy map allows the interpretation of the latter at near-atomic resolution, providing insight into the interactions between the components. Graphical software is presented that was designed for the interactive fitting and refinement of atomic models into electron-microscopy reconstructions. Several characteristics enable it to be applied over a wide range of cases and resolutions. Firstly, calculations are performed in reciprocal space, which results in fast algorithms. This allows the entire reconstruction (or at least a sizeable portion of it) to be used by taking into account the symmetry of the reconstruction both in the calculations and in the graphical display. Secondly, atomic models can be placed graphically in the map while the correlation between the model-based electron density and the electron-microscopy reconstruction is computed and displayed in real time. The positions and orientations of the models are refined by a least-squares minimization. Thirdly, normal-mode calculations can be used to simulate conformational changes between the atomic model of an individual component and its corresponding density within a macromolecular complex determined by electron microscopy. These features are illustrated using three practical cases with different symmetries and resolutions. The software, together with examples and user instructions, is available free of charge at http://mem.ibs.fr/UROX/. [source] Confidence intervals for fitting of atomic models into low-resolution densitiesACTA CRYSTALLOGRAPHICA SECTION D, Issue 7 2009Niels Volkmann The fitting of high-resolution structures into low-resolution densities obtained from techniques such as electron microscopy or small-angle X-ray scattering can yield powerful new insights. While several algorithms for achieving optimal fits have recently been developed, relatively little effort has been devoted to developing objective measures for judging the quality of the resulting fits, in particular with regard to the danger of overfitting. Here, a general method is presented for obtaining confidence intervals for atomic coordinates resulting from fitting of atomic resolution domain structures into low-resolution densities using well established statistical tools. It is demonstrated that the resulting confidence intervals are sufficiently accurate to allow meaningful statistical tests and to provide tools for detecting potential overfitting. [source] Fitting atomic models into electron-microscopy mapsACTA CRYSTALLOGRAPHICA SECTION D, Issue 10 2000Michael G. Rossmann Combining X-ray crystallographically determined atomic structures of component domains or subunits with cryo-electron microscopic three-dimensional images at around 22,Å resolution can produce structural information that is accurate to about 2.2,Å resolution. In an initial step, it is necessary to determine accurately the absolute scale and absolute hand of the cryo-electron microscopy map, the former of which can be off by up to 5%. It is also necessary to determine the relative height of density by using a suitable scaling function. Difference maps can identify, for instance, sites of glycosylation, the position of which helps to fit the component structures into the EM density maps. Examples are given from the analysis of alphaviruses, rhinovirus,receptor interactions and poliovirus,receptor interactions. [source] | ||||||||||