- Record: found
- Abstract: found
- Article: found
ClpP protease activation results from the reorganization of the electrostatic interaction networks at the entrance pores
research-article
Author(s):
Mark F. Mabanglo
1 ,
Elisa Leung
1 ,
Siavash Vahidi
1
,
2
,
3
,
4 ,
Thiago V. Seraphim
1
,
5 ,
Bryan T. Eger
1 ,
Steve Bryson
1
,
6 ,
Vaibhav Bhandari
1 ,
Jin Lin Zhou
3 ,
Yu-Qian Mao
1 ,
Kamran Rizzolo
1 ,
Marim M. Barghash
1 ,
Jordan D. Goodreid
3 ,
Sadhna Phanse
1
,
5 ,
Mohan Babu
5 ,
Leandro R. S. Barbosa
7 ,
Carlos H. I. Ramos
8 ,
Robert A. Batey
3 ,
Lewis E. Kay
1
,
2
,
3
,
4 ,
Emil F. Pai
1
,
2
,
6
,
9 ,
Walid A. Houry
1
,
3
,
Publication date (Electronic):
13 November 2019
Journal:
Communications Biology
Publisher:
Nature Publishing Group UK
Read this article at
There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.
Abstract
Bacterial ClpP is a highly conserved, cylindrical, self-compartmentalizing serine protease required for maintaining cellular proteostasis. Small molecule acyldepsipeptides (ADEPs) and activators of self-compartmentalized proteases 1 (ACP1s) cause dysregulation and activation of ClpP, leading to bacterial cell death, highlighting their potential use as novel antibiotics. Structural changes in Neisseria meningitidis and Escherichia coli ClpP upon binding to novel ACP1 and ADEP analogs were probed by X-ray crystallography, methyl-TROSY NMR, and small angle X-ray scattering. ACP1 and ADEP induce distinct conformational changes in the ClpP structure. However, reorganization of electrostatic interaction networks at the ClpP entrance pores is necessary and sufficient for activation. Further activation is achieved by formation of ordered N-terminal axial loops and reduction in the structural heterogeneity of the ClpP cylinder. Activating mutations recapitulate the structural effects of small molecule activator binding. Our data, together with previous findings, provide a structural basis for a unified mechanism of compound-based ClpP activation.
Abstract
Mabanglo, Leung, Vahidi, Seraphim et al. examine the structural changes to ClpP from Neisseria meningitidis and Escherichia coli upon binding to two novel activators. They show that reorganization of the electrostatic interaction networks at the ClpP entrance pores is needed for activation.
Related collections
Most cited references35
- Record: found
- Abstract: found
- Article: not found
An introduction to data reduction: space-group determination, scaling and intensity statistics
Philip R Evans, Piyush Kalakoti (2011)
1. Introduction Estimates of integrated intensities from X-ray diffraction images are not generally suitable for immediate use in structure determination. Theoretically, the measured intensity I h of a reflection h is proportional to the square of the underlying structure factor |F h |2, which is the quantity that we want, with an associated measurement error, but systematic effects of the diffraction experiment break this proportionality. Such systematic effects include changes in the beam intensity, changes in the exposed volume of the crystal, radiation damage, bad areas of the detector and physical obstruction of the detector (e.g. by the backstop or cryostream). If data from different crystals (or different sweeps of the same crystal) are being merged, corrections must also be applied for changes in exposure time and rotation rate. In order to infer |F h |2 from I h , we need to put the measured intensities on the same scale by modelling the experiment and inverting its effects. This is generally performed in a scaling process that makes the data internally consistent by adjusting the scaling model to minimize the difference between symmetry-related observations. This process requires us to know the point-group symmetry of the diffraction pattern, so we need to determine this symmetry prior to scaling. The scaling process produces an estimate of the intensity of each unique reflection by averaging over all of the corrected intensities, together with an estimate of its error σ(I h ). The final stage in data reduction is estimation of the structure amplitude |F h | from the intensity, which is approximately I h 1/2 (but with a skewing factor for intensities that are below or close to background noise, e.g. ‘negative’ intensities); at the same time, the intensity statistics can be examined to detect pathologies such as twinning. This paper presents a brief overview of how to run CCP4 programs for data reduction through the CCP4 graphical interface ccp4i and points out some issues that need to be considered. No attempt is made to be comprehensive nor to provide full references for everything. Automated pipelines such as xia2 (Winter, 2010 ▶) are often useful and generally work well, but sometimes in difficult cases finer control is needed. In the current version of ccp4i (CCP4 release 6.1.3) the ‘Data Reduction’ module contains two major relevant tasks: ‘Find or Match Laue Group’, which determines the crystal symmetry, and ‘Scale and Merge Intensities’, which outputs a file containing averaged structure amplitudes. Future GUI versions may combine these steps into a simplified interface. Much of the advice given here is also present in the CCP4 wiki (http://www.ccp4wiki.org/). 2. Space-group determination The true space group is only a hypothesis until the structure has been solved, since it can be hard to distinguish between exact crystallographic symmetry and approximate noncrystallographic symmetry. However, it is useful to find the likely symmetry early on in the structure-determination pipeline, since it is required for scaling and indeed may affect the data-collection strategy. The program POINTLESS (Evans, 2006 ▶) examines the symmetry of the diffraction pattern and scores the possible crystallographic symmetry. Indexing in the integration program (e.g. MOSFLM) only indicates the lattice symmetry, i.e. the geometry of the lattice giving constraints on the cell dimensions (e.g. α = β = γ = 90° for an orthorhombic lattice), but such relationships can arise accidentally and may not reflect the true symmetry. For example, a primitive hexagonal lattice may belong to point groups 3, 321, 312, 6, 622 or indeed lower symmetry (C222, 2 or 1). A rotational axis of symmetry produces identical true intensities for reflections related by that axis, so examination of the observed symmetry in the diffraction pattern allows us to determine the likely point group and hence the Laue group (a point group with added Friedel symmetry) and the Patterson group (with any lattice centring): note that the Patterson group is labelled ‘Laue group’ in the output from POINTLESS. Translational symmetry operators that define the space group (e.g. the distinction between a pure dyad and a screw dyad) are only visible in the observed diffraction pattern as systematic absences, along the principal axes for screws, and these are less reliable indicators since there are relatively few axial reflections in a full three-dimensional data set and some of these may be unrecorded. The protocol for determination of space group in POINTLESS is as follows. (i) From the unit-cell dimensions and lattice centring, find the highest compatible lattice symmetry within some tolerance, ignoring any input symmetry information. (ii) Score each potential rotational symmetry element belonging to the lattice symmetry using all pairs of observations related by that element. (iii) Score combinations of symmetry elements for all possible subgroups of the lattice-symmetry group (Laue or Patterson groups). (iv) Score possible space groups from axial systematic absences (the space group is not needed for scaling but is required later for structure solution). (v) Scores for rotational symmetry operations are based on correlation coefficients rather than R factors, since they are less dependent on the unknown scales. A probability is estimated from the correlation coefficient, using equivalent-size samples of unrelated observations to estimate the width of the probability distribution (see Appendix A ). 2.1. A simple example POINTLESS may be run from the ‘Data Reduction’ module of ccp4i with the task ‘Find or Match Laue Group’ or from the ‘QuickSymm’ option of the iMOSFLM interface (Battye et al., 2011 ▶). Unless the space group is known from previous crystals, the appropriate major option is ‘Determine Laue group’. To use this, fill in the boxes for the title, the input and output file names and the project, crystal and data-set names (if not already set in MOSFLM). Table 1 ▶ shows the results for a straightforward example in space group P212121. Table 1 ▶(a) shows the scores for the three possible dyad axes in the orthorhombic lattice, all of which are clearly present. Combining these (Table 1 ▶ b) shows that the Laue group is mmm with a primitive lattice, Patterson group Pmmm. Fourier analysis of systematic absences along the three principal axes shows that all three have alternating strong (even) and weak (odd) intensities (Fig. 1 ▶ and Table 1 ▶ c), so are likely to be screw axes, implying that the space group is P212121. However, there are only three h00 reflections recorded along the a* axis, so confidence in the space-group assignment is not as high as the confidence in the Laue-group assignment (Table 1 ▶ d). With so few observations along this axis, it is impossible to be confident that P212121 is the true space group rather than P22121. 2.2. A pseudo-cubic example Table 2 ▶ shows the scores for individual symmetry elements for a pseudo-cubic case with a ≃ b ≃ c. It is clear that only the orthorhombic symmetry elements are present: these are the high-scoring elements marked ‘***’. Neither the fourfolds characteristic of tetragonal groups nor the body-diagonal threefolds (along 111 etc.) characteristic of cubic groups are present. The joint probability score for the Laue group Pmmm is 0.989. The suggested solution (not shown) interchanges k and l to make a 1 if the anomalous differences are on average greater than their error. Another way of detecting a significant anomalous signal is to compare the two estimates of ΔI anom from random half data sets, ΔI 1 and ΔI 2 (provided there are at least two measurements of each, i.e. a multiplicity of roughly 4). Figs. 5 ▶(b) and 5 ▶(f) show the correlation coefficient between ΔI 1 and ΔI 2 as a function of resolution: Fig. 5 ▶(f) shows little statistically significance beyond about 4.5 Å resolution. Figs. 5 ▶(c) and 5 ▶(g) show scatter plots of ΔI 1 against ΔI 2: this plot is elongated along the diagonal if there is a large anomalous signal and this can be quantitated as the ‘r.m.s. correlation ratio’, which is defined as (root-mean-square deviation along the diagonal)/(root-mean-square deviation perpendicular to the diagonal) and is shown as a function of resolution in Figs. 5 ▶(d) and 5 ▶(h). The plots against resolution give a suggestion of where the data might be cut for substructure determination, but it is important to note that useful albeit weak phase information extends well beyond the point at which these statistics show a significant signal. 5. Estimation of amplitude |F| from intensity I If we knew the true intensity J we could just take the square root, |F| = J 1/2. However, measured intensities have an error, so a weak intensity may well be measured as negative (i.e. below background); indeed, multiple measurements of a true intensity of zero should be equally positive and negative. This is one reason why when possible it is better to use I rather than |F| in structure determination and refinement. The ‘best’ (most likely) estimate of |F| is larger than I 1/2 for weak intensities, since we know |F| > 0, but |F| = I 1/2 is a good estimate for stronger intensities, roughly those with I > 3σ(I). The programs TRUNCATE and its newer version CTRUNCATE estimate |F| from I and σ(I) as where the prior probability of the true intensity p(J) is estimated from the average intensity in the same resolution range (French & Wilson, 1978 ▶). 6. Intensity statistics and crystal pathologies At the end stage of data reduction, after scaling and merging, the distribution of intensities and its variation with resolution can indicate problems with the data, notably twinning (see, for example, Lebedev et al., 2006 ▶; Zwart et al., 2008 ▶). The simplest expected intensity statistics as a function of resolution s = sinθ/λ arise from assuming that atoms are randomly placed in the unit cell, in which case 〈I〉(s) = 〈FF*〉(s) = g(j, s)2, where g(j, s) is the scattering from the jth atom at resolution s. This average intensity falls off with resolution mainly because of atomic motions (B factors). If all atoms were equal and had equal B factors, then 〈I〉(s) = Cexp(−2Bs 2) and the ‘Wilson plot’ of log[〈I〉(s)] against s 2 would be a straight line of slope −2B. The Wilson plot for proteins shows peaks at ∼10 and 4 Å and a dip at ∼6 Å arising from the distribution of interatomic spacings in polypeptides (fewer atoms 6 Å apart than 4 Å apart), but the slope at higher resolution does give an indication of the average B factor and an unusual shape can indicate a problem (e.g. 〈I〉 increasing at the outer limit, spuriously large 〈I〉 owing to ice rings etc.). For detection of crystal pathologies we are not so interested in resolution dependence, so we can use normalized intensities Z = I/〈I〉(s) ≃ |E|2 which are independent of resolution and should ideally be corrected for anisotropy (as is performed in CTRUNCATE). Two useful statistics on Z are plotted by CTRUNCATE: the moments of Z as a function of resolution and its cumulative distribution. While 〈Z〉(s) = 1.0 by definition, its second moment 〈Z 2〉(s) (equivalent to the fourth moment of E) is >1.0 and is larger if the distribution of Z is wider. The ideal value of 〈E 4〉 is 2.0, but it will be smaller for the narrower intensity distribution from a merohedral twin (too few weak reflections), equal to 1.5 for a perfect twin and larger if there are too many weak reflections, e.g. from a noncrystallographic translation which leads to a whole class of reflections being weak. The cumulative distribution plot of N(z), the fraction of reflections with Z |L| and N(|L|) = |L|(3 − L 2)/2 for a perfect twin. This test seems to be largely unaffected by anisotropy or translational noncrystallographic symmetry which may affect tests on Z. The calculation of Z = I/〈I〉(s) depends on using a suitable value for I/〈I〉(s) and noncrystallographic translations or uncorrected anisotropy lead to the use of an inappropriate value for 〈I〉(s). These statistical tests are all unweighted, so it may be better to exclude weak high-resolution data or to examine the resolution dependence of, for example, the moments of Z (or possibly L). It is also worth noting that fewer weak reflections than expected may arise from unresolved closely spaced spots along a long real-space axis, so that weak reflections are contaminated by neighbouring strong reflections, thus mimicking the effect of twinning. 7. Summary: questions and decisions In the process of data reduction, a number of decisions need to be taken either by the programs or by the user. The main questions and considerations are as follows. (i) What is the point group or Laue group? This is usually unambiguous, but pseudosymmetry may confuse the programs and the user. Close examination of the scores for individual symmetry elements from POINTLESS may suggest lower symmetry groups to try. (ii) What is the space group? Distinction between screw axes and pure rotations from axial systematic absences is often unreliable and it is generally a good idea to try all the likely space groups (consistent with the Laue group) in the key structure-solution step: either molecular-replacement searches or substructure searches in experimental phasing. For example, in a primitive orthorhombic system the eight possible groups P2 x 2 x 2 x should be tried. This has the added advantage of providing some negative controls on the success of the structure solution. (iii) Is there radiation damage: should data collected after the crystal has had a high dose of radiation be ignored (possibly at the expense of resolution)? Cutting back data from the end may reduce completeness and the optimum trade-off is hard to choose. (iv) What is the best resolution cutoff? An appropriate choice of resolution cutoff is difficult and sometimes seems to be performed mainly to satisfy referees. On the one hand, cutting back too far risks excluding data that do contain some useful information. On the other hand, extending the resolution further makes all statistics look worse and may in the end degrade maps. The choice is perhaps not as important as is sometimes thought: maps calculated with slightly different resolution cutoffs are almost indistinguishable. (v) Is there an anomalous signal detectable in the intensity statistics? Note that a weak anomalous signal may still be useful even if it is not detectable in the statistics. The statistics do give a good guide to a suitable resolution limit for location of the substructure, but the whole resolution range should be used in phasing. (vi) Are the data twinned? Highly twinned data sets can be solved by molecular replacement and refined, but probably not solved, by experimental phasing methods. Partially twinned data sets can often be solved by ignoring the twinning and then refined as a twin. (vii) Is this data set better or worse than those previously collected? One of the best things to do with a bad data set is to throw it away in favour of a better one. With modern synchrotrons, data collection is so fast that we usually have the freedom to collect data from several equivalent crystals and choose the best. In most cases the data-reduction process is straightforward, but in difficult cases critical examination of the results may make the difference between solving and not solving the structure.
- Record: found
- Abstract: found
- Article: found
ShelXle: a Qt graphical user interface for SHELXL
1. Introduction The SHELX programs as originally developed in the 1970s were intended for use with photographic intensity data, punched cards and computers multiple orders of mangitude slower than even the most basic models on the market today (Sheldrick, 2008 ▶). In the early days of SHELX, a crystal structure refinement usually involved examining a lineprinter output – i.e. drawing lines between the numbers to create a ‘picture’ of the structure – followed by editing a few of the input and output cards with a card-punch and combining the cards to create the input deck for the next refinement job, which usually ran overnight. The way crystal structure determinations are performed today is clearly different, but – somewhat surprisingly – SHELXL is still used in most small-molecule structure refinements. More recently, a number of excellent graphical user interfaces (GUIs) [e.g. WINGX (Farrugia, 1999 ▶), OLEX2 (Dolomanov et al., 2009 ▶), XSEED (Barbour, 2001 ▶), PLATON and SYSTEM-S (Spek, 2009 ▶), and the Bruker programs XP (Nicolet, 1981 ▶) and XSHELL (Bruker, 2000 ▶)] have been developed to facilitate structure refinement with SHELXL as the underlying program, but in general the punched-card way of thinking that was central to the design of SHELXL has proven awkward to integrate into a modern interactive computer-graphics environment without losing at least some of the unique capabilities of the original program. Despite the availability of a very informative International Union of Crystallography monograph (Müller et al., 2006 ▶) describing the application of SHELXL, we felt that there was still a need for a simple, intuitive and robust GUI that uses state-of-the-art programming techniques but retains as much as possible of the original SHELX flavour and capabilities. For this purpose, ShelXle was developed. ShelXle shares some concepts with earlier programs, such as MoleCoolQt (Hübschle & Dittrich, 2011 ▶), but most of the code was rewritten. 2. Technical description and functionality ShelXle opens a SHELX-format .res file from a structure solution program or a SHELXL refinement. The .ins/.res file in SHELX format is shown in an interactive editor window (on the right side of the graphical interface) and (on the left side) the mono or stereo visualization of the three-dimensional structure is displayed. The display and editor are strongly coupled. The editor uses colour highlighting to identify the currently chosen atom and also possible syntax errors. Clicking on an atom in the displayed structure moves the text cursor to the corresponding atom in the editor. An atom can also be selected by right clicking on a line in the editor containing an atom, which is then centred in the display. The GUI is controlled by menus and toolbars; command-line input is neither required nor implemented. Fig. 1 ▶ gives a general impression of the appearance and functionality of ShelXle. ShelXle is written entirely in C++ using the Qt4 (http://qt.nokia.com/products/) and the FFTW (http://www.fftw.org/) libraries, and so is able to exploit the latest developments in computer graphics as well as being highly portable. 2.1. Electron density maps If the previous SHELXL refinement used the ‘LIST 6’ instruction, F o and F o–F c maps are calculated and visualized as mesh-style isosurfaces. The colour scheme used is the same as in the program COOT (Emsley et al., 2010 ▶). The isocontour level of such maps can be controlled by using either the mouse wheel or a dialogue window. The contour level of the difference map may be changed with the mouse wheel while pressing the control key (or the command key under Mac-OS), and the contour level of the F o map is changed in the same way but using the shift key. Initial isocontour levels are 2.7σ for the F o–F c map and 1.2σ for the F o map, where σ is the square root of the average variance of the density. These maps are in principle infinite in all directions, but the region displayed is restricted by clipping planes perpendicular to the viewing direction. If deemed desirable, in order to simplify the view, it is possible to display only density within 1.41 Å ( ) of any visible atom or ‘Q peak’ (difference electron density peak from SHELXL). It may sometimes occur that the parameters of the SHELXL PLAN instruction are not sufficient to generate a Q peak at a desired position, for example when dominant heavy atoms are present. In such cases ShelXle can generate further Q peaks by searching for peaks in the F o–F c residual density that are higher than the current isosurface value. 2.2. Special handling of difference electron density maxima (‘Q peaks’) Q peaks are visualized as small colour-coded icosahedra. The colour of a Q peak corresponds to the peak height. A separate Q-peak list shows the correspondence between colours and peak heights. By moving the mouse over this list, labels of Q peaks with the same peak height are highlighted. If the mouse pointer hovers over a Q peak, the region representing its height is highlighted in the list. Q peaks below a certain threshold may be hidden temporarily by clicking on the Q-peak list. Once some of the Q peaks have been hidden in this way, the cutoff value can be adjusted by scrolling with the mouse wheel while the mouse pointer is over the list. 2.3. Adding H atoms The ‘add H atoms’ function in ShelXle places hydrogen atoms automatically by generating the corresponding AFIX instructions in the file being edited. If the F o–F c map is available, the difference electron density may be used to find optimal positions for H atoms in CH3 groups in a similar manner to the way in which the ‘HFIX 137’ command in SHELXL operates. As methyl groups are often disordered, there is a facility to place six H atoms in idealized positions and to refine an occupancy parameter to describe the disorder using one additional free variable that is generated automatically. Fig. 2 ▶ illustrates the usefulness of the difference electron density in placing the H atoms correctly. 2.4. The editor: syntax highlighting and codeword completion One of the core functionalities of ShelXle is the editor and its ability to perform syntax highlighting. All known SHELXL commands are highlighted in the same way (dark red over light green). Permanent comments (REM cards or following ‘!’) are coloured in blue, while temporary comments (lines beginning with a space when the line before does not end with ‘ = ’) are coloured dark blue and are underlined. Lines longer than 80 characters are flagged by a red background colour, since characters after column 80 (not compatible with punched cards) are ignored by SHELXL. After the first one or two characters of a new line have been entered, a code-completer function opens, suggesting commands beginning with the given letters. Accepting a suggestion by striking the ‘enter’ key inserts the command in capital letters (whether or not they were entered in upper case). Care is taken to keep track of the ‘free variables’, a defining feature of SHELXL. When a number in the editor window implicitly references a free variable and the mouse pointer hovers over it for several seconds, a popup window appears with the interpretation. Analogously, a brief description of each SHELXL command is given when the mouse is placed over a line starting with a command. If lines containing atoms are selected in the editor, right clicking in the selected area in the editor achieves atom selection. The editor is also equipped with a ‘search and replace’ tool that highlights matches in the editor in yellow. Entire parts (‘PART’) and residues (‘RESI’) can also be selected. This function allows the selection of disordered PARTs, either separately or in combination with the ordered PART. Unselected atoms can optionally be hidden. A residue may also be selected using a residue list. In addition, facilities are provided for rearranging the windows. When desired, or prior to performing a refinement, the three-dimensional display and the editor are synchronized and the editor contents are saved. More esoteric SHELXL instructions – e.g. FRAG…FEND or the third number on the L.S. command – can easily be added using the editor. 2.5. Refinement history facility Like OLEX2 (Dolomanov et al., 2009 ▶), ShelXle is equipped with a refinement history, where every refinement step is saved and represented within the GUI by a bar. The colour and height of the bar symbolize the R value of each refinement step. By left clicking on a bar, a particular refinement step can be loaded into the editor and displayed graphically. In this way users can go back to a previous refinement step, which can be useful if the refinement becomes unstable or the strategy employed proved to be a dead end. The refinement history can be pruned or a preview can be displayed by right clicking. In addition to the refinement history, ShelXle stores a backup each time the editor contents are saved. One of these backup versions can be selected in a dialogue window; this dialogue also contains a preview, where every line that is different from the current version of the file is highlighted in dark orange. All history files are stored in a subdirectory called ‘shelXlesaves’, which is placed in the directory where the structure file is located. ShelXle does not generate hidden or write-protected files or directories. 2.6. The information window All text output is collected and displayed in the information window. Hydrogen bonds found in the structure are tabulated. The contents of this window are stored internally as HTML; any part of it can easily be marked, copied and pasted to word-processing programs. Distances, angles, torsion angles and the differences of mean-square displacement amplitudes (DMSDAs; Hirshfeld, 1976 ▶; Rosenfield et al., 1978 ▶) may be displayed in the information window. Where appropriate, crystallographic symmetry operators are displayed. Values of free variables and how often they are used can also be found in the information window, as can statistical details of the electron density maps. 2.7. Labelling and renaming atoms When ‘rename mode’ is selected, a popup window displays the element type, a numerical index and a suffix. By clicking on an atom or a Q peak, these values are applied to that atom and the numerical index is increased by one. It is also possible to use this mode to set PART numbers, residue numbers and residue names. When PART numbers not equal to zero are applied, there is an option to tie the occupancy to a free variable (or to one minus the free variable). If the free variable is not yet defined, it is generated and inserted into the FVAR instruction. The original atom record is retained as a temporary comment. If an existing atom has the same combination of atom name, PART and RESI number, the colour of the new atom name changes to red to warn the user; when the combination is unique the atom name is green. The user is allowed to create duplicate atoms but should resolve such SHELXL incompatibilities before starting the next refinement. When there is more than one chemically identical molecule in the asymmetric unit, ShelXle provides an option to label subsequent molecules in the same way as the first. Each identical molecule is assigned a different residue number. This is achieved in a semi-automated manner in which the user can assign atoms of the target molecule to be equivalent to specified atoms of the source molecule a ‘drag and drop’ dialogue. Fig. 3 ▶ illustrates the way in which a disordered ‘PART -1’ molecule lying close to a symmetry element is displayed. 2.8. Other convenient functions The built-in editor gives the user full control over the SHELXL input file. This means that more advanced SHELXL commands can be added directly. Nevertheless, many tasks in routine structure refinement can be repetitive and time consuming, so ShelXle provides the functionality to expedite some of them. Examples are applying the suggested weighting scheme or updating the cell contents in the UNIT instruction to make it consistent with the atom list. After all necessary changes have been made, selecting the appropriate menu option or pressing the function key ‘F2’ causes the currently edited .res file to be saved as a .ins file and a SHELXL refinement job to be started. The refinement can be followed in an output window, with important items highlighted to improve readability. On completion of the refinement the user can choose between updating the editor window or discarding the results; updating is blocked to prevent accidents if a critical error has occurred in the refinement. Sometimes it happens that molecules lie outside the primary unit cell with , , . Often this is first noticed on checking the refinement results with checkCIF (http://checkcif.iucr.org). Optionally ShelXle applies an algorithm to move the centre of gravity of each molecule into the primary unit cell, whilst ensuring that the molecules are as close as possible to each other. It is also possible to call additional programs from within ShelXle, e.g. PLATON (Spek, 2009 ▶) to perform diagnostics before the refinement is completed or to make ORTEP (Johnson & Burnett, 1996 ▶) style plots etc. as an alternative to the screenshot provided by ShelXle. 3. Program availability ShelXle is available at no cost for most modern Windows, Linux and Mac-OS X systems. For details on how to obtain ShelXle, see http://www.moliso.de/shelxle/.
- Record: found
- Abstract: found
- Article: not found
Prediction of hydrodynamic and other solution properties of rigid proteins from atomic- and residue-level models.
A. Ortega, D Amorós, J García de la Torre (2011)
Here we extend the ability to predict hydrodynamic coefficients and other solution properties of rigid macromolecular structures from atomic-level structures, implemented in the computer program HYDROPRO, to models with lower, residue-level resolution. Whereas in the former case there is one bead per nonhydrogen atom, the latter contains one bead per amino acid (or nucleotide) residue, thus allowing calculations when atomic resolution is not available or coarse-grained models are preferred. We parameterized the effective hydrodynamic radius of the elements in the atomic- and residue-level models using a very large set of experimental data for translational and rotational coefficients (intrinsic viscosity and radius of gyration) for >50 proteins. We also extended the calculations to very large proteins and macromolecular complexes, such as the whole 70S ribosome. We show that with proper parameterization, the two levels of resolution yield similar and rather good agreement with experimental data. The new version of HYDROPRO, in addition to considering various computational and modeling schemes, is far more efficient computationally and can be handled with the use of a graphical interface. Copyright © 2011 Biophysical Society. Published by Elsevier Inc. All rights reserved.
Author and article information
Contributors
Walid A. Houry:
ORCID: http://orcid.org/0000-0002-1861-3441
walid.houry@utoronto.ca
Journal
Journal ID (nlm-ta): Commun Biol
Journal ID (iso-abbrev): Commun Biol
Title:
Communications Biology
Publisher:
Nature Publishing Group UK
(London
)
ISSN
(Electronic):
2399-3642
Publication date
(Electronic):
13
November
2019
Publication date PMC-release: 13
November
2019
Publication date Collection: 2019
Volume: 2
Electronic Location Identifier: 410
Affiliations
[1
]ISNI 0000 0001 2157 2938, GRID grid.17063.33, Department of Biochemistry, , University of Toronto, ; Toronto, Ontario M5G 1M1 Canada
[2
]ISNI 0000 0001 2157 2938, GRID grid.17063.33, Department of Molecular Genetics, , University of Toronto, ; Toronto, Ontario M5S 1A8 Canada
[3
]ISNI 0000 0001 2157 2938, GRID grid.17063.33, Department of Chemistry, , University of Toronto, ; Toronto, Ontario M5S 3H6 Canada
[4
]ISNI 0000 0004 0473 9646, GRID grid.42327.30, Program in Molecular Medicine, The Hospital for Sick Children Research Institute,
; Toronto, Ontario M5G 0A4 Canada
[5
]ISNI 0000 0004 1936 9131, GRID grid.57926.3f, Department of Biochemistry, , University of Regina, ; Regina, Saskatchewan S4S 0A2 Canada
[6
]ISNI 0000 0001 2150 066X, GRID grid.415224.4, Ontario Cancer Institute/Princess Margaret Hospital, Campbell Family Institute for
Cancer Research, ; Toronto, Ontario M5G 1L7 Canada
[7
]ISNI 0000 0004 1937 0722, GRID grid.11899.38, Institute of Physics, , University of São Paulo, ; São Paulo SP, 05508-090 Brazil
Author information
Leandro R. S. Barbosa
http://orcid.org/0000-0001-5997-2160
Walid A. Houry
http://orcid.org/0000-0002-1861-3441
Article
Publisher ID: 656DOI: 10.1038/s42003-019-0656-3
PMC ID: 6853987
PubMed ID: 30701199
SO-VID: 2de35ae9-e152-4b0c-a3a2-4eeeda2496bd
Copyright © © The Author(s) 2019
License:
Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
History
Date
received
: 13
May
2019
Date
accepted
: 17
October
2019
Funding
Funded by: FundRef https://doi.org/10.13039/501100000024, Gouvernement du Canada | Canadian Institutes of Health Research (Instituts de Recherche
en Santé du Canada);
Award ID: PJT-148564
Award ID: XNE-86945
Award Recipient
:
Walid A. Houry
Funded by: FundRef https://doi.org/10.13039/501100000038, Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada
(Conseil de Recherches en Sciences Naturelles et en Génie du Canada);
Award ID: RGPIN-2015- 04877
Award Recipient
:
Walid A. Houry
Categories
Subject:
Article
Custom metadata
issue-copyright-statement © The Author(s) 2018
Data availability:
Comments
Comment on this article
scite_
0
0
0
0
Smart Citations0
0
0
0
Citing PublicationsSupportingMentioningContrasting
See how this article has been cited at scite.ai
scite shows how a scientific paper has been cited by providing the context of the citation, a classification describing whether it supports, mentions, or contrasts the cited claim, and a label indicating in which section the citation was made.