Towards the automatic crystal structure solution of nucleic acids: automated model building using the new CAB program

2021 ◽  
Vol 77 (12) ◽  
Author(s):  
Giovanni Luca Cascarano ◽  
Carmelo Giacovazzo
Keyword(s):  
Nucleic Acids ◽  
Prior Information ◽  
Model Building ◽  
Phase Error ◽  
Heavy Atoms ◽  
Density Maps ◽  
Structure Solution ◽  
Nucleic Acid Structures ◽  
Automated Model Building ◽  
Model Chain

CAB, a recently described automated model-building (AMB) program, has been modified to work effectively with nucleic acids. To this end, several new algorithms have been introduced and the libraries have been updated. To reduce the input average phase error, ligand heavy atoms are now located before starting the CAB interpretation of the electron-density maps. Furthermore, alternative approaches are used depending on whether the ligands belong to the target or to the model chain used in the molecular-replacement step. Robust criteria are then applied to decide whether the AMB model is acceptable or whether it must be modified to fit prior information on the target structure. In the latter case, the model chains are rearranged to fit prior information on the target chains. Here, the performance of the new AMB program CAB applied to various nucleic acid structures is discussed. Other well documented programs such as Nautilus, ARP/wARP and phenix.autobuild were also applied and the experimental results are described.

scholarly journals Automated nucleic acid chain tracing in real time

IUCrJ ◽  
2014 ◽  
Vol 1 (6) ◽  
pp. 387-392 ◽  
Author(s):  
Kevin Cowtan
Keyword(s):  
Electron Density ◽  
Model Building ◽  
Protein Structures ◽  
Current View ◽  
Crystallographic Structure ◽  
Large Structures ◽  
Density Maps ◽  
Structure Solution ◽  
Automated Model Building ◽  
Electron Density Map

The crystallographic structure solution of nucleotides and nucleotide complexes is now commonplace. The resulting electron-density maps are often poorer than for proteins, and as a result interpretation in terms of an atomic model can require significant effort, particularly in the case of large structures. While model building can be performed automatically, as with proteins, the process is time-consuming, taking minutes to days depending on the software and the size of the structure. A method is presented for the automatic building of nucleotide chains into electron density which is fast enough to be used in interactive model-building software, with extended chain fragments built around the current view position in a fraction of a second. The speed of the method arises from the determination of the `fingerprint' of the sugar and phosphate groups in terms of conserved high-density and low-density features, coupled with a highly efficient scoring algorithm. Use cases include the rapid evaluation of an initial electron-density map, addition of nucleotide fragments to prebuilt protein structures, and in favourable cases the completion of the structure while automated model-building software is still running. The method has been incorporated into theCootsoftware package.

scholarly journals Cyclic Automated Model Building (CAB) Applied to Nucleic Acids

Crystals ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 280
Author(s):  
Maria Cristina Burla ◽  
Benedetta Carrozzini ◽  
Giovanni Luca Cascarano ◽  
Carmelo Giacovazzo ◽  
Giampiero Polidori
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Model Building ◽  
State Of The Art ◽  
Molecular Replacement ◽  
Dna And Rna ◽  
Protein Model ◽  
Rna Fragments ◽  
Nucleic Acid Structures ◽  
Automated Model Building

Obtaining high-quality models for nucleic acid structures by automated model building programs (AMB) is still a challenge. The main reasons are the rather low resolution of the diffraction data and the large number of rotatable bonds in the main chains. The application of the most popular and documented AMB programs (e.g., PHENIX.AUTOBUILD, NAUTILUS and ARP/wARP) may provide a good assessment of the state of the art. Quite recently, a cyclic automated model building (CAB) package was described; it is a new AMB approach that makes the use of BUCCANEER for protein model building cyclic without modifying its basic algorithms. The applications showed that CAB improves the efficiency of BUCCANEER. The success suggested an extension of CAB to nucleic acids—in particular, to check if cyclically including NAUTILUS in CAB may improve its effectiveness. To accomplish this task, CAB algorithms designed for protein model building were modified to adapt them to the nucleic acid crystallochemistry. CAB was tested using 29 nucleic acids (DNA and RNA fragments). The phase estimates obtained via molecular replacement (MR) techniques were automatically submitted to phase refinement and then used as input for CAB. The experimental results from CAB were compared with those obtained by NAUTILUS, ARP/wARP and PHENIX.AUTOBUILD.

Phased rotation, conformation and translation function: performance with mononucleotides

2008 ◽  
Vol 41 (1) ◽  
pp. 62-67 ◽  
Author(s):  
Frantisek Pavelcik
Keyword(s):  
Nucleic Acid ◽  
Degrees Of Freedom ◽  
Model Building ◽  
Protein Crystallography ◽  
Torsion Angles ◽  
Heavy Atoms ◽  
Promising Tool ◽  
Translation Function ◽  
Nucleic Acid Structures ◽  
Automatic Model Building

A phased rotation, conformation and translation function (PRCTF) is a novel and promising tool for automatic model building in protein crystallography. Its performance has been tested on nucleic acid structures. A mononucleotide fragment of phosphate-to-phosphate type with seven conformation degrees of freedom was used as a search fragment. The position, orientation and internal torsion angles of all localized fragments are refined by a phased flexible refinement. In general, 50 to 93% of the fragments can be found by the PRCTF. Results depend on resolution and phase quality. The ability of the PRCTF to locate bases is significantly lower (3–30%), owing to the lack of heavy atoms. Individual localized fragments can be connected into polynucleotide chains.

Is single-wavelength anomalous scattering sufficient for solving phases? A comparison of different methods for a 2.1 Å structure solution

1999 ◽  
Vol 55 (9) ◽  
pp. 1620-1622 ◽  
Author(s):  
Liu Yu-dong ◽  
I. Harvey ◽  
Gu Yuan-xin ◽  
Zheng Chao-de ◽  
He Yi-zong ◽  
...  
Keyword(s):  
Electron Density ◽  
Phase Error ◽  
Direct Methods ◽  
Anomalous Scattering ◽  
Refined Model ◽  
Native Protein ◽  
Acta Cryst ◽  
Density Maps ◽  
Structure Solution ◽  
Unknown Structure

The structure of rusticyanin is the largest unknown structure (Mr = 16.8 kDa) which has been recently solved by the direct-methods approach using only single-wavelength anomalous scattering (SAS) data from the native protein [Harvey et al. (1998). Acta Cryst. D54, 629–635]. Here, the results of the Sim distribution approach [Hendrickson & Teeter (1981). Nature (London), 290, 107–113] and of the CCP4 procedure MLPHARE [Collaborative Computational Project, Number 4 (1994). Acta Cryst. D50, 760–763] are compared with those from direct methods. Analysis against the final refined model shows that direct methods produced significantly better phases (average phase error 56°) and therefore significantly better electron-density maps than the Sim distribution and MLPHARE approaches (average phase error was around 63° in both cases).

scholarly journals Challenges and surprises that arise with nucleic acids during model building and refinement

2012 ◽  
Vol 68 (4) ◽  
pp. 441-445 ◽  
Author(s):  
William G. Scott
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Model Building ◽  
Heavy Atom ◽  
Three Dimensional ◽  
Isomorphous Replacement ◽  
Density Map ◽  
Nucleic Acid Structures ◽  
Electron Density Map ◽  
Experimental Electron Density

The process of building and refining crystal structures of nucleic acids, although similar to that for proteins, has some peculiarities that give rise to both various complications and various benefits. Although conventional isomorphous replacement phasing techniques are typically used to generate an experimental electron-density map for the purposes of determining novel nucleic acid structures, it is also possible to couple the phasing and model-building steps to permit the solution of complex and novel RNA three-dimensional structures without the need for conventional heavy-atom phasing approaches.

scholarly journals Freeze Frames vs. Movies

2014 ◽  
Vol 70 (a1) ◽  
pp. C178-C178
Author(s):  
Carola Müller ◽  
Sven Lidin
Keyword(s):  
Intermetallic Compounds ◽  
Degrees Of Freedom ◽  
Model Building ◽  
Electronic Devices ◽  
Atomic Arrangement ◽  
Modulation Wave ◽  
Structure Solution ◽  
Methodological Errors ◽  
In The Beginning ◽  
Lock In

Sometimes, model building in crystallography is like resolving a puzzle: All obvious symmetrical or methodological errors are excluded, you apparently understand the measured patterns in 3D, but the structure solution and/or refinement is just not working. One such nerve-stretching problem arises from metrically commensurate structures (MCS). This expression means that the observed values of the components of the modulation wave vectors are rational by chance and not because of a lock-in. Hence, it is not a superstructure - although the boundaries between the two descriptions are blurry. Using a superstructure model for a MCS decreases the degrees of freedom, and forces the atomic arrangement to an artificial state of ordering. Just imagine it as looking at a freeze frame from a movie instead of watching the whole film. The consequences in structure solution and refinement of MCS are not always as dramatically as stated in the beginning. On the contrary, treating a superstructure like a MCS might be a worthwhile idea. Converting from a superstructure model to a superspace model may lead to a substantial decrease in the number of parameters needed to model the structure. Further, it can permit for the refinement of parameters that the paucity of data does not allow in a conventional description. However, it is well known that families of superstructures can be described elegantly by the use of superspace models that collectively treat a whole range of structures, commensurate and incommensurate. Nevertheless, practical complications in the refinement are not uncommon. Instances are overlapping satellites from different orders and parameter correlations. Notably, MCS occur in intermetallic compounds that are important for the performance of next-generation electronic devices. Based on examples of their (pseudo)hexagonal 3+1D and 3+2D structures, we will discuss the detection and occurrence of MCS as well as the benefits and limitations of implementing them artificially.

Synergy among phase-refinement techniques in macromolecular crystallography

2017 ◽  
Vol 73 (11) ◽  
pp. 877-888 ◽  
Author(s):  
Maria Cristina Burla ◽  
Giovanni Luca Cascarano ◽  
Carmelo Giacovazzo ◽  
Giampiero Polidori
Keyword(s):  
Ab Initio ◽  
Electron Density ◽  
Molecular Model ◽  
Experimental Tests ◽  
Protein Chemistry ◽  
Sources Of Information ◽  
Density Maps ◽  
Structure Solution ◽  
Molecular Interpretation ◽  
The Difference

Ab initioand non-ab initiophasing methods are often unable to provide phases of sufficient quality to allow the molecular interpretation of the resulting electron-density maps. Phase extension and refinement is therefore a necessary step: its success or failure can make the difference between solution and nonsolution of the crystal structure. Today phase refinement is trusted to electron-density modification (EDM) techniques, and in practice to dual-space methods which try,viasuitable constraints in direct and in reciprocal space, to generate higher quality electron-density maps. The most popular EDM approaches, denoted here as mainstream methods, are usually part of packages which assist crystallographers in all of the structure-solution steps from initial phasing to the point where the molecular model perfectly fits the known features of protein chemistry. Other phase-refinement approaches that are based on different sources of information, denoted here as out-of-mainstream methods, are not frequently employed. This paper aims to show that mainstream and out-of-mainstream methods may be combined and may lead to dramatic advances in the present state of the art. The statement is confirmed by experimental tests using molecular-replacement, SAD–MAD andab initiotechniques.

Application of constrained real-space refinement of flexible molecular fragments to automatic model building of RNA structures

2012 ◽  
Vol 45 (2) ◽  
pp. 309-315 ◽  
Author(s):  
Frantisek Pavelcik
Keyword(s):  
Nucleic Acid ◽  
Model Building ◽  
Real Space ◽  
Rna Structures ◽  
Molecular Fragments ◽  
Source Codes ◽  
Translation Function ◽  
Base Method ◽  
Nucleic Acid Structures ◽  
Automatic Model Building

New methods have been developed for locating phosphate groups and nucleic acid bases in the electron density of RNA structures. These methods utilize a constrained real-space refinement of molecular fragments and a phased rotation–conformation–translation function. Real-space refinement has also contributed to the improvement of the bone/base method of RNA model building and to redesigning the method of building double helices in nucleic acid structures. This improvement is reflected in the increased accuracy of the model building and the ability to better distinguish between correct and false solutions. A program,RSR, was created, and the programsNUT,HELandDHLwere upgraded and organized into a program system, which is CCP4 oriented. Source codes will also be released.

Protein phasing at non-atomic resolution by combining Patterson andVLDtechniques

2014 ◽  
Vol 70 (7) ◽  
pp. 1994-2006 ◽  
Author(s):  
Rocco Caliandro ◽  
Benedetta Carrozzini ◽  
Giovanni Luca Cascarano ◽  
Giuliana Comunale ◽  
Carmelo Giacovazzo ◽  
...  
Keyword(s):  
Model Building ◽  
Protein Structures ◽  
Experimental Information ◽  
Atomic Resolution ◽  
Data Sets ◽  
Density Maps ◽  
Combined Use ◽  
Final Electron ◽  
Automatic Model Building

Phasing proteins at non-atomic resolution is still a challenge for anyab initiomethod. A variety of algorithms [Patterson deconvolution, superposition techniques, a cross-correlation function (Cmap), theVLD(vive la difference) approach, the FF function, a nonlinear iterative peak-clipping algorithm (SNIP) for defining the background of a map and thefree lunchextrapolation method] have been combined to overcome the lack of experimental information at non-atomic resolution. The method has been applied to a large number of protein diffraction data sets with resolutions varying from atomic to 2.1 Å, with the condition that S or heavier atoms are present in the protein structure. The applications include the use ofARP/wARPto check the quality of the final electron-density maps in an objective way. The results show that resolution is still the maximum obstacle to protein phasing, but also suggest that the solution of protein structures at 2.1 Å resolution is a feasible, even if still an exceptional, task for the combined set of algorithms implemented in the phasing program. The approach described here is more efficient than the previously described procedures:e.g.the combined use of the algorithms mentioned above is frequently able to provide phases of sufficiently high quality to allow automatic model building. The method is implemented in the current version ofSIR2014.

Sign in / Sign up

Export Citation Format

Share Document