Ab initiophasing of proteins with heavy atoms at non-atomic resolution: pushing the size limit of solvable structures up to 7890 non-H atoms in the asymmetric unit

2008 ◽  
Vol 41 (3) ◽  
pp. 548-553 ◽  
Author(s):  
Rocco Caliandro ◽  
Benedetta Carrozzini ◽  
Giovanni Luca Cascarano ◽  
Liberato De Caro ◽  
Carmelo Giacovazzo ◽  
...  
Keyword(s):  
Ab Initio ◽  
State Of The Art ◽  
Structural Complexity ◽  
Direct Methods ◽  
Atomic Resolution ◽  
Asymmetric Unit ◽  
Resolution Limit ◽  
Heavy Atoms ◽  
Data Resolution ◽  
Two Parameters

The success of theab initiophasing process mainly depends on two parameters: data resolution and structural complexity. In agreement with the Sheldrick rule, the presence of heavy atoms can also play a nonnegligible role in the success of direct methods. The increased efficiency of the Patterson methods and the advent of new phasing techniques based on extrapolated reflections have changed the state of the art. In particular, it is not clear how much the resolution limit and the structural complexity may be pushed in the presence of heavy atoms. In this paper, it is shown that the limits fixed by the Sheldrick rule may be relaxed if the structure contains heavy atoms and thatab initiotechniques can succeed even when the data resolution is about 2 Å, a limit unthinkable a few years ago. The method is successful in solving a structure with 7890 non-H atoms in the asymmetric unit at a resolution of 1.65 Å, a considerable advance on the previous record of 6319 atoms at atomic resolution.

Solving proteins at non-atomic resolution by direct methods

2015 ◽  
Vol 48 (6) ◽  
pp. 1692-1698 ◽  
Author(s):  
Maria Cristina Burla ◽  
Benedetta Carrozzini ◽  
Giovanni Luca Cascarano ◽  
Carmelo Giacovazzo ◽  
Giampiero Polidori
Keyword(s):  
Ab Initio ◽  
Protein Structures ◽  
Structural Complexity ◽  
Direct Methods ◽  
Atomic Resolution ◽  
Asymmetric Unit ◽  
Hydrogen Atoms ◽  
Heavy Atoms ◽  
Density Map ◽  
Electron Density Map

A new probabilistic formula estimating triplet invariants and capable of exploiting a model electron-density map gradually created during theab initiophasing process has been tested on a set of protein structures with data at non-atomic resolution. All the structures contain heavy atoms larger than Ca, and show a structural complexity which may attain the level of about 8000 non-hydrogen atoms in the asymmetric unit. It is shown that the majority of such structures may be solved by our direct methods procedure, which, in combination with a number of ancillary phasing tools, weakens the traditional expectation that atomic resolution is a necessary ingredient for the success of a directab initiophasing.

scholarly journals Direct-methods structure determination of a trypanosome RNA-editing substrate fragment with translational pseudosymmetry

2016 ◽  
Vol 72 (4) ◽  
pp. 477-487 ◽  
Author(s):  
Blaine H. M. Mooers
Keyword(s):  
Crystal Structure ◽  
Random Phase ◽  
Direct Methods ◽  
Automated Detection ◽  
Asymmetric Unit ◽  
Resolution Limit ◽  
Data Resolution ◽  
Rna Hairpin ◽  
Correct Structure

Using direct methods starting from random phases, the crystal structure of a 32-base-pair RNA (675 non-H RNA atoms in the asymmetric unit) was determined using only the native diffraction data (resolution limit 1.05 Å) and the computer programSIR2014. The almost three helical turns of the RNA in the asymmetric unit introduced partial or imperfect translational pseudosymmetry (TPS) that modulated the intensities when averaged by thelMiller indices but still escaped automated detection. Almost six times as many random phase sets had to be tested on average to reach a correct structure compared with a similar-sized RNA hairpin (27 nucleotides, 580 non-H RNA atoms) without TPS. More sensitive methods are needed for the automated detection of partial TPS.

Ab initio solution and refinement of two high-potential iron protein structures at atomic resolution

1999 ◽  
Vol 55 (11) ◽  
pp. 1773-1784 ◽  
Author(s):  
Emilio Parisini ◽  
Francesco Capozzi ◽  
Paolo Lubini ◽  
Victor Lamzin ◽  
Claudio Luchinat ◽  
...  
Keyword(s):  
Ab Initio ◽  
Protein Structures ◽  
Direct Methods ◽  
High Potential ◽  
Chromatium Vinosum ◽  
Atomic Resolution ◽  
Crystal Modification ◽  
Redox Potentials ◽  
Asymmetric Unit ◽  
Iron Protein

The crystal structure of the reduced high-potential iron protein (HiPIP) from Chromatium vinosum has been redetermined in a new orthorhombic crystal modification, and the structure of its H42Q mutant has been determined in orthorhombic (H42Q-1) and cubic (H42Q-2) modifications. The first two were solved by ab initio direct methods using data collected to atomic resolution (1.20 and 0.93 Å, respectively). The recombinant wild type (rc-WT) with two HiPIP molecules in the asymmetric unit has 1264 protein atoms and 335 solvent sites, and is the second largest structure reported so far that has been solved by pure direct methods. The solutions were obtained in a fully automated way and included more than 80% of the protein atoms. Restrained anisotropic refinement for rc-WT and H42Q-1 converged to R_1=\sum\big||F_o|-|F_c|\big|\big/\sum|F_o| of 12.0 and 13.6%, respectively [data with I>2\sigma(I)], and 12.8 and 15.5% (all data). H42Q-2 contains two molecules in the asymmetric unit and diffracted only to 2.6 Å. In both molecules of rc-WT and in the single unique molecule of H42Q-1 the [Fe4S4]2+ cluster dimensions are very similar and show a characteristic tetragonal distortion with four short Fe—S bonds along four approximately parallel cube edges, and eight long Fe—S bonds. The unique protein molecules in H42Q-2 and rc-WT are also very similar in other respects, except for the hydrogen bonding around the mutated residue that is at the surface of the protein, supporting the hypothesis that the difference in redox potentials at lower pH values is caused primarily by differences in the charge distribution near the surface of the protein rather than by structural differences in the cluster region.

SIR2004: an improved tool for crystal structure determination and refinement

2005 ◽  
Vol 38 (2) ◽  
pp. 381-388 ◽  
Author(s):  
Maria C. Burla ◽  
Rocco Caliandro ◽  
Mercedes Camalli ◽  
Benedetta Carrozzini ◽  
Giovanni L. Cascarano ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Ab Initio ◽  
Structure Determination ◽  
Protein Structures ◽  
Medium Size ◽  
Graphical Interface ◽  
Asymmetric Unit ◽  
Density Maps ◽  
Data Resolution ◽  
User Friendly

SIR2004is the evolution of theSIR2002program [Burla, Camalli, Carrozzini, Cascarano, Giacovazzo, Polidori & Spagna (2003).J. Appl. Cryst.36, 1103]. It is devoted to the solution of crystal structures by direct and Patterson methods. Several new features implemented inSIR2004make this program efficient: it is able to solveab initioboth small/medium-size structures as well as macromolecules (up to 2000 atoms in the asymmetric unit). In favourable circumstances, the program is also able to solve protein structures with data resolution up to 1.4–1.5 Å, and to provide interpretable electron density maps. A powerful user-friendly graphical interface is provided.

Use of Patterson-based methods automatically to determine the structures of heavy-atom-containing proteins with up to 6000 non-hydrogen atoms in the asymmetric unit

2006 ◽  
Vol 39 (5) ◽  
pp. 728-734 ◽  
Author(s):  
Maria Cristina Burla ◽  
Rocco Caliandro ◽  
Benedetta Carrozzini ◽  
Giovanni Luca Cascarano ◽  
Liberato De Caro ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Protein Data Bank ◽  
Heavy Atom ◽  
Data Bank ◽  
Atomic Resolution ◽  
Asymmetric Unit ◽  
Hydrogen Atoms ◽  
Heavy Atoms ◽  
Density Maps ◽  
Resolution Data

The Patterson superposition methods described by Burlaet al.[J. Appl. Cryst.(2006),39, 527–535], based on the use of the `multiple implication functions', have been enriched by supplementary filtering techniques based on some general (resolution-dependent) features of both the Patterson and the electron density maps. The method has been implemented in a modified version of the programSIR2004and tested using a set of 20 crystal structures selected from the Protein Data Bank, having a number of non-hydrogen atoms in the asymmetric unit larger than 2000, atomic resolution data and some heavy atoms (equal to or heavier than Ca). The new phasing procedure is able to solve most of the test structures, among which there are two proteins with more than 6000 non-hydrogen atoms in the asymmetric unit, so extending by far the complexity today commonly considered as the limit for Patterson-based methods (i.e.about 2000 non-hydrogen atoms).

The revenge of the Patterson methods. I. Proteinab initiophasing

2006 ◽  
Vol 39 (4) ◽  
pp. 527-535 ◽  
Author(s):  
Maria C. Burla ◽  
Rocco Caliandro ◽  
Benedetta Carrozzini ◽  
Giovanni Luca Cascarano ◽  
Liberato De Caro ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Computing Time ◽  
Direct Methods ◽  
Data Bank ◽  
Atomic Resolution ◽  
Atomic Data ◽  
Large Set ◽  
Hydrogen Atoms ◽  
Data Resolution ◽  
Structure Complexity

Direct methods combined with direct-space refinement procedures are the standard tools forab initiocrystal structure solution of macromoleculesviadiffraction data collected up to atomic or quasi-atomic resolution. An entirely direct-space approach is described here: it includes an automated Patterson deconvolution method, based on the minimum superposition function, followed by an effective direct-space refinement, consisting of cycles of electron density modification. The new approach has been implemented in a new version of theSIR2004program and tested on a large set of test structures selected from the Protein Data Bank, with data resolution better than 1.6 Å and number of non-hydrogen atoms in the asymmetric unit up to 2000. The new procedure proved to be extremely efficient and very fast in solving crystal structures with atomic resolution data and heavy atoms: their solution and refinement requires a computing time roughly comparable with that necessary for solving small-molecule crystal structuresviaa modern computer program. It markedly overcomes direct methods, even for crystal structures with atomic data resolution and heaviest atomic species up to calcium, as well as for crystal structures with quasi-atomic data resolution (i.e.1.2–1.6 Å). The Patterson approach proved to be loosely dependent on the structure complexity.

Solving proteins at non-atomic resolution by direct methods: update

2017 ◽  
Vol 50 (4) ◽  
pp. 1048-1055 ◽  
Author(s):  
Maria Cristina Burla ◽  
Benedetta Carrozzini ◽  
Giovanni Luca Cascarano ◽  
Carmelo Giacovazzo ◽  
Giampiero Polidori
Keyword(s):  
Structural Complexity ◽  
Direct Methods ◽  
Atomic Resolution ◽  
Free Lunch ◽  
Fourier Synthesis ◽  
Structure Solution ◽  
Full Structure ◽  
Subsequent Phase ◽  
Difference Fourier ◽  
New Phase

Direct methods can be used to solve proteins of great structural complexity even when diffraction data are at non-atomic resolution. However, one of the main obstacles to the wider application of direct methods is that they reliably phase only a small fraction of the observed reflections, those with a sufficiently large value of the normalized structure factor amplitude. The subsequent phase expansion and refinement required for full structure solution are difficult. Here a new phase refinement procedure is described, which combines (1–2) difference Fourier synthesis with electron density modification techniques and thevive la differenceand Free Lunch algorithms. This procedure is able to solve data resistant to other direct space refinement procedures.

Advances inab initioprotein phasing by Patterson deconvolution techniques

2007 ◽  
Vol 40 (5) ◽  
pp. 883-890 ◽  
Author(s):  
Rocco Caliandro ◽  
Benedetta Carrozzini ◽  
Giovanni Luca Cascarano ◽  
Liberato De Caro ◽  
Carmelo Giacovazzo ◽  
...  
Keyword(s):  
Molecular Model ◽  
Large Set ◽  
Resolution Limit ◽  
Heavy Atoms ◽  
Data Resolution ◽  
Correct Location ◽  
True Position ◽  
Definition Of ◽  
Deconvolution Techniques ◽  
New Algorithms

New algorithms have been devised and implemented in the programSIR2007for the deconvolution of Patterson mapsviathe use of implication transformations and of the minimum superposition function. The new algorithms concern several practical aspects, such as the use of weighted Patterson syntheses to simplify the recognition of useful pivot peaks, the definition of a ranking criterion for them, the introduction of an early figure of merit to discard useless pivots and the fast Fourier transform transposition of theRELAXalgorithm, aiming to find the correct location when the current molecular model is translated with respect to the true position. The advantages of the new procedure have been assessed using a large set of test structures. The results have been analysed with respect to four parameters: the CPU time necessary for obtaining and recognizing the correct solution, the presence of heavy atoms, the complexity limit of the structures solvableab initio, and the data resolution limit.

scholarly journals The Degree of Oxidation of Graphene Oxide

Nanomaterials ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 560
Author(s):  
Alexandra Carvalho ◽  
Mariana C. F. Costa ◽  
Valeria S. Marangoni ◽  
Pei Rou Ng ◽  
Thi Le Hang Nguyen ◽  
...  
Keyword(s):  
Graphene Oxide ◽  
Ab Initio ◽  
State Of The Art ◽  
High Accuracy ◽  
Precise Determination ◽  
Photoemission Spectroscopy ◽  
Pristine Graphene ◽  
X Ray ◽  
Degree Of Oxidation

We show that the degree of oxidation of graphene oxide (GO) can be obtained by using a combination of state-of-the-art ab initio computational modeling and X-ray photoemission spectroscopy (XPS). We show that the shift of the XPS C1s peak relative to pristine graphene, ΔEC1s, can be described with high accuracy by ΔEC1s=A(cO−cl)2+E0, where c0 is the oxygen concentration, A=52.3 eV, cl=0.122, and E0=1.22 eV. Our results demonstrate a precise determination of the oxygen content of GO samples.

Cellulose organic solvents: V. Conformational aspects of N,N-dimethyl ethanolamine N-oxide in its crystalline and diluted states

1984 ◽  
Vol 62 (1) ◽  
pp. 6-10 ◽  
Author(s):  
E. R. Maia ◽  
A. Péguy ◽  
S. Pérez
Keyword(s):  
Tertiary Amine ◽  
Amine Oxide ◽  
Direct Methods ◽  
Monoclinic Space Group ◽  
Cyclic Form ◽  
Asymmetric Unit ◽  
Ir And Nmr Spectroscopy ◽  
Conformational Investigation ◽  
Intramolecular Hydrogen ◽  
Strong Intramolecular Hydrogen Bond

N,N-Dimethyl ethanolamine N-oxide (DMEAO) belongs to the class of tertiary amine oxide molecules that are good solvents for cellulose, although not being cyclic. Crystallographic investigation shows that anhydrous DMEAO is monoclinic, space group Cc, a = 25.725(9), b = 7.023(4), c = 9.483(5) Å, β = 101.16(10)°, Z = 12. The crystal structure has been solved by direct methods and refined to a final R value of 0.063 for 575 observed reflexions. Three independent molecules are found within the asymmetric unit; one of these displays a pseudo-cyclic form dictated by the occurrence of a strong intramolecular hydrogen bond. Conformational investigation of DMEAO in solution, using ir and nmr spectroscopy shows that this pseudo-cyclic form is more likely to occur in diluted states. These findings are related to the ability of this tertiary amine oxide to act as a good solvent, up to a water content of one water molecule per DMEAO molecule.

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