A Connected Set Algorithm for the Identification of Spatially Contiguous Regions in Crystallographic Envelopes

Hunt, J.F.; Vellieux, F.M.D.; Deisenhofer, Johann

doi:10.1107/s0907444997001431

Cited by 3 publications

(3 citation statements)

References 10 publications

(11 reference statements)

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“…The original algorithm implemented in DynDom1D was found to be far too slow for very large molecules like the ribosome, and so a faster algorithm was developed for DynDom3D. The algorithm is based on one devised for the refinement of electron density maps from X‐ray crystallography implemented in the CNCTDENV program 14. In that application, contacts between neighboring cells in a digitized electron density map were considered, whereas for DynDom3D contacts between atoms situated anywhere in space are considered.…”

Section: Methodsmentioning

confidence: 99%

A method for the analysis of domain movements in large biomolecular complexes

et al. 2009

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A new method for the analysis of domain movements in large, multichain, biomolecular complexes is presented. The method is applicable to any molecule for which two atomic structures are available that represent a conformational change indicating a possible domain movement. The method is blind to atomic bonding and atom type and can, therefore, be applied to biomolecular complexes containing different constituent molecules such as protein, RNA, or DNA. At the heart of the method is the use of blocks located at grid points spanning the whole molecule. The rotation vector for the rotation of atoms from each block between the two conformations is calculated. Treating components of these vectors as coordinates means that each block is associated with a point in a "rotation space" and that blocks with atoms that rotate together, perhaps as part of the same rigid domain, will have colocated points. Thus a domain can be identified from the clustering of points from blocks that span it. Domain pairs are accepted for analysis of their relative movements in terms of screw axes based upon a set of reasonable criteria. Here, we report on the application of the method to biomolecules covering a considerable size range: hemoglobin, liver alcohol dehydrogenase, S-Adenosylhomocysteine hydrolase, aspartate transcarbamylase, and the 70S ribosome. The results provide a depiction of the conformational change within each molecule that is easily understood, giving a perspective that is expected to lead to new insights. Of particular interest is the allosteric mechanism in some of these molecules. Results indicate that common boundaries between subunits and domains are good regions to focus on as movement in one subunit can be transmitted to another subunit through such interfaces.

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Section: Methodsmentioning

confidence: 99%

A method for the analysis of domain movements in large biomolecular complexes

et al. 2009

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“…If a gridpoint distance is greater than a user-defined cutoff radius, it is designated as a channel. The channel gridpoints are then broken into groups based on nearest neighbour connectivity, using a procedure essentially identical to an algorithm reported for identifying connected sets in protein envelopes (Hunt et al, 1997). Space-group symmetry and unit-cell translation are accounted for so that unit-cell faces do not interrupt connected groups.…”

Section: Map_channels Strategymentioning

confidence: 99%

MAP_CHANNELS: a computation tool to aid in the visualization and characterization of solvent channels in macromolecular crystals

Juers

Ruffin

2014

J Appl Crystallogr

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A computation tool is described that facilitates visualization and characterization of solvent channels or pores within macromolecular crystals. A scalar field mapping the shortest distance to protein surfaces is calculated on a grid covering the unit cell and is written as a map file. The map provides a multiscale representation of the solvent channels, which when viewed in standard macromolecular crystallographic software packages gives an intuitive sense of the solvent channel architecture. The map is analysed to yield descriptors of the topology and the morphology of the solvent channels, including bottleneck radii, tortuosity, width variation and anisotropy.

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“…Once the clustering has been performed, the translational shifts needed to bring the envelopes onto a common origin are applied, and the consensus envelope is calculated for each cluster by taking the modal value for each sample point in the envelope, across all members of the cluster. The consensus envelope is subsequently edited using a previously published connectivity algorithm (Hunt et al, 1997), erasing small islands, and filling small voids, that can sometimes be created by the averaging procedure.…”

Section: Clustering Algorithms and The Computation Of Consensus Envel...mentioning

confidence: 99%

A general method for directly phasing diffraction data from high-solvent-content protein crystals

Kingston¹,

Millane²

2022

IUCrJ

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A procedure is described for direct phase determination in protein crystallography, applicable to crystals with high solvent content. The procedure requires only the diffraction data and an estimate of the solvent content as input. Direct phase determination is treated as a constraint satisfaction problem, in which an image is sought that is consistent with both the diffraction data and generic constraints on the density distribution in the crystal. The problem is solved using an iterative projection algorithm, the Difference Map algorithm, which has good global convergence properties, and can locate the correct solution without any initial phase information. Computational efficiency is improved by breaking the problem down into two stages; initial approximation of the molecular envelope at low resolution, followed by subsequent phase determination using all of the data. The molecular envelope is continually updated during the phase determination step. At both stages, the algorithm is initiated with many different and random phase sets, which are evolved subject to the constraints. A clustering procedure is used to identify consistent results across multiple runs, which are then averaged to generate consensus envelopes or phase sets. The emergence of highly consistent phase sets is diagnostic of success. The effectiveness of the procedure is demonstrated by application to 42 known structures of solvent fraction 0.60–0.85. The procedure works robustly at intermediate resolutions (1.9–3.5 Å) but is strongly dependent on crystal solvent content, only working routinely with solvent fractions greater than 0.70.

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A Connected Set Algorithm for the Identification of Spatially Contiguous Regions in Crystallographic Envelopes

Cited by 3 publications

References 10 publications

A method for the analysis of domain movements in large biomolecular complexes

A method for the analysis of domain movements in large biomolecular complexes

MAP_CHANNELS: a computation tool to aid in the visualization and characterization of solvent channels in macromolecular crystals

A general method for directly phasing diffraction data from high-solvent-content protein crystals

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