scholarly journals Unraveling low-resolution structural data of large biomolecules by constructing atomic models with experiment-targeted parallel cascade selection simulations

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Junhui Peng ◽  
Zhiyong Zhang
Keyword(s):  
Structural Data ◽  
Low Resolution ◽  
Atomic Models

scholarly journals Covalently modified carboxyl side chains on cell surface leads to a novel method toward topology analysis of transmembrane proteins

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Anna Müller ◽  
Tamás Langó ◽  
Lilla Turiák ◽  
András Ács ◽  
György Várady ◽  
...  
Keyword(s):  
Cell Surface ◽  
Transmembrane Proteins ◽  
Structural Data ◽  
Covalent Modification ◽  
Peptide Fragments ◽  
Low Resolution ◽  
Topology Analysis ◽  
High Resolution Structure ◽  
Accessible Surface ◽  
Resolution Structure

Abstract The research on transmembrane proteins (TMPs) is quite widespread due to their biological importance. Unfortunately, only a little amount of structural data is available of TMPs. Since technical difficulties arise during their high-resolution structure determination, bioinformatics and other experimental approaches are widely used to characterize their low-resolution structure, namely topology. Experimental and computational methods alone are still limited to determine TMP topology, but their combination becomes significant for the production of reliable structural data. By applying amino acid specific membrane-impermeable labelling agents, it is possible to identify the accessible surface of TMPs. Depending on the residue-specific modifications, new extracellular topology data is gathered, allowing the identification of more extracellular segments for TMPs. A new method has been developed for the experimental analysis of TMPs: covalent modification of the carboxyl groups on the accessible cell surface, followed by the isolation and digestion of these proteins. The labelled peptide fragments and their exact modification sites are identified by nanoLC-MS/MS. The determined peptides are mapped to the primary sequences of TMPs and the labelled sites are utilised as extracellular constraints in topology predictions that contribute to the refined low-resolution structure data of these proteins.

Low Resolution Refinement of Atomic Models Against Crystallographic Data

2017 ◽  
pp. 565-593 ◽  
Author(s):  
Robert A. Nicholls ◽  
Oleg Kovalevskiy ◽  
Garib N. Murshudov
Keyword(s):  
Crystallographic Data ◽  
Low Resolution ◽  
Atomic Models

Low-Resolution Density Maps from Atomic Models: How Stepping “Back” Can Be a Step “Forward”

1999 ◽  
Vol 125 (2-3) ◽  
pp. 166-175 ◽  
Author(s):  
David M. Belnap ◽  
Abhinav Kumar ◽  
Jon T. Folk ◽  
Thomas J. Smith ◽  
Timothy S. Baker
Keyword(s):  
Low Resolution ◽  
Atomic Models ◽  
Density Maps

scholarly journals Real-space refinement in Phenix for cryo-EM and crystallography

2018 ◽  
Author(s):  
Pavel V. Afonine ◽  
Billy K. Poon ◽  
Randy J. Read ◽  
Oleg V. Sobolev ◽  
Thomas C. Terwilliger ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Target Function ◽  
Real Space ◽  
Molecular Symmetry ◽  
Low Resolution ◽  
Fast Calculation ◽  
Additional Information ◽  
Extra Information ◽  
Atomic Models ◽  
Resolution Data

AbstractThis article describes the implementation of real-space refinement in the phenix.real_space_refine program from the Phenix suite. Use of a simplified refinement target function enables fast calculation, which in turn makes it possible to identify optimal data-restraints weight as part of routine refinements with little runtime cost. Refinement of atomic models against low-resolution data benefits from the inclusion of as much additional information as is available. In addition to standard restraints on covalent geometry, phenix.real_space_refine makes use of extra information such as secondary-structure and rotamer-specific restraints, as well as restraints or constraints on internal molecular symmetry. Re-refinement of 385 cryo-EM derived models available in the PDB at resolutions of 6 Å or better shows significant improvement of models and the fit of these models to the target maps.SynopsisA description of the implementation of real-space refinement in the phenix.real_space_refine program from the Phenix suite and its application to re-refinement of cryo-EM derived models.

scholarly journals TEMPy: a Python library for assessment of three-dimensional electron microscopy density fits

2015 ◽  
Vol 48 (4) ◽  
pp. 1314-1323 ◽  
Author(s):  
Irene Farabella ◽  
Daven Vasishtan ◽  
Agnel Praveen Joseph ◽  
Arun Prasad Pandurangan ◽  
Harpal Sahota ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Three Dimensional ◽  
Dimensional Electron ◽  
Low Resolution ◽  
Macromolecular Assemblies ◽  
Atomic Models ◽  
Density Maps ◽  
Consensus Scoring ◽  
Ensemble Generation ◽  
Modular Nature

Three-dimensional electron microscopy is currently one of the most promising techniques used to study macromolecular assemblies. Rigid and flexible fitting of atomic models into density maps is often essential to gain further insights into the assemblies they represent. Currently, tools that facilitate the assessment of fitted atomic models and maps are needed.TEMPy(template and electron microscopy comparison using Python) is a toolkit designed for this purpose. The library includes a set of methods to assess density fits in intermediate-to-low resolution maps, both globally and locally. It also provides procedures for single-fit assessment, ensemble generation of fits, clustering, and multiple and consensus scoring, as well as plots and output files for visualization purposes to help the user in analysing rigid and flexible fits. The modular nature ofTEMPyhelps the integration of scoring and assessment of fits into large pipelines, making it a tool suitable for both novice and expert structural biologists.

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