Xtrapol8 enables automatic elucidation of low-occupancy intermediate-states in crystallographic studies

被引:20
作者
De Zitter, Elke [1 ]
Coquelle, Nicolas [2 ]
Oeser, Paula [1 ]
Barends, Thomas R. M. [3 ]
Colletier, Jacques-Philippe [1 ]
机构
[1] Univ Grenoble Alpes, CNRS, CEA, Inst Biol Struct, F-38000 Grenoble, France
[2] European Synchrotron Radiat Facil ESRF, BP 220, F-38043 Grenoble, France
[3] Max Planck Inst Med Res, Jahnstr 29, D-69120 Heidelberg, Germany
关键词
REFINEMENT; PROTEIN; PHOTOCYCLE; DYNAMICS; SUITE;
D O I
10.1038/s42003-022-03575-7
中图分类号
Q [生物科学];
学科分类号
07 ; 0710 ; 09 ;
摘要
Unstable states studied in kinetic, time-resolved and ligand-based crystallography are often characterized by a low occupancy, which hinders structure determination by conventional methods. To automatically extract structural information pertaining to these states, we developed Xtrapol8, a program which (i) applies various flavors of Bayesian-statistics weighting to generate the most informative Fourier difference maps; (ii) determines the occupancy of the intermediate states by use of methods hitherto not available; (iii) calculates extrapolated structure factors using the various proposed formalisms while handling the issue of negative structure factor amplitudes, and (iv) refines the corresponding structures in real and reciprocal-space. The use of Xtrapol8 could accelerate data processing in kinetic and time-resolved crystallographic studies, and as well foster the identification of drug-targetable states in ligand-based crystallography. The software Xtrapol8 extracts low occupancy states and can thereby accelerate and facilitate data processing in kinetic, timeresolved and ligand-based crystallographic studies.
引用
收藏
页数:11
相关论文
共 37 条
[1]   Bulk-solvent and overall scaling revisited: faster calculations, improved results [J].
Afonine, P. V. ;
Grosse-Kunstleve, R. W. ;
Adams, P. D. ;
Urzhumtsev, A. .
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2013, 69 :625-634
[2]   Real-space refinement in PHENIX for cryo-EM and crystallography [J].
Afonine, Pavel V. ;
Poon, Billy K. ;
Read, Randy J. ;
Sobolev, Oleg V. ;
Terwilliger, Thomas C. ;
Urzhumtsev, Alexandre ;
Adams, Paul D. .
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2018, 74 :531-544
[3]   Towards automated crystallographic structure refinement with phenix.refine [J].
Afonine, Pavel V. ;
Grosse-Kunstleve, Ralf W. ;
Echols, Nathaniel ;
Headd, Jeffrey J. ;
Moriarty, Nigel W. ;
Mustyakimov, Marat ;
Terwilliger, Thomas C. ;
Urzhumtsev, Alexandre ;
Zwart, Peter H. ;
Adams, Paul D. .
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2012, 68 :352-367
[4]   Advances and challenges in time-resolved macromolecular crystallography [J].
Branden, Gisela ;
Neutze, Richard .
SCIENCE, 2021, 373 (6558)
[5]   Crystallography & NMR system:: A new software suite for macromolecular structure determination [J].
Brunger, AT ;
Adams, PD ;
Clore, GM ;
DeLano, WL ;
Gros, P ;
Grosse-Kunstleve, RW ;
Jiang, JS ;
Kuszewski, J ;
Nilges, M ;
Pannu, NS ;
Read, RJ ;
Rice, LM ;
Simonson, T ;
Warren, GL .
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 1998, 54 :905-921
[6]   Shoot-and-Trap: Use of specific x-ray damage to study structural protein dynamics by temperature-control led cryo-crystallography [J].
Colletier, Jacques-Philippe ;
Bourgeois, Dominique ;
Sanson, Benoit ;
Fournier, Didier ;
Sussman, Joel L. ;
Silman, Israel ;
Weik, Martin .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2008, 105 (33) :11742-11747
[7]   Use of a 'caged' analogue to study the traffic of choline within acetylcholinesterase by kinetic crystallography [J].
Colletier, Jacques-Philippe ;
Royant, Antoine ;
Specht, Alexandre ;
Sanson, Benoit ;
Nachon, Florian ;
Masson, Patrick ;
Zaccai, Giuseppe ;
Sussman, Joel L. ;
Goeldner, Maurice ;
Silman, Israel ;
Bourgeois, Dominique ;
Weik, Martin .
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2007, 63 :1115-1128
[8]  
Coquelle N, 2018, NAT CHEM, V10, P31, DOI [10.1038/NCHEM.2853, 10.1038/nchem.2853]
[9]  
De Zitter E., XTRAPOL8 V0 9 5 BETA, DOI [10.5281/ZENODO.6560832(2022, DOI 10.5281/ZENODO.6560832(2022]
[10]   Mechanistic investigation of mEos4b reveals a strategy to reduce track interruptions in sptPALM [J].
De Zitter, Elke ;
Thedie, Daniel ;
Monkemoller, Viola ;
Hugelier, Siewert ;
Beaudouin, Joel ;
Adam, Virgile ;
Byrdin, Martin ;
Van Meervelt, Luc ;
Dedecker, Peter ;
Bourgeois, Dominique .
NATURE METHODS, 2019, 16 (08) :707-+