Literature DB >> 32142641

XFEL and NMR Structures of Francisella Lipoprotein Reveal Conformational Space of Drug Target against Tularemia.

James Zook1, Mrinal Shekhar2, Debra Hansen1, Chelsie Conrad3, Thomas Grant4, Chitrak Gupta1, Thomas White5, Anton Barty5, Shibom Basu6, Yun Zhao7, Nadia Zatsepin1, Andrii Ishchenko8, Alex Batyuk9, Cornelius Gati5, Chufeng Li7, Lorenzo Galli5, Jesse Coe10, Mark Hunter9, Meng Liang9, Uwe Weierstall1, Garret Nelson7, Daniel James11, Benjamin Stauch3, Felicia Craciunescu1, Darren Thifault1, Wei Liu12, Vadim Cherezov8, Abhishek Singharoy13, Petra Fromme14.   

Abstract

Francisella tularensis is the causative agent for the potentially fatal disease tularemia. The lipoprotein Flpp3 has been identified as a virulence determinant of tularemia with no sequence homology outside the Francisella genus. We report a room temperature structure of Flpp3 determined by serial femtosecond crystallography that exists in a significantly different conformation than previously described by the NMR-determined structure. Furthermore, we investigated the conformational space and energy barriers between these two structures by molecular dynamics umbrella sampling and identified three low-energy intermediate states, transitions between which readily occur at room temperature. We have also begun to investigate organic compounds in silico that may act as inhibitors to Flpp3. This work paves the road to developing targeted therapeutics against tularemia and aides in our understanding of the disease mechanisms of tularemia. Published by Elsevier Ltd.

Entities:  

Keywords:  Francisella tularensis; NMR spectroscopy; X-ray crystallography; computational chemistry; drug discovery; intergrative modeling; molecular biophysics; serial femtosecond crystallography

Mesh:

Substances:

Year:  2020        PMID: 32142641      PMCID: PMC9014820          DOI: 10.1016/j.str.2020.02.005

Source DB:  PubMed          Journal:  Structure        ISSN: 0969-2126            Impact factor:   5.871


  44 in total

1.  Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation.

Authors:  Araz Jakalian; David B Jack; Christopher I Bayly
Journal:  J Comput Chem       Date:  2002-12       Impact factor: 3.376

2.  Scalable molecular dynamics with NAMD.

Authors:  James C Phillips; Rosemary Braun; Wei Wang; James Gumbart; Emad Tajkhorshid; Elizabeth Villa; Christophe Chipot; Robert D Skeel; Laxmikant Kalé; Klaus Schulten
Journal:  J Comput Chem       Date:  2005-12       Impact factor: 3.376

3.  AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading.

Authors:  Oleg Trott; Arthur J Olson
Journal:  J Comput Chem       Date:  2010-01-30       Impact factor: 3.376

4.  Prediction of hydrodynamic and other solution properties of rigid proteins from atomic- and residue-level models.

Authors:  A Ortega; D Amorós; J García de la Torre
Journal:  Biophys J       Date:  2011-08-17       Impact factor: 4.033

5.  Simple, yet powerful methodologies for conformational sampling of proteins.

Authors:  Ryuhei Harada; Yu Takano; Takeshi Baba; Yasuteru Shigeta
Journal:  Phys Chem Chem Phys       Date:  2015-03-07       Impact factor: 3.676

Review 6.  Tularemia as a biological weapon: medical and public health management.

Authors:  D T Dennis; T V Inglesby; D A Henderson; J G Bartlett; M S Ascher; E Eitzen; A D Fine; A M Friedlander; J Hauer; M Layton; S R Lillibridge; J E McDade; M T Osterholm; T O'Toole; G Parker; T M Perl; P K Russell; K Tonat
Journal:  JAMA       Date:  2001-06-06       Impact factor: 56.272

7.  Chemomechanical Coupling in Hexameric Protein-Protein Interfaces Harnesses Energy within V-Type ATPases.

Authors:  Abhishek Singharoy; Christophe Chipot; Mahmoud Moradi; Klaus Schulten
Journal:  J Am Chem Soc       Date:  2016-12-23       Impact factor: 15.419

8.  The crystal structure of the Escherichia coli lipocalin Blc suggests a possible role in phospholipid binding.

Authors:  Valérie Campanacci; Didier Nurizzo; Silvia Spinelli; Christel Valencia; Mariella Tegoni; Christian Cambillau
Journal:  FEBS Lett       Date:  2004-03-26       Impact factor: 4.124

9.  Francisella tularensis Confronts the Complement System.

Authors:  Susan R Brock; Michael J Parmely
Journal:  Front Cell Infect Microbiol       Date:  2017-12-19       Impact factor: 5.293

10.  Recent developments in CrystFEL.

Authors:  Thomas A White; Valerio Mariani; Wolfgang Brehm; Oleksandr Yefanov; Anton Barty; Kenneth R Beyerlein; Fedor Chervinskii; Lorenzo Galli; Cornelius Gati; Takanori Nakane; Alexandra Tolstikova; Keitaro Yamashita; Chun Hong Yoon; Kay Diederichs; Henry N Chapman
Journal:  J Appl Crystallogr       Date:  2016-03-29       Impact factor: 3.304

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  3 in total

1.  Data-guided Multi-Map variables for ensemble refinement of molecular movies.

Authors:  John W Vant; Daipayan Sarkar; Ellen Streitwieser; Giacomo Fiorin; Robert Skeel; Josh V Vermaas; Abhishek Singharoy
Journal:  J Chem Phys       Date:  2020-12-07       Impact factor: 3.488

2.  CryoFold: determining protein structures and data-guided ensembles from cryo-EM density maps.

Authors:  Mrinal Shekhar; Genki Terashi; Chitrak Gupta; Daipayan Sarkar; Gaspard Debussche; Nicholas J Sisco; Jonathan Nguyen; Arup Mondal; John Vant; Petra Fromme; Wade D Van Horn; Emad Tajkhorshid; Daisuke Kihara; Ken Dill; Alberto Perez; Abhishek Singharoy
Journal:  Matter       Date:  2021-09-22

Review 3.  The surface lipoproteins of gram-negative bacteria: Protectors and foragers in harsh environments.

Authors:  Gregory B Cole; Thomas J Bateman; Trevor F Moraes
Journal:  J Biol Chem       Date:  2020-12-10       Impact factor: 5.157

  3 in total

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