Literature DB >> 34135339

Ultrafast coherent motion and helix rearrangement of homodimeric hemoglobin visualized with femtosecond X-ray solution scattering.

Yunbeom Lee1,2, Jong Goo Kim1,2, Sang Jin Lee1,2, Srinivasan Muniyappan1,2, Tae Wu Kim1,2, Hosung Ki1,2, Hanui Kim1,2, Junbeom Jo1,2, So Ri Yun1,2, Hyosub Lee1,2, Kyung Won Lee1,2, Seong Ok Kim1,2, Marco Cammarata3, Hyotcherl Ihee4,5.   

Abstract

Ultrafast motion of molecules, particularly the coherent motion, has been intensively investigated as a key factor guiding the reaction pathways. Recently, X-ray free-electron lasers (XFELs) have been utilized to elucidate the ultrafast motion of molecules. However, the studies on proteins using XFELs have been typically limited to the crystalline phase, and proteins in solution have rarely been investigated. Here we applied femtosecond time-resolved X-ray solution scattering (fs-TRXSS) and a structure refinement method to visualize the ultrafast motion of a protein. We succeeded in revealing detailed ultrafast structural changes of homodimeric hemoglobin involving the coherent motion. In addition to the motion of the protein itself, the time-dependent change of electron density of the hydration shell was tracked. Besides, the analysis on the fs-TRXSS data of myoglobin allows for observing the effect of the oligomeric state on the ultrafast coherent motion.

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Year:  2021        PMID: 34135339     DOI: 10.1038/s41467-021-23947-7

Source DB:  PubMed          Journal:  Nat Commun        ISSN: 2041-1723            Impact factor:   14.919


  44 in total

1.  Ligand migration and binding in the dimeric hemoglobin of Scapharca inaequivalvis.

Authors:  Karin Nienhaus; James E Knapp; Pasquale Palladino; William E Royer; G Ulrich Nienhaus
Journal:  Biochemistry       Date:  2007-11-15       Impact factor: 3.162

Review 2.  Time-resolved x-ray crystallography of heme proteins.

Authors:  Vukica Srajer; William E Royer
Journal:  Methods Enzymol       Date:  2008       Impact factor: 1.600

3.  Protein conformational dynamics of homodimeric hemoglobin revealed by combined time-resolved spectroscopic probes.

Authors:  Jungkweon Choi; Srinivasan Muniyappan; John T Wallis; William E Royer; Hyotcherl Ihee
Journal:  Chemphyschem       Date:  2010-01-18       Impact factor: 3.102

4.  Communication maps computed for homodimeric hemoglobin: computational study of water-mediated energy transport in proteins.

Authors:  Ramachandran Gnanasekaran; Johnson K Agbo; David M Leitner
Journal:  J Chem Phys       Date:  2011-08-14       Impact factor: 3.488

5.  Dynamics of cyanide binding to ferrous Scapharca inaequivalvis homodimeric hemoglobin.

Authors:  A Boffi; E Chiancone; E S Peterson; J Wang; D L Rousseau; J M Friedman
Journal:  Biochemistry       Date:  1997-04-15       Impact factor: 3.162

6.  Dynamics of water clusters confined in proteins: a molecular dynamics simulation study of interfacial waters in a dimeric hemoglobin.

Authors:  Ramachandran Gnanasekaran; Yao Xu; David M Leitner
Journal:  J Phys Chem B       Date:  2010-12-02       Impact factor: 2.991

7.  Ligand binding and conformation change in the dimeric hemoglobin of the clam Scapharca inaequivalvis.

Authors:  E Chiancone; R Elber; W E Royer; R Regan; Q H Gibson
Journal:  J Biol Chem       Date:  1993-03-15       Impact factor: 5.157

8.  Degeneration and regeneration of unmyelinated fibers in experimental leprous neuropathy.

Authors:  V P Shetty; N H Antia
Journal:  Int J Lepr Other Mycobact Dis       Date:  1981-09

9.  Kinetics of ligand binding and quaternary conformational change in the homodimeric hemoglobin from Scapharca inaequivalvis.

Authors:  E Antonini; F Ascoli; M Brunori; E Chiancone; D Verzili; R J Morris; Q H Gibson
Journal:  J Biol Chem       Date:  1984-06-10       Impact factor: 5.157

10.  Heme-heme interactions in a homodimeric cooperative hemoglobin. Evidence from transient Raman scattering.

Authors:  D L Rousseau; S Song; J M Friedman; A Boffi; E Chiancone
Journal:  J Biol Chem       Date:  1993-03-15       Impact factor: 5.157

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  6 in total

Review 1.  Reaction dynamics studied via femtosecond X-ray liquidography at X-ray free-electron lasers.

Authors:  Eun Hyuk Choi; Yunbeom Lee; Jun Heo; Hyotcherl Ihee
Journal:  Chem Sci       Date:  2022-06-06       Impact factor: 9.969

2.  Light-induced protein structural dynamics in bacteriophytochrome revealed by time-resolved x-ray solution scattering.

Authors:  Sang Jin Lee; Tae Wu Kim; Jong Goo Kim; Cheolhee Yang; So Ri Yun; Changin Kim; Zhong Ren; Indika Kumarapperuma; Jane Kuk; Keith Moffat; Xiaojing Yang; Hyotcherl Ihee
Journal:  Sci Adv       Date:  2022-05-27       Impact factor: 14.957

3.  Determining the charge distribution and the direction of bond cleavage with femtosecond anisotropic x-ray liquidography.

Authors:  Jun Heo; Jong Goo Kim; Eun Hyuk Choi; Hosung Ki; Doo-Sik Ahn; Jungmin Kim; Seonggon Lee; Hyotcherl Ihee
Journal:  Nat Commun       Date:  2022-01-26       Impact factor: 14.919

4.  Filming ultrafast roaming-mediated isomerization of bismuth triiodide in solution.

Authors:  Eun Hyuk Choi; Jong Goo Kim; Jungmin Kim; Hosung Ki; Yunbeom Lee; Seonggon Lee; Kihwan Yoon; Joonghan Kim; Jeongho Kim; Hyotcherl Ihee
Journal:  Nat Commun       Date:  2021-08-05       Impact factor: 14.919

5.  Tracking the ATP-binding response in adenylate kinase in real time.

Authors:  Fredrik Orädd; Harsha Ravishankar; Jack Goodman; Per Rogne; Lars Backman; Annette Duelli; Martin Nors Pedersen; Matteo Levantino; Michael Wulff; Magnus Wolf-Watz; Magnus Andersson
Journal:  Sci Adv       Date:  2021-11-17       Impact factor: 14.136

6.  Reversible molecular motional switch based on circular photoactive protein oligomers exhibits unexpected photo-induced contraction.

Authors:  Sang Jin Lee; Youngmin Kim; Tae Wu Kim; Cheolhee Yang; Kamatchi Thamilselvan; Hyeongseop Jeong; Jaekyung Hyun; Hyotcherl Ihee
Journal:  Cell Rep Phys Sci       Date:  2021-07-22
  6 in total

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