Literature DB >> 12847289

Complex landscape of protein structural dynamics unveiled by nanosecond Laue crystallography.

Dominique Bourgeois1, Beatrice Vallone, Friedrich Schotte, Alessandro Arcovito, Adriana E Miele, Giuliano Sciara, Michael Wulff, Philip Anfinrud, Maurizio Brunori.   

Abstract

Although conformational changes are essential for the function of proteins, little is known about their structural dynamics at atomic level resolution. Myoglobin (Mb) is the paradigm to investigate conformational dynamics because it is a simple globular heme protein displaying a photosensitivity of the iron-ligand bond. Upon laser photodissociation of carboxymyoglobin Mb a nonequilibrium population of protein structures is generated that relaxes over a broad time range extending from picoseconds to milliseconds. This process is associated with migration of the ligand to cavities in the matrix and with a reduction in the geminate rebinding rate by several orders of magnitude. Here we report nanosecond time-resolved Laue diffraction data to 1.55-A resolution on a Mb mutant, which depicts the sequence of structural events associated with this extended relaxation. Motions of the distal E-helix, including the mutated residue Gln-64(E7), and of the CD-turn are found to lag significantly (100-300 ns) behind local rearrangements around the heme such as heme tilting, iron motion out of the heme plane, and swinging of the mutated residue Tyr-29(B10), all of which occur promptly (< or =3 ns). Over the same delayed time range, CO is observed to migrate from a cavity distal to the heme known to bind xenon (called Xe4) to another such cavity proximal to the heme (Xe1). We propose that the extended relaxation of the globin moiety reflects reequilibration among conformational substates known to play an essential role in controlling protein function.

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Year:  2003        PMID: 12847289      PMCID: PMC166376          DOI: 10.1073/pnas.1430900100

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  29 in total

1.  Towards automated Laue data processing: application to the choice of optimal X-ray spectrum.

Authors:  D Bourgeois; U Wagner; M Wulff
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2000-08

2.  The effect of ligand dynamics on heme electronic transition band III in myoglobin.

Authors:  Karin Nienhaus; Don C Lamb; Pengchi Deng; G Ulrich Nienhaus
Journal:  Biophys J       Date:  2002-02       Impact factor: 4.033

3.  Slaving: solvent fluctuations dominate protein dynamics and functions.

Authors:  P W Fenimore; H Frauenfelder; B H McMahon; F G Parak
Journal:  Proc Natl Acad Sci U S A       Date:  2002-11-20       Impact factor: 11.205

4.  Ligand binding to heme proteins: connection between dynamics and function.

Authors:  P J Steinbach; A Ansari; J Berendzen; D Braunstein; K Chu; B R Cowen; D Ehrenstein; H Frauenfelder; J B Johnson; D C Lamb
Journal:  Biochemistry       Date:  1991-04-23       Impact factor: 3.162

5.  The energy landscapes and motions of proteins.

Authors:  H Frauenfelder; S G Sligar; P G Wolynes
Journal:  Science       Date:  1991-12-13       Impact factor: 47.728

6.  An extensively modified version of MolScript that includes greatly enhanced coloring capabilities.

Authors:  R M Esnouf
Journal:  J Mol Graph Model       Date:  1997-04       Impact factor: 2.518

7.  Ligand migration in sperm whale myoglobin.

Authors:  E E Scott; Q H Gibson
Journal:  Biochemistry       Date:  1997-09-30       Impact factor: 3.162

8.  The role of cavities in protein dynamics: crystal structure of a photolytic intermediate of a mutant myoglobin.

Authors:  M Brunori; B Vallone; F Cutruzzola; C Travaglini-Allocatelli; J Berendzen; K Chu; R M Sweet; I Schlichting
Journal:  Proc Natl Acad Sci U S A       Date:  2000-02-29       Impact factor: 11.205

9.  Cavities in proteins: structure of a metmyoglobin-xenon complex solved to 1.9 A.

Authors:  R F Tilton; I D Kuntz; G A Petsko
Journal:  Biochemistry       Date:  1984-06-19       Impact factor: 3.162

10.  Mapping the pathways for O2 entry into and exit from myoglobin.

Authors:  E E Scott; Q H Gibson; J S Olson
Journal:  J Biol Chem       Date:  2000-10-03       Impact factor: 5.157

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  63 in total

Review 1.  Myoglobin: the hydrogen atom of biology and a paradigm of complexity.

Authors:  H Frauenfelder; B H McMahon; P W Fenimore
Journal:  Proc Natl Acad Sci U S A       Date:  2003-07-14       Impact factor: 11.205

2.  Extended molecular dynamics simulation of the carbon monoxide migration in sperm whale myoglobin.

Authors:  Cecilia Bossa; Massimiliano Anselmi; Danilo Roccatano; Andrea Amadei; Beatrice Vallone; Maurizio Brunori; Alfredo Di Nola
Journal:  Biophys J       Date:  2004-06       Impact factor: 4.033

3.  Bulk-solvent and hydration-shell fluctuations, similar to alpha- and beta-fluctuations in glasses, control protein motions and functions.

Authors:  P W Fenimore; Hans Frauenfelder; B H McMahon; R D Young
Journal:  Proc Natl Acad Sci U S A       Date:  2004-09-24       Impact factor: 11.205

4.  Photochemical tools to study dynamic biological processes.

Authors:  Alexandre Specht; Frédéric Bolze; Ziad Omran; Jean-François Nicoud; Maurice Goeldner
Journal:  HFSP J       Date:  2009-05-22

5.  NO binding kinetics in myoglobin investigated by picosecond Fe K-edge absorption spectroscopy.

Authors:  Mahsa Silatani; Frederico A Lima; Thomas J Penfold; Jochen Rittmann; Marco E Reinhard; Hannelore M Rittmann-Frank; Camelia Borca; Daniel Grolimund; Christopher J Milne; Majed Chergui
Journal:  Proc Natl Acad Sci U S A       Date:  2015-10-05       Impact factor: 11.205

6.  Imaging the migration pathways for O2, CO, NO, and Xe inside myoglobin.

Authors:  Jordi Cohen; Anton Arkhipov; Rosemary Braun; Klaus Schulten
Journal:  Biophys J       Date:  2006-06-02       Impact factor: 4.033

7.  Exploring the common dynamics of homologous proteins. Application to the globin family.

Authors:  Sandra Maguid; Sebastian Fernandez-Alberti; Leticia Ferrelli; Julian Echave
Journal:  Biophys J       Date:  2005-03-04       Impact factor: 4.033

8.  Membrane-induced changes in the holomyoglobin tertiary structure: interplay with function.

Authors:  Liana V Basova; Elisaveta I Tiktopulo; Victor P Kutyshenko; Stanislav I Klenin; Vitalii A Balobanov; Valentina E Bychkova
Journal:  Eur Biophys J       Date:  2014-05-11       Impact factor: 1.733

9.  An engineered heme-copper center in myoglobin: CO migration and binding.

Authors:  Karin Nienhaus; John S Olson; G Ulrich Nienhaus
Journal:  Biochim Biophys Acta       Date:  2013-02-28

Review 10.  Myoglobin strikes back.

Authors:  Maurizio Brunori
Journal:  Protein Sci       Date:  2010-02       Impact factor: 6.725

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