Literature DB >> 16547137

Extended subnanosecond structural dynamics of myoglobin revealed by Laue crystallography.

Dominique Bourgeois1, Beatrice Vallone, Alessandro Arcovito, Giuliano Sciara, Friedrich Schotte, Philip A Anfinrud, Maurizio Brunori.   

Abstract

Work carried out over the last 30 years unveiled the role of structural dynamics in controlling protein function. Cavity networks modulate structural dynamics trajectories and are functionally relevant; in globins they have been assigned a role in ligand migration and docking. These findings raised renewed interest for time-resolved structural investigations of myoglobin (Mb), a simple heme protein displaying a photosensitive iron-ligand bond. Photodissociation of MbCO generates a nonequilibrium population of protein structures relaxing over a time range extending from picoseconds to milliseconds. This process triggers ligand migration to matrix cavities with clear-cut effects on the rate and yield of geminate rebinding. Here, we report subnanosecond time-resolved Laue diffraction data on the triple mutant YQR-Mb [Leu-29(B10)Tyr, His-64(E7)Gln, Thr-67(E10)Arg] that depict the sequence of structural events associated with heme and protein relaxation from 100 ps to 316 ns and above. The photodissociated ligand rapidly (<0.1 ns) populates the Xe-binding cavity distal to the heme. Moreover, the heme relaxation toward the deoxy configuration is heterogeneous, with a slower phase ( approximately ns) evident in these experiments. Damping of the heme response appears to result from a strain exerted by the E-helix via the CD-turn; Phe-43(CD1), in close contact with heme, opposes tilt until the strain is relieved. A comparison with crystallographic data on wild-type Mb and mutants Leu(29)Phe or Leu(29)Trp suggests that the internal structure controls the rate and amplitude of the relaxation events. A correlation between structural dynamics as unveiled by Laue crystallography and functional properties of Mb is presented.

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Year:  2006        PMID: 16547137      PMCID: PMC1458771          DOI: 10.1073/pnas.0508880103

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


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

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Journal:  Biochemistry       Date:  1991-04-23       Impact factor: 3.162

4.  Ligand binding and protein relaxation in heme proteins: a room temperature analysis of NO geminate recombination.

Authors:  J W Petrich; J C Lambry; K Kuczera; M Karplus; C Poyart; J L Martin
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.  Ligand migration in sperm whale myoglobin.

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

7.  Ligand migration pathway and protein dynamics in myoglobin: a time-resolved crystallographic study on L29W MbCO.

Authors:  Marius Schmidt; Karin Nienhaus; Reinhard Pahl; Angela Krasselt; Spencer Anderson; Fritz Parak; G Ulrich Nienhaus; Vukica Srajer
Journal:  Proc Natl Acad Sci U S A       Date:  2005-08-05       Impact factor: 11.205

8.  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

9.  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

10.  Distal pocket residues affect picosecond ligand recombination in myoglobin. An experimental and molecular dynamics study of position 29 mutants.

Authors:  Q H Gibson; R Regan; R Elber; J S Olson; T E Carver
Journal:  J Biol Chem       Date:  1992-11-05       Impact factor: 5.157

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  36 in total

1.  Picosecond primary structural transition of the heme is retarded after nitric oxide binding to heme proteins.

Authors:  Sergei G Kruglik; Byung-Kuk Yoo; Stefan Franzen; Marten H Vos; Jean-Louis Martin; Michel Negrerie
Journal:  Proc Natl Acad Sci U S A       Date:  2010-07-19       Impact factor: 11.205

2.  Full kinetics of CO entry, internal diffusion, and exit in myoglobin from transition-path theory simulations.

Authors:  Tang-Qing Yu; Mauro Lapelosa; Eric Vanden-Eijnden; Cameron F Abrams
Journal:  J Am Chem Soc       Date:  2015-02-23       Impact factor: 15.419

Review 3.  Ligand recombination and a hierarchy of solvent slaved dynamics: the origin of kinetic phases in hemeproteins.

Authors:  Uri Samuni; David Dantsker; Camille J Roche; Joel M Friedman
Journal:  Gene       Date:  2007-05-10       Impact factor: 3.688

Review 4.  Application of structural dynamic approaches provide novel insights into the enzymatic mechanism of the tumor necrosis factor-alpha-converting enzyme.

Authors:  Irit Sagi; Marcos E Milla
Journal:  Anal Biochem       Date:  2007-09-26       Impact factor: 3.365

5.  The RATIO method for time-resolved Laue crystallography.

Authors:  Philip Coppens; Mateusz Pitak; Milan Gembicky; Marc Messerschmidt; Stephan Scheins; Jason Benedict; Shin Ichi Adachi; Tokushi Sato; Shunsuke Nozawa; Kohei Ichiyanagi; Matthieu Chollet; Shin Ya Koshihara
Journal:  J Synchrotron Radiat       Date:  2009-01-10       Impact factor: 2.616

Review 6.  Time-resolved x-ray crystallography of heme proteins.

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

7.  BioCARS: a synchrotron resource for time-resolved X-ray science.

Authors:  T Graber; S Anderson; H Brewer; Y S Chen; H S Cho; N Dashdorj; R W Henning; I Kosheleva; G Macha; M Meron; R Pahl; Z Ren; S Ruan; F Schotte; V Srajer; P J Viccaro; F Westferro; P Anfinrud; K Moffat
Journal:  J Synchrotron Radiat       Date:  2011-05-12       Impact factor: 2.616

8.  Cluster analysis of time-dependent crystallographic data: Direct identification of time-independent structural intermediates.

Authors:  Konstantin S Kostov; Keith Moffat
Journal:  Biophys J       Date:  2011-01-19       Impact factor: 4.033

Review 9.  Myoglobin strikes back.

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

10.  Identification of Mutational Hot Spots for Substrate Diffusion: Application to Myoglobin.

Authors:  David De Sancho; Adam Kubas; Po-Hung Wang; Jochen Blumberger; Robert B Best
Journal:  J Chem Theory Comput       Date:  2015-04-14       Impact factor: 6.006

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