Literature DB >> 12773621

Ligand dynamics in a protein internal cavity.

Jan M Kriegl1, Karin Nienhaus, Pengchi Deng, Jochen Fuchs, G Ulrich Nienhaus.   

Abstract

We have studied the temperature dependence of the IR stretch bands of carbon monoxide (CO) in the Xe 4 internal cavity of myoglobin mutant L29W-S108L at cryogenic temperatures. Pronounced changes of band areas and positions were analyzed quantitatively by using a simple dynamic model in which CO rotation in the cavity is constrained by a static potential. The librational dynamics of the CO causes a decrease of the total spectral area. A strong local electric field splits the CO stretch absorption into a doublet, indicating that CO can assume opposite orientations in the cavity. With increasing temperature, the two peaks approach each other, because the average angle of the CO with respect to the electric field increases. A combined classical and quantum-mechanical analysis precisely reproduces the observed temperature dependencies of both spectral area and peak shifts. It yields the height of the energy barrier between the two wells associated with opposite CO orientations, V0 approximately 2 kJ/mol, and the frequency of oscillation within a well, omega approximately 25 cm(-1). The electric field in the protein cavity was estimated as 10 MV/cm.

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Year:  2003        PMID: 12773621      PMCID: PMC165831          DOI: 10.1073/pnas.1231856100

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


  20 in total

1.  Protein conformational relaxation and ligand migration in myoglobin: a nanosecond to millisecond molecular movie from time-resolved Laue X-ray diffraction.

Authors:  V Srajer; Z Ren; T Y Teng; M Schmidt; T Ursby; D Bourgeois; C Pradervand; W Schildkamp; M Wulff; K Moffat
Journal:  Biochemistry       Date:  2001-11-20       Impact factor: 3.162

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.  Temperature-derivative spectroscopy: a tool for protein dynamics.

Authors:  J Berendzen; D Braunstein
Journal:  Proc Natl Acad Sci U S A       Date:  1990-01       Impact factor: 11.205

4.  Ultrafast rotation and trapping of carbon monoxide dissociated from myoglobin.

Authors:  M Lim; T A Jackson; P A Anfinrud
Journal:  Nat Struct Biol       Date:  1997-03

5.  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

6.  Ligand binding to heme proteins: II. Transitions in the heme pocket of myoglobin.

Authors:  J R Mourant; D P Braunstein; K Chu; H Frauenfelder; G U Nienhaus; P Ormos; R D Young
Journal:  Biophys J       Date:  1993-10       Impact factor: 4.033

7.  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

8.  Infrared spectroscopy of photodissociated carboxymyoglobin at low temperatures.

Authors:  J O Alben; D Beece; S F Bowne; W Doster; L Eisenstein; H Frauenfelder; D Good; J D McDonald; M C Marden; P P Moh; L Reinisch; A H Reynolds; E Shyamsunder; K T Yue
Journal:  Proc Natl Acad Sci U S A       Date:  1982-06       Impact factor: 11.205

9.  Photolysis-induced structural changes in single crystals of carbonmonoxy myoglobin at 40 K.

Authors:  T Y Teng; V Srajer; K Moffat
Journal:  Nat Struct Biol       Date:  1994-10

10.  Myoglobin, a paradigm in the study of protein dynamics.

Authors:  Fritz G Parak; G Ulrich Nienhaus
Journal:  Chemphyschem       Date:  2002-03-12       Impact factor: 3.102

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  20 in total

1.  Small-world communication of residues and significance for protein dynamics.

Authors:  Ali Rana Atilgan; Pelin Akan; Canan Baysal
Journal:  Biophys J       Date:  2004-01       Impact factor: 4.033

2.  Time-resolved visible and infrared study of the cyano complexes of myoglobin and of hemoglobin I from Lucina pectinata.

Authors:  Jan Helbing; Luigi Bonacina; Ruth Pietri; Jens Bredenbeck; Peter Hamm; Frank van Mourik; Frédéric Chaussard; Alejandro Gonzalez-Gonzalez; Majed Chergui; Cacimar Ramos-Alvarez; Carlos Ruiz; Juan López-Garriga
Journal:  Biophys J       Date:  2004-09       Impact factor: 4.033

3.  Probing electric fields in protein cavities by using the vibrational stark effect of carbon monoxide.

Authors:  Hartwig Lehle; Jan M Kriegl; Karin Nienhaus; Pengchi Deng; Stephanus Fengler; G Ulrich Nienhaus
Journal:  Biophys J       Date:  2004-12-13       Impact factor: 4.033

4.  Protein ligand migration mapped by nonequilibrium 2D-IR exchange spectroscopy.

Authors:  Jens Bredenbeck; Jan Helbing; Karin Nienhaus; G Ulrich Nienhaus; Peter Hamm
Journal:  Proc Natl Acad Sci U S A       Date:  2007-01-29       Impact factor: 11.205

5.  CO migration pathways in cytochrome P450cam studied by molecular dynamics simulations.

Authors:  Liliane Mouawad; Catherine Tetreau; Safwat Abdel-Azeim; David Perahia; Daniel Lavalette
Journal:  Protein Sci       Date:  2007-03-30       Impact factor: 6.725

Review 6.  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

7.  Transient ligand docking sites in Cerebratulus lacteus mini-hemoglobin.

Authors:  Pengchi Deng; Karin Nienhaus; Pasquale Palladino; John S Olson; George Blouin; Luc Moens; Sylvia Dewilde; Eva Geuens; G Ulrich Nienhaus
Journal:  Gene       Date:  2007-04-29       Impact factor: 3.688

8.  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

9.  Vibrational stark effect probes for nucleic acids.

Authors:  Lisa N Silverman; Michael E Pitzer; Peter O Ankomah; Steven G Boxer; Edward E Fenlon
Journal:  J Phys Chem B       Date:  2007-09-18       Impact factor: 2.991

10.  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
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