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Title: Bending of the reduced porphyrin of factor F430 can accommodate a trigonal-bipyramidal geometry at nickel: A conformational analysis of this nickel-containing tetrapyrrole, in reaction to archaebacterial methanogenesis

Abstract

A full search of the conformational space of factor F430 shows that it can easily accommodate both square-planar (SPL) and, by bending, trigonal-bipyramidal (TBP) coordination geometric about nickel. Both Ni(I) species and organometallic Ni(Il) compounds tend to adopt the TBP geometry, and so this bending may be important in enabling facile reduction of the Ni(II) form to a Ni(I) species, observed in the holoenzyme by EPR spectroscopy. A TBP geometry would also be suitable for a Ni(II)-methyl intermediate, which could be formed from the Ni(I) species by abstraction of a methyl group from methyl coenzyme M. These ideas imply that the bent TBP form is probably the conformer bound to the protein and that direct binding of amino acid side chains to Ni is probably not important. Recent biophysical evidence for the protein-bound form of F430 seems to support this view. Of the common biologically significant metals, only Ni is expected to allow the bent conformation to be adopted, and so binding of the bent form may also allow the apoprotein to choose the correctly metalated tetrapyrrole. Porphyrin compounds contract their tetrapyrrole cavity by a characteristic 54 distortion, termed ruffling. The molecular mechanical calculations show that because factor F430 hasmore » two adjacent flexible meso methylene groups it does not need to ruffle in order to contract its cavity. The hole in factor F430 accommodates the larger Ni(Il) high-spin or Ni(I) ions better than the low-spin Ni(ll) form. In the case of Ni(II) low-spin, the cavity contracts with less ruffling than might have been expected; most of the strain energy brought about by contraction is absorbed by distortions involving the saturated meso carbons.« less

Authors:
;  [1]
  1. Yale Univ., New Haven, CT (USA)
Publication Date:
OSTI Identifier:
6944913
Resource Type:
Journal Article
Journal Name:
Journal of the American Chemical Society; (USA)
Additional Journal Information:
Journal Volume: 112:3; Journal ID: ISSN 0002-7863
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY; 59 BASIC BIOLOGICAL SCIENCES; PORPHYRINS; CONFORMATIONAL CHANGES; PYRROLES; CALCULATION METHODS; DATA ANALYSIS; GEOMETRY; MATHEMATICAL MODELS; METHANOGENIC BACTERIA; NICKEL; AZOLES; BACTERIA; CARBOXYLIC ACIDS; ELEMENTS; HETEROCYCLIC ACIDS; HETEROCYCLIC COMPOUNDS; MATHEMATICS; METALS; MICROORGANISMS; ORGANIC ACIDS; ORGANIC COMPOUNDS; ORGANIC NITROGEN COMPOUNDS; TRANSITION ELEMENTS; 400201* - Chemical & Physicochemical Properties; 550500 - Metabolism

Citation Formats

Zimmer, M, and Crabtree, R H. Bending of the reduced porphyrin of factor F430 can accommodate a trigonal-bipyramidal geometry at nickel: A conformational analysis of this nickel-containing tetrapyrrole, in reaction to archaebacterial methanogenesis. United States: N. p., 1990. Web. doi:10.1021/ja00159a027.
Zimmer, M, & Crabtree, R H. Bending of the reduced porphyrin of factor F430 can accommodate a trigonal-bipyramidal geometry at nickel: A conformational analysis of this nickel-containing tetrapyrrole, in reaction to archaebacterial methanogenesis. United States. doi:10.1021/ja00159a027.
Zimmer, M, and Crabtree, R H. Wed . "Bending of the reduced porphyrin of factor F430 can accommodate a trigonal-bipyramidal geometry at nickel: A conformational analysis of this nickel-containing tetrapyrrole, in reaction to archaebacterial methanogenesis". United States. doi:10.1021/ja00159a027.
@article{osti_6944913,
title = {Bending of the reduced porphyrin of factor F430 can accommodate a trigonal-bipyramidal geometry at nickel: A conformational analysis of this nickel-containing tetrapyrrole, in reaction to archaebacterial methanogenesis},
author = {Zimmer, M and Crabtree, R H},
abstractNote = {A full search of the conformational space of factor F430 shows that it can easily accommodate both square-planar (SPL) and, by bending, trigonal-bipyramidal (TBP) coordination geometric about nickel. Both Ni(I) species and organometallic Ni(Il) compounds tend to adopt the TBP geometry, and so this bending may be important in enabling facile reduction of the Ni(II) form to a Ni(I) species, observed in the holoenzyme by EPR spectroscopy. A TBP geometry would also be suitable for a Ni(II)-methyl intermediate, which could be formed from the Ni(I) species by abstraction of a methyl group from methyl coenzyme M. These ideas imply that the bent TBP form is probably the conformer bound to the protein and that direct binding of amino acid side chains to Ni is probably not important. Recent biophysical evidence for the protein-bound form of F430 seems to support this view. Of the common biologically significant metals, only Ni is expected to allow the bent conformation to be adopted, and so binding of the bent form may also allow the apoprotein to choose the correctly metalated tetrapyrrole. Porphyrin compounds contract their tetrapyrrole cavity by a characteristic 54 distortion, termed ruffling. The molecular mechanical calculations show that because factor F430 has two adjacent flexible meso methylene groups it does not need to ruffle in order to contract its cavity. The hole in factor F430 accommodates the larger Ni(Il) high-spin or Ni(I) ions better than the low-spin Ni(ll) form. In the case of Ni(II) low-spin, the cavity contracts with less ruffling than might have been expected; most of the strain energy brought about by contraction is absorbed by distortions involving the saturated meso carbons.},
doi = {10.1021/ja00159a027},
journal = {Journal of the American Chemical Society; (USA)},
issn = {0002-7863},
number = ,
volume = 112:3,
place = {United States},
year = {1990},
month = {1}
}