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
- Yale Univ., New Haven, CT (USA)
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.
- OSTI ID:
- 6944913
- Journal Information:
- Journal of the American Chemical Society; (USA), Journal Name: Journal of the American Chemical Society; (USA) Vol. 112:3; ISSN 0002-7863; ISSN JACSA
- Country of Publication:
- United States
- Language:
- English
Similar Records
Structural consequences of nickel versus macrocycle reductions in F430 models: EXAFS studies of a Ni(I) anion and Ni(II). pi. anion radicals
Spectroscopic and computational studies of reduction of the metalversus the tetrapyrrole ring of coenzyme F-430 from methyl-coenzyme Mreductase
Related Subjects
400201* -- Chemical & Physicochemical Properties
550500 -- Metabolism
59 BASIC BIOLOGICAL SCIENCES
AZOLES
BACTERIA
CALCULATION METHODS
CARBOXYLIC ACIDS
CONFORMATIONAL CHANGES
DATA ANALYSIS
ELEMENTS
GEOMETRY
HETEROCYCLIC ACIDS
HETEROCYCLIC COMPOUNDS
MATHEMATICAL MODELS
MATHEMATICS
METALS
METHANOGENIC BACTERIA
MICROORGANISMS
NICKEL
ORGANIC ACIDS
ORGANIC COMPOUNDS
ORGANIC NITROGEN COMPOUNDS
PORPHYRINS
PYRROLES
TRANSITION ELEMENTS