Indian Journal of Chemistry
Sect. A: Inorganic, Bio-inorganic, Physical, Theoretical & Analytical
VOLUME 41A
NUMBER 1
JANUARY 2002
CONTENTS
Papers
13
Zn catalyzed alkyl-transfer reactions: A new
class of biological Zn sites
James E Penner-Hahn
22
Structure/function studies of arsenite
oxidoreductase and xanthine oxidase
Recently solved X-ray crystal structure of the molybdenumcontaining arsenite oxidoreductase from Alcaligenes
faecalis is discussed keeping in view the known
mechanistic and spectroscopic information regarding the
protein in a structural context. In addition, recent
mechanistic studies of xanthine oxidase are covered, with
the conclusion that the reaction mechanism is initiated by
nucleophilic attack of a Mo-OH group on substrate.
Palanichamy Manikandan, Paul Ellis, Peter
Kuhn, Eun-Young Choi, Brian Hoffman &
Russ Hille*
32
Oxygen utilization by nonvertebrate globins: A
resonance Raman investigation
Tapan Kanti Das
Resonance Raman spectroscopy
reveals how nature
tinkered the active site structure of globins to accomplish
diverse biological functions.
39
Dynamics in the electron transfer complexes of
plastocyanin with cytochrome f and
cytochrome c
Electron transfer complexes are short-lived and the
dynamics within the complex vary from highly disordered
to a single, well-defined complex. The dynamics can be
probed with NMR.
Marcellus Ubbink
46
New insights into lignin peroxidase
During the past three years, based on structural-functional
investigations, a wealth of new information about the
haem containing enzyme lignin peroxidase has been
accumulated. In this mini-review an overview of the
corresponding work is given with emphasis on substrate
interaction and redox activity.
Klaus Piontek
54
Metal ions and the thermodynamics and
kinetics of tertiary RNA folding
Tobin Sosnick*, Tao Pan, Xingwang Fang,
Valerie Shelton, P Thiyagarajan & K Littrel
65
An inorganic approach to drug design: Novel
inorganic nucleases
J A Cowan
73
Abstracts of Lectures
Copper aminoglycosides are highly efficient DNA and
RNA cleavage agents and show considerable promise for
the development of novel anti-viral agents.
98
Posters
Authors for correspondence are indicated by (*)
Indian Journal of Chemistry
Vol. 41A, January 2002, p.p 13-21
Zn catalyzed alkyl-transfer reactions: A new class of biological Zn sites
James E Penner-Hahn
The use of X-ray absorption to characterize a novel class of Zn alkyl-transfer enzymes is illustrated,
using examples taken from the recent literature, with emphasis on characterization of the Zn sites in the
methionine synthase enzymes. By probing directly the structure of the Zn site, X-ray spectroscopy was
used to demonstrate that Zn is intimately involved in the catalytic reaction of both the MetE and the MetH
methionine synthases. From extended X-ray absorption fine structure (EXAFS) measurements, it is
possible to demonstrate that thiolate-containing substrates bind directly to the Zn site. Although EXAFS is
limited in its ability to characterize individual ligands, the combination of EXAFS with site directed
mutagenesis is able to identify the specific amino acids that are bound to the Zn in methionine synthase.
Recent results using X-ray absorption near edge structure (XANES) suggest intriguing geometrical
difference between the Zn sites of related alkyl-transfer enzymes.
Indian Journal of Chemistry
Vol. 41A, January 2002, pp. 22-31
Structure/function studies of arsenite oxidoreductase and xanthine oxidase
Palanichamy Manikandan, Paul Ellis, Peter Kuhn, Eun-Young Choi, Brian Hoffman &Russ Hille
The recently solved X-ray crystal structure of the molybdenum-containing arsenite oxidoreductase
from Alcaligenes faecalis, is discussed, keeping in view the known mechanistic and spectroscopic
information regarding the protein in a structural context. In addition, recent mechanistic studies of
xanthine oxidase are covered, with the conclusion that the reaction mechanism is initiated by nucleophilic
attack of a Mo-OH group on substrate.
Indian Journal of Chemistry
Vol. 41A, January 2002, pp. 32-38
Oxygen utilization by nonvertebrate globins: A resonance Raman
investigation
Tapan Kanti Das
There has been a renewed interest in understanding the function of hemoglobins in recent years because
of their diverse cellular locations and unique physical properties. Although the nonvertebrate hemoglobins
bind dioxygen and other ligands just as the vertebrate hemoglobins, the kinetic and structural properties of
the oxygen complexes differ significantly suggesting functional diversity. This paper describes our recent
work on a series of nonvertebrate hemoglobins using state-of-the-art resonance Raman spectroscopy with the
aim of deciphering various biological oxygen utilization mechanisms.
Indian Journal of Chemistry
Vol. 41A, January 2002, pp. 39-45
Dynamics in the electron transfer complexes of plastocyanin with
cytochrome f and cytochrome c
Marcellus Ubbink
The complex of the photosynthetic redox proteins plastocyanin and cytochrome f is compared with
that of plastocyanin and cytochrome c. On the basis of nuclear magnetic resonance chemical shift data, it
is concluded that the dynamics of the two complexes differs greatly. The complex of plastocyanin and
cytochrome f exists predominantly in a single orientation, stabilised by both electrostatic and hydrophobic
interactions. The complex of plastocyanin and cytochrome c consists of an ensemble of orientations of a
purely electrostatic nature. The results explain the differences in reaction rates between the complexes.
Indian Journal of Chemistry
Vol. 41A, January 2002, pp. 46-53
New insights into lignin peroxidase
Klaus Piontek
Lignin peroxidase an extracellular haem containing gylcoprotein is able to oxidise nonphenolic aromatic compounds with redox potentials exceeding 1.4 V. This enzyme is employed by
ligninolytic fungi to degrade the recalcitrant bio-polymer lignin, a cell wall constituent of woody plants.
Due to its enlarged substrate range in the presence of specific mediators and due to its high redox potential
this enzyme has the potentiality for the application in various industrial processes. But, until recently
information concerning the binding mode of the substrate with the enzyme was lacking, therefore
hampering progress in the elucidation of the catalytic mechanism. The finding of an unprecedented amino
acid modification at a surface tryptophan initiated several investigations during the past few years on the
role of this residue, which resulted in the identification of two distinct substrate interaction sites in lignin
peroxidase. This mini-review summarises the major outcome of these investigations and describes the
underlying structural factors that govern substrate interaction and electron transfer in lignin peroxidase.
Indian Journal of Chemistry
Vol. 41A, January 2002, pp. 54-64
Metal ions and the thermodynamics and kinetics of tertiary RNA
folding
Tobin Sosnick, Tao Pan, Xingwang Fang, Valerie Shelton, P Thiyagarajan & K Littrel
Divalent cations play a fundamental role in the stability and folding of tertiary RNAs. We have
applied multiple spectroscopic, chemical and enzymatic probes to examine the cooperativity and stability
of tertiary RNAs. We present a framework to quantify the free energy for tertiary RNA folding using
Mg2+ and urea titrations. We describe the compaction process along the Mg-induced thermodynamic
folding pathway. The kinetic pathway of this and other large RNAs is complex and often fraught with
multiple kinetic traps. Intermediates can exist on certain pathways and folding can be under kinetic
control. However, we show that a large ribozyme can fold all the way to the biological active state in 0.1
second (orders of magnitude faster than previously observed) without falling into kinetic traps. We
introduce the Mg2+ and urea “chevron” plots and conduct the first complete, quantitative analysis of
tertiary RNA folding pathway. A folding scheme containing two kinetic intermediates accounts for all the
free energy, number of bound Mg2+ ions, and surface burial of the equilibrium transition. The folding of
this ribozyme is best described by a classical pathway populated by discrete intermediates. These results
indicate that the conformational search in tertiary RNA folding can be very fast and occur along a smooth
energy landscape.
Indian Journal of Chemistry
Vol. 41A, January 2002, pp. 65-72
An inorganic approach to drug design: Novel inorganic nucleases
J A Cowan
Copper aminoglycosides are demonstrated to be highly efficient cleavage catalysts for DNA and RNA
targets. Such catalysts mediate both oxidative and hydrolytic pathways and their cleavage reactions display
enzyme-like Michaelis-Menten kinetic behaviour. An unusual double-strand cleavage of DNA has been
observed. Degradation of RNA viral motifs have been demonstrated in vitro, and the efficacy of such
molecules against an in vivo target has also been established using a novel in vivo assay. Chemical
mechanisms underlying the cleavage of RNA and DNA targets, recognition strategies, mechanisms of
cellular delivery, and the design of in vivo assays have been presented.
Indian Journal of Chemistry
Vol. 41A, January 2002, pp. 73-97
Lecture abstracts
Indian Journal of Chemistry
Vol. 41A, January 2002, pp. 98-142
Posters