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

 

 

 

 

 

 

 

 

Palanichamy Manikandan, Paul Ellis, Peter Kuhn, Eun-Young Choi, Brian Hoffman & Russ Hille*

 

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.

 

 

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

 

 

 

Marcellus Ubbink

 

 

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.

 

46

New insights into lignin peroxidase

 

 

 

 

 

 

Klaus Piontek

 

 

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.

 

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

 

 

Copper aminoglycosides are highly efficient DNA and RNA cleavage agents and show considerable promise for the development of novel anti-viral agents.

73

Abstracts of Lectures

 

 

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 non-phenolic 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