Macromolecular crystallography in India. A historical overview

India has a distinguished tradition in crystallography and structural biology. However, biological macromolecular crystallography in the country has had a somewhat delayed start on account of paucity of adequate funds and insufficient interactions between crystallographers and biochemists. Preliminary results in the area began to appear in the early eighties. The support provided by the Department of Science & Technology in the mid eighties under its thrust area programme for macromolecular crystallographic studies at the Molecular Biophysics Unit of the Indian Institute of Science gave a major impetus to work in the area. The Bangalore centre also came to be recognised as a national nucleus for the development of the area in the country. Since then, over the years, biological macromolecular crystallography has grown into a major activity in India encompassing nearly 20 institutions and close to twice as many research groups. It is also now at the centre stage of modern biological research in India. The problems addressed by biological crystallographers in the country span a wide spectrum and their efforts have made considerable international impact. Collective initiatives such as those involving microbial pathogens and structure-based inhibitor design have also begun to emerge

Structural genomics of microbial pathogens - an Indian programme

Structural genomics, simply stated, seeks to determine the structures of all proteins coded by genomes of known sequence, using X-ray crystallography, NMR and bioinformatics. The known principles of protein architecture and the available information on the structural and functional classification of proteins, make this an approachable objective. The early excessive preoccupation with folds has now been substantially overcome. The emphasis is now on the determination of a collection of related proteins coded by a given genome or a set of similar proteins coded by different genomes. Taking advantage of the existing strengths in the country, a national programme on the structural genomics of microbial pathogens is being pursued. A major component of the programme is concerned with proteins from Mycobacterium tuberculosis. Comparative structural genomics of viruses forms another important component. Although not part of the concerted effort, structural studies on proteins from parasites are also gathering momentum. India has reasonably well-equipped laboratories for carrying out the programme. A major lacuna in the effort is caused by the absence of an Indian synchrotron X-ray facility. The results obtained so far in the programme have been encouraging. Particular attention is being paid to marry the requirements of quantity and quality. The overall objective of the programme is to advance our detailed understanding of selected microbial pathogens at the molecular level and to promote applications that flow from it where possible, under the overall umbrella provided by the genomics effort in the country

Structural mobility and transformations in globular proteins

Although globular proteins are endowed with well defined three-dimensional structures, they exhibit substantial mobility within the framework of the given three-dimensional structure. The different types of mobility found in proteins by and large correspond to the different levels of organisational hierarchy in protein architecture. They are of considerable structural and functional significance, and can be broadly classified into (a) thermal and conformational fluctuations, (b) segmental mobility, (c) interdomain mobility and (d) intersubunit mobility. Protein crystallographic studies has provided a wealth of information on all of them. The temperature factors derived from X-ray diffraction studies provide a measure of atomic displacements caused by thermal and conformational fluctuations. The variation of displacement along the polypeptide chain have provided functionally significant information on the flexibility of different regions of the molecule in proteins such as myoglobin, lysozyme and prealbumin. Segmental mobility often involves the movement of a region or a segment of a molecule with respect to the rest, as in the transition between the apo and the holo structures of lactate dehydrogenase. It may also involve rigidification of a disordered region of the molecule as in the activation of the zymogens of serine proteases. Transitions between the apo and the holo structures of alcohol dehydrogenase, and between the free and the sugar bound forms of hexokinase, are good examples of interdomain mobility caused by hinge-bending. The capability of different domains to move semi-independently contributes greatly to the versatility of immunoglobulin molecules. Interdomain mobility in citrate synthase appears to be more complex and its study has led to an alternative description of domain closure. The classical and the most thoroughly studied case of intersubunit mobility is that in haemoglobin. The stereochemical mechanism of the action of this allosteric protein clearly brings out the functional subtilities that could be achieved through intersubunit movements. In addition to ligand binding and activation, environmental changes also often cause structural transformations. The reversible transformation between 2 Zn insulin and 4 Zn insulin is caused by changes in the ionic strength of the medium. Adenylate Kinase provides a good example for functionally significant reversible conformational transitions induced by variation in pH. Available evidences indicate that reversible structural transformations in proteins could also be caused by changes in the aqueous environment, including those in the amount of water surrounding protein molecules