Research in biophysics had an early startin India in the late nineteenth centurywhen the renowned physicist J.C. Bosebegan his pioneering work on the

behaviour of cells under external stimulii. He alsoinvented many delicate and sensitive instruments.The best known among them is the crescograph forrecording plant growth.

Among the modern biophysicists of India, andindeed of the world, the name of G.N. Ramachandranstands out as the most outstanding scientist to haveworked in Independent India. The structure of thefibrous protein collagen, proposed by him andGopinath Kartha in the first half of the 1950s, has beenan intellectual achievement of the highest order andhas stood the test of time. The Ramachandran plot,devised in the early 1960s, still remains the simplestand the most commonly used descriptor and versatiletool for the validation of protein structures. Hiscontributions to the foundations of crystallographyhave been immense and in the area of imagereconstruction he made major contributions. Heinitiated and pursued conformational studies on allmajor biopolymers and laid the foundations of thecurrently thriving field of molecular modelling. Hefounded two renowned schools of biophysics andstructural biology, one at Chennai and the other atBangalore. Although Ramachandran left the fieldnearly a quarter of a century ago and died recently,his work continues to exert great influence onstructural studies of biomolecules.

N.N. Dasgupta of Kolkata has been anotherpioneer in the field of biophysics in India. Heconstructed an electron microscope in the middle ofthe last century and, among other things, visualisedthe cholera phage DNA. Another leading scientistassociated with the early development of biophysicsin the country has been A.R. Gopal-Iyengar who,working at Mumbai, made outstanding contributionsin the basic and the applied aspects of radiobiology,radiation biophysics, cellular biophysics and relatedareas. Both of them left behind flourishing schools ofbiophysics. The others involved in pioneering effortsin the 1950s and the 1960s include D.M. Bose, N.N.Saha, S.N. Chatterjee, R.K. Poddar (all from Kolkata),S.R. Bawa (Chandigarh), R.K. Mishra (Delhi) and K.S.Korgaonkar (Mumbai).

In addition to the students and colleagues ofthe early pioneers of biophysics in the country, asubstantial section of the present leaders ofbiophysics and structural biology in India enteredthe field through doctoral or postdoctoral studiesat leading schools in different parts of the world.Thus, the biophysics and structural biologycommunity in India today is a vibrant mosaic madeup of different strands of traditions and expertise.

CURRENT STATUS

Today, close to a hundred research groups distrib-uted in different institutions in the country are

engaged in research in the field of biophysics.Among them, they cover almost all aspects of bio-

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BIOPHYSICS AND STRUCTURALBIOLOGY

C H A P T E R X I X

physics, especially at the molecular level. The rangeof activities is so extensive that it is impossible tocover all of them in a brief summary and the fact thatthe boundaries of biophysics are too porous to bedefined makes the task all the more difficult. Theeffort here, therefore, is to give a gist of current bio-physics research in India without making anyattempt to be comprehensive. The strongest compo-nent of biophysics research in the country, and per-haps in the world, is concerned with molecular bio-physics which, in modern parlance, is called struc-tural biology. The emphasis here would thus be nat-urally on structural biology.

Proteins and Peptides: G.N. Ramachandran and hiscolleagues were pioneers in structural studies onproteins at the international level. Much of theirwork has been computational or theoretical. Themost important approach to studies on proteinstructure involves biological macromolecularcrystallography. Work in this area was initiated earlyin the 1980s at the Indian Institute of Science (IISc)Bangalore, and the Bhabha Atomic Research Centre,Bombay. The endeavour gathered momentum with

the implementation of the Thrust Area Programmeof the Department of Science & Technology (DST)in 1983, when Bangalore was identified as a nationalnucleus for the development of this research area inthe country. Since then, particularly in the 1990s, anumber of research groups in macromolecularcrystallography came into being in different partsof India with support from DST, the Department ofBiotechnology (DBT) and the Council for Scientificand Industrial Research (CSIR). There are currentlya dozen such groups located at nine institutions.The Indian effort in this area has been wellcoordinated and has a significant internationalpresence.

The macromolecular crystallographic studies inIndia range across a wide spectrum. Crystallographicstudies on lectins, in conjunction with biochemicaland physico-chemical investigations, carried out inIndia has had considerable international impact. Thestructure analysis of two plant viruses has beenamong the landmarks in the development ofstructural biology in India while studies oflactoferrins from different sources constitute an imp-ortant component, as do those on phospholipases

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Space-filling model of sesbania mosaic virus (left) and physalis mottle virus (right). Sesbania mosaic virus

has a smoother surface when compared to physalis mottle virus which displays prominent protrusions at the

5-fold symmetry axis.

Phot

o: M

.R.N

. M

urth

y

and xylanases. Carbonic anhydrase and itscomplexes have been extensively studied in thecountry and work on ribosome-inactivating protein,and proteolytic enzymes and their inhibitors deservemention. Substantial contributions have emanatedfrom India in structural approaches to molecularmimicry. Crystallographic and related studies onimmunological systems are now gatheringmomentum. Yet another crystallographiccontribution from India pertains to the hydration,plasticity and action of proteins. An exciting recentdevelopment in the area is the concerted effort on

proteins from Mycobacterium tuberculosis. Nuclear Magnetic Resonance (NMR) is widely

used in chemistry and biology, and structuredetermination of proteins using NMR is currentlygathering momentum in India. The structures of acouple of proteins, a calcium-binding protein anda novel neurotoxin, have already been determinedat the Tata Institute of Fundamental Research,Mumbai, which houses the largest national NMRfacility in the country. Serious efforts in the area arenow underway in a few more centres in thecountry. In addition to working on individual or

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GOPALASAMUDRAM NARAYANA RAMACHANDRAN1922-2001

Considered one of the founders of molecular biophysics, G. N. Ramachandran was also a crystallogra-pher of international repute. He was fascinated by the arrangement of molecules in proteins and so

decided to take up research in this field. His work on the collagen molecule brought him worldwidereknown in the scientific community.

Ramachandran was born on October 8,1922 in Ernakulam district of Kerala. He studied for aMaster's degree in electrical engineering in 1940. He received his D.Sc. from the University of Madrasin 1948 and completed his Ph.D. from the University of Cambridge in 1949. In 1951, he went back toCambridge, England, to work with Sir William Lawrence Bragg, the 1915 Nobel Laureate in physics,and W.A. Wooster, and returned home with another Ph.D.

Ramachandran is credited with the establishment of the Department of Physics at the Universityof Madras in 1952. He began work on modeling collagen from fibre diffraction in 1952-53, when J.D.Bernal, who did pioneering work in X-ray crystallography, visited him in Madras and suggested that thestructure of collagen was one of the greatest unsolved problems. In 1954, Ramachandran arrived at thetriple helix model which had two hydrogen bonds per unit. Dr Francis Crick, co-discoverer of thestructure of the DNA molecule, had independently deduced one hydrogen bond per collagen unit.More recent single crystal work has shown the result to be 1.5 hydrogen bonds per unit, a compromisebetween these two proposals.

In 1968, he was made the Jawaharlal Nehru Fellow at the University of Madras. In 1971, the IndianInstitute of Science in Bangalore invited Ramachandran to set up the Department of MolecularBiophysics. Soon he managed to raise the Department to an international status where research wascarried out on several giant molecules of biological importance, for example, nucleic acids andpolysaccharides.

In the 1970s, he turned to problems of mathematical logic and proposed a new method for structuralanalysis in 1990. RamachandranÕs work with A. V. Lakshminarayanan has been acclaimed as the startingpoint of the CAT scan technique in radiography.

Ramachandran who was honoured with the prestigious Ewald Prize in 1999 for his outstandingcontribution in the field of crystallography, died in Chennai on April 7, 2001 after a long illness.

groups of molecules, the Mumbai centre and theNMR centre at the IISc, Bangalore, which houses awidely used national facility, have made importantcontributions to the methodology of 2D and 3DNMR spectroscopy.

Computational approaches to protein structurecontinues to be an important component ofbiophysical research in India. The work in the areaencompasses homology modelling, protein-ligand

interactions, study of secondary and other specialstructural features, and data analysis.

Biophysical chemistry is central to modernbiology. There was a phase in India when studies inthis area appeared to be on the decline but in recentyears, work in the area has gathered greatmomentum, particularly in relation to the folding,stability and design of proteins. High-quality workof international standard on protein folding is

currently being carried out in several laboratoriesin India. Some of them primarily address generalquestions, while others tend to concentrate onparticular systems. The systems encompass proteinsfrom widely different families. Protein stability, toa substantial degree, is related to protein folding.This is reflected in the work carried out in manylaboratories. The role of water, metal ions, ligandsand additives in protein stability also form a topicof detailed investigations.

Molecular design provides a link betweenproteins and peptides. Design and synthesis ofoligopeptides with desired conformations, parti-cularly using conformationally restrictive aminoacids, have been an area of considerable strength inthe country. Such peptides are then used as modularunits for the subsequent synthesis of proteins.Imaginative use of crystallography and NMR hasplayed an important part in this effort. Interactionsinvolving amino acids and peptides and theirrelevance to present-day biological systems, as wellas to processes involved in the origin of life, havebeen investigated in considerable detail. Synthetic,spectroscopic, crystallographic and theoreticalstudies have also been carried out on severalpeptide systems.

Nucleic Acids: Theoretical conformational studieson nucleic acids were initiated by G.N.Ramachandran and were carried forward by V.Sasisekharan and his colleagues. In structuralstudies, using crystallography, on DNA, M.A.Viswamitra has been another pioneer.Computational and crystallographic studies,particularly on the sequence-dependent structureof DNA, continue to be pursued seriously in severallaboratories. Extensive work on the structuredetermination of oligonucleotides using NMR hasemerged, particularly from the TIFR, Mumbai.Work at this centre has produced a wealth ofinformation on unusual DNA structures. In theprocess, important contributions to NMRmethodology specifically applicable to DNA, have

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Transaxial T1-weighted proton MR image of a

patient showing clearly the tumor near the 3rd

ventricle region of the brain.

Phot

o: N

.R.

Jaga

nnat

han

also been made. DNA-ligand interactions arepursued vigorously, mainly using spectroscopic andphysico-chemical techniques. The recentlyrecognized importance of trinucleotide and otherrepeats has added a new dimension to the structuralstudies on DNA.

Membranes: The biological membrane, theubiquitous multimolecular system found in livingorganisms, and related models, have receivedconsiderable attention from biophysicists. India hasbeen no exception in this regard. The organization,heterogeniety, dynamics and asymmetry ofmembranes have been studied extensively, usingspectroscopic and physico-chemical approaches.The Indian contribution towards the synthetic,spectroscopic, crystallographic and computational

studies on ionophores has been very substantial.The same is true about the interaction of drugs andother active molecules with the membrane.Significant contributions have also been recentlymade from India to ion channels with implications,among other things, for neurobiology.

Carbohydrates: Carbohydrates have emerged asvery interesting molecules during the past coupleof decades. A substantial part of biologicalrecognition is mediated by sugars. Work on proteinsthat bind sugars such as lectins, has already beenreferred to. Pioneering efforts of V.S.R. Rao and hiscolleagues on polysaccharide conformation havebeen noteworthy. Yet, work on carbohydrates andglycoconjugates in the country is much lessextensive than it ought to be, although there aresome groups working in the area.Computational Biology and Bioinformatics: Indianshave been in the forefront of international efforts incomputational biology during the emergent phase of

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The unusual quarternary structure of peanut lectin

(left) and a subunit of jacaline which exhibits a

novel lectin fold (right).

the field and work in the field continues to be pursuedvigorously in the country. Some components of it havebeen referred to above. There are groups of scientists,distributed over the country in different centres, whoare exclusively concerned with computational biology.Thanks to a major initiative of DBT, India has beenamong the first countries to embark on a concertedeffort in the allied field of bioinformatics. Anetwork ofbioinformatics centres have been established coveringall regions of the country for the dissemination andanalysis of different data bases. This network hasplayed an invaluable role in taking bioinformatics tothe biology community as a whole. The emphasis ofthe bioinformatics programme is shifting fromdissemination to generation of data bases and software.

Whole Systems: Structural biology has to someextent dominated biophysics in recent years.However, biophysical studies at higher levels oforganization continue to be pursued as for instancein NMR investigations of whole cells and metabolicprocesses and, importantly, in MRI studies onneurological processes. Optical studies of differenttypes on biological systems are being carried out ina few centres. Radiation biophysics is another areain which significant activity exists while work inmedical biophysics and on biomaterials is beingpursued at a few centres.

Unlike in the case of computational biophysics,mathematical biology has had only limitedfollowing in the country. However, a trend towardswider acceptance of the area is now discernible.Theoreticians, particularly theoretical physicists, arecurrently showing increased interest in themathematical modeling of biological systems.

TRENDS AND PROSPECTS

Even in normal circumstances, predictions rarelycome true in science. This is even more so at

present when rapid and revolutionary changes aretaking place in almost all branches of biology. Allthat one can reasonably do is to indicate some trends.

For long, much of the biophysics research in

India, impressive though it was, took placeindependently of the bulk of the biological researchactivities in the country. Work in crystallographyand computational biology exemplifies thesituation. Most of the workers in these areas usedto be physicists and had little professional contactwith biologists. The situation is rapidly changing.A number of multi-disciplinary collaborations havedeveloped. Structural biologists are now very muchpart of the biology community and biologylaboratories are rapidly becoming natural habitats ofcrystallographers and computational biologists.This trend is likely to accelerate in the years to come.

The development of biological macromolecularcrystallography in India provides a good exampleof a concerted effort towards building upmomentum in an important scientific programmein the country. The area of biological macro-molecular crystallography is well past the stage ofcapacity building and many important problemshave already been successfully addressed at aglobally competitive level. Work using thecrystallographic approach is poised to take furthermajor strides, with the active involvement ofbiologists working in other areas. A further impetusin this direction is expected to be provided by therecently evolved multi-institutional programme onthe structural genomics of microbial pathogens. Asindicated earlier, macromolecular structuredetermination using NMR is well underway in onemajor centre in the country and major results in thearea are expected in the near future, from at leasttwo more centres. However, in experimentalapproaches to macromolecular structure deter-mination, a major gap area in the country is cryo-electron microscopy. Efforts to fill this gap will bevery worthwhile. The major thrust of biologicalstructural studies in India has been concerned withproteins that act on carbohydrates, plant viruses,lactotransferrins, proteolytic enzymes and theirinhibitors, protein hydration, molecular mimicryand structural variability of DNA. These lines ofinvestigation are expected to be further

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strengthened. Work on immunologically relevantproblems, which has already been initiated, is likelyto gather additional momentum in the near future.A major new thrust is expected in structural studieson proteins from microbial pathogens.

A major theme of structural studies on peptideshas been concerned with protein folding and design.Physico-chemical, thermodynamic, structural andtheoretical studies in this area will continue to be animportant element of structural biology in thecountry while biophysical and theoreticalapproaches should continue to play a major role inmultifarious studies on membranes.

The primary emphasis of the bioinformaticsprogramme in India so far has been on thedissemination of information. That phase is nowover. Efforts are already underway for the creationof novel data bases and the development of web-based software. These efforts, which are nowgathering momentum, are likely to occupy centrestage of bioinformatics in the country in the future.The initiatives in genome analysis have added anew dimension to these efforts. In general, withthe departure of giants of yesteryears, the visibilityof computational biology as a distinct approach,diminished somewhat during the closing decades

of the twentieth century. This trend is now beingreversed as a new generation of practitioners in thearea have appeared and seem to be set to make asignificant impact on biology.

Work on whole systems, particularly usingimaging techniques, is expected to be further carriedforward in the years to come. There is currently aclearly discernible and welcome trend towardsharmonizing studies at the molecular and theorganismal levels. This trend needs to be, and islikely to be, strengthened in the future.

Recent years have witnessed the rapidevolution of a host of new approaches and noveltechniques to deal with biology at different levelsof organization. Most of them involve a great dealof what is conventionally described as biophysics.However, the borders between different sub-disciplines of biology are becoming increasinglyblurred. Studies at different levels of biologicalorganization have also begun to get progressivelyintegrated. In this rapidly changing scenario, it isdifficult to foretell how the new approaches andtechniques will develop in the country. However,modern biological research in India is sufficientlymature and resilient to be able to cope with therapid developments and contribute to them.

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