Prof Homendra Naorem
It is only natural for humans to be visual-centric which led to the foundation of the perception of ‘Seeing is Believing’. Given a choice, everyone would prefer to be in front of a TV set than to tune in a radio! Because seeing is not only believing but also helps in shaping our reality, if there is anything such as reality – as Einstein once remarked, ‘reality is merely an illusion, albeit a very persistent one’. If you see something for yourself, you will believe it to exist or be true despite being unusual or unexpected necessarily implying that what is not seen is not believing, however real it may be! The recently created‘anti-corruption’ cell of the Government of Manipur apparently works on this principle of ‘seeing is believing and not seeing is not believing’ since any complaint therein must be duly authenticated by a photo or a video (unedited of course) evidence to get the accused person penalized! Any circumstantial or indirect evidences, however convincing they may be, is not good enough to be entertained. But, in realm of spiritual or religious matters it is the ‘Seeing in Believing’ principle which is more important than the ‘Seeing is Believing’ principle, making so many people believing in God despite the fact that no one has ever seen God!
Similarly, the progress of science and scientific developments owe much more on the principle of seeing what you believe in rather than on ‘seeing is believing’ principle. For example, no one can see the molecules of gases present in the atmosphere, yet one cannot deny their existence. Theory guides us in shaping the nature of the molecules of such gases and then we begin to see them through our intellect-eyes. That, of course, does not make us anything less visual-centric! In fact, the dawn of the digital era and better mega-pixels have further escalated the visual-centric nature of the humans to the extent that ‘seeing’ has become the necessary evil before anything is to be believed or accepted to be true. This tendency has also deeply penetrated into the realm of science.
Chemistry is essentially a science based on atoms and molecules and, at heart, chemistry is about the interaction of different atoms and molecules, their structures, properties, reactions, and the ways in which they are held together by the so called chemical bonds.The world we live in is made of atoms. So also the human body. Every student of chemistry is familiar with structural drawings of atoms and molecules and chemical bonds in any chemistry text, which may at times be difficult to translate into reality. However, the currently accepted atomic model is based on the principles of quantum mechanics and hence the model of atom often seen in any standard text is, indeed, a mathematical object generated using appropriate wave functions. Yet we understand, to a larger extent, the behavior of the atoms and the molecules through their wave functions and the mathematical objects in terms of their respective effects despite the fact that no one has ever seen an atom – its doubtful if one can ever see one even with the best technology or technique. Imagine, if the stick-ball model of the molecules were see-able and can be imaged using some imaging techniques with molecules showing the real atoms and bonds! Imagine if we can control the future of the universe through manipulation of the atoms and bonds present therein! Imagine! Yes, scientists have been dreaming of photographing the molecules in action. Arguably the most challenging chemistry is within the human body – the wonderful chemical reactions and machineries thereof occurring nonstop at constant body temperature without any malfunctioning for years together, save a few aberrations here and there! Who won’t like to see them watching live in action? The pace at which the imaging techniques evolve signals that we may soon have detailed images of life’s complex reactions and machineries in atomic resolution.
The Royal Swedish Academy of Sciences has announced that the 2017 Chemistry Nobel Prize will be jointly awarded to the three scientists; (1) Jacques Dubochet of the University of Lausanne, Switzerland (2) Joachim Frank of Columbia University, New York, USA, and (3) Richard Henderson of the MRC Laboratory of Molecular Biology, Cambridge, UK for developing cryo-electron microscopy (cryo-EM) for the high-resolution structure determination of biomolecules in solution which both simplifies and improves the imaging of biomolecules. What is cryo-EM? In the scientific jargon, ‘Cryo’ (or cryogenic) refers to very low temperatures generally less than minus 150°C though the actual temperature is not well defined. Therefore, cryo-EM refers to the technique of electron microscopy to get the native (not denatured) picture of the bio-macromolecules after being frozen or supercooled at its natural state. This method has been so effective that in recent times the three dimensional (3D) images of the Zika virus at atomic resolution has been produced using cryo-EM which paved the way for searching for potential targets for pharmaceuticals.
The physical methods generally employed in the determination of structure of molecules in chemistry may broadly be categorized into two: (i) indirect method based on analysis of the signals obtained using the molecule, like in spectroscopic methods including NMR (nuclear magnetic resonance) spectrometer, XRD (X-ray diffractometer), etc. and (ii) direct method based on taking the picture of the molecule, like microscopy. Until recently, XRD and NMRwere among the best method to obtain structures of complex biomolecules whereas electron microscopes were believed to give images for dead matter since the powerful electron beam destroys the biological material. Perhaps the first breakthrough in understanding the structure of biomolecules came through the famous double-helix structure of DNA using XRD by Creek, Watson and Wilkins (Medicine Nobel Prize-1962) followed by development of 3D structure of bio-macromolecules in solution by Wuthrich, Tanaka and Fenn using NMR technique (Nobel Prize-2002). Images may be developed based on NMR signals as in Magnetic Resonance Imaging (MRI) which by now has become a popular diagnostic tool. Both the techniques require deep understanding of chemistry and analysis and assignment of the signals to appropriate atoms before arriving at the final structure. Some of the shortcomings of these methods, inter alia, are the development of a good single crystal for XRD (which may be very tedious job in certain cases) and the fact that the techniques of NMR is limited mostly to protons (H+) and few species like Carbon (13C), etc.
On the other hand, microscopy is the technique of viewing objects and areas of objects that cannot be seen with the naked eye. In any microscope, a light source is required for production of image and a technique for magnification of the image. Depending upon the nature of the light used, it is termed as optical or electron microscope. In optical or light microscopes ‘light waves’ are used to produce the image and magnification is obtained by a system of optical lenses. In electron microscope an ‘electron beam’ is used to produce the image of the object and magnification is obtained by techniques based on the electromagnetic fields. The magnification or the resolving power of a microscope is related to the wavelength of the light used – the smaller the wavelength of light used greater is its resolving power. The average wavelength of visible light is about 500 nm (say) while that of electron is about 0.005 nm which is about one hundred thousand (one lac) times smaller than that of the visible light. On an average, an electron microscope can resolve objects as small as 1.0 nm as compared to 200 nm by a light microscope which roughly means that the resolving power of an electron microscope is about 200 times greater than that of an optical microscope. There are three types of electron microscopes: (i) Scanning electron microscope SEM, (ii) Transmission electron microscope TEM and (iii) Scanning and Transmission electron microscope STEM. By the 20thcentury, electron microscopy has already emerged as one of the popular methods for looking into the cell and observe the tiny beings that play such an important role in our lives such as viruses. But unfortunately the powerful ‘electronbeam’ would lead to evaporation of water and also destroying the biological material, limiting such a powerful technique only for dead cells and dead organisms. Can this powerful technique be used for imaging of biomolecules in solution and in their native states?
It was in the 1970s when Henderson and his colleagues were attempting to determine the 3D image of bacteriorhodopsin by blasting a frozen solution of the sample with weak electron beam and averaging the multiple images obtained thereof. It was Frank who developed image-processing technology for converting the conventional two-dimensional electron microscopy pictures into 3-D structures. Finally, in 1990 Henderson achieved his goal and was able to present a structure of bacteriorhodopsin at atomic resolution. This however has not completely solved the problem of imaging biological molecules in their native states or in solution since the samples get de-natured under the electron beam of the microscope at normal temperatures.
Around the same time Dubochet was trying to solve another of the electron microscope’s basic problems: how biological samples can be imaged in solution or in their native state, or in other words how to add water to electron microscopy! He believed that if water is allowed to freeze rapidly it could freeze into a disordered state like in the case of glass – glass is not a solid but a supercooled liquid in which individual molecules are arranged at random instead of a periodic crystalline solid structure. The supercooled glassy form of water, which is known as vitrified water, would not dry up when exposed to the electron beam. Dubochet developed a rapid freezing method using liquid ethane, which prevented the biomolecules from drying out and distorting under the electron beams. By the early 1980s, Dubochet succeeded in vitrifying water – he cooled water so rapidly that it solidified in its liquid form around a biological sample, allowing the biomolecules to retain their natural shape even in a vacuum. By 1984 he published the first images of a number of different viruses, round and hexagonal, that are shown in sharp contrast against the background of vitrified water.
The Swedish academy has recognized the three scientists for their pioneering works that led to the development of the cryo-EM in which a beam of electrons is sent through a molecular sample that has been supercooled, typically with liquid ethane. The material deflects the electrons in a way that permits researchers to determine the sample’s structure without getting damaged or dehydrated in the electron microscope’s vacuum chamber. Structures obtained by cryo-EM at molecular resolution has greatly advanced the understanding of life chemistry and help scientists develop drugs by elucidating the way they interact. Another advantage of cryo-EM is the fact that it can handle much larger structures than is possible with NMR or even X-ray crystallography. As Sarah Butcher of the University of Helsinki, a cryo-EM specialist, stated, ‘the technique can structurally analyze objects probably 100-fold larger than crystallography can handle, including whole viruses and even frozen cells making much, much more adaptable to lots of different types of biological questions than NMR or X-ray crystallography’. That is until another break or path breaking features are added to NMR or XRD! Another imaging technique which is almost at the verge of atomic level is the non-contact atomic force microscopy (ncAFM). Already the images captured by ncAFM have added another dimension to how we learn about bonding in chemical compounds. Sooner or later this technique may also arrest the attention of the Swedish Academy.
(Prof Homendra Naorem works at Chemistry Department, Manipur University)
Source: The Sangai Express