BioWiki

Protein spotlight

http://www.expasy.org/spotlight/

「Protein Spotlight」 (ISSN 1424-4721) は、スイスバイオインフォマティクス研究所Swiss-Protチームの月間レビューである。特定のタンパク質やタンパク質ファミリーについて、やさしく解説している。

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  • on versatility by vgerrits (2019/06/11 18:00)
    Diversity is one of Nature's fortes. See how she has spread life and let it flow into Earth's every nook and cranny: oceans and seas, rivers and lakes, woodland, forests and jungles, mountains, valleys, deserts, marshland and glaciers, and even stifled cities where weeds push their way through bricks - and flies, rats and pigeons feed on our waste. Though humans seem set on diminishing diversity, there is still a great variety of living organisms on most of the planet's surfaces. It continues on a smaller scale too. Consider a cell and the myriads of different molecules inside it all working together in relative harmony, to keep the cell alive and healthy. It may seem a paradox but the principle of economy is one of diversity's driving forces, and the world of proteins illustrates this beautifully. Imagine a basic sequence, a template if you like, then add a methyl group here or remove a phosphate group there, and you have a protein that behaves in two different ways. This is the realm of post-translational modifications, or PTMs. In cells, special enzymes - of which there are many - have the task of adding or removing molecules onto or from proteins to this end. One of these is SET domain protein 3, or SETD3 which shifts the behaviour of a certain kind of actin.
  • twisting fate by vgerrits (2019/05/10 14:21)
    Life thrives on reproduction. Over time, it has found very imaginative ways to proliferate in multitudinous forms - from protozoa wriggling in the bottom of pools to big cats racing across the African plains and birds flying swiftly through the air. All forms of life - or certainly the great majority - require help of some sort to reproduce: mammals need a partner, plants rely on insects for pollination and many amphibians are dependent on favourable conditions for spawning. There are life forms, too, that not only count on others to multiply but also damage them in the process, frequently to the extent of killing them. This is the realm of infection. Though their ultimate aim is not to kill their hosts, pathogens such as viruses, bacteria or fungi invade other organisms to take advantage of their resources - so doing, if left unchecked, they can destroy their hosts. In this way, the AIDS virus diminishes our immune cells, the poliovirus attacks our motor neurons and a variety of fungi infect plant cells, ultimately wiping out complete crops. Phytophthora infestans is a fungus-like organism that invades potato plants in particular. Scientists are slowly unveiling how P.infestans uses potato cells to develop, and which molecules are involved. Notably: a protein known as PexRD54.
  • another kind of harmony by vgerrits (2019/04/12 09:48)
    Would Nature not tend instinctively towards symmetry? In our eyes, symmetry often spells equilibrium, a source of beauty. Consider the work of architects, or engineers. Houses, skyscrapers, bridges and dams are usually symmetric which is not only, and in a mysterious way, emotionally reassuring but also in keeping with the laws of physics. In the same vein, a face that strikes us as being attractive is a face whose sides echo one another. Anything that drifts from these unsaid boundaries strikes us as being odd, if not ugly: think of the Elephant Man. Despite this, life is defined by an underlying lack of symmetry. In fact, Nature frequently seeks a way to break symmetry. Take humans: our heart is not symmetric, neither is the arrangement of our organs inside us, and our brain hemispheres are involved in very different aspects of intelligence. Why has Nature chosen asymmetry? And how does it occur in the first place? The field of research is relatively recent and the answers to these questions are still far from satisfactory. However, we do know that a certain form of myosin, known as myosin 1D, is directly involved in paving the paths of asymmetry in zebrafish.
  • paths of discomfort by vgerrits (2019/03/15 09:34)
    We are all bound to become prey, predator or competitor one day. Whichever way you look at it. That is why, over time, all living beings have acquired their very own palette of defence mechanisms. Roses grow thorns. Bacteria fire toxins. Panthers run fast, chameleons blend into the environment and humans hurl a few well-chosen words. The whole point of developing such mechanisms is to shun the threat of some sort of insult, or worse: death. Bees sting, dogs bite, ivy poisons, humans humiliate... Everything that has to do with defence frequently involves hurt or physical pain. Why? Because it is the best way to say: "go away, and don't come back". Cone snails have developed one of the most varied and plentiful venomous cocktails that are known, which have been extensively studied. Recently, researchers discovered that one component of such a cocktail makes humans itch. This is an intriguing discovery since itching is - so scientists believe - not far removed from pain. The component is a particular conotoxin, a venom peptide coined conorfamide.
  • dark horse by vgerrits (2019/02/13 16:08)
    There are many proteins crouching in the recesses of databanks whose role in vivo eludes researchers. Despite similarities of all kinds they may share with other proteins, they seem to have been designed for another purpose. A few of them may even have an unexpected function in an organism that does not synthesize them at all - much in the way a pair of scissors can be used to hammer a nail into the wall. This is precisely the case of a protein known as gamma-conglutin, found in the seeds of lupins. Unlike the majority of proteins in lupin seeds, gamma-conglutin does not seem to be used as a source of nourishment for seedlings. However, it does have an effect on sugar levels in our blood! Lupin seeds have been part of our diet in various parts of the world for centuries and their beneficial effects on our health long acknowledged. Today, thanks to technological advances, scientists are able to discern what is going on at the molecular level.
  • silent walls by vgerrits (2019/01/17 12:05)
    Though it may seem a paradox, life is riddled with barriers. This is because it is sometimes necessary to create dead ends to keep things at a healthy distance. Obstructions of this kind exist at all levels of living matter. Specialized pores are found in membranes surrounding cells but also within cells, to ensure that only specific molecules are able to cross while the transit of others is barred. Aquaporin and sodium channels are two examples through which only water molecules or sodium ions fit, respectively. Another vital barrier is the one that keeps spermatozoa that belongs to one species from fertilizing eggs that belong to another - which would only bring about chaos. Though the mingling of germinal fluids and how life ensues have been discussed since the days of Aristotle, on the molecular level very little is known, still, on how species keep to themselves. A recent find in zebrafish has lifted a veil: scientists discovered a protein on the membranes of zebrafish eggs, which only allows access to zebrafish sperm. They called it Bouncer.
  • ice whisperer by vgerrits (2018/12/19 15:30)
    No one likes the cold. Humans wear scarves, fur boots, quilted coats and woollen hats to keep the harshness of winter out while other creatures grow their own fur or line their bodies with a thick layer of blubber. There are those, too, who have a more subtle approach to dealing with extreme temperatures and, instead of sporting a protective coating of fur or fat, tame the cold by acting upon its actual source. As an example, various species of fish or bacteria who live in Arctic environments have evolved systems to keep ice crystals from developing further inside them or sometimes even in the surrounding extracellular medium. For what reason? Because ice crystals can damage cell membranes by puncturing them or causing them to rip, which is life threatening. One particular Arctic yeast known as Leucosporidium has developed a system that - in freezing conditions - hinders the growth of ice crystals by secreting a protein that binds to them and ultimately lowers their freezing point. This particular protein has been coined Leucosporidium ice-binding protein, or more simply LeIBP.
  • on mar and motion by vgerrits (2018/11/16 09:15)
    Movement is what sustains life. Organisms need to move to find food, seek shelter and to reproduce. Mobility is also essential inside organisms where cells are continuously dividing and migrating. There is also unceasing movement inside every cell where myriads of molecules are being trafficked, and cellular compartments of all shapes and sizes shifted. What keeps things moving? Years ago, scientists discovered a protein they coined actin. Actin is a small globular protein that has many different roles in eukaryotic cells. One characteristic feature is its capacity to polymerize into microfilaments that stretch from one end of a cell to another to form the cell's cytoskeleton - which speaks for itself. Though the formation of a cell's cytoskeleton is perhaps considered as actin's fundamental role in the cytoplasm, the protein is also involved in many other activities, one of which is mobility. Actin is also present in the nucleus but, until recently, scientists believed that microfilaments did not form there. It turns out that they do: damaged DNA seems to be oriented towards repair centres thanks to actin microfilaments whose growth is prompted by a protein complex known as Arp2/3.
  • best left unsaid by vgerrits (2018/09/28 09:42)
    There are times in life when things are best left unsaid. So you bite your tongue or someone bites it for you. Either way, you are silenced and no - or less - harm is done. Nature also has its techniques for muffling genes whose products are not necessary at a given time, or that are perhaps harmful once expressed. One technique, which seems to have been with us for a very long time, is DNA methylation. DNA methylation is like locking a door with a key that you promptly throw away: you're making things difficult for someone to open it and see what's on the other side. In the same vein, DNA methylation has the capacity to keep a gene in a locked - or silent - state, thus hindering the production of an undesirable protein and a probable adverse downstream metabolic pathway. DNA methyltransferase 3C is one of the many enzymes able to gag a gene. Although not any old gene: DNA methyltransferase 3C seems to silence specifically retrotransposons.
  • on the right track by vgerrits (2018/08/24 08:45)
    Left only to the passage of time, everything gravitates towards chaos. Gardens become overgrown. Roads gather potholes and cracks. Relationships wither, and teeth rot. We have ways of dealing with this however. Gardeners look after the lawns, engineers inspect the roads, therapists have a go at unravelling relationships, and dentists tend to our mouths. Life, too, has its keepers. Left unattended, the very essence of life - our DNA - will collect unfortunate mutations that have the power to wreak havoc inside us. Over time, our cells have found ways of coping with this by promoting, for example, self-destruction so as not to propagate what has become unhealthy, or by repairing damaged DNA. As a result, cells are kept on the right track. Who, though, is the keeper? Different keepers are summoned at different stages and depending on the cell's fate. One protein, however, seems to be the orchestrator. Its name is p53, and it has been studied extensively since the 1970s because when it goes wrong, life is at stake.