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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  • a way in by vgerrits (2020/03/26 21:04)
    As children in Scotland, back home from school and when the weather was dry, we would fling our schoolbags into the hall and grab a few golf clubs, a ball and a tee. There was no need for a change of clothes or shoes, whatever we were wearing was good enough. The course was along the coast on the edge of the North Sea, and the balls we used were found in the dunes where they had been lost by more experienced players. We had four clubs - a driver, two irons and a putter. Putting was the best part of the game. You would aim carefully for the long slim rod with the little red flag, taking into account the odd clump of grass or small mounds on the green and then, holding your breath, watch the little white ball as it made its meandering way to the base of the rod to drop, almost as an afterthought, into the hole. Well... it so happens that viruses infect cells in a similar manner... Viruses need to get inside cells in order to multiply, and this is what brings on infection. Like the flagged pole that marked the way in for our golf ball, viruses recognise molecules on the surface of cells to which they bind, thus enabling them - or parts of them - to enter the host cells where they rapidly spread. The coronavirus which is wreaking havoc across the planet as I write these words, is able to recognise a protein on the surface of a variety of human cells known as angiotensin-converting enzyme 2, or ACE2.
  • "the unwalkable disease" by vgerrits (2020/02/21 18:38)
    Health is really all a question of balance. Not too much of this, not too little of that. Gout is no exception. Throughout history, this particular form of arthrosis has been associated with the exaggerated consumption of rich foods and excessive alcohol, and consequently described as "arthritis of the rich" since, in the early days, only the higher classes of society seemed to suffer from it. However, as the excessive indulgence in over-rich foods has spread across a great part of the world, gout too has spread - and not only on a geographical scale but also throughout the various strata of human society. Gout is an inflammation caused by the accumulation of needle-like crystals of uric acid deposited in joints, tendons or their surrounding tissues. Uric acid comes from the breakdown of purine we ingest from the food we eat, and is usually processed by our kidneys and then eliminated with our urine. When too much uric acid is produced however, it precipitates as urate crystals that slowly build up finally causing excruciating pain - surprisingly at the base of the big toe in about half of gout cases. Why is uric acid elimination sometimes insufficient? Besides certain diets, there are a number of other reasons and one of them is the inherited dysfunction of a protein pump known as ABCG2.
  • backlash by vgerrits (2020/01/17 20:02)
    Every cell is a world of its own. Within its boundaries, there are entities of all shapes and sizes each busy accomplishing specific activities - transcribing genes, synthesizing proteins, modifying proteins, ferrying molecules from one part of the cell to another, building molecular motorways, erecting scaffoldings, repairing scaffoldings, collecting waste, shifting waste, digesting waste... To keep this state of affairs going, there needs to be a continuous exchange between the cell and the outside world as various goods are shuttled across its membrane in both directions. There are checkpoints nevertheless, which is why cell membranes are riddled with canals or pumps that are more or less selective: not everything can come in or go out, while some things must come in and others are better out. It is a case of survival. Toxic compounds that find their way into microorganisms, for instance, are usually funnelled out by what are known as efflux pumps. These pumps pose one problem for humans however, and that is drug resistance. One such pump is the Trichophyton rubrum ABC multidrug transporter MDR3.
  • dropping barriers by vgerrits (2019/12/18 19:26)
    Blood. It is deep red, liquid and essential to life, and courses through us from the very early stages of our development to our final gasp. It cannot have taken long for our ancestors to make the link between blood and life. They will have seen the rich red fluid seep from wounds alongside the lifeless bodies of animals they had just hunted down, and understood that the same fluid flows through their own bodies. Blood is indeed a tissue (albeit liquid) of vital importance, composed of myriads of crucial cells and nutrients, which is why - when lost - it is transfused. There is a snag however: no two bloods are identical. But all human bloods can be sorted into well-defined groups of which the most representative are the A, B, AB and O blood groups. The O blood group can be transfused to everyone, while the other blood groups cannot. This is why scientists have been searching for ways, literally, to shift A, B and AB blood types to the 'universal' O blood type - which could resolve the problem of insufficient stocks in blood banks. There have been several attempts, none of which conclusive. One more promising attempt involves bacteria from our gut microbiome, and two enzymes: a D-galactosamine deacetylase and a D-galactosamine galactosaminidase.
  • sting by vgerrits (2019/11/19 19:16)
    Venom has a language of its own. The recurring message is not a nice one, and usually expresses one thing: back off. Certain animals use venom - a cocktail of molecules - to ward off predators or, at the very least, to divert oncoming danger. We all know what a wasp's sting is like and many of us may have felt the sting of a jellyfish, or perhaps even the bite of a snake. It is a painful experience. To what end? The reason is twofold: one, we at once recoil from the animal that has just caused pain and two, our body is instantly told where it hurts. Concomitantly, the animal takes flight while our body attends to our wound. The feeling of pain itself is caused by the opening and closing of minute channels that riddle the membranes of our nerve cells just under our skin. This gives rise to pain signals that originate at the location of the sting, or bite, and are relayed to our brain. Understanding how pain occurs on the molecular plane helps scientists find ways of designing pain relievers. However, more often than not, pain is usually accompanied by swelling which has a protective role. So we face a conundrum: how do you relieve pain while preserving inflammation? One particular scorpion toxin, the Black Rock scorpion toxin known as the wasabi receptor toxin or WaTx, may well provide an answer.
  • lure by vgerrits (2019/10/18 01:55)
    Walking down a busy main street a few days ago, from the corner of my eye I saw a teenager rooting rapidly through a wallet he had just pulled out of a girl's backpack. Before I had registered what was going on, a young man approached me to ask where he could catch a bus. Flustered, I told him. In between times, the teenager and the stolen wallet had disappeared. Minutes later, I realised what had just occurred. The young man who had asked me about a bus had - successfully - diverted my attention from what his accomplice was doing. This is very similar to the kind of lure a plant pathogen known as Phytophthora sojae uses to confound soybean's immune response to infection. P.sojae secretes a protein known as XEG1 into the soybean plant where it can do significant harm. Soybean, however, reacts to the infection and muffles the effects of XEG1 thanks to a protein known as GIP1. To bypass this inconvenience, P.sojae promptly secretes a second protein - XLP1 - that soybean GIP1 mistakes for XEG1. XEG1 is then free to continue infection while the plant's immune system is tricked to attend to XLP1. This is a perfect example, in Nature, of two entities working together to confound a third.
  • a sense of direction by vgerrits (2019/09/19 20:21)
    Survival depends on cues, mobility and a medium to evolve in. Cues - such as scents, sounds or colours for example - will attract organisms towards food, mating grounds and an environment in which they feel protected and are happy to stay. Thanks to them, organisms usually head off in a direction they expect will be to their advantage, using the means of locomotion they have, to cross all sorts of media. A few organisms use yet additional systems to reach a given destination. An example? Magnetotactic bacteria have learned to use the Earth's magnetic field as a speedy highway to travel to nutrients of interest. They do this by way of minute iron-rich pouches - or magnetosomes - that are aligned along their middle and act much like a compass would. Many macromolecules are required to model this fascinating system. One of particular interest is a protein known as MamB which is at the heart of magnetosome initiation. Magnetosomes have also long intrigued those behind the microbiology blog Small Things Considered, and this article echoes a lovely piece on magnetotactic bacteria and their navigation skills written by Christoph Weigel earlier this week, and whose artwork illustrates this text.
  • the scent of guile by vgerrits (2019/08/01 20:12)
    All kinds of strategies are used by living beings for their survival. Humans lay down traps to catch prey, chameleons melt into their environment to hide from predators and foxes cross water to bewilder those hunting them. Because of their inability to move, plants have devised the most elaborate ways of deceiving their environment in order to grow. They can exude scents or even produce fake fruit to attract pollinators for instance. They can also synthesize hosts of different molecules that, once released, fight off microbes. But there is yet another master plan used by many plant species as a means of defence. European maize, for example, is able to synthesize a molecule known as (E)-β-caryophyllene which is released by the plant's leaves and roots in the presence of larvae feeding on them. (E)-β-caryophyllene does not actually kill off the larvae but attracts yet other organisms that will feed on the herbivorous parasites, thus stalling harm that could be made to the plant. The enzyme at the heart of (E)-β-caryophyllene synthesis is a terpene synthase, known as TPS23.
  • on versatility by vgerrits (2019/06/12 03:00)
    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 23:21)
    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.