Excerpts from Recent Articles from 2006

2006 Back Issues

Proteic grace - December 2006
Rarely do we give a thought to the minute world within us that keeps us going. Yet were it not for thousands of proteins, we would not be able to breathe. Or walk. Or smell. Hear, see or even think. How would we go to the shops? Drive a car? Take the bus? Write a letter? Read the newspaper? Or make a cup of tea? When things are fine, we feel invincible. It takes very little though to remind us how fragile we really are. The tiniest of entities can ground us. A virus can cripple us. Cells gone haywire can kill us. Chemicals can indispose us. A faulty gene can condemn us. And, more often than not, this molecular havoc is caused by proteins whose function has been diverted, modified or lost. Textbooks can explain it to us and even show some of it to us but the elegance of it is rarely grasped, at least by the layman. That is why art – in all its forms – can be a unique way of shifting the tiny into the world of the big. Mara Haseltine, an American artist and sculptor, has done just that by shaping a handful of proteins, to show both their beauty but also perhaps their ugliness on a human scale. (PDF version - 53K bytes)
Swiss-Prot cross references
BLyS, Homo sapiens (Human) : Q9Y275
Rhodopsin, Homo sapiens (Human) : Q16414
Follicle-stimulating hormone alpha chain, Homo sapiens (Human) : P01215
Replicase polyprotein 1ab, Human coronavirus : Q05002

Life shuttle - November 2006
There is no life without energy. Much in the way a car needs petrol to run, we also need something essential to keep us going. And it is called adenosine tri-phosphate or ATP. ATP runs through every nook and cranny of our body to keep our heart pumping, our fingers moving and our thoughts alive. But – like petrol – we do not get it for free. We have to make it. So, in the great majority of our cells, we have powerhouses – known as mitochondria – that spend their time synthesizing ATP and distributing it where need be. Not surprisingly, hordes of proteins are involved in this process, one of which has been known for decades: cytochrome c. Human cytochrome c happens to be the very first protein sequence that was entered into the Swiss-Prot database. And the beginning of an adventure which is heading into its 21st year. (PDF version - 564K bytes)
Swiss-Prot cross references
Cytochrome c, Homo sapiens (Human) : P00001
Cytochrome c, Equus caballus (Horse) : P00004

The accidental crippler - October 2006
All organisms need other organisms to survive. Flowers need bees. Frogs need flies. Humans need vegetables. And viruses need us. Poliovirus in particular squats human cells preferentially, where it uses their machinery to replicate and multiply since it cannot do it on its own. In doing so, poliovirus – like all viruses – hinders not only the host cell’s welfare but also any activity it should have undertaken. However, before a virus stands a chance of invading a cell, let alone propagating inside it, something has to let it in. For poliovirus that something is a protein receptor, known as the poliovirus receptor. These receptors are sprinkled on the surface of certain types of cells and are specifically recognised by poliovirus, which docks to them and subsequently finds a way to wriggle inside. (PDF version - 121K bytes)
Swiss-Prot cross references
Poliovirus receptor, Homo sapiens (Human) : P15151

Skin-deep - September 2006
The colour of human skin has been – and still frequently is – at the heart of violent controversy. Political, social and physical. Yet, as the science of human genetics unfolds, we are reminded over and over again that any given human population cannot be defined according to its pigmentation since any skin hue blends gradually into another. However, there is no doubt that there are dark skins, and there are light ones. The darkness – as the lightness – of skin depends on the amount of melanin present in the epidermal cells. And the amount of melanin depends directly – though not solely – on the existence of a protein that has been christened ‘solute carrier family 24 member 5’ or ‘SLC24A5’. (PDF version - 53K bytes)
Swiss-Prot cross references
Golden protein, Brachydanio rerio (Zebrafish): Q49SH1
Solute carrier family 24 member 5, Homo sapiens (Human): Q71RS6
Molecular embrace - August 2006
We take our three dimensional architecture for granted. Yet, were it not for biological scaffoldings of different kinds, all living entities would probably be quite flat. Besides acting as something from which muscles and internal organs can hang, skeletons bestow on humans a characteristic shape. As they do on giraffes. On a far smaller scale, any specific cell also has a distinctive contour, given to it by what is known as the cytoskeleton. The cytoskeleton is made up – for the most part – of actin filaments, which are themselves assemblies of thousands of globular actin monomers. Cytoskeletons – like any scaffolding – need builders to be erected, and the protein twinfilin is one such builder. Twinfilin is intimately involved in actin filament dynamics, and without it there is not much that living entities could do. (PDF version - 35K bytes)
Swiss-Prot cross references
Twinfilin, Homo sapiens (Human): Q12792
Twinfilin, Saccharomyces cerevisiae (Baker's yeast): P53250
Twinfilin, Xenopus laevis (African clawed frog): Q68F50
Twinfilin, Gallus gallus (Chicken): Q5ZM35

Entanglement - July 2006
Getting tangled into knots is rarely a desirable situation. Yet there is a protein whose entanglement is not only profitable but also so final that it can kill off bacteria that interfere with its host’s feeding or living space. Microcin J25 is a small antibacterial peptide synthesized by certain strains of Escherichia coli during times of hardship. Its knotted structure is such that it interferes with the victim’s RNA polymerases hindering RNA polymerization and hence protein synthesis. As a consequence, the targeted bacteria die off leaving refreshment and room for their rivals. (PDF version - 179K bytes)
Swiss-Prot cross references
Microcin J25, Escherichia coli : Q9X2V7

Nematode tempo - June 2006
Hearts beat, throats swallow and Fallopian tubes squeeze. Many parts of us are pumping, pushing, and expanding at regular intervals all day long. And the regularity of these intervals depends on intricate molecular pathways that we are only beginning to understand. Part of the secret is being unveiled thanks to a minute nematode – Caenorhabditis elegans – whose rhythmic movements are easy to follow simply because of its transparency. A protein similar to proteins already discovered in humans, and known as Vav-1, seems to be at the heart of rhythms in the worm, which allow it not only to swallow but also to conceive and – less romantically – to expel waste. (PDF version - 50K bytes)
Swiss-Prot cross references
Vav-1, Caenorhabditis elegans : Q45FX5

All things dwarfed and beautiful - May 2006
The world population increases daily, and with it the number of mouths to feed. As a consequence, finding ways to improve crop yield has become a major issue. Since the 1960s, grain production has grown exponentially. And while it took 10 000 years to produce the first billion tons of grain, it has only taken 40 years to produce the second, thanks to fertilisers, pesticides and intensive cross-breeding. As is frequently the case, the molecular mechanisms underlying the commercially improved phenotype are largely unknown. However, it appears that hormones known as gibberellins – along with the proteins they stimulate – have a central role in plant growth and development, and could be the molecules upon which to act in the future, to design cereals – or indeed other plants – that are favourable in terms of agronomy and economy. (PDF version - 128K bytes)
Swiss-Prot cross references
DELLA protein Rht-1, Triticum aestivum (Wheat): Q9ST59
DELLA protein dwarf-8, Zea mays (Maize): Q9ST48
DELLA protein Gai1, Vitis vinifera (Grapevine): Q8S4W7

Nerve regrowth: nipped by a no-go - April 2006
Injury to the adult central nervous system (CNS) and neurodegenerative diseases often engender lifelong consequences to the organism. Could the key to the mysteries of nerve regeneration lie concealed in the amino terminus of a notorious protein? Independent research groups working on either side of the Atlantic have answered in the affirmative. Indeed, the legendary inability of neurons to regenerate and repair lesions in the adult CNS can be attributed to a battery of inhibitory and repellent proteins, one of which - dubbed Nogo - is released by nerve fibres following injury. (PDF version - 70K bytes)
Swiss-Prot cross references
Nogo protein, Homo sapiens (Human): Q9NQC3
Nogo-66 receptor, Homo sapiens (Human): Q9BZR6

Vita minima - March 2006
Trees are beginning to blossom, flowers are easing their way through the earth and frogs will soon begin their slow march out of hibernation. In short, Spring is on its way. And for the faultless unfolding of these awakenings, hosts of proteins will be summoned. Tau protein is one. Tau has become very popular since it was discovered that its presence seemed to coincide with the evolution of Alzheimer’s disease. Though it may sound contradictory, tau protein could have a protective role towards neurons, as suggested by the process of hibernation in the European ground squirrel... (PDF version - 75K bytes)
Swiss-Prot cross references
Microtubule-associated protein tau, Homo sapiens (Human): P10636
Microtubule-associated protein tau, Spermophilus citellus (European suslik): Q6TS35

Of earwax and migration - February 2006
The month of February is usually dedicated to romanticism. We, however, shall dedicate it to the intricacies of earwax. Less charming, perhaps, but just as colourful. Many of us are acquainted with the yellowish/brownish soft substance which lines our inner ear. Regarded mainly as dirt, we spend our time extracting it. Yet there is good reason for it to be there. And one of the reasons is due to the existence of cerumen apocrine glands in the external auditory canal, which secrete cerumen along with a host of other biomolecules. Secretion demands canals and pumps. And one protein pump – the multiple drug resistance protein 8 (MRP8) – has a direct role not only in the production of earwax but also its texture. (PDF version - 34K bytes)
Swiss-Prot cross references
ATP-binding cassette transporter subfamily C member 11 (Multidrug resistance-associated protein 8), Homo sapiens (Human): Q96J66

Gut feelings - January 2006
The sensation of hunger would seem trivial to most, and yet – besides being vital – it implies complex molecular pathways both in our guts and our brain, as too does the perception of food sufficiency. Most of the time we are unaware, but we own a built-in system which tells us when our bodies could do with a little fuel, and when they can do without. An empty stomach – like a full one – does not go unnoticed. What is it that makes us feel hungry? Or full? Research on gut sensations has been blooming for years now, what with obesity spreading worldwide, and the molecular processes underlying appetite, or satiety, are slowly emerging. Ghrelin and obestatin are just two proteins which are an integral part of such processes, and are particular in that not only are they coded by the same gene but they have opposing actions. Indeed, ghrelin triggers off the desire for food, while obestatin reports adequacy. (PDF version - 106K bytes)
Swiss-Prot cross references
Appetite regulating hormones ghrelin and obestatin, Homo sapiens (Human): Q9UBU3
Appetite regulating hormones ghrelin and obestatin, Rattus norvegicus (Rat): Q9QYH7


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