Most of us would agree with the poet John Keats, who wrote in 1818 "A thing of beauty is a joy forever." Once we start to reflect on the topic, of course, we realize that we are surrounded by beauty! There is the beauty of natural land­scapes, whether barren or lush. We might reflect on the crea­tures of coral reefs, or of the tropical rainforest, or of the boreal forest. Of course flowers come to mind as things of astonishing beauty:

Consider the lilies of the field, how they grow: they nei­ther toil nor spin, yet I tell you, even Solomon in all his glory was not arrayed like one of these"

Matt. 6:28-29 ESV

Indeed our lists of beautiful things could go on and on.

There is however one topic that most of us might miss, and that is the beauty of functional proteins in the cells of our bodies. Anybody studying biology today is aware that proteins form the molecular machines that keep the compo­nent cells of our bodies healthy. But how many students are told that these proteins are actually beautiful?

Pretty, with a Purpose⤒🔗

Imagine a scene which could be taking place now in your body. A killer T cell (a kind of white blood cell) has de­tected that a virus has invaded a cell in your body. The killer T cell squeezes right up close to the cell in question. Then the killer T cell forms a tiny but beautiful vase-like structure. The vase consists of three large protein molecules attached end to end together. Then twenty of these composites are attached side by side in a circular formation to make an elaborate vase with 20-fold symmetry.

But this vase is not just pretty, it has a purpose. There is a large, very specifically sized opening all the way through the vase, from top to bottom. The vase projects through the killer T cell's enclosing membrane, across any intervening space and through the membrane of the cell containing the virus. The vase is called "perforin" since it perforates the mem­branes of these cells.

Then the killer T cell releases a protein-dissolving gran­ule into the other cell. The pore in the perforin vase must be of the correct size to allow this chemical weapon to enter the target cell. The infected host cell now duly disintegrates and along with it, the invading virus. Whew! That is one less vi­rus infection to worry about. It is to be hoped that the killer T cells catch most or all of your cells infected by this virus (Nature online October 31, 2010).

Proteins Created with Precision←⤒🔗

Another study (Nature on line November 4, 2010) dis­cussed how tiny changes in the structure of a protein called HLA-B, enable 1 out of 300 people with HIV to control the virus rather than succumb to its effects. Apparently just four modifications, out of hundreds of component parts in the protein, enable these people to stay healthy.

What happens is this. The HLA-B protein grabs frag­ments of the HIV virus and carries them to the cell mem­brane, sticking them on the outside where they act like flags to call in the killer T cells and you know what the killer T cells do.

Obviously it is not only the beauty, but the precise way in which the proteins are constructed, which amazes biolo­gists today. Proteins are formed when certain small mole­cules, called amino acids, are strung end to end like beads on a string.

Amyloid Lumps vs. Precise Proteins←⤒🔗

At first we just have a long ungainly strand. Left to its own devices, this strand would most likely collapse into a useless clump called amyloid. Thus a commentator, Jim Schnabel, remarked in an article entitled The Dark Side of Proteins:

The amyloid state is more like the default state of a protein, and in the absence of specific protective mecha­nisms, many of our proteins could fall into it.

Nature April 8, 2010 p. 828

This, of course, is not what usually happens in our bodies.

While the proteins start as long chains of amino acids, most of them fold up by means of a precise order of events, into complicated three dimensional shapes.

But how does this come about when the default position is the nasty amyloids? The author of this news features, Jim Schnabel points out that:

Most modern proteins fold into globular structures. But their folding patterns are so complex that they couldn't have evolved by accident.

p. 829

He points out that randomly assembled strings of amino ac­ids would almost never fold into a stable shape. For them to fold in a useful form the string of amino acids must first be assembled in a suitable order (and while Schnabel wouldn't say it, we can't help but think of design!).

Need to Be in the Right Order and Properly "Chaperoned"←⤒🔗

Even if the string of amino acids were ever so carefully chosen and assembled, the protein under construction still needs special hardware, provided by the living cell, in order to collapse the strand into the correct 3-dimensional shape. Thus the commentator in Nature declares:

When proteins are first synthesized and start to fold, 'chaperone' proteins and related molecules are there to guard against amyloid formation.

p. 829

These "chaperones" are structures in the cell which are es­sential for the survival of all proper-functioning in cells. The chaperone makes sure that the protein folds correctly.

All large complex proteins require the supervision of particularly fancy molecular machines called chaperonins. Two basic types have been described. Both enclose the newly minted protein chain inside a central cavity where folding takes place.

The one design consists of two barrel shaped cavities placed end to end with the openings facing outward. A pro­tein enters one end, and a cap moves in to trap the protein inside where it folds. The cap is then released to allow the newly folded protein to emerge. Meanwhile another pro­tein chain enters the barrel at the other end as the finished product emerges from the first end. Thus in this seesaw de­sign, one end or other always has a protein folding inside the cavity.

The other chaperonin model consists of only one cav­ity. A protein chain enters the cavity and the top closes like the iris diaphragm of a camera. Once the protein is folded, another iris diaphragm opens at the other end of the struc­ture and the finished protein is pushed out. The really im­portant work of protein folding obviously all happens inside the chaperonins.

What's Happening behind the Closed Doors?←⤒🔗

Scientists naturally are curious persons, otherwise they would never bother to research these difficult topics. Naturally they would like to know what happens inside the chaperonins. What is it about that enclosed space which en­courages proteins to fold in the appropriate way? It is now more than 50 years ago since scientists first proposed that the order of the amino acids on the strand is what determines how they will fold into their correct shapes. Three people Stanford Moore, William Stein and Christian Anfinsen won the 1972 Nobel Prize in Chemistry for this explanation. This, however, is just the beginning of understanding proteins. The problem is that even a relatively small protein can col­lapse into a huge number of possible shapes. It depends upon which folds come first, what the final shape is. Obviously, also, it is much harder to figure out interactions in a large protein. The factors in general determining the order of fold­ing involve the shapes of the various component amino acids in the strand and the electrical charges on these same com­ponent parts.

How Many Different Ways Is It Possible for Them to Fold?←⤒🔗

Scientists thus would love to discover all the ways that strings of amino acids could potentially fold and the ways in which they actually do fold. The Protein Structure Initiative was set up in 2000 to seek a complete understanding of the elaborate protein folds. Using fancy techniques, this center, based in Bethesda, Maryland, seeks to map the "protein uni­verse," or all the ways that a protein can fold. Critics claim that in the past 10 years, this laboratory has studied main­ly easier proteins, of little biological significance. Thus of the 5,000 protein structures for which the folds have been mapped, only 128 are human proteins.

Human proteins, for their part, tend to be larger and more difficult to work with than microbial proteins. The in­terest in mapping the human proteins, of course, is to de­velop suitable drugs against various diseases.

An ambitious project established by the Japanese in 2002 set out to produce a reference library of representa­tive protein folds. The hope was that scientists would then be able to translate information on the order of amino ac­ids in proteins into predictions on the overall structure of the larger molecules. Critics however suggested that the solu­tions obtained from this $70 million program, were the easy proteins involving many relatively similar folds. Initially it was hoped that the project would solve about one third of the 10,000 different folds then believed to exist. Experts lat­er placed the number of different folds at 16,000 or 30,000 (Nature September 28, 2006 p. 382). Thus after millions of dollars spent to date on a worldwide basis on protein folds, an expert in July 2010 concluded that perhaps about 6% of the protein folds had now been mapped and he declared that this achievement was "actually quite impressive." When we consider that an early objective of a former study was 33% mapped, 6% does not look so good (Nature July 29, 2010 p. 544).

A further illustration of the extreme complexity of pro­teins concerns the difficulties of some scientists who have sought to design proteins for specific functions. If one could figure out what determines folding patterns, then one could design strings of amino acids which would fit desired roles. Thus protein design is considered to be a cutting edge field which not only seeks to understand nature, but also to im­prove upon it. This has been the endeavor, for example, of Homme Hellinga of Duke University in Durham, North Carolina. In 2002 Dr. Hellinga undertook to radically recon­figure one protein. The new molecule would exhibit enzy­matic activity not present in the starting structure. Claiming victory, the Hellinga team published on their results in 2004 and 2007. However others were unable to make the system work. It indeed appears that no new protein had been pro­duced after all and the papers were withdrawn in 2008. Then in 2009, another paper published by Dr. Hellinga came un­der scrutiny. Widely hailed as a milestone, the paper claimed that computer algorithms could be used to design proteins with specific desired functions. Subsequent studies howev­er have found no evidence that the designed proteins func­tioned properly at all.

Other scientists are using the world's fastest supercom­puters to simulate all the possible ways that a given protein could fold. The idea is to use massive computing power to dis­cover correct folding patterns in proteins. But the difficulties are huge.

The number of possible configurations of atoms in larger molecules, over time and in three dimensions, is astro­nomical. If these kinds of simulation could be sped up 1,000-fold, which even then could take a month of computing time, the pay-off could be high. They might, for instance, reveal binding sites for new drugs to tackle a wide range of medical problems.

Nature January 17, 2008 P. 241

So this approach might show promise if we had supercomputers 1000 times faster than today! That tells us something about the scope of the problem. Once the results are all in, other computers would mine the data for promising results.

So Beautiful, So Amazing!←⤒🔗

So here we are, faced with complex and beautiful pro­teins which our best technology and worldwide teams of sci­entists have not even begun to understand. They can't predict the shape a given order of amino acids will assume once it folds into a protein nor can they manipulate those strands to make the protein do something else. It is obvious that the living cell, made up of many different kinds of protein, is an absolute miracle! With so many folding options, how does a cell ever achieve a correctly folded protein? Few phenomena in nature demonstrate the absolute necessity for an intelli­gent designer as clearly as the wonders of protein construc­tion. All praise to our Creator God!