Reasons to Believe

Protein Life Times: Just-Right Evidence for Design

A recent study by scientists from Belgium and Spain exemplifies the unremitting stream of apologetically significant research in biochemistry. It turns out that protein amino acid sequences, production rates, and the duration of protein existence inside the cell are carefully optimized so these “workhorse molecules of life” possess maximum structural stability, while minimizing the likelihood that they will aggregate.

Systems and objects produced by human designers are also optimized. In fact, optimization in an engineered system requires extensive planning and forethought and, therefore, stands as a hallmark of intelligent design. Indeed, optimization is often synonymous with superior design.

I am often asked what convinced me that a Creator exists, and that life stems from His handiwork. To be brief, I was convinced by the elegance, sophistication, and cleverness of biochemical systems—the most basic, fundamental components of life. (See The Cell’s Design for a detailed discussion of these systems.)

Week after week, scientific journals publish new discoveries that continue to highlight the awe-inspiring properties of biochemical systems—and at the same time advance the case for the Creator. One study that recently caught my attention was published by a research team from Belgium and Spain.1

These scientists determined that the lifetimes of proteins are carefully optimized so that those with the greatest propensity for aggregation exist only for a short duration within the cell. On the other hand, proteins with a reduced tendency to clump together have longer life spans.

So why does this insight help make the case for intelligent design? Some background information will make it possible to appreciate why I think this discovery is so significant.

Proteins

These biomolecules are the workhorse molecules of life, taking part in virtually every cellular structure and activity. Proteins catalyze (assist) chemical reactions, store and transport molecules, harvest chemical energy, and assemble and become part of the cell’s structures. Simply put, every structure and activity inside the cell involves multiple proteins working in conjunction with one another.

Proteins are chain-like molecules that fold into precise three-dimensional structures. A protein’s shape uniquely determines its functional and/or structural role. If that structure is compromised, the protein will not function properly and it becomes a detriment to the cell. Protein chains are made-up of amino acids, smaller molecules linked together in a head-to-tail manner. The sequence of amino acids dictates the folding pattern of the protein chain and, consequently, determines the protein’s functional properties.

The video below shows the structure of a typical protein molecule (depicted in a variety of ways) and illustrates how it folds in three-dimensional space.




Protein Lifetimes and Turnover

Proteins assume different roles inside the cell. As a consequence, they have varying lifetimes. Some proteins perform highly specific functions required only at specific points in the cell cycle. The cell’s machinery makes these proteins as needed, and then quickly destroys them after they carry out their assignment.

Other proteins persist for long periods of time. These proteins carry out activities necessary throughout the cell cycle. Over time, these enduring biomolecules become worn out and begin to break down. This breakdown then causes the proteins to unfold, adopting an unnatural three-dimensional shape in a process called denaturation.

When proteins become denatured, an elaborate mechanism kicks in to destroy and dispose of these unfolded biomolecules. (Go here and here to read about this removal process and why it also constitutes evidence for intelligent design.)

This disposal operation is critical for the cell, because unfolded proteins tend to interact with each other, clumping together to form aggregates. These tangled proteins will gum up cellular operations. In fact, aggregated proteins are part of the etiology of diseases like Alzheimer’s and Parkinson’s.

Designed to Minimize Aggregation...

A few years ago, researchers discovered that when proteins become denatured and unfold, they expose stretches of amino acids (called a hydrophobic β–sheet structure) that possess a strong tendency to clump with other like sequences. Normally, these sequences are buried deep within the interior of the folded protein and can’t come into contact with corresponding sequences in other proteins. It’s only when proteins become denatured and either partially or completely unfold that these aggregation-promoting sequences are exposed to other proteins, exerting their deleterious effects.

But researchers also discovered amino acid residues adjacent to the hydrophobic β–sheet sequences that disrupt protein aggregation.2 These aggregation-reducing amino acids are called “gate-keeping” residues. It turns out that strongly aggregating sequences are flanked by more gate-keeping residues than those that are weakly aggregating. Proteins’ amino acid sequences appear carefully designed to minimize aggregation.3

…And Optimized to Ensure Structural Stability

But a trade-off exists. The strongly aggregating sequences are necessary to stabilize proteins when they fold into their naturally intended three-dimensional shapes. Researchers learned that the amino acid sequences are exquisitely arranged to precisely balance the need for structural stability, while minimizing aggregation propensity.

That’s not all. Scientists also discovered a few years ago that proteins with the greatest tendency to aggregate are produced less frequently and at lower levels than proteins with a reduced tendency to clump together.4 (The rate and the amount of protein production is called gene expression.) Gene expression appears optimized with a tendency toward aggregation.

And, as the latest work by the scientists from Belgium and Spain indicates, so are protein lifetimes. Proteins with the longest lifetimes tend to have a reduced tendency to aggregate; whereas proteins with the greatest likelihood of clumping together have the shortest lifetimes.

Yet the optimization of proteins is not limited to their aggregation propensities. A cascade of optimization characterizes protein structure and function. In The Cell’s Design, I described a number of other ways that protein structure is optimized.

Protein Optimization and the Case for Intelligent Design

Human designers optimize the systems and objects they produce. Optimization in an engineered system requires extensive planning and forethought and, therefore, stands as a hallmark of intelligent design. In fact, optimization is often synonymous with superior design.

As I describe in The Cell’s Design, life scientists have discovered that, like human designs, many biochemical systems are optimized according to a purpose. The optimization that surrounds protein structure, production, and lifetimes with respect to aggregation tendency mark just one more example. But there is more—the protein optimization displays a clever molecular logic, of sorts. It also bespeaks of the work of a Mind.

The more that we learn about biochemical systems, the more convinced I am that they are the Creator’s handiwork.

Subjects: Biochemical Design

Dr. Fazale Rana

In 1999, I left my position in R&D at a Fortune 500 company to join Reasons to Believe because I felt the most important thing I could do as a scientist is to communicate to skeptics and believers alike the powerful scientific evidence—evidence that is being uncovered day after day—for God’s existence and the reliability of Scripture. Read more about Dr. Fazale Rana

Endnotes:

1.    Greet De Baets et al., “An Evolutionary Trade-Off between Protein Turnover Rate and Protein Aggregation Favors a Higher Aggregation Propensity in Fast Degrading Proteins,” PLoS Computational Biology 7 (June 2011): e002090.

2.    Joke Reumers et al., “Protein Sequences Encode Safeguards against Aggregation,” Human Mutation 30 (March 2009): 431–39.

3.    Elodie Monsellier et al., “The Distribution of Residues in a Polypeptide Sequence Is a Determinant of Aggregation Optimization,” Biophysical Journal 93 (December 2007): 4382–91; Elodie Monsellier et al., “Aggregation Propensity of the Human Proteome,” PLoS Computational Biology 4, (October 2008): e1000199; Natalia S. de Groot and Salvador Ventura, “Protein Aggregation Profile of the Bacterial Cytosol,” PLoS One 5 (February 2010): e9383.

4.    Gian Gaetano Tartaglia et al., “Life on the Edge: A Link between Gene Expression Levels and Aggregation Rates of Human Proteins,” TRENDS in Biochemical Sciences 32 (2007): 204–206.