February 3, 2006 | David F. Coppedge

Precision of Cell Quality Control Described

Two research papers in Molecular Cell give more glimpses into the precision of cellular controls to ensure mistakes are detected and weeded out before harm occurs.  Vogel, Bukau and Mayer1 found that the molecular “chaperone” Hsp70 has a “proline switch,” found in all living organisms.  This switch regulates when the polypeptide needing to be folded is attached for processing, then ejected:

Crucial to the function of Hsp70 chaperones is the nucleotide-regulated transition between two conformational states, the ATP bound state with high association and dissociation rates for substrates and the ADP bound state with two and three orders of magnitude lower association and dissociation rates.  The spontaneous transition between the two states is extremely slow, indicating a high energy barrier for the switch that regulates the transition.  Here we provide evidence that a universally conserved proline in the ATPase domain constitutes the switch that assumes alternate conformations in response to ATP binding and hydrolysis.  The conformation of the proline, acting through an invariant arginine as relay, determines and stabilizes the opened and closed conformation of the substrate binding domain and thereby regulates the chaperone activity of Hsp70.   (Emphasis added in all quotes.)

What is Hsp70 used for?  “The 70 kDa heat shock proteins (Hsp70) are molecular chaperones that assist folding of newly synthesized polypeptides, refolding of misfolded proteins, and translocation of proteins through biological membranes, and in addition have regulatory functions in signal transduction, cell cycle [i.e., cell division], and apoptosis [i.e., programmed cell death].”
    Another paper in the same issue by Gromadski, Daviter and Rodnina2 looked at a quality-control mechanism in the ribosome, where proteins are synthesized before going to the chaperone for folding.  They found a way that the machine recognizes typos in transfer-RNA (tRNA) molecules, by authenticating each molecule in a series of precision molecular contacts at the docking site.  Mismatches slow down the assembly line from 120-260 per second to 3-4 per second, and result in a thousandfold faster ejection of errors, regardless of their shape:

Ribosomes take an active part in aminoacyl-tRNA selection by distinguishing correct and incorrect codon-anticodon pairs.  Correct codon-anticodon complexes are recognized by a network of ribosome contacts that are specific for each position of the codon-anticodon duplex and involve A-minor RNA interactions.  Here, we show by kinetic analysis that single mismatches at any position of the codon-anticodon complex result in slower forward reactions and a uniformly 1000-fold faster dissociation of the tRNA from the ribosome.  This suggests that high-fidelity tRNA selection is achieved by a conformational switch of the decoding site between accepting and rejecting modes, regardless of the thermodynamic stability of the respective codon-anticodon complexes or their docking partners at the decoding site.  The forward reactions on mismatched codons were particularly sensitive to the disruption of the A-minor interactions with 16S rRNA and determined the variations in the misreading efficiency of near-cognate codons.

The scientists calculated that this one proofreading step reduces errors from somewhere between one in 1,000 to one in 100,000.3  There was no mention of evolution in either of these papers.

1Vogel, Bukau and Mayer, “Allosteric Regulation of Hsp70 Chaperones by a Proline Switch,” Molecular Cell, Volume 21, Issue 3, 3 February 2006, Pages 359-367, doi:10.1016/j.molcel.2005.12.017.
2Gromadski, Daviter and Rodnina, “A Uniform Response to Mismatches in Codon-Anticodon Complexes Ensures Ribosomal Fidelity,” Molecular Cell, Volume 21, Issue 3, 3 February 2006, Pages 369-377, http://dx.doi.org/10.1016/j.molcel.2005.12.018.
3There are many other proofreading steps in the process.  There are quality-control mechanisms when the DNA is decoded, when the messenger RNA is assembled, when it enters the ribosome, when the amino acids are attached to the proper transfer-RNA, when the tRNA enters the ribosome (as shown here), when the polypeptide exits the ribosome, when the polypeptide is folded in the chaperone, and even later, when post-translational modifications take place in the endoplasmic reticulum.

In the film Unlocking the Mystery of Life, biochemist Dean Kenyon remarked that it is precisely at this molecular level that we find the most powerful evidence for intelligent design on the earth.  We couldn’t possibly report on all such stories flowing daily out of the scientific journals.  We just provide tidbits from time to time to show you what the Darwinists are up against these days.  Their answer is a mysterious silence.

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