Research papers into the processes of molecular machines continue to reveal moving parts: “fingers” that open and close, ratchets that lock into place, and feet that move along tracks. Here are a few samples from the voluminous literature that continues to pour from biophysics labs.
1. DNA Polymerase I: Scientific papers tend to be reserved in their language, but the authors of a paper in Structure1 couldn’t help themselves: “DNA polymerases are spectacular molecular machines that can accurately copy genetic material with error rates on the order of 1 in 105 bases incorporated, not including the contributions of proofreading exonucleases.” Their paper went into detail on how the “fingers” and “thumb” of the machine open and close in precise sequence as the machine moves along the DNA strand base by base. Part of the machine rotates 50° as the machine translocates along the DNA. These machines copy millions of base pairs of DNA every cell division so that each daughter cell gets an accurate copy. The research was done on a bacterium that lives in hot springs.
Pata and Jaeger, who reviewed the paper by Golosov et al in Structure,2 included a diagram showing the “conformational changes” that DNA polymerase I undergoes in its action along the DNA strand. “After more than fifty years of research, the DNA polymerases responsible for copying the genetic material are some of the most well characterized enzymes in all of biology,” they said. “Although the polymerases are divided into several different families, they all share a common two metal-ion catalytic mechanism, and most of them are described as having fingers, palm, and thumb domains: the palm contains metal-binding catalytic residues, the thumb contacts DNA duplex, and the fingers form one side of the pocket surrounding the nascent base pair.” Three phases occur during each step along the DNA chain: the fingers open, the machine moves one base pair as it rotates, then the base in the “palm” is placed into the “preinsertion site,” while another moving part prevents further movement till the operation is completed. Then the process repeats — millions of times per operation….
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