Genome complexity: controlling DNA in the cell (Introduction)

by David Turell , Sunday, November 04, 2018, 19:52 (2212 days ago) @ David Turell

There are molecules which lasso DNA:

https://www.sciencedaily.com/releases/2018/11/181102105950.htm

"The Rice lab of José Onuchic has determined the structure of the condensin protein complex. The work settles the controversy over whether the complex is a single ring that lassos two double strands of DNA or a molecular "handcuff" composed of two connected rings that each wrangle a double strand.

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"Their work is the first step toward understanding the activity of proteins over the structure of chromosomes throughout mitosis and all phases of the cell life cycle.

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"Condensin does what the word suggests: It helps condense the chromosomes into the cell's nucleus. Recent research has demonstrated that condensin and its protein partner cohesin extrude DNA. But until now, nobody has settled on how condensin proteins come together into their functional forms.

"Krepel started her analysis from bacterial condensin complexes made up of five subunits, including two structural maintenance of chromosomes (SMC) proteins that come together as a hinge and long kleisin proteins that make up the rest of the ring. Complexes in human eukaryotic nuclei -- a target for future analysis -- are similar to their more archaic counterparts.

" Krepel pieced the puzzle together by combining and comparing existing data about the atomic structures and genetic sequences of the individual proteins. The structures came from available X-ray crystallography of protein fragments, and sequence information through direct coupling analysis (DCA), a statistics-based program introduced by Onuchic and his colleagues in 2011 that compares amino acid residues in proteins that coevolve.

"'We used DCA to infer coevolving pairs of amino acids, and we had little bits of protein fragments from experiments," Krepel said. "That was a good starting point, and then we had to put them together like a puzzle. We wanted to get a full structure and settle the conflict over whether it's a single or double ring."

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"Onuchic's group at Rice's Center for Theoretical Biological Physics (CTBP) has published a series of papers that extend its theories on protein folding to the much larger genome. He expects ongoing work will eventually reveal condensin's mechanisms. "These things have to condense the chromosomes," he said. "People know that. But nobody knows how they do it."

"Onuchic said studies by others suggest the flexible hinge may help open and close the ring, serving as a gate that allows DNA strands in and out, a process also hinted at by the Rice study. But without knowing the position of every molecule in the complex, there is no way to completely understand its function and dynamics.

"'We know the condensin complex is involved, because if you remove it, mitosis doesn't happen," he said. "But nobody understands the mechanism. Now that we have this structure, we have the first shot at understanding the molecular details.'"

Comment: Translation of this paper: we can see what the molecules do, but we do not know how the molecules are controlled. Molecules cannot act on their own, but are driven by reactions that are intelligently purposeful. The complexity requires design.