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Molecular dynamics simulation of Escherichia coli dihydrofolate reductase and its protein fragments: Relative stabilities in experiment and simulations

¹ Laboratory of Experimental and Computational Biology, National Cancer Institute-Frederick, Frederick, Maryland 21702, USA
² Intramural Research Support Program–SAIC, Laboratory of Experimental and Computational Biology, National Cancer Institute-Frederick, Frederick, Maryland 21702, USA
³ Sackler Institute of Molecular Medicine Department of Human Genetics, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel

Reprint requests to: Dr. Ruth Nussinov, NCI-FCRF Bldg. 469, Rm. 151, Frederick, Maryland 21702, USA; e-mail: ruthn{at}ncifcrf.gov; fax: (301) 846-5598.

We have carried out molecular dynamics simulations of the native dihydrofolate reductase from Escherichia coli and several of its folded protein fragments at standard temperature. The simulations have shown fragments 1–36, 37–88, and 89–159 to be unstable, with a CRMSD (C root mean squared deviation) >5 Å after 3.0 nsec of simulation. The unfolding of fragment 1–36 was immediate, whereas fragments 37–88 and 89–159 gradually unfolded because of the presence of the ß-sheet core structure. In the absence of residues 1–36, the two distinct domains comprising fragment 39–159 associated with each other, resulting in a stable conformation. This conformation retained most of its native structural elements. We have further simulated fragments derived from computational protein cutting. These were also found to be unstable, with the exception of fragment 104–159. In the absence of ₄, the loose loop region of residues 120–127 exhibited a ß-strand-like behavior, associating itself with the ß-sheet core of the protein fragment. The current study suggests that the folding of dihydrofolate reductase involves cooperative folding of distinct domains which otherwise would have been unstable as independent folded units in solution. Finally, the critical role of residues 1–36 in allowing the two distinct domains of fragment 104–159 to fold into the final native conformation is discussed.

Keywords: Protein stability; protein folding; molecular dissection; intramolecular chaperone; molecular modeling; building blocks

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