DOI: 10.1110/ps.062724307. Conformational change of the methionine 20 loop of <i>Escherichia coli</i> dihydrofolate reductase modulates pK<sub>a</sub> of the bound dihydrofolate

Conformational change of the methionine 20 loop of Escherichia coli dihydrofolate reductase modulates pKa of the bound dihydrofolate

10.1110/ps.062724307

Crossref journal-article

Wiley

Protein Science (311)

Abstract

AbstractWe evaluate the pKa of dihydrofolate (H2F) at the N5 position in three ternary complexes with Escherichia coli dihydrofolate reductase (ecDHFR), namely ecDHFR(NADP+:H2F) in the closed form (1), and the Michaelis complexes ecDHFR(NADPH:H2F) in the closed (2) and occluded (3) forms, by performing free energy perturbation with molecular dynamics simulations (FEP/MD). Our simulations suggest that in the Michaelis complex the pKa is modulated by the Met20 loop fluctuations, providing the largest pKa shift in substates with a “tightly closed” loop conformation; in the “partially closed/open” substates, the pKa is similar to that in the occluded complex. Conducive to the protonation, tightly closing the Met20 loop enhances the interactions of the cofactor and the substrate with the Met20 side chain and aligns the nicotinamide ring of the cofactor coplanar with the pterin ring of the substrate. Overall, the present study favors the hypothesis that N5 is protonated directly from solution and provides further insights into the mechanism of the substrate protonation.

Bibliography

Khavrutskii, I. V., Price, D. J., Lee, J., & Brooks, C. L. (2007). Conformational change of the methionine 20 loop of Escherichia coli dihydrofolate reductase modulates pKa of the bound dihydrofolate. Protein Science, 16(6), 1087â1100. Portico.

Authors 4

Ilja V. Khavrutskii (first)
Daniel J. Price (additional)
Jinhyuk Lee (additional)
Charles L. Brooks (additional)

References 72 Referenced 34

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Dates

Type	When
Created	18 years, 3 months ago (May 2, 2007, 10:01 a.m.)
Deposited	1 year, 10 months ago (Sept. 29, 2023, 3:11 a.m.)
Indexed	1 year, 2 months ago (June 16, 2024, 1:51 p.m.)
Issued	18 years, 2 months ago (June 1, 2007)
Published	18 years, 2 months ago (June 1, 2007)
Published Online	16 years, 7 months ago (Jan. 2, 2009)
Published Print	18 years, 2 months ago (June 1, 2007)

Funders 0

None

BibTeX

@article{Khavrutskii_2007, title={Conformational change of the methionine 20 loop of Escherichia coli dihydrofolate reductase modulates pKa of the bound dihydrofolate}, volume={16}, ISSN={1469-896X}, url={http://dx.doi.org/10.1110/ps.062724307}, DOI={10.1110/ps.062724307}, number={6}, journal={Protein Science}, publisher={Wiley}, author={Khavrutskii, Ilja V. and Price, Daniel J. and Lee, Jinhyuk and Brooks, Charles L.}, year={2007}, month=jun, pages={1087–1100} }

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        "id-type": "doi",
        "id": "10.3410/f.1086898.539831",
        "asserted-by": "object"
      }
    ]
  },
  "ISSN": [
    "0961-8368",
    "1469-896X"
  ],
  "subject": [],
  "container-title-short": "Protein Science",
  "published": {
    "date-parts": [
      [
        2007,
        6
      ]
    ]
  }
}