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Cetin E, Guclu TF, Kantarcioglu I, Gaszek IK, Toprak E, Atilgan AR, Dedeoglu B, Atilgan C. Kinetic Barrier to Enzyme Inhibition Is Manipulated by Dynamical Local Interactions in E. coli DHFR. J Chem Inf Model 2023; 63:4839-4849. [PMID: 37491825 PMCID: PMC10428214 DOI: 10.1021/acs.jcim.3c00818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Indexed: 07/27/2023]
Abstract
Dihydrofolate reductase (DHFR) is an important drug target and a highly studied model protein for understanding enzyme dynamics. DHFR's crucial role in folate synthesis renders it an ideal candidate to understand protein function and protein evolution mechanisms. In this study, to understand how a newly proposed DHFR inhibitor, 4'-deoxy methyl trimethoprim (4'-DTMP), alters evolutionary trajectories, we studied interactions that lead to its superior performance over that of trimethoprim (TMP). To elucidate the inhibition mechanism of 4'-DTMP, we first confirmed, both computationally and experimentally, that the relative binding free energy cost for the mutation of TMP and 4'-DTMP is the same, pointing the origin of the characteristic differences to be kinetic rather than thermodynamic. We then employed an interaction-based analysis by focusing first on the active site and then on the whole enzyme. We confirmed that the polar modification in 4'-DTMP induces additional local interactions with the enzyme, particularly, the M20 loop. These changes are propagated to the whole enzyme as shifts in the hydrogen bond networks. To shed light on the allosteric interactions, we support our analysis with network-based community analysis and show that segmentation of the loop domain of inhibitor-bound DHFR must be avoided by a successful inhibitor.
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Affiliation(s)
- Ebru Cetin
- Faculty
of Engineering and Natural Sciences, Sabanci
University, Tuzla 34956, Istanbul, Turkey
| | - Tandac F. Guclu
- Faculty
of Engineering and Natural Sciences, Sabanci
University, Tuzla 34956, Istanbul, Turkey
| | - Isik Kantarcioglu
- Faculty
of Engineering and Natural Sciences, Sabanci
University, Tuzla 34956, Istanbul, Turkey
- Department
of Pharmacology, University of Texas Southwestern
Medical Center, Dallas 75390, Texas, United States
| | - Ilona K. Gaszek
- Department
of Pharmacology, University of Texas Southwestern
Medical Center, Dallas 75390, Texas, United States
| | - Erdal Toprak
- Department
of Pharmacology, University of Texas Southwestern
Medical Center, Dallas 75390, Texas, United States
| | - Ali Rana Atilgan
- Faculty
of Engineering and Natural Sciences, Sabanci
University, Tuzla 34956, Istanbul, Turkey
| | - Burcu Dedeoglu
- Department
of Chemistry, Gebze Technical University, Gebze 41400, Kocaeli, Turkey
| | - Canan Atilgan
- Faculty
of Engineering and Natural Sciences, Sabanci
University, Tuzla 34956, Istanbul, Turkey
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2
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Abdizadeh H, Tamer YT, Acar O, Toprak E, Atilgan AR, Atilgan C. Increased substrate affinity in the Escherichia coli L28R dihydrofolate reductase mutant causes trimethoprim resistance. Phys Chem Chem Phys 2018; 19:11416-11428. [PMID: 28422217 DOI: 10.1039/c7cp01458a] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Dihydrofolate reductase (DHFR) is a ubiquitous enzyme with an essential role in cell metabolism. DHFR catalyzes the reduction of dihydrofolate to tetrahydrofolate, which is a precursor for purine and thymidylate synthesis. Several DHFR targeting antifolate drugs including trimethoprim, a competitive antibacterial inhibitor, have therefore been developed and are clinically used. Evolution of resistance against antifolates is a common public health problem rendering these drugs ineffective. To combat the resistance problem, it is important to understand resistance-conferring changes in the DHFR structure and accordingly develop alternative strategies. Here, we structurally and dynamically characterize Escherichia coli DHFR in its wild type (WT) and trimethoprim resistant L28R mutant forms in the presence of the substrate and its inhibitor trimethoprim. We use molecular dynamics simulations to determine the conformational space, loop dynamics and hydrogen bond distributions at the active site of DHFR for the WT and the L28R mutant. We also report their experimental kcat, Km, and Ki values, accompanied by isothermal titration calorimetry measurements of DHFR that distinguish enthalpic and entropic contributions to trimethoprim binding. Although mutations that confer resistance to competitive inhibitors typically make enzymes more promiscuous and decrease affinity to both the substrate and the inhibitor, strikingly, we find that the L28R mutant has a unique resistance mechanism. While the binding affinity differences between the WT and the mutant for the inhibitor and the substrate are small, the newly formed extra hydrogen bonds with the aminobenzoyl glutamate tail of DHF in the L28R mutant leads to increased barriers for the dissociation of the substrate and the product. Therefore, the L28R mutant indirectly gains resistance by enjoying prolonged binding times in the enzyme-substrate complex. While this also leads to slower product release and decreases the catalytic rate of the L28R mutant, the overall effect is the maintenance of a sufficient product formation rate. Finally, the experimental and computational analyses together reveal the changes that occur in the energetic landscape of DHFR upon the resistance-conferring L28R mutation. We show that the negative entropy associated with the binding of trimethoprim in WT DHFR is due to water organization at the binding interface. Our study lays the framework to study structural changes in other trimethoprim resistant DHFR mutants.
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Affiliation(s)
- Haleh Abdizadeh
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey.
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3
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Søndergaard CR, Olsson MHM, Rostkowski M, Jensen JH. Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKa Values. J Chem Theory Comput 2011; 7:2284-95. [DOI: 10.1021/ct200133y] [Citation(s) in RCA: 1072] [Impact Index Per Article: 82.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Chresten R. Søndergaard
- Department of Chemistry and Center for Computational Molecular Sciences, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Mats H. M. Olsson
- Department of Chemistry and Center for Computational Molecular Sciences, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Michał Rostkowski
- Department of Chemistry and Center for Computational Molecular Sciences, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Jan H. Jensen
- Department of Chemistry and Center for Computational Molecular Sciences, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
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4
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Moretti L, Graham Richards W. Molecular alignment using multipole moments. Bioorg Med Chem Lett 2010; 20:5887-90. [DOI: 10.1016/j.bmcl.2010.07.107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2010] [Revised: 07/23/2010] [Accepted: 07/25/2010] [Indexed: 11/15/2022]
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5
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Bas DC, Rogers DM, Jensen JH. Very fast prediction and rationalization of pKa values for protein-ligand complexes. Proteins 2008; 73:765-83. [PMID: 18498103 DOI: 10.1002/prot.22102] [Citation(s) in RCA: 882] [Impact Index Per Article: 55.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Delphine C Bas
- Equipe de Chimie et Biochimie Théoriques, UMR 7565 - CNRS, Université Henri Poincaré, Nancy I, Boulevard des Aiguillettes BP 239, 54506 Vandoeuvre-lès-Nancy Cedex, France
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6
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Czodrowski P, Dramburg I, Sotriffer CA, Klebe G. Development, validation, and application of adapted PEOE charges to estimate pKa values of functional groups in protein-ligand complexes. Proteins 2006; 65:424-37. [PMID: 16927370 DOI: 10.1002/prot.21110] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
For routine pK(a) calculations of protein-ligand complexes in drug design, the PEOE method to compute partial charges was modified. The new method is applicable to a large scope of proteins and ligands. The adapted charges were parameterized using experimental free energies of solvation of amino acids and small organic ligands. For a data set of 80 small organic molecules, a correlation coefficient of r(2) = 0.78 between calculated and experimental solvation free energies was obtained. Continuum electrostatics pK(a) calculations based on the Poisson-Boltzmann equation were carried out on a validation set of nine proteins for which 132 experimental pK(a) values are known. In total, an overall RMSD of 0.88 log units between calculated and experimentally determined data is achieved. In particular, the predictions of significantly shifted pK(a) values are satisfactory, and reasonable estimates of protonation states in the active sites of lysozyme and xylanase could be obtained. Application of the charge-assignment and pK(a)-calculation procedure to protein-ligand complexes provides clear structural interpretations of experimentally observed changes of protonation states of functional groups upon complex formation. This information is essential for the interpretation of thermodynamic data of protein-ligand complex formation and provides the basis for the reliable factorization of the free energy of binding in enthalpic and entropic contributions. The modified charge-assignment procedure forms the basis for future automated pK(a) calculations of protein-ligand complexes.
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Affiliation(s)
- Paul Czodrowski
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
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Bennett B, Langan P, Coates L, Mustyakimov M, Schoenborn B, Howell EE, Dealwis C. Neutron diffraction studies of Escherichia coli dihydrofolate reductase complexed with methotrexate. Proc Natl Acad Sci U S A 2006; 103:18493-8. [PMID: 17130456 PMCID: PMC1664550 DOI: 10.1073/pnas.0604977103] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Hydrogen atoms play a central role in many biochemical processes yet are difficult to visualize by x-ray crystallography. Spallation neutron sources provide a new arena for protein crystallography with TOF measurements enhancing data collection efficiency and allowing hydrogen atoms to be located in smaller crystals of larger biological macromolecules. Here we report a 2.2-A resolution neutron structure of Escherichia coli dihydrofolate reductase (DHFR) in complex with methotrexate (MTX). Neutron data were collected on a 0.3-mm(3) D(2)O-soaked crystal at the Los Alamos Neutron Scattering Center. This study provides an example of using spallation neutrons to study protein dynamics, to identify protonation states directly from nuclear density maps, and to analyze solvent structure. Our structure reveals that the occluded loop conformation [monomer (mon.) A] of the DHFR.MTX complex undergoes greater H/D exchange compared with the closed-loop conformer (mon. B), partly because the Met-20 and beta(F-G) loops readily exchange in mon. A. The eight-stranded beta sheet of both DHFR molecules resists H/D exchange more than the helices and loops. However, the C-terminal strand, betaH, in mon. A is almost fully exchanged. Several D(2)Os form hydrogen bonds with exchanged amides. At the active site, the N1 atom of MTX is protonated and thus charged when bound to DHFR. Several D(2)Os are observed at hydrophobic surfaces, including two pockets near the MTX-binding site. A previously unidentified D(2)O hydrogen bonds with the catalytic D27 in mon. B, stabilizing its negative charge.
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Affiliation(s)
- Brad Bennett
- *Department of Biochemistry, Cellular and Molecular Biology, M407 Walters Life Sciences, University of Tennessee, Knoxville, TN 37996; and
| | - Paul Langan
- Los Alamos National Laboratory, Biosciences Division, Mail Stop MS M888, Los Alamos, NM 87545
| | - Leighton Coates
- Los Alamos National Laboratory, Biosciences Division, Mail Stop MS M888, Los Alamos, NM 87545
| | - Marat Mustyakimov
- Los Alamos National Laboratory, Biosciences Division, Mail Stop MS M888, Los Alamos, NM 87545
| | - Benno Schoenborn
- Los Alamos National Laboratory, Biosciences Division, Mail Stop MS M888, Los Alamos, NM 87545
| | - Elizabeth E. Howell
- *Department of Biochemistry, Cellular and Molecular Biology, M407 Walters Life Sciences, University of Tennessee, Knoxville, TN 37996; and
| | - Chris Dealwis
- *Department of Biochemistry, Cellular and Molecular Biology, M407 Walters Life Sciences, University of Tennessee, Knoxville, TN 37996; and
- To whom correspondence should be addressed. E-mail:
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8
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Blakley RL. Eukaryotic dihydrofolate reductase. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2006; 70:23-102. [PMID: 8638484 DOI: 10.1002/9780470123164.ch2] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- R L Blakley
- Department of Molecular Pharmacology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
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Pignatello R, Guccione S, Forte S, Di Giacomo C, Sorrenti V, Vicari L, Uccello Barretta G, Balzano F, Puglisi G. Lipophilic conjugates of methotrexate with short-chain alkylamino acids as DHFR inhibitors. Synthesis, biological evaluation, and molecular modeling. Bioorg Med Chem 2005; 12:2951-64. [PMID: 15142554 DOI: 10.1016/j.bmc.2004.03.040] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2003] [Accepted: 03/16/2004] [Indexed: 11/29/2022]
Abstract
Pursuing previous researches on lipophilic conjugates of methotrexate, aimed at over-crossing a form of transport resistance shown by some tumor cell lines toward the drug, a new series of derivatives is described in which the drug alpha- and gamma-carboxyl groups have been linked through amide bonds to short-chain alpha-alkylamino acids (4-6 carbon atoms). A specific NMR study was performed to delineate the stereochemistry of the conjugates. The inhibitory activity of these compounds against the target enzyme, (bovine liver) dihydrofolate reductase, and a sensitive (CCRF-CEM) and a transport-resistant tumor cell subline (CEM-MTX) were assessed. The conjugates showed the ability of retaining the same inhibitory activity also against the resistant cell subline, against which the parent drug was much less active than against the wild one; the alpha,gamma-bis(hexyl) derivative was the most active term of the series. Docking studies are in agreement with the proposed mode of interaction of these conjugates with the human DHFR.
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Affiliation(s)
- Rosario Pignatello
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Catania, Viale A. Doria 6, Città Universitaria, I-95125 Catania, Italy.
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Cummins PL, Gready JE. Combined Quantum and Molecular Mechanics (QM/MM) Study of the Ionization State of 8-Methylpterin Substrate Bound to Dihydrofolate Reductase. J Phys Chem B 2000. [DOI: 10.1021/jp993153l] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Peter L. Cummins
- Computational Molecular Biology and Drug Design Group, John Curtin School of Medical Research, Australian National University, P.O. BOX 334, Canberra ACT, 2601 Australia
| | - Jill E. Gready
- Computational Molecular Biology and Drug Design Group, John Curtin School of Medical Research, Australian National University, P.O. BOX 334, Canberra ACT, 2601 Australia
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12
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Cannon WR, Garrison BJ, Benkovic SJ. Consideration of the pH-dependent inhibition of dihydrofolate reductase by methotrexate. J Mol Biol 1997; 271:656-68. [PMID: 9281432 DOI: 10.1006/jmbi.1997.1173] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Poisson-Boltzmann calculations were used to determine the pKa of protein functional groups in the unliganded dihydrofolate reductase enzyme, and the pKa of protein and ligand groups in methotrexate-enzyme complexes. The results reported here are in conflict with two fundamental tenets of dihydrofolate reductase inhibition by methotrexate: (1) Asp27 is not expected to be protonated near pH 6.5 in the apoenzyme as previously proposed based on fitting of empirical equations to binding data, and (2) the calculated pKa for the pteridine N1 of the inhibitor while bound to the protein is significantly lower than that estimated for this group from interpretation of NMR data (>10). In fact, the electrostatic calculations and complementary quantum chemical calculations indicate that Asp27 is likely protonated when methotrexate is bound, resulting in a neutral dipole-dipole interaction rather than a salt-bridge between the enzyme and the inhibitor. Reasons for this discrepancy with the experimental data are discussed. Furthermore, His45 and Glu17 in the Escherichia coli enzyme are proposed to be in part responsible for the pH dependence of the conformational degeneracy in the inhibitor-enzyme complex.
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Affiliation(s)
- W R Cannon
- Department of Chemistry 152 Davey Laboratory, Pennsylvania State University, University Park, PA 16802, USA
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Yang QX, Huang FY, Lin TH, Gelbaum L, Howell EE, Huang TH. Dynamics of trimethoprim bound to dihydrofolate reductase--a deuterium NMR study. SOLID STATE NUCLEAR MAGNETIC RESONANCE 1996; 7:193-201. [PMID: 9050157 DOI: 10.1016/0926-2040(95)01223-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
We have employed deuterium NMR techniques to determine the dynamics of trimethoprim (TMP) in a binary complex with dihydrofolate reductase (DHFR) or in a ternary complex with DHFR and cofactor NADP+ in the fully hydrated state. TMP was deuterated at the following positions: (2',6'-D2)TMP, (3'-Ome-D3)TMP and (3',4'-Ome-D6)TMP. Dynamics of TMP were deduced from lineshape simulation and relaxation measurements of the deuterium NMR powder spectra of the three samples obtained at various temperatures. The results showed that in the polycrystalline state the TMP molecule is very rigid. The only detectable motion is the methyl group rotation at a rate of 10(10) s-1 at 25 degrees C, as determined from simulation of the partially relaxed powder patterns. When bound to DHFR a residual deuterium quadrupole splitting of 140 kHz was observed for (2',6'-D2)TMP at temperatures up to 30 degrees C, suggesting that the benzyl ring in the bound state is also very rigid. In contrast, in the binary complex with DHFR the methoxyl groups of TMP undergo librational motion of 10(7) s-1 about the C3-O bond at an amplitude of 54 degrees for the meta methoxyl group and about the C4-O bond at an amplitude of 70 degrees and similar rate for the para methoxyl group at 30 degrees C. The presence of the cofactor, NADP+, appears to tighten up the binding pocket such that the motion freedom of TMP is more restricted. The rigidity of TMP in a protein complex as revealed by our deuterium NMR results is in accord with the tight binding of TMP to DHFR.
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Affiliation(s)
- Q X Yang
- Division of Structural Biology, Academia Sinica, Nankang, Taipei, Taiwan
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Huang FY, Yang QX, Huang TH, Gelbaum L, Kuyper LF. The conformations of trimethoprim/E. coli dihydrofolate reductase complexes. A 15N and 31P NMR study. FEBS Lett 1991; 283:44-6. [PMID: 2037072 DOI: 10.1016/0014-5793(91)80549-i] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We have employed 15N and 31P NMR techniques to characterize the conformations of trimethoprim (TMP)/E. coli dihydrofolate reductase (DHFR) complexes in the presence and absence of NADPH and NADP+. A single conformation was observed for TMP/DHFR, NADP+/DHFR, NADPH/DHFR, and TMP/NADPH/DHFR complexes. In the ternary complex of TMP/NADP+/DHFR both the 15N and 31P spectra revealed the presence of two conformations. However, the conformations of TMP and NADP+ in the ternary complex may not be correlated, resulting in the possible existence of four conformations for the protein ternary complex.
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Affiliation(s)
- F Y Huang
- School of Physics, Georgia Institute of Technology, Atlanta 30332
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Davies JF, Delcamp TJ, Prendergast NJ, Ashford VA, Freisheim JH, Kraut J. Crystal structures of recombinant human dihydrofolate reductase complexed with folate and 5-deazafolate. Biochemistry 1990; 29:9467-79. [PMID: 2248959 DOI: 10.1021/bi00492a021] [Citation(s) in RCA: 140] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The 2.3-A crystal structure of recombinant human dihydrofolate reductase (EC 1.5.1.3, DHFR) has been solved as a binary complex with folate (a poor substrate at neutral pH) and also as a binary complex with an inhibitor, 5-deazafolate. The inhibitor appears to be protonated at N8 on binding, whereas folate is not. Rotation of the peptide plane joining I7 and V8 from its position in the folate complex permits hydrogen bonding of 5-deazafolate's protonated N8 to the backbone carbonyl of I7, thus contributing to the enzyme's greater affinity for 5-deazafolate than for folate. In this respect it is likely that bound 5-deazafolate furnishes a model for 7,8-dihydrofolate binding and, in addition, resembles the transition state for folate reduction. A hypothetical transition-state model for folate reduction, generated by superposition of the DHFR binary complexes human.5-deazafolate and chicken liver.NADPH, reveals a 1-A overlap of the binding sites for folate's pteridine ring and the dihydronicotinamide ring of NADPH. It is proposed that this binding-site overlap accelerates the reduction of both folate and 7,8-dihydrofolate by simultaneously binding substrate and cofactor with a sub van der Waals separation that is optimal for hydride transfer.
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Affiliation(s)
- J F Davies
- Department of Chemistry, University of California, San Diego, La Jolla 92093
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Abstract
NMR spectroscopy is a useful technique for studying interactions, conformations and dynamic processes within ligand-protein complexes. Several examples of the application of the method to studies of complexes of anti-folate drugs with their target enzyme, dihydrofolate reductase, are discussed.
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Affiliation(s)
- J Feeney
- National Institute for Medical Research, Mill Hill, London, U.K
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Appleman JR, Howell EE, Kraut J, Kühl M, Blakley RL. Role of aspartate 27 in the binding of methotrexate to dihydrofolate reductase from Escherichia coli. J Biol Chem 1988. [DOI: 10.1016/s0021-9258(19)76524-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Singh UC. Probing the salt bridge in the dihydrofolate reductase-methotrexate complex by using the coordinate-coupled free-energy perturbation method. Proc Natl Acad Sci U S A 1988; 85:4280-4. [PMID: 3380791 PMCID: PMC280412 DOI: 10.1073/pnas.85.12.4280] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The importance of the ionic interaction due to the formation of the salt bridge between the Asp-27 and the pteridine ring in Escherichia coli dihydrofolate reductase-methotrexate complex has been studied by using the free-energy perturbation method. The calculation suggests that the ion-pair contribution to the binding energy is insignificant, as the enzyme surroundings do not stabilize the salt bridge to the extent of the desolvation of the charged groups. The activation barrier for the proton exchange between the pteridine ring and the Asp-27 is calculated to be 20.1 kcal/mol (1 cal = 4.184 J) by using the coordinate-coupled perturbation method, implying that this may be a channel to the proton exchange from the pteridine ring to the solvent. The Gibbs-energy difference of binding between the Asn-27 and Ser-27 is calculated to be 3.2 kcal/mol and is mainly due to the electrostatic interactions.
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Affiliation(s)
- U C Singh
- Department of Molecular Biology, Scripps Clinic and Research Foundation, La Jolla, CA 92037
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19
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Shaw WV. Protein engineering. The design, synthesis and characterization of factitious proteins. Biochem J 1987; 246:1-17. [PMID: 3314863 PMCID: PMC1148234 DOI: 10.1042/bj2460001] [Citation(s) in RCA: 68] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- W V Shaw
- Department of Biochemistry, University of Leicester, U.K
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