1
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Mealka M, Sierra NA, Avellaneda Matteo D, Albekioni E, Khoury R, Mai T, Conley BM, Coleman NJ, Sabo KA, Komives EA, Bobkov AA, Cooksy AL, Silletti S, Schiffer JM, Huxford T, Sohl CD. Active site remodeling in tumor-relevant IDH1 mutants drives distinct kinetic features and potential resistance mechanisms. Nat Commun 2024; 15:3785. [PMID: 38710674 PMCID: PMC11074275 DOI: 10.1038/s41467-024-48277-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 04/26/2024] [Indexed: 05/08/2024] Open
Abstract
Mutations in human isocitrate dehydrogenase 1 (IDH1) drive tumor formation in a variety of cancers by replacing its conventional activity with a neomorphic activity that generates an oncometabolite. Little is understood of the mechanistic differences among tumor-driving IDH1 mutants. We previously reported that the R132Q mutant unusually preserves conventional activity while catalyzing robust oncometabolite production, allowing an opportunity to compare these reaction mechanisms within a single active site. Here, we employ static and dynamic structural methods and observe that, compared to R132H, the R132Q active site adopts a conformation primed for catalysis with optimized substrate binding and hydride transfer to drive improved conventional and neomorphic activity over R132H. This active site remodeling reveals a possible mechanism of resistance to selective mutant IDH1 therapeutic inhibitors. This work enhances our understanding of fundamental IDH1 mechanisms while pinpointing regions for improving inhibitor selectivity.
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Affiliation(s)
- Matthew Mealka
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Nicole A Sierra
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | | | - Elene Albekioni
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Rachel Khoury
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Timothy Mai
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Brittany M Conley
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Nalani J Coleman
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Kaitlyn A Sabo
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Elizabeth A Komives
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Andrey A Bobkov
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Andrew L Cooksy
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Steve Silletti
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, CA, USA
| | | | - Tom Huxford
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Christal D Sohl
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA.
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2
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Lin C, Mazor Y, Reppert M. Feeling the Strain: Quantifying Ligand Deformation in Photosynthesis. J Phys Chem B 2024; 128:2266-2280. [PMID: 38442033 DOI: 10.1021/acs.jpcb.3c06488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
Structural distortion of protein-bound ligands can play a critical role in enzyme function by tuning the electronic and chemical properties of the ligand molecule. However, quantifying these effects is difficult due to the limited resolution of protein structures and the difficulty of generating accurate structural restraints for nonprotein ligands. Here, we seek to quantify these effects through a statistical analysis of ligand distortion in chlorophyll proteins (CP), where ring deformation is thought to play a role in energy and electron transfer. To assess the accuracy of ring-deformation estimates from available structural data, we take advantage of the C2 symmetry of photosystem II (PSII), comparing ring-deformation estimates for equivalent sites both within and between 113 distinct X-ray and cryogenic electron microscopy PSII structures. Significantly, we find that several deformation modes exhibit considerable variability in predictions, even for equivalent monomers, down to a 2 Å resolution, to an extent that probably prevents their utilization in optical calculations. We further find that refinement restraints play a critical role in determining deformation values to resolution as low as 2 Å. However, for those modes that are well-resolved in the structural data, ring deformation in PSII is strongly conserved across all species tested from cyanobacteria to algae. These results highlight both the opportunities and limitations inherent in structure-based analyses of the bioenergetic and optical properties of CPs and other protein-ligand complexes.
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Affiliation(s)
- Chientzu Lin
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47920, United States
| | - Yuval Mazor
- School of Molecular Sciences, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Mike Reppert
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47920, United States
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3
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Mealka M, Sierra NA, Matteo DA, Albekioni E, Khoury R, Mai T, Conley BM, Coleman NJ, Sabo KA, Komives EA, Bobkov AA, Cooksy AL, Silletti S, Schiffer JM, Huxford T, Sohl CD. Active site remodeling in tumor-relevant IDH1 mutants drives distinct kinetic features and potential resistance mechanisms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.10.574970. [PMID: 38260668 PMCID: PMC10802581 DOI: 10.1101/2024.01.10.574970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Mutations in human isocitrate dehydrogenase 1 (IDH1) drive tumor formation in a variety of cancers by replacing its conventional activity with a neomorphic activity that generates an oncometabolite. Little is understood of the mechanistic differences among tumor-driving IDH1 mutants. We previously reported that the R132Q mutant uniquely preserves conventional activity while catalyzing robust oncometabolite production, allowing an opportunity to compare these reaction mechanisms within a single active site. Here, we employed static and dynamic structural methods and found that, compared to R132H, the R132Q active site adopted a conformation primed for catalysis with optimized substrate binding and hydride transfer to drive improved conventional and neomorphic activity over R132H. This active site remodeling revealed a possible mechanism of resistance to selective mutant IDH1 therapeutic inhibitors. This work enhances our understanding of fundamental IDH1 mechanisms while pinpointing regions for improving inhibitor selectivity.
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Affiliation(s)
- Matthew Mealka
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Nicole A. Sierra
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | | | - Elene Albekioni
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Rachel Khoury
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Timothy Mai
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Brittany M. Conley
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Nalani J. Coleman
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Kaitlyn A. Sabo
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Elizabeth A. Komives
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Andrey A. Bobkov
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA USA
| | - Andrew L. Cooksy
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Steve Silletti
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, CA, USA
| | | | - Tom Huxford
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Christal D. Sohl
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
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4
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Reyes AC, Amyes TL, Richard JP. A reevaluation of the origin of the rate acceleration for enzyme-catalyzed hydride transfer. Org Biomol Chem 2018; 15:8856-8866. [PMID: 28956050 DOI: 10.1039/c7ob01652b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
There is no consensus of opinion on the origin of the large rate accelerations observed for enzyme-catalyzed hydride transfer. The interpretation of recent results from studies on hydride transfer reactions catalyzed by alcohol dehydrogenase (ADH) focus on the proposal that the effective barrier height is reduced by quantum-mechanical tunneling through the energy barrier. This interpretation contrasts sharply with the notion that enzymatic rate accelerations are obtained through direct stabilization of the transition state for the nonenzymatic reaction in water. The binding energy of the dianion of substrate DHAP provides 11 kcal mol-1 stabilization of the transition state for the hydride transfer reaction catalyzed by glycerol-3-phosphate dehydrogenase (GPDH). We summarize evidence that the binding interactions between (GPDH) and dianion activators are utilized directly for stabilization of the transition state for enzyme-catalyzed hydride transfer. The possibility is considered, and then discounted, that these dianion binding interactions are utilized for the stabilization of a tunnel ready state (TRS) that enables efficient tunneling of the transferred hydride through the energy barrier, and underneath the energy maximum for the transition state. It is noted that the evidence to support the existence of a tunnel-ready state for the hydride transfer reactions catalyzed by ADH is ambiguous. We propose that the rate acceleration for ADH is due to the utilization of the binding energy of the cofactor NAD+/NADH in the stabilization of the transition state for enzyme-catalyzed hydride transfer.
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Affiliation(s)
- Archie C Reyes
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, USA.
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5
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Bourne CR, Wakeham N, Webb N, Nammalwar B, Bunce RA, Berlin KD, Barrow WW. The structure and competitive substrate inhibition of dihydrofolate reductase from Enterococcus faecalis reveal restrictions to cofactor docking. Biochemistry 2014; 53:1228-38. [PMID: 24495113 PMCID: PMC3985486 DOI: 10.1021/bi401104t] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
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We
are addressing bacterial resistance to antibiotics by repurposing
a well-established classic antimicrobial target, the dihydrofolate
reductase (DHFR) enzyme. In this work, we have focused on Enterococcus faecalis, a nosocomial pathogen that frequently
harbors antibiotic resistance determinants leading to complicated
and difficult-to-treat infections. An inhibitor series with a hydrophobic
dihydrophthalazine heterocycle was designed from the anti-folate trimethoprim.
We have examined the potency of this inhibitor series based on inhibition
of DHFR enzyme activity and bacterial growth, including in the presence
of the exogenous product analogue folinic acid. The resulting preferences
were rationalized using a cocrystal structure of the DHFR from this
organism with a propyl-bearing series member (RAB-propyl). In a companion
apo structure, we identify four buried waters that act as placeholders
for a conserved hydrogen-bonding network to the substrate and indicate
an important role in protein stability during catalytic cycling. In
these structures, the nicotinamide of the nicotinamide adenine dinucleotide
phosphate cofactor is visualized outside of its binding pocket, which
is exacerbated by RAB-propyl binding. Finally, homology models of
the TMPR sequences dfrK and dfrF were constructed. While the dfrK-encoded protein
shows clear sequence changes that would be detrimental to inhibitor
binding, the dfrF-encoded protein model suggests
the protein would be relatively unstable. These data suggest a utility
for anti-DHFR compounds for treating infections arising from E. faecalis. They also highlight a role for water in stabilizing
the DHFR substrate pocket and for competitive substrate inhibitors
that may gain advantages in potency by the perturbation of cofactor
dynamics.
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Affiliation(s)
- Christina R Bourne
- Department of Veterinary Pathobiology, Oklahoma State University , Stillwater, Oklahoma 74078, United States
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6
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Yahashiri A, Rubach JK, Plapp BV. Effects of cavities at the nicotinamide binding site of liver alcohol dehydrogenase on structure, dynamics and catalysis. Biochemistry 2014; 53:881-94. [PMID: 24437493 PMCID: PMC3969020 DOI: 10.1021/bi401583f] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
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A role
for protein dynamics in enzymatic catalysis of hydrogen
transfer has received substantial scientific support, but the connections
between protein structure and catalysis remain to be established.
Valine residues 203 and 207 are at the binding site for the nicotinamide
ring of the coenzyme in liver alcohol dehydrogenase and have been
suggested to facilitate catalysis with “protein-promoting vibrations”
(PPV). We find that the V207A substitution has small effects on steady-state
kinetic constants and the rate of hydrogen transfer; the introduced
cavity is empty and is tolerated with minimal effects on structure
(determined at 1.2 Å for the complex with NAD+ and
2,3,4,5,6-pentafluorobenzyl alcohol). Thus, no evidence is found to
support a role for Val-207 in the dynamics of catalysis. The protein
structures and ligand geometries (including donor–acceptor
distances) in the V203A enzyme complexed with NAD+ and
2,3,4,5,6-pentafluorobenzyl alcohol or 2,2,2-trifluoroethanol (determined
at 1.1 Å) are very similar to those for the wild-type enzyme,
except that the introduced cavity accommodates a new water molecule
that contacts the nicotinamide ring. The structures of the V203A enzyme
complexes suggest, in contrast to previous studies, that the diminished
tunneling and decreased rate of hydride transfer (16-fold, relative
to that of the wild-type enzyme) are not due to differences in ground-state
ligand geometries. The V203A substitution may alter the PPV and the
reorganization energy for hydrogen transfer, but the protein scaffold
and equilibrium thermal motions within the Michaelis complex may be
more significant for enzyme catalysis.
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Affiliation(s)
- Atsushi Yahashiri
- Department of Biochemistry, The University of Iowa , Iowa City, Iowa 52242-1109, United States
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7
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Bhowmik S, Jones DH, Chiu HP, Park IH, Chiu HJ, Axelrod HL, Farr CL, Tien HJ, Agarwalla S, Lesley SA. Structural and functional characterization of BaiA, an enzyme involved in secondary bile acid synthesis in human gut microbe. Proteins 2013; 82:216-29. [PMID: 23836456 DOI: 10.1002/prot.24353] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Revised: 06/07/2013] [Accepted: 06/17/2013] [Indexed: 12/19/2022]
Abstract
Despite significant influence of secondary bile acids on human health and disease, limited structural and biochemical information is available for the key gut microbial enzymes catalyzing its synthesis. Herein, we report apo- and cofactor bound crystal structures of BaiA2, a short chain dehydrogenase/reductase from Clostridium scindens VPI 12708 that represent the first protein structure of this pathway. The structures elucidated the basis of cofactor specificity and mechanism of proton relay. A conformational restriction involving Glu42 located in the cofactor binding site seems crucial in determining cofactor specificity. Limited flexibility of Glu42 results in imminent steric and electrostatic hindrance with 2'-phosphate group of NADP(H). Consistent with crystal structures, steady state kinetic characterization performed with both BaiA2 and BaiA1, a close homolog with 92% sequence identity, revealed specificity constant (kcat /KM ) of NADP(+) at least an order of magnitude lower than NAD(+) . Substitution of Glu42 with Ala improved specificity toward NADP(+) by 10-fold compared to wild type. The cofactor bound structure uncovered a novel nicotinamide-hydroxyl ion (NAD(+) -OH(-) ) adduct contraposing previously reported adducts. The OH(-) of the adduct in BaiA2 is distal to C4 atom of nicotinamide and proximal to 2'-hydroxyl group of the ribose moiety. Moreover, it is located at intermediary distances between terminal functional groups of active site residues Tyr157 (2.7 Å) and Lys161 (4.5 Å). Based on these observations, we propose an involvement of NAD(+) -OH(-) adduct in proton relay instead of hydride transfer as noted for previous adducts.
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Affiliation(s)
- Shiva Bhowmik
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, 92037; Joint Center for Structural Genomics
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8
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Verkhovskaya M, Bloch DA. Energy-converting respiratory Complex I: on the way to the molecular mechanism of the proton pump. Int J Biochem Cell Biol 2012; 45:491-511. [PMID: 22982742 DOI: 10.1016/j.biocel.2012.08.024] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Revised: 08/27/2012] [Accepted: 08/28/2012] [Indexed: 12/16/2022]
Abstract
In respiring organisms the major energy transduction flux employs the transmembrane electrochemical proton gradient as a physical link between exergonic redox reactions and endergonic ADP phosphorylation. Establishing the gradient involves electrogenic, transmembrane H(+) translocation by the membrane-embedded respiratory complexes. Among others, Complex I (NADH:ubiquinone oxidoreductase) is the most structurally complex and functionally enigmatic respiratory enzyme; its molecular mechanism is as yet unknown. Here we highlight recent progress and discuss the catalytic events during Complex I turnover in relation to their role in energy conversion and to the enzyme structure.
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Affiliation(s)
- Marina Verkhovskaya
- Helsinki Bioenergetics Group, Institute of Biotechnology, PO Box 65 (Viikinkaari 1) FIN-00014 University of Helsinki, Finland.
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9
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Plapp BV, Ramaswamy S. Atomic-resolution structures of horse liver alcohol dehydrogenase with NAD(+) and fluoroalcohols define strained Michaelis complexes. Biochemistry 2012; 51:4035-48. [PMID: 22531044 DOI: 10.1021/bi300378n] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Structures of horse liver alcohol dehydrogenase complexed with NAD(+) and unreactive substrate analogues, 2,2,2-trifluoroethanol or 2,3,4,5,6-pentafluorobenzyl alcohol, were determined at 100 K at 1.12 or 1.14 Å resolution, providing estimates of atomic positions with overall errors of ~0.02 Å, the geometry of ligand binding, descriptions of alternative conformations of amino acid residues and waters, and evidence of a strained nicotinamide ring. The four independent subunits from the two homodimeric structures differ only slightly in the peptide backbone conformation. Alternative conformations for amino acid side chains were identified for 50 of the 748 residues in each complex, and Leu-57 and Leu-116 adopt different conformations to accommodate the different alcohols at the active site. Each fluoroalcohol occupies one position, and the fluorines of the alcohols are well-resolved. These structures closely resemble the expected Michaelis complexes with the pro-R hydrogens of the methylene carbons of the alcohols directed toward the re face of C4N of the nicotinamide rings with a C-C distance of 3.40 Å. The oxygens of the alcohols are ligated to the catalytic zinc at a distance expected for a zinc alkoxide (1.96 Å) and participate in a low-barrier hydrogen bond (2.52 Å) with the hydroxyl group of Ser-48 in a proton relay system. As determined by X-ray refinement with no restraints on bond distances and planarity, the nicotinamide rings in the two complexes are slightly puckered (quasi-boat conformation, with torsion angles of 5.9° for C4N and 4.8° for N1N relative to the plane of the other atoms) and have bond distances that are somewhat different compared to those found for NAD(P)(+). It appears that the nicotinamide ring is strained toward the transition state on the path to alcohol oxidation.
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Affiliation(s)
- Bryce V Plapp
- Department of Biochemistry, The University of Iowa, Iowa City, IA 52242, USA.
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10
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Plapp BV. Conformational changes and catalysis by alcohol dehydrogenase. Arch Biochem Biophys 2009; 493:3-12. [PMID: 19583966 DOI: 10.1016/j.abb.2009.07.001] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2009] [Revised: 07/01/2009] [Accepted: 07/02/2009] [Indexed: 10/20/2022]
Abstract
As shown by X-ray crystallography, horse liver alcohol dehydrogenase undergoes a global conformational change upon binding of NAD(+) or NADH, involving a rotation of the catalytic domain relative to the coenzyme binding domain and the closing up of the active site to produce a catalytically efficient enzyme. The conformational change requires a complete coenzyme and is affected by various chemical or mutational substitutions that can increase the catalytic turnover by altering the kinetics of the isomerization and rate of dissociation of coenzymes. The binding of NAD(+) is kinetically limited by a unimolecular isomerization (corresponding to the conformational change) that is controlled by deprotonation of the catalytic zinc-water to produce a negatively-charged zinc-hydroxide, which can attract the positively-charged nicotinamide ring. The deprotonation is facilitated by His-51 acting through a hydrogen-bonded network to relay the proton to solvent. Binding of NADH also involves a conformational change, but the rate is very fast. After the enzyme binds NAD(+) and closes up, the substrate displaces the hydroxide bound to the catalytic zinc; this exchange may involve a double displacement reaction where the carboxylate group of a glutamate residue first displaces the hydroxide (inverting the tetrahedral coordination of the zinc), and then the exogenous ligand displaces the glutamate. The resulting enzyme-NAD(+)-alcoholate complex is poised for hydrogen transfer, and small conformational fluctuations may bring the reactants together so that the hydride ion is transferred by quantum mechanical tunneling. In the process, the nicotinamide ring may become puckered, as seen in structures of complexes of the enzyme with NADH. The conformational changes of alcohol dehydrogenase demonstrate the importance of protein dynamics in catalysis.
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Affiliation(s)
- Bryce V Plapp
- Department of Biochemistry, The University of Iowa, Iowa City, IA 52242-1109, USA.
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