CoChat
Sign Up
Cited by 12Metal-Catalyzed Oxygenation MechanismsProtein Structure and DynamicsEnzyme Structure and Function

Impact of Mutations on the Binding Pocket of Soybean Lipoxygenase: Implications for Proton-Coupled Electron Transfer

Open access
Li, Pengfei, Soudackov, Alexander V., Hammes-Schiffer, Sharon·2018·The Journal of Physical Chemistry Letters
DOI 10.1021/acs.jpclett.8b02945PMC PMC6402330
Open this paper in CoChat — free account

Abstract

Soybean lipoxygenase catalyzes a proton-coupled electron transfer (PCET) reaction and serves as a prototype for hydrogen tunneling in enzymes due to the unusually high kinetic isotope effect and significant modulation of the rate constant and kinetic isotope effect by mutation. Herein these experimental observations are interpreted in the context of changes to the substrate binding pocket in microsecond molecular dynamics simulations of wild-type and mutant soybean lipoxygenase. The binding pocket exhibits an hourglass shape with residues L546 and L754 bracketing the bottleneck, positioning the linoleic acid substrate for PCET. Mutation of I553 to less bulky residues slightly increases the width of the bottleneck and the volume of the binding pocket. Mutating L546 or L754 to a smaller residue also enlarges this width and volume, and mutating both has an even more dramatic effect. This analysis illustrates how mutation of the substrate binding pocket can be used as a strategy to tune the kinetics.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1021/acs.jpclett.8b02945

Cites

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • In wild-type soybean lipoxygenase, a high kinetic isotope effect of approximately 80 has been experimentally observed and verified using theory.

    “Furthermore, in a proton transfer reaction catalysed by enzyme soybean lipoxygenase, in the wild type, a high KIE of ~80 41 has been experimentally observed and verified using theory 42 .”

    From An open quantum systems approach to proton tunnelling in DNA (2022) · cites this paper as [42]

    The passage on wild-type SLO (section labelled Abstract; page unavailable) reports an experimentally observed KIE of approximately 80 at room temperature. The paper uses molecular-dynamics simulations and PCET theory to interpret experimental KIE trends, but does not report a theoretical verification of the specific value of 80. (LLM, conf=0.83)

    Experimental — accuracy not yet measured

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Cites

No references could be resolved yet.

Research works printed but not linked: 36

  1. [1]Grechkin A, Recent developments in biochemistry of the plant lipoxygenase pathway. Prog. Lipid Res. 1998, 37, 317– 352. 10209652
  2. [2]Schewe T; Ku H, Do 15-lipoxygenases have a common biological role? Trends Biochem. Sci 1991, 16, 369– 373. 1785138
  3. [3]Glickman MH; Klinman JP, Nature of rate-limiting steps in the soybean lipoxygenase- 1 reaction. Biochem. 1995, 34, 14077– 14092. 7578005
  4. [4]Rickert KW; Klinman JP, Nature of hydrogen transfer in soybean lipoxygenase 1: separation of primary and secondary isotope effects. Biochem. 1999, 38, 12218– 12228. 10493789
  5. [5]Meyer MP; Tomchick DR; Klinman JP, Enzyme structure and dynamics affect hydrogen tunneling: The impact of a remote side chain (I553) in soybean lipoxygenase-1. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 1146– 1151. 18216254 PMC2234106
  6. [6]Hu S; Sharma SC; Scouras AD; Soudackov AV; Carr CAM; Hammes-Schiffer S; Alber T; Klinman JP, Extremely elevated room-temperature kinetic isotope effects quantify the critical role of barrier width in enzymatic C-H activation. J. Am. Chem. Soc. 2014, 136, 8157– 8160. 24884374 PMC4188422
  7. [7]Hu S; Soudackov AV; Hammes-Schiffer S; Klinman JP, Enhanced Rigidification within a Double Mutant of Soybean Lipoxygenase Provides Experimental Support for Vibronically Nonadiabatic Proton-Coupled Electron Transfer Models. ACS Catal. 2017, 7, 3569– 3574. 29250456 PMC5724529
  8. [8]Newcomer ME; Brash AR, The structural basis for specificity in lipoxygenase catalysis. Protein Sci. 2015, 24, 298– 309. 25524168 PMC4353356
  9. [9]Knapp MJ; Rickert K; Klinman JP, Temperature-dependent isotope effects in soybean lipoxygenase-1: correlating hydrogen tunneling with protein dynamics. J. Am. Chem. Soc. 2002, 124, 3865– 3874. 11942823
  10. [10]Klinman JP; Offenbacher AR; Hu S, Origins of Enzyme Catalysis: Experimental Findings for C-H Activation, New Models, and Their Relevance to Prevailing Theoretical Constructs. J. Am. Chem. Soc. 2017, 139, 18409– 18427. 29244501 PMC5812730
  11. [11]Hatcher E; Soudackov AV; Hammes-Schiffer S, Proton-coupled electron transfer in soybean lipoxygenase. J. Am. Chem. Soc. 2004, 126, 5763– 5775. 15125669
  12. [12]Tejero I; Garcia-Viloca M; Gonzalez-Lafont A; Lluch JM; York DM, Enzyme dynamics and tunneling enhanced by compression in the hydrogen abstraction catalyzed by soybean lipoxygenase-1. J. Phys. Chem. B 2006, 110, 24708– 24719. 17134234
  13. [13]Hatcher E; Soudackov AV; Hammes-Schiffer S, Proton-coupled electron transfer in soybean lipoxygenase: dynamical behavior and temperature dependence of kinetic isotope effects. J. Am. Chem. Soc. 2007, 129, 187– 196. 17199298
  14. [14]Mavri J; Liu H; Olsson MH; Warshel A, Simulation of tunneling in enzyme catalysis by combining a biased propagation approach and the quantum classical path method: application to lipoxygenase. J. Phys. Chem. B 2008, 112, 5950– 5954. 18069813
  15. [15]Edwards SJ; Soudackov AV; Hammes-Schiffer S, Impact of distal mutation on hydrogen transfer interface and substrate conformation in soybean lipoxygenase. J. Phys. Chem. B 2010, 114, 6653– 6660. 20423074 PMC2880924
  16. [16]Phatak P; Venderley J; Debrota J; Li J; Iyengar SS, Active Site Dynamical Effects in the Hydrogen Transfer Rate-limiting Step in the Catalysis of Linoleic Acid by Soybean Lipoxygenase-1 (SLO-1): Primary and Secondary Isotope Contributions. J. Phys. Chem. B 2015, 119, 9532– 9546. 26079999
  17. [17]Salna B; Benabbas A; Russo D; Champion PM, Tunneling Kinetics and Non-Adiabatic Proton-Coupled Electron Transfer in Proteins: The Effect of Electric Fields and Anharmonic Donor-Acceptor Interactions. J. Phys. Chem. B 2017, 121, 6869– 6881. 28628313
  18. [18]Li P; Soudackov AV; Hammes-Schiffer S, Fundamental Insights into Proton-Coupled Electron Transfer in Soybean Lipoxygenase from Quantum Mechanical/Molecular Mechanical Free Energy Simulations. J. Am. Chem. Soc. 2018, 140, 3068– 3076. 29392938 PMC5849423
  19. [19]Hammes-Schiffer S; Soudackov AV, Proton-coupled electron transfer in solution, proteins, and electrochemistry. J. Phys. Chem. B 2008, 112, 14108– 14123. 18842015 PMC2720037
  20. [20]Sharma SC; Klinman JP, Kinetic Detection of Orthogonal Protein and Chemical Coordinates in Enzyme Catalysis: Double Mutants of Soybean Lipoxygenase. Biochem. 2015, 54, 5447– 5456. 26154975 PMC4565126
  21. [21]zHoritani M; Offenbacher AR; Carr CAM; Yu T; Hoeke V; Cutsail III GE; Hammes-Schiffer S; Klinman JP; Hoffman BM, 13C ENDOR Spectroscopy of Lipoxygenase-Substrate Complexes Reveals the Structural Basis for C-H Activation by Tunneling. J. Am. Chem. Soc. 2017, 139, 1984– 1997. 28121140 PMC5322796
  22. [22]Chruszcz M; Wlodawer A; Minor W, Determination of protein structures—a series of fortunate events. Biophys. J. 2008, 95, 1– 9. 18441029 PMC2426657
  23. [26]Morris GM; Huey R; Lindstrom W; Sanner MF; Belew RK; Goodsell DS; Olson AJ, AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J. Comput. Chem. 2009, 30, 2785– 2791. 19399780 PMC2760638
  24. [27]Trott O; Olson AJ, AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J. Comput. Chem. 2010, 31, 455– 461. 19499576 PMC3041641
  25. [28]Maier JA; Martinez C; Kasavajhala K; Wickstrom L; Hauser KE; Simmerling C, ff14SB: improving the accuracy of protein side chain and backbone parameters from ff99SB. J. Chem. Theory Comput. 2015, 11, 3696– 3713. 26574453 PMC4821407
  26. [29]Li P; Merz KM Jr, MCPB.py: A Python Based Metal Center Parameter Builder. J. Chem. Inf. Model. 2016, 56, 599– 604. 26913476
  27. [30]Li P; Roberts BP; Chakravorty DK; Merz KM Jr, Rational Design of Particle Mesh Ewald Compatible Lennard-Jones Parameters for +2 Metal Cations in Explicit Solvent. J. Chem. Theory Comput. 2013, 9, 2733– 2748. 23914143 PMC3728907
  28. [31]Jorgensen WL; Chandrasekhar J; Madura JD; Impey RW; Klein ML, Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 1983, 79, 926– 935.
  29. [32]Li P; Song LF; Merz KM Jr, Systematic Parameterization of Monovalent Ions Employing the Nonbonded Model. J. Chem. Theory Comput. 2015, 11, 1645– 1657. 26574374
  30. [33]Salomon-Ferrer R; Götz AW; Poole D; Le Grand S; Walker RC, Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald. J. Chem. Theory Comput. 2013, 9, 3878– 3888. 26592383
  31. [34]Durrant JD; Votapka L; Sorensen J; Amaro RE, POVME 2.0: an enhanced tool for determining pocket shape and volume characteristics. J. Chem. Theory Comput. 2014, 10, 5047– 5056. 25400521 PMC4230373
  32. [35]Minor W; Steczko J; Stec B; Otwinowski Z; Bolin JT; Walter R; Axelrod B, Crystal structure of soybean lipoxygenase L-1 at 1.4 A resolution. Biochem. 1996, 35, 10687– 10701. 8718858
  33. [36]Offenbacher AR; Hu S; Poss EM; Carr CAM; Scouras AD; Prigozhin DM; Iavarone AT; Palla A; Alber T; Fraser JS; Klinman JP, Hydrogen-Deuterium Exchange of Lipoxygenase Uncovers a Relationship between Distal, Solvent Exposed Protein Motions and the Thermal Activation Barrier for Catalytic Proton-Coupled Electron Tunneling. ACS Cent. Sci. 2017, 3, 570– 579. 28691068 PMC5492416
  34. [37]Kozlikova B; Sebestova E; Sustr V; Brezovsky J; Strnad O; Daniel L; Bednar D; Pavelka A; Manak M; Bezdeka M, CAVER Analyst 1.0: graphic tool for interactive visualization and analysis of tunnels and channels in protein structures. Bioinformatics 2014, 30, 2684– 2685. 24876375
  35. [38]Collazo L; Klinman JP, Control of the Position of Oxygen Delivery in Soybean Lipoxygenase-1 by Amino Acid Side Chains within a Gas Migration Channel. J. Biol. Chem. 2016, 291, 9052– 9059. 26867580 PMC4861474
  36. [39]Towns J; Cockerill T; Dahan M; Foster I; Gaither K; Grimshaw A; Hazlewood V; Lathrop S; Lifka D; Peterson GD, XSEDE: accelerating scientific discovery. Comput. Sci. Eng. 2014, 16, 62– 74.

Cited by

Sorted by citations

Authors
Li, P., Soudackov, A. V., & Hammes-Schiffer, S.
Affiliations
  • Yale University (US)
  • Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
ORCID
Venue
The Journal of Physical Chemistry Letters
Publisher
American Chemical Society (ACS)
Published
2018-10-25
Volume
9
Issue
22
Pages
6444-6449
ISSN
1948-7185 (ISSN-L)
DOI
10.1021/acs.jpclett.8b02945
PMC
PMC6402330
OpenAlex
W2898301210
Cited by
12
References
0
Citations by year
2025: 2 · 2023: 1 · 2022: 3 · 2021: 1 · 2020: 2 · 2019: 3
FWCI
0.55
Type
journal article
Language
en
Open access
Locations
  • The Journal of Physical Chemistry Letters (publishedVersion)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion)
Funders
National Institute of General Medical Sciences (GM056207)
Topics
  • Physical Sciences › Chemistry › Inorganic Chemistry › Metal-Catalyzed Oxygenation Mechanisms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
Keywords
soybean lipoxygenase, proton-coupled electron transfer, hydrogen tunneling, substrate binding pocket, kinetic isotope effects, linoleic acid, site-directed mutagenesis, enzyme kinetics, molecular dynamics simulation
MeSH terms
Binding Sites, Electrons, Kinetics, Lipoxygenase, Mutation, Protons, Glycine max, Soybean Proteins, Molecular Dynamics Simulation

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review