skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: X‑ray Emission Spectroscopy of Single Protein Crystals Yields Insights into Heme Enzyme Intermediates

Journal Article · · Journal of Physical Chemistry Letters

Enzyme reactivity is often enhanced by changes in oxidation state, spin state, and metal−ligand covalency of associated metallocofactors. The development of spectroscopic methods for studying these processes coincidentally with structural rearrangements is essential for elucidating metalloenzyme mechanisms. Herein, we demonstrate the feasibility of collecting X-ray emission spectra of metalloenzyme crystals at a third-generation synchrotron source. In particular, we report the development of a von Hamos spectrometer for the collection of Fe Kβ emission optimized for analysis of dilute biological samples. We further showcase its application in crystals of the immunosuppressive heme-dependent enzyme indoleamine 2,3-dioxygenase. Spectra from protein crystals in different states were compared with relevant reference compounds. Complementary density functional calculations assessing covalency support our spectroscopic analysis and identify active site conformations that correlate to high- and low-spin states. These experiments validate the suitability of an X-ray emission approach for determining spin states of previously uncharacterized metalloenzyme reaction intermediates.

Research Organization:
Argonne National Laboratory (ANL), Argonne, IL (United States)
Sponsoring Organization:
National Institutes of Health (NIH); National Science Foundation (NSF); Canadian Light Source, Inc.; USDOE Office of Science - Office of Basic Energy Sciences - Scientific User Facilities Division
DOE Contract Number:
AC02-06CH11357
OSTI ID:
2229096
Journal Information:
Journal of Physical Chemistry Letters, Vol. 14, Issue 1
Country of Publication:
United States
Language:
English

References (51)

Targeting Metalloenzymes for Therapeutic Intervention journal September 2018
Kinetic properties of crystalline enzymes. Carboxypeptidase A journal March 1977
The Activity of an Enzyme in the Crystalline State: Ribonuclease S journal July 1963
High resolution 1s core hole X-ray spectroscopy in 3d transition metal complexes—electronic and structural information journal January 2005
Taking snapshots of photosynthetic water oxidation using femtosecond X-ray diffraction and spectroscopy journal July 2014
The role of X-ray spectroscopy in understanding the geometric and electronic structure of nitrogenase journal June 2015
Rapid Evolution of the Photosystem II Electronic Structure during Water Splitting journal October 2018
X-ray Emission Spectroscopy as an in Situ Diagnostic Tool for X-ray Crystallography of Metalloproteins Using an X-ray Free-Electron Laser journal April 2018
Energy-dispersive X-ray emission spectroscopy using an X-ray free-electron laser in a shot-by-shot mode journal November 2012
Using X-ray free-electron lasers for spectroscopy of molecular catalysts and metalloenzymes journal March 2021
Effects of x-ray free-electron laser pulse intensity on the Mn Kβ1,3 x-ray emission spectrum in photosystem II—A case study for metalloprotein crystals and solutions journal November 2021
X-ray Emission Spectroscopy at X-ray Free Electron Lasers: Limits to Observation of the Classical Spectroscopic Response for Electronic Structure Analysis journal December 2018
Inception of electronic damage of matter by photon-driven post-ionization mechanisms journal March 2019
Kinetic Modeling of the X-ray-Induced Damage to a Metalloprotein journal July 2013
Specific chemical and structural damage to proteins produced by synchrotron radiation journal January 2000
Radiation damage and dose limits in serial synchrotron crystallography at cryo- and room temperatures journal February 2020
X-ray–induced photoreduction of heme metal centers rapidly induces active-site perturbations in a protein-independent manner journal September 2020
Kinetics and Mechanisms of Formation and Reactivity of Non-heme Iron Oxygen Intermediates journal May 2005
Oxygen Activation and Radical Transformations in Heme Proteins and Metalloporphyrins journal December 2017
Chemical Basis for Enzyme Catalysis journal May 2000
Indoleamine 2,3‐dioxygenase 1 (IDO1): an up‐to‐date overview of an eclectic immunoregulatory enzyme journal June 2021
Indoleamine 2,3-dioxygenase pathways of pathogenic inflammation and immune escape in cancer journal April 2014
Targeting the indoleamine 2,3-dioxygenase pathway in cancer journal December 2015
Tryptophan and the immune response journal August 2003
DIY XES-development of an inexpensive, versatile, and easy to fabricate XES analyzer and sample delivery system journal February 2019
Influence of the core hole on K β emission following photoionization or orbital electron capture: A comparison using MnO and 55 Fe 2 O 3 journal July 2001
High-resolution manganese x-ray fluorescence spectroscopy. Oxidation-state and spin-state sensitivity journal April 1994
Chemical Sensitivity of Kβ and Kα X-ray Emission from a Systematic Investigation of Iron Compounds journal August 2020
Metal Kβ X-ray emission spectra of first row transition metal compounds journal February 2001
Probing Physical Oxidation State by Resonant X‐ray Emission Spectroscopy: Applications to Iron Model Complexes and Nitrogenase journal March 2021
Importance of Direct Spin−Spin Coupling and Spin-Flip Excitations for the Zero-Field Splittings of Transition Metal Complexes:  A Case Study journal August 2006
Kβ Mainline X-ray Emission Spectroscopy as an Experimental Probe of Metal–Ligand Covalency
  • Pollock, Christopher J.; Delgado-Jaime, Mario Ulises; Atanasov, Mihail
  • Journal of the American Chemical Society, Vol. 136, Issue 26 https://doi.org/10.1021/ja504182n
journal June 2014
Probing Valence Orbital Composition with Iron Kβ X-ray Emission Spectroscopy journal July 2010
Probing the 3d Spin Momentum with X-ray Emission Spectroscopy:  The Case of Molecular-Spin Transitions journal June 2006
Cholorophthalocyanine iron(III) FePc(−2)Cl. A spin-admixed (S = / S = (frsol|5/2) system journal January 1984
Spin states in iron(III) phthalocyanines studied by Moessbauer, magnetic susceptibility, and ESR measurements journal July 1986
S = 1 Spin State of Divalent Iron. I. Magnetic Properties of Phthalocyanine Iron (II) journal October 1968
Magnetic properties of α -iron(II) phthalocyanine journal October 2002
High-resolution structures of inhibitor complexes of human indoleamine 2,3-dioxygenase 1 in a new crystal form journal October 2018
Probing the Ternary Complexes of Indoleamine and Tryptophan 2,3-Dioxygenases by Cryoreduction EPR and ENDOR Spectroscopy journal April 2010
Redox and Spectroscopic Properties of Human Indoleamine 2,3-Dioxygenase and A His303Ala Variant:  Implications for Catalysis journal October 2005
Crystal structure of human indoleamine 2,3-dioxygenase: Catalytic mechanism of O2 incorporation by a heme-containing dioxygenase journal February 2006
The Heme Environment of Recombinant Human Indoleamine 2,3-Dioxygenase journal May 2002
Local Coordination and Electronic Structure Ramifications of Guest-Dependent Spin Crossover in a Metal–Organic Framework: A Combined X-ray Absorption and Emission Spectroscopy Study journal June 2022
Indoleamine 2,3-dioxygenase. Equilibrium studies of the tryptophan binding to the ferric, ferrous, and CO-bound enzymes. journal March 1980
Influence of the presence of the heme cofactor on the JK-loop structure in indoleamine 2,3-dioxygenase 1 journal November 2020
Temporary Intermediates of L-Trp Along the Reaction Pathway of Human Indoleamine 2,3-Dioxygenase 1 and Identification of an Exo Site journal January 2021
Yeast cytochrome c peroxidase. Coordination and spin states of heme prosthetic group. journal July 1987
Coherence properties of the high-energy fourth-generation X-ray synchrotron sources journal November 2019
New era of synchrotron radiation: fourth-generation storage ring journal August 2021
Potential for biomolecular imaging with femtosecond X-ray pulses journal August 2000

Similar Records

Immune-modulating enzyme indoleamine 2,3-dioxygenase is effectively inhibited by targeting its apo-form
Journal Article · Mon Mar 12 00:00:00 EDT 2018 · Proceedings of the National Academy of Sciences of the United States of America · OSTI ID:2229096

Crystal Structure and Mechanism of Tryptophan 2,3-Dioxygenase, a Heme Enzyme Involved in Tryptophan Catabolism and in Quinolinate Biosynthesis
Journal Article · Mon Jan 01 00:00:00 EST 2007 · Biochemistry · OSTI ID:2229096

The Fe-heme structure of met-indoleamine 2,3-dioxygenase-2 determined by X-ray absorption fine structure
Journal Article · Fri Jul 18 00:00:00 EDT 2014 · Biochemical and Biophysical Research Communications · OSTI ID:2229096

Related Subjects