Probing the E1o-E2o and E1a-E2o Interactions in Binary Subcomplexes of the Human 2-Oxoglutarate Dehydrogenase and 2-Oxoadipate Dehydrogenase Complexes by Chemical Cross-Linking Mass Spectrometry and Molecular Dynamics Simulation

Oliver Ozohanics; Xu Zhang; Natalia S Nemeria; Attila Ambrus; Frank Jordan

doi:10.3390/ijms24054555

Probing the E1o-E2o and E1a-E2o Interactions in Binary Subcomplexes of the Human 2-Oxoglutarate Dehydrogenase and 2-Oxoadipate Dehydrogenase Complexes by Chemical Cross-Linking Mass Spectrometry and Molecular Dynamics Simulation

Int J Mol Sci. 2023 Feb 25;24(5):4555. doi: 10.3390/ijms24054555.

Authors

Oliver Ozohanics¹, Xu Zhang², Natalia S Nemeria², Attila Ambrus¹, Frank Jordan²

Affiliations

¹ Department of Biochemistry, Institute of Biochemistry and Molecular Biology, Semmelweis University, 1094 Budapest, Hungary.
² Department of Chemistry, Rutgers University, Newark, NJ 07102, USA.

Abstract

The human 2-oxoglutarate dehydrogenase complex (hOGDHc) is a key enzyme in the tricarboxylic acid cycle and is one of the main regulators of mitochondrial metabolism through NADH and reactive oxygen species levels. Evidence was obtained for formation of a hybrid complex between the hOGDHc and its homologue the 2-oxoadipate dehydrogenase complex (hOADHc) in the L-lysine metabolic pathway, suggesting a crosstalk between the two distinct pathways. Findings raised fundamental questions about the assembly of hE1a (2-oxoadipate-dependent E1 component) and hE1o (2-oxoglutarate-dependent E1) to the common hE2o core component. Here we report chemical cross-linking mass spectrometry (CL-MS) and molecular dynamics (MD) simulation analyses to understand assembly in binary subcomplexes. The CL-MS studies revealed the most prominent loci for hE1o-hE2o and hE1a-hE2o interactions and suggested different binding modes. The MD simulation studies led to the following conclusions: (i) The N-terminal regions in E1s are shielded by, but do not interact directly with hE2o. (ii) The hE2o linker region exhibits the highest number of H-bonds with the N-terminus and α/β1 helix of hE1o, yet with the interdomain linker and α/β1 helix of hE1a. (iii) The C-termini are involved in dynamic interactions in complexes, suggesting the presence of at least two conformations in solution.

Keywords: 2-oxoadipate dehydrogenase; 2-oxoglutarate dehydrogenase; chemical cross-linking mass spectrometry; dihydrolipoyl succinyltransferase; molecular dynamics simulations; protein–protein interactions.

MeSH terms

Citric Acid Cycle
Humans
Ketoglutarate Dehydrogenase Complex* / metabolism
Mass Spectrometry
Molecular Dynamics Simulation*
Reactive Oxygen Species / metabolism

Substances

Ketoglutarate Dehydrogenase Complex
Reactive Oxygen Species

Grants and funding

This research was funded by the National Institutes of Health (R15GM116077-01 to F.J.), the National Science Foundation (CHE-1402675 to F.J.), Rutgers–Newark Chancellor’s SEED Grants (F.J.), the Hungarian Brain Research Program 2 (2017-1.2.1-NKP-2017-00002 to Vera Adam-Vizi, Semmelweis University), Semmelweis University (STIA-OTKA-2021 grant to A.A.), the Hungarian Scientific Research Fund (OTKA grant 143627 to A.A.), and the National Research, Development and Innovation Fund (TKP2021-EGA-25 grant to A.A.). Project no. TKP2021-EGA-25 has been implemented with the support provided by the Ministry of Innovation and Technology of Hungary from the National Research, Development and Innovation Fund, financed under the TKP2021-EGA funding scheme.