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Morse PT, Wan J, Arroum T, Herroon MK, Kalpage HA, Bazylianska V, Lee I, Heath EI, Podgorski I, Hüttemann M. Prostate Cancer-Specific Lysine 53 Acetylation of Cytochrome c Drives Metabolic Reprogramming and Protects from Apoptosis in Intact Cells. Biomolecules 2024; 14:695. [PMID: 38927098 PMCID: PMC11201891 DOI: 10.3390/biom14060695] [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: 05/06/2024] [Revised: 06/07/2024] [Accepted: 06/09/2024] [Indexed: 06/28/2024] Open
Abstract
Cytochrome c (Cytc) is important for both mitochondrial respiration and apoptosis, both of which are altered in cancer cells that switch to Warburg metabolism and manage to evade apoptosis. We earlier reported that lysine 53 (K53) of Cytc is acetylated in prostate cancer. K53 is conserved in mammals that is known to be essential for binding to cytochrome c oxidase and apoptosis protease activating factor-1 (Apaf-1). Here we report the effects of this acetylation on the main functions of cytochrome c by expressing acetylmimetic K53Q in cytochrome c double knockout cells. Other cytochrome c variants analyzed were wild-type, K53R as a control that maintains the positive charge, and K53I, which is present in some non-mammalian species. Intact cells expressing K53Q cytochrome c showed 49% decreased mitochondrial respiration and a concomitant increase in glycolytic activity (Warburg effect). Furthermore, mitochondrial membrane potential was decreased, correlating with notably reduced basal mitochondrial superoxide levels and decreased cell death upon challenge with H2O2 or staurosporine. To test for markers of cancer aggressiveness and invasiveness, cells were grown in 3D spheroid culture. K53Q cytochrome c-expressing cells showed profoundly increased protrusions compared to WT, suggesting increased invasiveness. We propose that K53 acetylation of cytochrome c is an adaptive response that mediates prostate cancer metabolic reprogramming and evasion of apoptosis, which are two hallmarks of cancer, to better promote tumor survival and metastasis.
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Affiliation(s)
- Paul T. Morse
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA; (P.T.M.)
| | - Junmei Wan
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA; (P.T.M.)
| | - Tasnim Arroum
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA; (P.T.M.)
| | | | - Hasini A. Kalpage
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA; (P.T.M.)
| | - Viktoriia Bazylianska
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA; (P.T.M.)
- Department of Biochemistry, Microbiology and Immunology, Wayne State University, Detroit, MI 48201, USA
| | - Icksoo Lee
- College of Medicine, Dankook University, Cheonan-si 31116, Republic of Korea;
| | - Elisabeth I. Heath
- Karmanos Cancer Institute, Department of Oncology, Wayne State University, Detroit, MI 48201, USA
| | - Izabela Podgorski
- Department of Pharmacology, Wayne State University, Detroit, MI 48201, USA
| | - Maik Hüttemann
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA; (P.T.M.)
- Department of Biochemistry, Microbiology and Immunology, Wayne State University, Detroit, MI 48201, USA
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Morse PT, Arroum T, Wan J, Pham L, Vaishnav A, Bell J, Pavelich L, Malek MH, Sanderson TH, Edwards BFP, Hüttemann M. Phosphorylations and Acetylations of Cytochrome c Control Mitochondrial Respiration, Mitochondrial Membrane Potential, Energy, ROS, and Apoptosis. Cells 2024; 13:493. [PMID: 38534337 DOI: 10.3390/cells13060493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 03/07/2024] [Accepted: 03/09/2024] [Indexed: 03/28/2024] Open
Abstract
Cytochrome c (Cytc) has both life-sustaining and cellular death-related functions, depending on subcellular localization. Within mitochondria, Cytc acts as a single electron carrier as part of the electron transport chain (ETC). When released into the cytosol after cellular insult, Cytc triggers the assembly of the apoptosome, committing the cell to intrinsic apoptosis. Due to these dual natures, Cytc requires strong regulation by the cell, including post-translational modifications, such as phosphorylation and acetylation. Six phosphorylation sites and three acetylation sites have been detected on Cytc in vivo. Phosphorylations at T28, S47, Y48, T49, T58, and Y97 tend to be present under basal conditions in a tissue-specific manner. In contrast, the acetylations at K8, K39, and K53 tend to be present in specific pathophysiological conditions. All of the phosphorylation sites and two of the three acetylation sites partially inhibit respiration, which we propose serves to maintain an optimal, intermediate mitochondrial membrane potential (ΔΨm) to minimize reactive oxygen species (ROS) production. Cytc phosphorylations are lost during ischemia, which drives ETC hyperactivity and ΔΨm hyperpolarization, resulting in exponential ROS production thus causing reperfusion injury following ischemia. One of the acetylation sites, K39, shows a unique behavior in that it is gained during ischemia, stimulating respiration while blocking apoptosis, demonstrating that skeletal muscle, which is particularly resilient to ischemia-reperfusion injury compared to other organs, possesses a different metabolic strategy to handle ischemic stress. The regulation of Cytc by these post-translational modifications underscores the importance of Cytc for the ETC, ΔΨm, ROS production, apoptosis, and the cell as a whole.
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Affiliation(s)
- Paul T Morse
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA
| | - Tasnim Arroum
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA
| | - Junmei Wan
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA
| | - Lucynda Pham
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA
| | - Asmita Vaishnav
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University, Detroit, MI 48201, USA
| | - Jamie Bell
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA
- Division of Pediatric Critical Care, Children's Hospital of Michigan, Central Michigan University, Detroit, MI 48201, USA
| | - Lauren Pavelich
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University, Detroit, MI 48201, USA
| | - Moh H Malek
- Department of Health Care Sciences, Eugene Applebaum College of Pharmacy & Health Sciences, Wayne State University, Detroit, MI 48201, USA
| | - Thomas H Sanderson
- Department of Emergency Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Brian F P Edwards
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University, Detroit, MI 48201, USA
| | - Maik Hüttemann
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University, Detroit, MI 48201, USA
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3
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Morse PT, Pérez-Mejías G, Wan J, Turner AA, Márquez I, Kalpage HA, Vaishnav A, Zurek MP, Huettemann PP, Kim K, Arroum T, De la Rosa MA, Chowdhury DD, Lee I, Brunzelle JS, Sanderson TH, Malek MH, Meierhofer D, Edwards BFP, Díaz-Moreno I, Hüttemann M. Cytochrome c lysine acetylation regulates cellular respiration and cell death in ischemic skeletal muscle. Nat Commun 2023; 14:4166. [PMID: 37443314 PMCID: PMC10345088 DOI: 10.1038/s41467-023-39820-8] [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: 10/11/2022] [Accepted: 06/30/2023] [Indexed: 07/15/2023] Open
Abstract
Skeletal muscle is more resilient to ischemia-reperfusion injury than other organs. Tissue specific post-translational modifications of cytochrome c (Cytc) are involved in ischemia-reperfusion injury by regulating mitochondrial respiration and apoptosis. Here, we describe an acetylation site of Cytc, lysine 39 (K39), which was mapped in ischemic porcine skeletal muscle and removed by sirtuin5 in vitro. Using purified protein and cellular double knockout models, we show that K39 acetylation and acetylmimetic K39Q replacement increases cytochrome c oxidase (COX) activity and ROS scavenging while inhibiting apoptosis via decreased binding to Apaf-1, caspase cleavage and activity, and cardiolipin peroxidase activity. These results are discussed with X-ray crystallography structures of K39 acetylated (1.50 Å) and acetylmimetic K39Q Cytc (1.36 Å) and NMR dynamics. We propose that K39 acetylation is an adaptive response that controls electron transport chain flux, allowing skeletal muscle to meet heightened energy demand while simultaneously providing the tissue with robust resilience to ischemia-reperfusion injury.
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Affiliation(s)
- Paul T Morse
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, USA
| | - Gonzalo Pérez-Mejías
- Instituto de Investigaciones Químicas, Universidad de Sevilla - CSIC, 41092, Sevilla, Spain
| | - Junmei Wan
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, USA
| | - Alice A Turner
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, USA
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University, Detroit, MI, 48201, USA
| | - Inmaculada Márquez
- Instituto de Investigaciones Químicas, Universidad de Sevilla - CSIC, 41092, Sevilla, Spain
| | - Hasini A Kalpage
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, USA
| | - Asmita Vaishnav
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University, Detroit, MI, 48201, USA
| | - Matthew P Zurek
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, USA
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University, Detroit, MI, 48201, USA
| | - Philipp P Huettemann
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, USA
| | - Katherine Kim
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, USA
| | - Tasnim Arroum
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, USA
| | - Miguel A De la Rosa
- Instituto de Investigaciones Químicas, Universidad de Sevilla - CSIC, 41092, Sevilla, Spain
| | - Dipanwita Dutta Chowdhury
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University, Detroit, MI, 48201, USA
| | - Icksoo Lee
- College of Medicine, Dankook University, Cheonan-si, Chungcheongnam-do 31116, Republic of Korea
| | - Joseph S Brunzelle
- Life Sciences Collaborative Access Team, Northwestern University, Center for Synchrotron Research, Argonne, IL, 60439, USA
| | - Thomas H Sanderson
- Department of Emergency Medicine, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Moh H Malek
- Department of Health Care Sciences, Eugene Applebaum College of Pharmacy & Health Sciences, Wayne State University, Detroit, MI, 48201, USA
| | - David Meierhofer
- Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Brian F P Edwards
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University, Detroit, MI, 48201, USA
| | - Irene Díaz-Moreno
- Instituto de Investigaciones Químicas, Universidad de Sevilla - CSIC, 41092, Sevilla, Spain.
| | - Maik Hüttemann
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, USA.
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University, Detroit, MI, 48201, USA.
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Brand SE, Scharlau M, Geren L, Hendrix M, Parson C, Elmendorf T, Neel E, Pianalto K, Silva-Nash J, Durham B, Millett F. Accelerated Evolution of Cytochrome c in Higher Primates, and Regulation of the Reaction between Cytochrome c and Cytochrome Oxidase by Phosphorylation. Cells 2022; 11:cells11244014. [PMID: 36552779 PMCID: PMC9777161 DOI: 10.3390/cells11244014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/24/2022] [Accepted: 12/01/2022] [Indexed: 12/14/2022] Open
Abstract
Cytochrome c (Cc) underwent accelerated evolution from the stem of the anthropoid primates to humans. Of the 11 amino acid changes that occurred from horse Cc to human Cc, five were at Cc residues near the binding site of the Cc:CcO complex. Single-point mutants of horse and human Cc were made at each of these positions. The Cc:CcO dissociation constant KD of the horse mutants decreased in the order: T89E > native horse Cc > V11I Cc > Q12M > D50A > A83V > native human. The largest effect was observed for the mutants at residue 50, where the horse Cc D50A mutant decreased KD from 28.4 to 11.8 μM, and the human Cc A50D increased KD from 4.7 to 15.7 μM. To investigate the role of Cc phosphorylation in regulating the reaction with CcO, phosphomimetic human Cc mutants were prepared. The Cc T28E, S47E, and Y48E mutants increased the dissociation rate constant kd, decreased the formation rate constant kf, and increased the equilibrium dissociation constant KD of the Cc:CcO complex. These studies indicate that phosphorylation of these residues plays an important role in regulating mitochondrial electron transport and membrane potential ΔΨ.
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Affiliation(s)
| | - Martha Scharlau
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Lois Geren
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Marissa Hendrix
- Independent Researcher, P.O. Box 603, Dardanelle, AR 72834, USA
| | - Clayre Parson
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Tyler Elmendorf
- School of Medicine, University of Kansas Medical Center, 2060 W 39th Ave, Kansas City, KS 66103, USA
| | - Earl Neel
- Tulsa Bone and Joint Associates, Tulsa, OK 74146, USA
| | - Kaila Pianalto
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | | | - Bill Durham
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Francis Millett
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
- Correspondence:
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Morse PT, Wan J, Bell J, Lee I, Goebel DJ, Malek MH, Sanderson TH, Hüttemann M. Sometimes less is more: inhibitory infrared light during early reperfusion calms hyperactive mitochondria and suppresses reperfusion injury. Biochem Soc Trans 2022; 50:1377-1388. [PMID: 36066188 PMCID: PMC10121102 DOI: 10.1042/bst20220446] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/20/2022] [Accepted: 08/22/2022] [Indexed: 11/17/2022]
Abstract
Ischemic stroke affects over 77 million people annually around the globe. Due to the blockage of a blood vessel caused by a stroke, brain tissue becomes ischemic. While prompt restoration of blood flow is necessary to save brain tissue, it also causes reperfusion injury. Mitochondria play a crucial role in early ischemia-reperfusion injury due to the generation of reactive oxygen species (ROS). During ischemia, mitochondria sense energy depletion and futilely attempt to up-regulate energy production. When reperfusion occurs, mitochondria become hyperactive and produce large amounts of ROS which damages neuronal tissue. This ROS burst damages mitochondria and the cell, which results in an eventual decrease in mitochondrial activity and pushes the fate of the cell toward death. This review covers the relationship between the mitochondrial membrane potential (ΔΨm) and ROS production. We also discuss physiological mechanisms that couple mitochondrial energy production to cellular energy demand, focusing on serine 47 dephosphorylation of cytochrome c (Cytc) in the brain during ischemia, which contributes to ischemia-reperfusion injury. Finally, we discuss the use of near infrared light (IRL) to treat stroke. IRL can both stimulate or inhibit mitochondrial activity depending on the wavelength. We emphasize that the use of the correct wavelength is crucial for outcome: inhibitory IRL, applied early during reperfusion, can prevent the ROS burst from occurring, thus preserving neurological tissue.
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Affiliation(s)
- Paul T. Morse
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA
| | - Junmei Wan
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA
| | - Jamie Bell
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA
- Division of Pediatric Critical Care, Children’s Hospital of Michigan, Central Michigan University, Detroit, MI 48201, USA
| | - Icksoo Lee
- College of Medicine, Dankook University, Cheonan-si, Chungcheongnam-do 31116, Republic of Korea
| | - Dennis J. Goebel
- Department of Ophthalmology, Visual and Anatomical Sciences, Wayne State University, Detroit, MI 48201, USA
| | - Moh H. Malek
- Department of Health Care Sciences, Eugene Applebaum College of Pharmacy & Health Sciences, Wayne State University, Detroit, MI 48201, USA
| | - Thomas H. Sanderson
- Department of Emergency Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Maik Hüttemann
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University, Detroit, MI 48201, USA
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Khoroshyy P, Tenger K, Chertkova RV, Bocharova OV, Kirpichnikov MP, Borovok N, Groma GI, Dolgikh DA, Kotlyar AB, Zimányi L. Kinetics and Energetics of Intramolecular Electron Transfer in Single-Point Labeled TUPS-Cytochrome c Derivatives. Molecules 2021; 26:molecules26226976. [PMID: 34834068 PMCID: PMC8621336 DOI: 10.3390/molecules26226976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 11/13/2021] [Accepted: 11/16/2021] [Indexed: 11/16/2022] Open
Abstract
Electron transfer within and between proteins is a fundamental biological phenomenon, in which efficiency depends on several physical parameters. We have engineered a number of horse heart cytochrome c single-point mutants with cysteine substitutions at various positions of the protein surface. To these cysteines, as well as to several native lysine side chains, the photoinduced redox label 8-thiouredopyrene-1,3,6-trisulfonate (TUPS) was covalently attached. The long-lived, low potential triplet excited state of TUPS, generated with high quantum efficiency, serves as an electron donor to the oxidized heme c. The rates of the forward (from the label to the heme) and the reverse (from the reduced heme back to the oxidized label) electron transfer reactions were obtained from multichannel and single wavelength flash photolysis absorption kinetic experiments. The electronic coupling term and the reorganization energy for electron transfer in this system were estimated from temperature-dependent experiments and compared with calculated parameters using the crystal and the solution NMR structure of the protein. These results together with the observation of multiexponential kinetics strongly support earlier conclusions that the flexible arm connecting TUPS to the protein allows several shortcut routes for the electron involving through space jumps between the label and the protein surface.
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Affiliation(s)
- Petro Khoroshyy
- Institute of Biophysics, Biological Research Centre, Temesvári Körút 62, H-6726 Szeged, Hungary; (P.K.); (K.T.); (G.I.G.)
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Flemingovo Náměstí 542/2, 16000 Prague, Czech Republic
| | - Katalin Tenger
- Institute of Biophysics, Biological Research Centre, Temesvári Körút 62, H-6726 Szeged, Hungary; (P.K.); (K.T.); (G.I.G.)
| | - Rita V. Chertkova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; (R.V.C.); (O.V.B.); (M.P.K.); (D.A.D.)
| | - Olga V. Bocharova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; (R.V.C.); (O.V.B.); (M.P.K.); (D.A.D.)
| | - Mikhail P. Kirpichnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; (R.V.C.); (O.V.B.); (M.P.K.); (D.A.D.)
- Biology Department, Lomonosov Moscow State University, Leninskie Gory 1/12, 119899 Moscow, Russia
| | - Natalia Borovok
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel; (N.B.); (A.B.K.)
| | - Géza I. Groma
- Institute of Biophysics, Biological Research Centre, Temesvári Körút 62, H-6726 Szeged, Hungary; (P.K.); (K.T.); (G.I.G.)
| | - Dmitry A. Dolgikh
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; (R.V.C.); (O.V.B.); (M.P.K.); (D.A.D.)
- Biology Department, Lomonosov Moscow State University, Leninskie Gory 1/12, 119899 Moscow, Russia
| | - Alexander B. Kotlyar
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel; (N.B.); (A.B.K.)
| | - László Zimányi
- Institute of Biophysics, Biological Research Centre, Temesvári Körút 62, H-6726 Szeged, Hungary; (P.K.); (K.T.); (G.I.G.)
- Correspondence:
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Gideon DA, Nirusimhan V, E JC, Sudarsha K, Manoj KM. Mechanism of electron transfers mediated by cytochromes c and b5 in mitochondria and endoplasmic reticulum: classical and murburn perspectives. J Biomol Struct Dyn 2021; 40:9235-9252. [PMID: 33998974 DOI: 10.1080/07391102.2021.1925154] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We explore the mechanism of electron transfers mediated by cytochrome c, a soluble protein involved in mitochondrial oxidative phosphorylation and cytochrome b5, a microsomal membrane protein acting as a redox aide in xenobiotic metabolism. We found minimal conservation in the sequence and surface amino acid residues of cytochrome c/b5 proteins among divergent species. Therefore, we question the evolutionary logic for electron transfer (ET) occurring through affinity binding via recognition of specific surface residues/topography. Also, analysis of putative protein-protein interactions in the crystal structures of these proteins and their redox partners did not point to any specific interaction logic. A comparison of the kinetic and thermodynamic constants of wildtype vs. mutants did not provide strong evidence to support the binding-based ET paradigm, but indicated support for diffusible reactive species (DRS)-mediated process. Topographically divergent cytochromes from one species have been substituted for reaction with proteins from other species, implying the involvement of non-specific interactions. We provide a viable alternative (murburn concept) to classical protein-protein binding-based long range ET mechanism. To account for the promiscuity of interactions and solvent-accessible hemes, we propose that the two proteins act as non- specific redox capacitors, mediating one-electron redox equilibriums involving DRS and unbound ions.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Daniel Andrew Gideon
- Satyamjayatu: The Science & Ethics Foundation, Palakkad District, Kerala State, India.,Department of Biotechnology and Bioinformatics, Bishop Heber College (Autonomous), Tiruchirappalli, Tamil Nadu, India
| | - Vijay Nirusimhan
- Department of Biotechnology and Bioinformatics, Bishop Heber College (Autonomous), Tiruchirappalli, Tamil Nadu, India
| | - Jesu Castin E
- Department of Biotechnology and Bioinformatics, Bishop Heber College (Autonomous), Tiruchirappalli, Tamil Nadu, India
| | - Karthik Sudarsha
- Department of Biotechnology and Bioinformatics, Bishop Heber College (Autonomous), Tiruchirappalli, Tamil Nadu, India
| | - Kelath Murali Manoj
- Satyamjayatu: The Science & Ethics Foundation, Palakkad District, Kerala State, India
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8
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Fedotovskaya O, Albertsson I, Nordlund G, Hong S, Gennis RB, Brzezinski P, Ädelroth P. Identification of a cytochrome bc 1-aa 3 supercomplex in Rhodobacter sphaeroides. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2021; 1862:148433. [PMID: 33932366 DOI: 10.1016/j.bbabio.2021.148433] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 04/19/2021] [Accepted: 04/20/2021] [Indexed: 10/21/2022]
Abstract
Respiration is carried out by a series of membrane-bound complexes in the inner mitochondrial membrane or in the cytoplasmic membrane of bacteria. Increasing evidence shows that these complexes organize into larger supercomplexes. In this work, we identified a supercomplex composed of cytochrome (cyt.) bc1 and aa3-type cyt. c oxidase in Rhodobacter sphaeroides. We purified the supercomplex using a His-tag on either of these complexes. The results from activity assays, native and denaturing PAGE, size exclusion chromatography, electron microscopy, optical absorption spectroscopy and kinetic studies on the purified samples support the formation and coupled quinol oxidation:O2 reduction activity of the cyt. bc1-aa3 supercomplex. The potential role of the membrane-anchored cyt. cy as a component in supercomplexes was also investigated.
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Affiliation(s)
- Olga Fedotovskaya
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Ingrid Albertsson
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Gustav Nordlund
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Sangjin Hong
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801, USA
| | - Robert B Gennis
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801, USA
| | - Peter Brzezinski
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Pia Ädelroth
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden.
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9
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Bazylianska V, Kalpage HA, Wan J, Vaishnav A, Mahapatra G, Turner AA, Chowdhury DD, Kim K, Morse PT, Lee I, Brunzelle JS, Polin L, Subedi P, Heath EI, Podgorski I, Marcus K, Edwards BF, Hüttemann M. Lysine 53 Acetylation of Cytochrome c in Prostate Cancer: Warburg Metabolism and Evasion of Apoptosis. Cells 2021; 10:802. [PMID: 33916826 PMCID: PMC8066186 DOI: 10.3390/cells10040802] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 03/28/2021] [Accepted: 04/01/2021] [Indexed: 02/07/2023] Open
Abstract
Prostate cancer is the second leading cause of cancer-related death in men. Two classic cancer hallmarks are a metabolic switch from oxidative phosphorylation (OxPhos) to glycolysis, known as the Warburg effect, and resistance to cell death. Cytochrome c (Cytc) is at the intersection of both pathways, as it is essential for electron transport in mitochondrial respiration and a trigger of intrinsic apoptosis when released from the mitochondria. However, its functional role in cancer has never been studied. Our data show that Cytc is acetylated on lysine 53 in both androgen hormone-resistant and -sensitive human prostate cancer xenografts. To characterize the functional effects of K53 modification in vitro, K53 was mutated to acetylmimetic glutamine (K53Q), and to arginine (K53R) and isoleucine (K53I) as controls. Cytochrome c oxidase (COX) activity analyzed with purified Cytc variants showed reduced oxygen consumption with acetylmimetic Cytc compared to the non-acetylated Cytc (WT), supporting the Warburg effect. In contrast to WT, K53Q Cytc had significantly lower caspase-3 activity, suggesting that modification of Cytc K53 helps cancer cells evade apoptosis. Cardiolipin peroxidase activity, which is another proapoptotic function of the protein, was lower in acetylmimetic Cytc. Acetylmimetic Cytc also had a higher capacity to scavenge reactive oxygen species (ROS), another pro-survival feature. We discuss our experimental results in light of structural features of K53Q Cytc, which we crystallized at a resolution of 1.31 Å, together with molecular dynamics simulations. In conclusion, we propose that K53 acetylation of Cytc affects two hallmarks of cancer by regulating respiration and apoptosis in prostate cancer xenografts.
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Affiliation(s)
- Viktoriia Bazylianska
- Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University, Detroit, MI 48201, USA; (V.B.); (H.A.K.); (J.W.); (G.M.); (A.A.T.); (K.K.); (P.T.M.); (I.L.)
- Department of Biochemistry, Microbiology, and Immunology, School of Medicine, Wayne State University, Detroit, MI 48201, USA; (A.V.); (D.D.C.); (B.F.P.E.)
| | - Hasini A. Kalpage
- Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University, Detroit, MI 48201, USA; (V.B.); (H.A.K.); (J.W.); (G.M.); (A.A.T.); (K.K.); (P.T.M.); (I.L.)
| | - Junmei Wan
- Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University, Detroit, MI 48201, USA; (V.B.); (H.A.K.); (J.W.); (G.M.); (A.A.T.); (K.K.); (P.T.M.); (I.L.)
| | - Asmita Vaishnav
- Department of Biochemistry, Microbiology, and Immunology, School of Medicine, Wayne State University, Detroit, MI 48201, USA; (A.V.); (D.D.C.); (B.F.P.E.)
| | - Gargi Mahapatra
- Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University, Detroit, MI 48201, USA; (V.B.); (H.A.K.); (J.W.); (G.M.); (A.A.T.); (K.K.); (P.T.M.); (I.L.)
- Department of Biochemistry, Microbiology, and Immunology, School of Medicine, Wayne State University, Detroit, MI 48201, USA; (A.V.); (D.D.C.); (B.F.P.E.)
| | - Alice A. Turner
- Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University, Detroit, MI 48201, USA; (V.B.); (H.A.K.); (J.W.); (G.M.); (A.A.T.); (K.K.); (P.T.M.); (I.L.)
- Department of Biochemistry, Microbiology, and Immunology, School of Medicine, Wayne State University, Detroit, MI 48201, USA; (A.V.); (D.D.C.); (B.F.P.E.)
| | - Dipanwita Dutta Chowdhury
- Department of Biochemistry, Microbiology, and Immunology, School of Medicine, Wayne State University, Detroit, MI 48201, USA; (A.V.); (D.D.C.); (B.F.P.E.)
| | - Katherine Kim
- Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University, Detroit, MI 48201, USA; (V.B.); (H.A.K.); (J.W.); (G.M.); (A.A.T.); (K.K.); (P.T.M.); (I.L.)
| | - Paul T. Morse
- Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University, Detroit, MI 48201, USA; (V.B.); (H.A.K.); (J.W.); (G.M.); (A.A.T.); (K.K.); (P.T.M.); (I.L.)
| | - Icksoo Lee
- Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University, Detroit, MI 48201, USA; (V.B.); (H.A.K.); (J.W.); (G.M.); (A.A.T.); (K.K.); (P.T.M.); (I.L.)
- College of Medicine, Dankook University, Cheonan-si, Chungcheongnam-do 31116, Korea
| | - Joseph S. Brunzelle
- Life Sciences Collaborative Access Team, Center for Synchrotron Research, Northwestern University, Argonne, IL 60439, USA;
| | - Lisa Polin
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI 48201, USA; (L.P.); (E.I.H.)
| | - Prabal Subedi
- Medical Proteomics/Bioanalytics-Center, Ruhr-University Bochum, 44789 Bochum, Germany; (P.S.); (K.M.)
| | - Elisabeth I. Heath
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI 48201, USA; (L.P.); (E.I.H.)
| | - Izabela Podgorski
- Department of Pharmacology, Wayne State University, Detroit, MI 48201, USA;
| | - Katrin Marcus
- Medical Proteomics/Bioanalytics-Center, Ruhr-University Bochum, 44789 Bochum, Germany; (P.S.); (K.M.)
| | - Brian F.P. Edwards
- Department of Biochemistry, Microbiology, and Immunology, School of Medicine, Wayne State University, Detroit, MI 48201, USA; (A.V.); (D.D.C.); (B.F.P.E.)
| | - Maik Hüttemann
- Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University, Detroit, MI 48201, USA; (V.B.); (H.A.K.); (J.W.); (G.M.); (A.A.T.); (K.K.); (P.T.M.); (I.L.)
- Department of Biochemistry, Microbiology, and Immunology, School of Medicine, Wayne State University, Detroit, MI 48201, USA; (A.V.); (D.D.C.); (B.F.P.E.)
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10
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Gladyck S, Aras S, Hüttemann M, Grossman LI. Regulation of COX Assembly and Function by Twin CX 9C Proteins-Implications for Human Disease. Cells 2021; 10:197. [PMID: 33498264 PMCID: PMC7909247 DOI: 10.3390/cells10020197] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/11/2021] [Accepted: 01/12/2021] [Indexed: 12/29/2022] Open
Abstract
Oxidative phosphorylation is a tightly regulated process in mammals that takes place in and across the inner mitochondrial membrane and consists of the electron transport chain and ATP synthase. Complex IV, or cytochrome c oxidase (COX), is the terminal enzyme of the electron transport chain, responsible for accepting electrons from cytochrome c, pumping protons to contribute to the gradient utilized by ATP synthase to produce ATP, and reducing oxygen to water. As such, COX is tightly regulated through numerous mechanisms including protein-protein interactions. The twin CX9C family of proteins has recently been shown to be involved in COX regulation by assisting with complex assembly, biogenesis, and activity. The twin CX9C motif allows for the import of these proteins into the intermembrane space of the mitochondria using the redox import machinery of Mia40/CHCHD4. Studies have shown that knockdown of the proteins discussed in this review results in decreased or completely deficient aerobic respiration in experimental models ranging from yeast to human cells, as the proteins are conserved across species. This article highlights and discusses the importance of COX regulation by twin CX9C proteins in the mitochondria via COX assembly and control of its activity through protein-protein interactions, which is further modulated by cell signaling pathways. Interestingly, select members of the CX9C protein family, including MNRR1 and CHCHD10, show a novel feature in that they not only localize to the mitochondria but also to the nucleus, where they mediate oxygen- and stress-induced transcriptional regulation, opening a new view of mitochondrial-nuclear crosstalk and its involvement in human disease.
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Affiliation(s)
- Stephanie Gladyck
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA; (S.G.); (S.A.); (M.H.)
| | - Siddhesh Aras
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA; (S.G.); (S.A.); (M.H.)
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland and Detroit, MI 48201, USA
| | - Maik Hüttemann
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA; (S.G.); (S.A.); (M.H.)
| | - Lawrence I. Grossman
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA; (S.G.); (S.A.); (M.H.)
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland and Detroit, MI 48201, USA
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11
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Saikia S, Bordoloi M. Molecular Docking: Challenges, Advances and its Use in Drug Discovery Perspective. Curr Drug Targets 2020; 20:501-521. [PMID: 30360733 DOI: 10.2174/1389450119666181022153016] [Citation(s) in RCA: 203] [Impact Index Per Article: 50.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 06/08/2018] [Accepted: 08/28/2018] [Indexed: 01/21/2023]
Abstract
Molecular docking is a process through which small molecules are docked into the macromolecular structures for scoring its complementary values at the binding sites. It is a vibrant research area with dynamic utility in structure-based drug-designing, lead optimization, biochemical pathway and for drug designing being the most attractive tools. Two pillars for a successful docking experiment are correct pose and affinity prediction. Each program has its own advantages and drawbacks with respect to their docking accuracy, ranking accuracy and time consumption so a general conclusion cannot be drawn. Moreover, users don't always consider sufficient diversity in their test sets which results in certain programs to outperform others. In this review, the prime focus has been laid on the challenges of docking and troubleshooters in existing programs, underlying algorithmic background of docking, preferences regarding the use of docking programs for best results illustrated with examples, comparison of performance for existing tools and algorithms, state of art in docking, recent trends of diseases and current drug industries, evidence from clinical trials and post-marketing surveillance are discussed. These aspects of the molecular drug designing paradigm are quite controversial and challenging and this review would be an asset to the bioinformatics and drug designing communities.
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Affiliation(s)
- Surovi Saikia
- Natural Products Chemistry Group, CSIR North East Institute of Science & Technology, Jorhat-785006, Assam, India
| | - Manobjyoti Bordoloi
- Natural Products Chemistry Group, CSIR North East Institute of Science & Technology, Jorhat-785006, Assam, India
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12
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Cytochrome c phosphorylation: Control of mitochondrial electron transport chain flux and apoptosis. Int J Biochem Cell Biol 2020; 121:105704. [PMID: 32023432 DOI: 10.1016/j.biocel.2020.105704] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 01/30/2020] [Accepted: 01/31/2020] [Indexed: 12/30/2022]
Abstract
Cytochrome c (Cytc)1is a cellular life and death decision molecule that regulates cellular energy supply and apoptosis through tissue specific post-translational modifications. Cytc is an electron carrier in the mitochondrial electron transport chain (ETC) and thus central for aerobic energy production. Under conditions of cellular stress, Cytc release from the mitochondria is a committing step for apoptosis, leading to apoptosome formation, caspase activation, and cell death. Recently, Cytc was shown to be a target of cellular signaling pathways that regulate the functions of Cytc by tissue-specific phosphorylations. So far five phosphorylation sites of Cytc have been mapped and functionally characterized, Tyr97, Tyr48, Thr28, Ser47, and Thr58. All five phosphorylations partially inhibit respiration, which we propose results in optimal intermediate mitochondrial membrane potentials and low ROS production under normal conditions. Four of the phosphorylations result in inhibition of the apoptotic functions of Cytc, suggesting a cytoprotective role for phosphorylated Cytc. Interestingly, these phosphorylations are lost during stress conditions such as ischemia. This results in maximal ETC flux during reperfusion, mitochondrial membrane potential hyperpolarization, excessive ROS generation, and apoptosis. We here present a new model proposing that the electron transfer from Cytc to cytochrome c oxidase is the rate-limiting step of the ETC, which is regulated via post-translational modifications of Cytc. This regulation may be dysfunctional in disease conditions such as ischemia-reperfusion injury and neurodegenerative disorders through increased ROS, or cancer, where post-translational modifications on Cytc may provide a mechanism to evade apoptosis.
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13
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Regulation of Respiration and Apoptosis by Cytochrome c Threonine 58 Phosphorylation. Sci Rep 2019; 9:15815. [PMID: 31676852 PMCID: PMC6825195 DOI: 10.1038/s41598-019-52101-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 10/02/2019] [Indexed: 12/16/2022] Open
Abstract
Cytochrome c (Cytc) is a multifunctional protein, acting as an electron carrier in the electron transport chain (ETC), where it shuttles electrons from bc1 complex to cytochrome c oxidase (COX), and as a trigger of type II apoptosis when released from the mitochondria. We previously showed that Cytc is regulated in a highly tissue-specific manner: Cytc isolated from heart, liver, and kidney is phosphorylated on Y97, Y48, and T28, respectively. Here, we have analyzed the effect of a new Cytc phosphorylation site, threonine 58, which we mapped in rat kidney Cytc by mass spectrometry. We generated and overexpressed wild-type, phosphomimetic T58E, and two controls, T58A and T58I Cytc; the latter replacement is found in human and testis-specific Cytc. In vitro, COX activity, caspase-3 activity, and heme degradation in the presence of H2O2 were decreased with phosphomimetic Cytc compared to wild-type. Cytc-knockout cells expressing T58E or T58I Cytc showed a reduction in intact cell respiration, mitochondrial membrane potential (∆Ψm), ROS production, and apoptotic activity compared to wild-type. We propose that, under physiological conditions, Cytc is phosphorylated, which controls mitochondrial respiration and apoptosis. Under conditions of stress Cytc phosphorylations are lost leading to maximal respiration rates, ∆Ψm hyperpolarization, ROS production, and apoptosis.
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14
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Kalpage HA, Vaishnav A, Liu J, Varughese A, Wan J, Turner AA, Ji Q, Zurek MP, Kapralov AA, Kagan VE, Brunzelle JS, Recanati MA, Grossman LI, Sanderson TH, Lee I, Salomon AR, Edwards BFP, Hüttemann M. Serine-47 phosphorylation of cytochrome c in the mammalian brain regulates cytochrome c oxidase and caspase-3 activity. FASEB J 2019; 33:13503-13514. [PMID: 31570002 DOI: 10.1096/fj.201901120r] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Cytochrome c (Cytc) is a multifunctional protein that operates as an electron carrier in the mitochondrial electron transport chain and plays a key role in apoptosis. We have previously shown that tissue-specific phosphorylations of Cytc in the heart, liver, and kidney play an important role in the regulation of cellular respiration and cell death. Here, we report that Cytc purified from mammalian brain is phosphorylated on S47 and that this phosphorylation is lost during ischemia. We have characterized the functional effects in vitro using phosphorylated Cytc purified from pig brain tissue and a recombinant phosphomimetic mutant (S47E). We crystallized S47E phosphomimetic Cytc at 1.55 Å and suggest that it spatially matches S47-phosphorylated Cytc, making it a good model system. Both S47-phosphorylated and phosphomimetic Cytc showed a lower oxygen consumption rate in reaction with isolated Cytc oxidase, which we propose maintains intermediate mitochondrial membrane potentials under physiologic conditions, thus minimizing production of reactive oxygen species. S47-phosphorylated and phosphomimetic Cytc showed lower caspase-3 activity. Furthermore, phosphomimetic Cytc had decreased cardiolipin peroxidase activity and is more stable in the presence of H2O2. Our data suggest that S47 phosphorylation of Cytc is tissue protective and promotes cell survival in the brain.-Kalpage, H. A., Vaishnav, A., Liu, J., Varughese, A., Wan, J., Turner, A. A., Ji, Q., Zurek, M. P., Kapralov, A. A., Kagan, V. E., Brunzelle, J. S., Recanati, M.-A., Grossman, L. I., Sanderson, T. H., Lee, I., Salomon, A. R., Edwards, B. F. P, Hüttemann, M. Serine-47 phosphorylation of cytochrome c in the mammalian brain regulates cytochrome c oxidase and caspase-3 activity.
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Affiliation(s)
- Hasini A Kalpage
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, USA
| | - Asmita Vaishnav
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University, Detroit, Michigan, USA
| | - Jenney Liu
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, USA
| | - Ashwathy Varughese
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, USA.,Department of Biochemistry, Microbiology, and Immunology, Wayne State University, Detroit, Michigan, USA
| | - Junmei Wan
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, USA.,Department of Biochemistry, Microbiology, and Immunology, Wayne State University, Detroit, Michigan, USA
| | - Alice A Turner
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, USA.,Department of Biochemistry, Microbiology, and Immunology, Wayne State University, Detroit, Michigan, USA
| | - Qinqin Ji
- Department of Chemistry, Brown University, Providence, Rhode Island, USA
| | - Matthew P Zurek
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, USA
| | - Alexandr A Kapralov
- Department of Environmental and Occupational Health, Center for Free Radical and Antioxidant Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Valerian E Kagan
- Department of Environmental and Occupational Health, Center for Free Radical and Antioxidant Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Laboratory of Navigational Redox Lipidomics, I. M. Sechenov Moscow Medical State University, Moscow, Russia
| | - Joseph S Brunzelle
- Center for Synchrotron Research, Northwestern University, Argonne, Illinois, USA
| | - Maurice-Andre Recanati
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, USA.,Department of Obstetrics and Gynecology, Wayne State University, Detroit, Michigan, USA
| | - Lawrence I Grossman
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, USA
| | - Thomas H Sanderson
- Department of Emergency Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA.,Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, Michigan, USA.,Cardiovascular Research Institute, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Icksoo Lee
- College of Medicine, Dankook University, Cheonan-si, South Korea
| | - Arthur R Salomon
- Department of Chemistry, Brown University, Providence, Rhode Island, USA
| | - Brian F P Edwards
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University, Detroit, Michigan, USA
| | - Maik Hüttemann
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, USA.,Department of Biochemistry, Microbiology, and Immunology, Wayne State University, Detroit, Michigan, USA.,Cardiovascular Research Institute, Wayne State University School of Medicine, Detroit, Michigan, USA
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15
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Scharlau M, Geren L, Zhen EY, Ma L, Rajagukguk R, Ferguson-Miller S, Durham B, Millett F. Definition of the Interaction Domain and Electron Transfer Route between Cytochrome c and Cytochrome Oxidase. Biochemistry 2019; 58:4125-4135. [PMID: 31532642 DOI: 10.1021/acs.biochem.9b00646] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The reaction between cytochrome c (Cc) and cytochrome c oxidase (CcO) was studied using horse cytochrome c derivatives labeled with ruthenium trisbipyridine at Cys 39 (Ru-39-Cc). Flash photolysis of a 1:1 complex between Ru-39-Cc and bovine CcO at a low ionic strength resulted in the electron transfer from photoreduced heme c to CuA with an intracomplex rate constant of k3 = 6 × 104 s-1. The K13A, K72A, K86A, and K87A Ru-39-Cc mutants had nearly the same k3 value but bound much more weakly to bovine CcO than wild-type Ru-39-Cc, indicating that lysines 13, 72, 86, and 87 were involved in electrostatic binding to CcO, but were not involved in the electron transfer pathway. The Rhodobacter sphaeroides (Rs) W143F mutant (bovine W104) caused a 450-fold decrease in k3 but did not affect the binding strength with CcO or the redox potential of CuA. These results are consistent with a computational model for Cc-CcO (Roberts and Pique ( 1999 ) J. Biol. Chem. 274 , 38051 - 38060 ) with the following electron transfer pathway: heme c → CcO-W104 → CcO-M207 → CuA. A crystal structure for the Cc-CcO complex with the proposed electron transfer pathway heme c → Cc-C14 → Cc-K13 → CcO-Y105 → CcO-M207 → CuA ( S. Shimada ( 2017 ) EMBO J. 36 , 291 - 300 ) is not consistent with the kinetic results because the K13A mutation had no effect on k3. Addition of 40% ethylene glycol (as present during the crystal preparation) decreased k3 significantly, indicating that it affected the conformation of the complex. This may explain the discrepancy between the current results and the crystallographic structure.
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Affiliation(s)
- Martha Scharlau
- Department of Chemistry and Biochemistry , University of Arkansas , Fayetteville , Arkansas 72701 , United States
| | - Lois Geren
- Department of Chemistry and Biochemistry , University of Arkansas , Fayetteville , Arkansas 72701 , United States
| | - Eugene Y Zhen
- Department of Biochemistry and Molecular Biology , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Ling Ma
- Department of Chemistry and Biochemistry , University of Arkansas , Fayetteville , Arkansas 72701 , United States
| | - Ray Rajagukguk
- Department of Chemistry and Biochemistry , University of Arkansas , Fayetteville , Arkansas 72701 , United States
| | - Shelagh Ferguson-Miller
- Department of Biochemistry and Molecular Biology , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Bill Durham
- Department of Chemistry and Biochemistry , University of Arkansas , Fayetteville , Arkansas 72701 , United States
| | - Francis Millett
- Department of Chemistry and Biochemistry , University of Arkansas , Fayetteville , Arkansas 72701 , United States
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16
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Pérez-Mejías G, Guerra-Castellano A, Díaz-Quintana A, De la Rosa MA, Díaz-Moreno I. Cytochrome c: Surfing Off of the Mitochondrial Membrane on the Tops of Complexes III and IV. Comput Struct Biotechnol J 2019; 17:654-660. [PMID: 31193759 PMCID: PMC6542325 DOI: 10.1016/j.csbj.2019.05.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 04/29/2019] [Accepted: 05/04/2019] [Indexed: 11/30/2022] Open
Abstract
The proper arrangement of protein components within the respiratory electron transport chain is nowadays a matter of intense debate, since altering it leads to cell aging and other related pathologies. Here, we discuss three current views—the so-called solid, fluid and plasticity models—which describe the organization of the main membrane-embedded mitochondrial protein complexes and the key elements that regulate and/or facilitate supercomplex assembly. The soluble electron carrier cytochrome c has recently emerged as an essential factor in the assembly and function of respiratory supercomplexes. In fact, a ‘restricted diffusion pathway’ mechanism for electron transfer between complexes III and IV has been proposed based on the secondary, distal binding sites for cytochrome c at its two membrane partners recently discovered. This channeling pathway facilitates the surfing of cytochrome c on both respiratory complexes, thereby tuning the efficiency of oxidative phosphorylation and diminishing the production of reactive oxygen species. The well-documented post-translational modifications of cytochrome c could further contribute to the rapid adjustment of electron flow in response to changing cellular conditions.
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Affiliation(s)
- Gonzalo Pérez-Mejías
- Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla - Consejo Superior de Investigaciones Científicas (CSIC), Avda. Américo Vespucio 49, Sevilla 41092, Spain
| | - Alejandra Guerra-Castellano
- Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla - Consejo Superior de Investigaciones Científicas (CSIC), Avda. Américo Vespucio 49, Sevilla 41092, Spain
| | - Antonio Díaz-Quintana
- Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla - Consejo Superior de Investigaciones Científicas (CSIC), Avda. Américo Vespucio 49, Sevilla 41092, Spain
| | - Miguel A De la Rosa
- Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla - Consejo Superior de Investigaciones Científicas (CSIC), Avda. Américo Vespucio 49, Sevilla 41092, Spain
| | - Irene Díaz-Moreno
- Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla - Consejo Superior de Investigaciones Científicas (CSIC), Avda. Américo Vespucio 49, Sevilla 41092, Spain
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17
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Deng Y, Zhong F, Alden SL, Hoke KR, Pletneva EV. The K79G Mutation Reshapes the Heme Crevice and Alters Redox Properties of Cytochrome c. Biochemistry 2018; 57:5827-5840. [PMID: 30142276 DOI: 10.1021/acs.biochem.8b00650] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The two roles of cytochrome c (cyt c), in oxidative phosphorylation and apoptosis, critically depend on redox properties of its heme iron center. The K79G mutant has served as a parent protein for a series of mutants of yeast iso-1 cyt c. The mutation preserves the Met80 coordination to the heme iron, as found in WT* (K72A/C102S), and many spectroscopic properties of K79G and WT* are indistinguishable. The K79G mutation does not alter the global stability, fold, rate of Met80 dissociation, or thermodynamics of the alkaline transition (p Ka) of the protein. However, the reduction potential of the heme iron decreases; further, the p KH of the trigger group and the rate of the Met-to-Lys ligand exchange associated with the alkaline transition decrease, suggesting changes in the environment of the heme. The rates of electron self-exchange and bimolecular electron transfer (ET) with positively charged inorganic complexes increase, as does the intrinsic peroxidase activity. Analysis of the reaction rates suggests that there is increased accessibility of the heme edge in K79G and supports the importance of the Lys79 site for bimolecular ET reactions of cyt c, including those with some of its native redox partners. Structural modeling rationalizes the observed effects to arise from changes in the volume of the heme pocket and solvent accessibility of the heme group. Kinetic and structural analyses of WT* characterize the properties of the heme crevice of this commonly employed reference variant. This study highlights the important role of Lys79 for defining functional redox properties of cyt c.
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Affiliation(s)
- Yunling Deng
- Department of Chemistry , Dartmouth College , Hanover , New Hampshire 03755 , United States
| | - Fangfang Zhong
- Department of Chemistry , Dartmouth College , Hanover , New Hampshire 03755 , United States
| | - Stephanie L Alden
- Department of Chemistry , Dartmouth College , Hanover , New Hampshire 03755 , United States
| | - Kevin R Hoke
- Department of Chemistry and Biochemistry , Berry College , Mount Berry , Georgia 30149 , United States
| | - Ekaterina V Pletneva
- Department of Chemistry , Dartmouth College , Hanover , New Hampshire 03755 , United States
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18
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Comparative biochemistry of cytochrome c oxidase in animals. Comp Biochem Physiol B Biochem Mol Biol 2017; 224:170-184. [PMID: 29180239 DOI: 10.1016/j.cbpb.2017.11.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 11/06/2017] [Accepted: 11/07/2017] [Indexed: 12/19/2022]
Abstract
Cytochrome c oxidase (COX), the terminal enzyme of the electron transport system, is central to aerobic metabolism of animals. Many aspects of its structure and function are highly conserved, yet, paradoxically, it is also an important model for studying the evolution of the metabolic phenotype. In this review, part of a special issue honouring Peter Hochachka, we consider the biology of COX from the perspective of comparative and evolutionary biochemistry. The approach is to consider what is known about the enzyme in the context of conventional biochemistry, but focus on how evolutionary researchers have used this background to explore the role of the enzyme in biochemical adaptation of animals. In synthesizing the conventional and evolutionary biochemistry, we hope to identify synergies and future research opportunities. COX represents a rare opportunity for researchers to design studies that span the breadth of biology: molecular genetics, protein biochemistry, enzymology, metabolic physiology, organismal performance, evolutionary biology, and phylogeography.
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19
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Alvarez-Paggi D, Hannibal L, Castro MA, Oviedo-Rouco S, Demicheli V, Tórtora V, Tomasina F, Radi R, Murgida DH. Multifunctional Cytochrome c: Learning New Tricks from an Old Dog. Chem Rev 2017; 117:13382-13460. [DOI: 10.1021/acs.chemrev.7b00257] [Citation(s) in RCA: 135] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Damián Alvarez-Paggi
- Departamento
de Química Inorgánica, Analítica y Química
Física and INQUIMAE (CONICET-UBA), Facultad de Ciencias Exactas
y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, piso 1, Buenos Aires C1428EHA, Argentina
| | - Luciana Hannibal
- Department
of Pediatrics, Universitätsklinikum Freiburg, Mathildenstrasse 1, Freiburg 79106, Germany
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Av.
Gral. Flores 2125, Montevideo 11800, Uruguay
| | - María A. Castro
- Departamento
de Química Inorgánica, Analítica y Química
Física and INQUIMAE (CONICET-UBA), Facultad de Ciencias Exactas
y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, piso 1, Buenos Aires C1428EHA, Argentina
| | - Santiago Oviedo-Rouco
- Departamento
de Química Inorgánica, Analítica y Química
Física and INQUIMAE (CONICET-UBA), Facultad de Ciencias Exactas
y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, piso 1, Buenos Aires C1428EHA, Argentina
| | - Veronica Demicheli
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Av.
Gral. Flores 2125, Montevideo 11800, Uruguay
| | - Veronica Tórtora
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Av.
Gral. Flores 2125, Montevideo 11800, Uruguay
| | - Florencia Tomasina
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Av.
Gral. Flores 2125, Montevideo 11800, Uruguay
| | - Rafael Radi
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Av.
Gral. Flores 2125, Montevideo 11800, Uruguay
| | - Daniel H. Murgida
- Departamento
de Química Inorgánica, Analítica y Química
Física and INQUIMAE (CONICET-UBA), Facultad de Ciencias Exactas
y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, piso 1, Buenos Aires C1428EHA, Argentina
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20
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Alleyne T, Ignacio DN, Sampson VB, Ashe D, Wilson M. Simulating the slow to fast switch in cytochrome c oxidase catalysis by introducing a loop flip near the enzyme's cytochrome c (substrate) binding site. Biotechnol Appl Biochem 2017; 64:677-685. [PMID: 27489224 DOI: 10.1002/bab.1526] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 07/30/2016] [Indexed: 01/03/2023]
Affiliation(s)
- Trevor Alleyne
- Biochemistry Unit, Faculty of Medical Sciences, The University of the West Indies, St. Augustine Campus, Trinidad and Tobago
| | - Diane N Ignacio
- Biochemistry Unit, Faculty of Medical Sciences, The University of the West Indies, St. Augustine Campus, Trinidad and Tobago
| | - Valerie B Sampson
- Nemours Center for Cancer and Blood Disorders, Alfred I. duPont Hospital for Children, Wilmington, DE, USA
| | - Damian Ashe
- Biochemistry Unit, Faculty of Medical Sciences, The University of the West Indies, St. Augustine Campus, Trinidad and Tobago
| | - Michael Wilson
- School of Biological Sciences, University of Essex, Colchester, Essex, UK
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21
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Chertkova RV, Brazhe NA, Bryantseva TV, Nekrasov AN, Dolgikh DA, Yusipovich AI, Sosnovtseva O, Maksimov GV, Rubin AB, Kirpichnikov MP. New insight into the mechanism of mitochondrial cytochrome c function. PLoS One 2017; 12:e0178280. [PMID: 28562658 PMCID: PMC5451065 DOI: 10.1371/journal.pone.0178280] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 05/10/2017] [Indexed: 11/22/2022] Open
Abstract
We investigate functional role of the P76GTKMIFA83 fragment of the primary structure of cytochrome c. Based on the data obtained by the analysis of informational structure (ANIS), we propose a model of functioning of cytochrome c. According to this model, conformational rearrangements of the P76GTKMIFA83 loop fragment have a significant effect on conformational mobility of the heme. It is suggested that the conformational mobility of cytochrome c heme is responsible for its optimal orientation with respect to electron donor and acceptor within ubiquinol–cytochrome c oxidoreductase (complex III) and cytochrome c oxidase (complex IV), respectively, thus, ensuring electron transfer from complex III to complex IV. To validate the model, we design several mutant variants of horse cytochrome c with multiple substitutions of amino acid residues in the P76GTKMIFA83 sequence that reduce its ability to undergo conformational rearrangements. With this, we study the succinate–cytochrome c reductase and cytochrome c oxidase activities of rat liver mitoplasts in the presence of mutant variants of cytochrome c. The electron transport activity of the mutant variants decreases to different extent. Resonance Raman spectroscopy (RRS) and surface-enhanced Raman spectroscopy (SERS) data demonstrate, that all mutant cytochromes possess heme with the higher degree of ruffling deformation, than that of the wild-type (WT) cytochrome c. The increase in the ruffled deformation of the heme of oxidized cytochromes correlated with the decrease in the electron transport rate of ubiquinol–cytochrome c reductase (complex III). Besides, all mutant cytochromes have lower mobility of the pyrrol rings and methine bridges, than WT cytochrome c. We show that a decrease in electron transport activity in the mutant variants correlates with conformational changes and reduced mobility of heme porphyrin. This points to a significant role of the P76GTKMIFA83 fragment in the electron transport function of cytochrome c.
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Affiliation(s)
- Rita V. Chertkova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, The Russian Academy of Sciences, Moscow, Russia
- * E-mail: (RVC); (NAB)
| | - Nadezda A. Brazhe
- Biophysics Department, Biological faculty, M.V. Lomonosov Moscow State University, Moscow, Russia
- * E-mail: (RVC); (NAB)
| | - Tatiana V. Bryantseva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, The Russian Academy of Sciences, Moscow, Russia
- Biophysics Department, Biological faculty, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Alexey N. Nekrasov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, The Russian Academy of Sciences, Moscow, Russia
| | - Dmitry A. Dolgikh
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, The Russian Academy of Sciences, Moscow, Russia
- Biophysics Department, Biological faculty, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Alexander I. Yusipovich
- Biophysics Department, Biological faculty, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Olga Sosnovtseva
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, Copenhagen University, Copenhagen, Denmark
| | - Georgy V. Maksimov
- Biophysics Department, Biological faculty, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Andrei B. Rubin
- Biophysics Department, Biological faculty, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Mikhail P. Kirpichnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, The Russian Academy of Sciences, Moscow, Russia
- Biophysics Department, Biological faculty, M.V. Lomonosov Moscow State University, Moscow, Russia
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22
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Hall A, Lächelt U, Bartek J, Wagner E, Moghimi SM. Polyplex Evolution: Understanding Biology, Optimizing Performance. Mol Ther 2017; 25:1476-1490. [PMID: 28274797 DOI: 10.1016/j.ymthe.2017.01.024] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 01/25/2017] [Accepted: 01/25/2017] [Indexed: 02/06/2023] Open
Abstract
Polyethylenimine (PEI) is a gold standard polycationic transfectant. However, the highly efficient transfecting activity of PEI and many of its derivatives is accompanied by serious cytotoxic complications and safety concerns at innate immune levels, which impedes the development of therapeutic polycationic nucleic acid carriers in general and their clinical applications. In recent years, the dilemma between transfection efficacy and adverse PEI activities has been addressed from in-depth investigations of cellular processes during transfection and elucidation of molecular mechanisms of PEI-mediated toxicity and translation of these integrated events to chemical engineering of novel PEI derivatives with an improved benefit-to-risk ratio. This review addresses these perspectives and discusses molecular events pertaining to dynamic and multifaceted PEI-mediated cytotoxicity, including membrane destabilization, mitochondrial dysfunction, and perturbations of glycolytic flux and redox homeostasis as well as chemical strategies for the generation of better tolerated polycations. We further examine the effect of PEI and its derivatives on complement activation and interaction with Toll-like receptors. These perspectives are intended to lay the foundation for an improved understanding of interlinked mechanisms controlling transfection and toxicity and their translation for improved engineering of polycation-based transfectants.
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Affiliation(s)
- Arnaldur Hall
- Genome Integrity Unit, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark
| | - Ulrich Lächelt
- Pharmaceutical Biotechnology, Department of Pharmacy, Ludwig-Maximilians-Universität, 81377 Munich, Germany; Nanosystems Initiative Munich, 80799 Munich, Germany
| | - Jiri Bartek
- Genome Integrity Unit, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark; Department of Medical Biochemistry and Biophysics, Science for Life Laboratory, Karolinska Institute, 171 65 Solna, Sweden
| | - Ernst Wagner
- Pharmaceutical Biotechnology, Department of Pharmacy, Ludwig-Maximilians-Universität, 81377 Munich, Germany; Nanosystems Initiative Munich, 80799 Munich, Germany.
| | - Seyed Moein Moghimi
- School of Medicine, Pharmacy and Health, Durham University, Queen's Campus, Stockton-on-Tees TS17 6BH, UK.
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23
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Pagadala NS, Syed K, Tuszynski J. Software for molecular docking: a review. Biophys Rev 2017; 9:91-102. [PMID: 28510083 DOI: 10.1007/s12551-016-0247-1] [Citation(s) in RCA: 644] [Impact Index Per Article: 92.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2016] [Accepted: 12/27/2016] [Indexed: 11/26/2022] Open
Abstract
Molecular docking methodology explores the behavior of small molecules in the binding site of a target protein. As more protein structures are determined experimentally using X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy, molecular docking is increasingly used as a tool in drug discovery. Docking against homology-modeled targets also becomes possible for proteins whose structures are not known. With the docking strategies, the druggability of the compounds and their specificity against a particular target can be calculated for further lead optimization processes. Molecular docking programs perform a search algorithm in which the conformation of the ligand is evaluated recursively until the convergence to the minimum energy is reached. Finally, an affinity scoring function, ΔG [U total in kcal/mol], is employed to rank the candidate poses as the sum of the electrostatic and van der Waals energies. The driving forces for these specific interactions in biological systems aim toward complementarities between the shape and electrostatics of the binding site surfaces and the ligand or substrate.
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Affiliation(s)
- Nataraj S Pagadala
- Department of Medical Microbiology and Immunology, Li Ka Shing Institute of Virology, 6-020 Katz Group Centre, University of Alberta, Edmonton, Alberta, T6G 2E1, Canada.
| | - Khajamohiddin Syed
- Unit for Drug Discovery Research, Department of Health Sciences, Faculty of Health and Environmental Sciences, Central University of Technology, Bloemfontein, 9300, Free State, South Africa
| | - Jack Tuszynski
- Department of Experimental Oncology, Cross Cancer Institute, Edmonton, Alberta, Canada
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada
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24
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Shimada S, Shinzawa-Itoh K, Baba J, Aoe S, Shimada A, Yamashita E, Kang J, Tateno M, Yoshikawa S, Tsukihara T. Complex structure of cytochrome c-cytochrome c oxidase reveals a novel protein-protein interaction mode. EMBO J 2016; 36:291-300. [PMID: 27979921 PMCID: PMC5286356 DOI: 10.15252/embj.201695021] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 10/21/2016] [Accepted: 11/16/2016] [Indexed: 12/21/2022] Open
Abstract
Mitochondrial cytochrome c oxidase (CcO) transfers electrons from cytochrome c (Cyt.c) to O2 to generate H2O, a process coupled to proton pumping. To elucidate the mechanism of electron transfer, we determined the structure of the mammalian Cyt.c–CcO complex at 2.0‐Å resolution and identified an electron transfer pathway from Cyt.c to CcO. The specific interaction between Cyt.c and CcO is stabilized by a few electrostatic interactions between side chains within a small contact surface area. Between the two proteins are three water layers with a long inter‐molecular span, one of which lies between the other two layers without significant direct interaction with either protein. Cyt.c undergoes large structural fluctuations, using the interacting regions with CcO as a fulcrum. These features of the protein–protein interaction at the docking interface represent the first known example of a new class of protein–protein interaction, which we term “soft and specific”. This interaction is likely to contribute to the rapid association/dissociation of the Cyt.c–CcO complex, which facilitates the sequential supply of four electrons for the O2 reduction reaction.
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Affiliation(s)
- Satoru Shimada
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, Akoh, Hyogo, Japan
| | - Kyoko Shinzawa-Itoh
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, Akoh, Hyogo, Japan
| | - Junpei Baba
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, Akoh, Hyogo, Japan
| | - Shimpei Aoe
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, Akoh, Hyogo, Japan
| | - Atsuhiro Shimada
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, Akoh, Hyogo, Japan
| | - Eiki Yamashita
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Jiyoung Kang
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, Akoh, Hyogo, Japan
| | - Masaru Tateno
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, Akoh, Hyogo, Japan
| | - Shinya Yoshikawa
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, Akoh, Hyogo, Japan
| | - Tomitake Tsukihara
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, Akoh, Hyogo, Japan .,Institute for Protein Research, Osaka University, Suita, Osaka, Japan.,JST, CREST, Kawaguchi, Saitama, Japan
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25
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Mahapatra G, Varughese A, Ji Q, Lee I, Liu J, Vaishnav A, Sinkler C, Kapralov AA, Moraes CT, Sanderson TH, Stemmler TL, Grossman LI, Kagan VE, Brunzelle JS, Salomon AR, Edwards BFP, Hüttemann M. Phosphorylation of Cytochrome c Threonine 28 Regulates Electron Transport Chain Activity in Kidney: IMPLICATIONS FOR AMP KINASE. J Biol Chem 2016; 292:64-79. [PMID: 27758862 DOI: 10.1074/jbc.m116.744664] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 09/20/2016] [Indexed: 11/06/2022] Open
Abstract
Mammalian cytochrome c (Cytc) plays a key role in cellular life and death decisions, functioning as an electron carrier in the electron transport chain and as a trigger of apoptosis when released from the mitochondria. However, its regulation is not well understood. We show that the major fraction of Cytc isolated from kidneys is phosphorylated on Thr28, leading to a partial inhibition of respiration in the reaction with cytochrome c oxidase. To further study the effect of Cytc phosphorylation in vitro, we generated T28E phosphomimetic Cytc, revealing superior behavior regarding protein stability and its ability to degrade reactive oxygen species compared with wild-type unphosphorylated Cytc Introduction of T28E phosphomimetic Cytc into Cytc knock-out cells shows that intact cell respiration, mitochondrial membrane potential (ΔΨm), and ROS levels are reduced compared with wild type. As we show by high resolution crystallography of wild-type and T28E Cytc in combination with molecular dynamics simulations, Thr28 is located at a central position near the heme crevice, the most flexible epitope of the protein apart from the N and C termini. Finally, in silico prediction and our experimental data suggest that AMP kinase, which phosphorylates Cytc on Thr28 in vitro and colocalizes with Cytc to the mitochondrial intermembrane space in the kidney, is the most likely candidate to phosphorylate Thr28 in vivo We conclude that Cytc phosphorylation is mediated in a tissue-specific manner and leads to regulation of electron transport chain flux via "controlled respiration," preventing ΔΨm hyperpolarization, a known cause of ROS and trigger of apoptosis.
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Affiliation(s)
- Gargi Mahapatra
- From the Center for Molecular Medicine and Genetics and.,the Departments of Biochemistry and Molecular Biology
| | - Ashwathy Varughese
- From the Center for Molecular Medicine and Genetics and.,the Departments of Biochemistry and Molecular Biology
| | | | - Icksoo Lee
- From the Center for Molecular Medicine and Genetics and.,the College of Medicine, Dankook University, Cheonan-si, Chungcheongnam-do 31116, Republic of Korea
| | - Jenney Liu
- From the Center for Molecular Medicine and Genetics and
| | | | | | - Alexandr A Kapralov
- the Center for Free Radical and Antioxidant Health and the Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, Pennsylvania 15219
| | - Carlos T Moraes
- the Department of Neurology, University of Miami School of Medicine, Miami, Florida 33136, and
| | | | - Timothy L Stemmler
- Pharmaceutical Sciences, Wayne State University, Detroit, Michigan 48201
| | | | - Valerian E Kagan
- the Center for Free Radical and Antioxidant Health and the Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, Pennsylvania 15219
| | - Joseph S Brunzelle
- the Life Sciences Collaborative Access Team, Northwestern University, Center for Synchrotron Research, Argonne, Illinois 60439
| | - Arthur R Salomon
- the MCB Department, Brown University, Providence, Rhode Island 02912
| | | | - Maik Hüttemann
- From the Center for Molecular Medicine and Genetics and .,the Departments of Biochemistry and Molecular Biology
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26
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Sato W, Hitaoka S, Inoue K, Imai M, Saio T, Uchida T, Shinzawa-Itoh K, Yoshikawa S, Yoshizawa K, Ishimori K. Energetic Mechanism of Cytochrome c-Cytochrome c Oxidase Electron Transfer Complex Formation under Turnover Conditions Revealed by Mutational Effects and Docking Simulation. J Biol Chem 2016; 291:15320-31. [PMID: 27226541 DOI: 10.1074/jbc.m115.708065] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Indexed: 11/06/2022] Open
Abstract
Based on the mutational effects on the steady-state kinetics of the electron transfer reaction and our NMR analysis of the interaction site (Sakamoto, K., Kamiya, M., Imai, M., Shinzawa-Itoh, K., Uchida, T., Kawano, K., Yoshikawa, S., and Ishimori, K. (2011) Proc. Natl. Acad. Sci. U.S.A. 108, 12271-12276), we determined the structure of the electron transfer complex between cytochrome c (Cyt c) and cytochrome c oxidase (CcO) under turnover conditions and energetically characterized the interactions essential for complex formation. The complex structures predicted by the protein docking simulation were computationally selected and validated by the experimental kinetic data for mutant Cyt c in the electron transfer reaction to CcO. The interaction analysis using the selected Cyt c-CcO complex structure revealed the electrostatic and hydrophobic contributions of each amino acid residue to the free energy required for complex formation. Several charged residues showed large unfavorable (desolvation) electrostatic interactions that were almost cancelled out by large favorable (Columbic) electrostatic interactions but resulted in the destabilization of the complex. The residual destabilizing free energy is compensated by the van der Waals interactions mediated by hydrophobic amino acid residues to give the stabilized complex. Thus, hydrophobic interactions are the primary factors that promote complex formation between Cyt c and CcO under turnover conditions, whereas the change in the electrostatic destabilization free energy provides the variance of the binding free energy in the mutants. The distribution of favorable and unfavorable electrostatic interactions in the interaction site determines the orientation of the binding of Cyt c on CcO.
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Affiliation(s)
- Wataru Sato
- From the Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628
| | - Seiji Hitaoka
- the Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka 819-0315
| | - Kaoru Inoue
- the Division of Chemistry, Graduate School of Science, and
| | - Mizue Imai
- From the Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628
| | - Tomohide Saio
- From the Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, and
| | - Takeshi Uchida
- From the Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, and
| | - Kyoko Shinzawa-Itoh
- the Department of Life Science, Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan
| | - Shinya Yoshikawa
- the Department of Life Science, Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan
| | - Kazunari Yoshizawa
- the Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka 819-0315
| | - Koichiro Ishimori
- From the Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, and
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27
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Hannibal L, Tomasina F, Capdevila DA, Demicheli V, Tórtora V, Alvarez-Paggi D, Jemmerson R, Murgida DH, Radi R. Alternative Conformations of Cytochrome c: Structure, Function, and Detection. Biochemistry 2016; 55:407-28. [DOI: 10.1021/acs.biochem.5b01385] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Luciana Hannibal
- Departamento
de Bioquímica, Facultad de Medicina, Universidad de la República, Avda. General Flores 2125, 11800 Montevideo, Uruguay
- Centro
de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Avda. General Flores 2125, 11800 Montevideo, Uruguay
- Center
for Pediatrics and Adolescent Medicine, Medical Center, University of Freiburg, Mathildenstrasse 1, Freiburg D-79106, Germany
| | - Florencia Tomasina
- Departamento
de Bioquímica, Facultad de Medicina, Universidad de la República, Avda. General Flores 2125, 11800 Montevideo, Uruguay
- Centro
de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Avda. General Flores 2125, 11800 Montevideo, Uruguay
| | - Daiana A. Capdevila
- Departamento
de Química Inorgánica, Analítica y Química
Física/INQUIMAE, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellón 2, Ciudad Universitaria, C1428EHA Buenos Aires, Argentina
| | - Verónica Demicheli
- Departamento
de Bioquímica, Facultad de Medicina, Universidad de la República, Avda. General Flores 2125, 11800 Montevideo, Uruguay
- Centro
de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Avda. General Flores 2125, 11800 Montevideo, Uruguay
| | - Verónica Tórtora
- Departamento
de Bioquímica, Facultad de Medicina, Universidad de la República, Avda. General Flores 2125, 11800 Montevideo, Uruguay
- Centro
de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Avda. General Flores 2125, 11800 Montevideo, Uruguay
| | - Damián Alvarez-Paggi
- Departamento
de Química Inorgánica, Analítica y Química
Física/INQUIMAE, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellón 2, Ciudad Universitaria, C1428EHA Buenos Aires, Argentina
| | - Ronald Jemmerson
- Department
of Microbiology and Immunology, University of Minnesota, MMC 196,
420 Delaware Street, Southeast, Minneapolis, Minnesota 55455, United States
| | - Daniel H. Murgida
- Departamento
de Química Inorgánica, Analítica y Química
Física/INQUIMAE, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellón 2, Ciudad Universitaria, C1428EHA Buenos Aires, Argentina
| | - Rafael Radi
- Departamento
de Bioquímica, Facultad de Medicina, Universidad de la República, Avda. General Flores 2125, 11800 Montevideo, Uruguay
- Centro
de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Avda. General Flores 2125, 11800 Montevideo, Uruguay
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Lyons JA, Hilbers F, Caffrey M. Structure and Function of Bacterial Cytochrome c Oxidases. ADVANCES IN PHOTOSYNTHESIS AND RESPIRATION 2016. [DOI: 10.1007/978-94-017-7481-9_16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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29
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De March M, Brancatelli G, Demitri N, De Zorzi R, Hickey N, Geremia S. A general exit strategy of monoheme cytochromes c and c2 in electron transfer complexes? IUBMB Life 2015; 67:694-700. [PMID: 26311433 DOI: 10.1002/iub.1410] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 07/28/2015] [Indexed: 11/06/2022]
Abstract
Using our previously reported maps of the electrostatic surface of horse heart ferri- and ferro-cyt c, comparisons were made between the complementary electrostatic surfaces of three cyt c peroxidase-cyt c complexes and the photosynthetic reaction center-cyt c complex, considering both iron oxidation states. The results obtained were consistent with a sliding mechanism for the electron shuttle on the surface of the protein complexes, promoted by the change in iron oxidation state. This mechanism was found to be in agreement with theoretical and NMR studies reported in the literature. Importantly, the analysis also provided a rationale for recognition of nonproductive associations. As we have previously reported the same conclusion on examination of redox partners of cyt c in the mitochondrial respiratory pathway, our hypothesis is that the proposed mechanism could represent a general exit strategy of monoheme cyts c and c2 in electron transfer complexes.
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Affiliation(s)
- Matteo De March
- Department of Chemical and Pharmaceutical Sciences, Centre of Excellence in Biocrystallography, University of Trieste, Trieste, Italy
| | - Giovanna Brancatelli
- Department of Chemical and Pharmaceutical Sciences, Centre of Excellence in Biocrystallography, University of Trieste, Trieste, Italy
| | - Nicola Demitri
- Department of Chemical and Pharmaceutical Sciences, Centre of Excellence in Biocrystallography, University of Trieste, Trieste, Italy
| | - Rita De Zorzi
- Department of Chemical and Pharmaceutical Sciences, Centre of Excellence in Biocrystallography, University of Trieste, Trieste, Italy
| | - Neal Hickey
- Department of Chemical and Pharmaceutical Sciences, Centre of Excellence in Biocrystallography, University of Trieste, Trieste, Italy
| | - Silvano Geremia
- Department of Chemical and Pharmaceutical Sciences, Centre of Excellence in Biocrystallography, University of Trieste, Trieste, Italy
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Shalaeva DN, Dibrova DV, Galperin MY, Mulkidjanian AY. Modeling of interaction between cytochrome c and the WD domains of Apaf-1: bifurcated salt bridges underlying apoptosome assembly. Biol Direct 2015. [PMID: 26014357 DOI: 10.1186/s13062-015-0059- 4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Binding of cytochrome c, released from the damaged mitochondria, to the apoptotic protease activating factor 1 (Apaf-1) is a key event in the apoptotic signaling cascade. The binding triggers a major domain rearrangement in Apaf-1, which leads to oligomerization of Apaf-1/cytochrome c complexes into an apoptosome. Despite the availability of crystal structures of cytochrome c and Apaf-1 and cryo-electron microscopy models of the entire apoptosome, the binding mode of cytochrome c to Apaf-1, as well as the nature of the amino acid residues of Apaf-1 involved remain obscure. RESULTS We investigated the interaction between cytochrome c and Apaf-1 by combining several modeling approaches. We have applied protein-protein docking and energy minimization, evaluated the resulting models of the Apaf-1/cytochrome c complex, and carried out a further analysis by means of molecular dynamics simulations. We ended up with a single model structure where all the lysine residues of cytochrome c that are known as functionally-relevant were involved in forming salt bridges with acidic residues of Apaf-1. This model has revealed three distinctive bifurcated salt bridges, each involving a single lysine residue of cytochrome c and two neighboring acidic resides of Apaf-1. Salt bridge-forming amino acids of Apaf-1 showed a clear evolutionary pattern within Metazoa, with pairs of acidic residues of Apaf-1, involved in bifurcated salt bridges, reaching their highest numbers in the sequences of vertebrates, in which the cytochrome c-mediated mechanism of apoptosome formation seems to be typical. CONCLUSIONS The reported model of an Apaf-1/cytochrome c complex provides insights in the nature of protein-protein interactions which are hard to observe in crystallographic or electron microscopy studies. Bifurcated salt bridges can be expected to be stronger than simple salt bridges, and their formation might promote the conformational change of Apaf-1, leading to the formation of an apoptosome. Combination of structural and sequence analyses provides hints on the evolution of the cytochrome c-mediated apoptosis.
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Affiliation(s)
- Daria N Shalaeva
- School of Physics, Osnabrück University, 49069, Osnabrück, Germany. .,School of Bioengineering and Bioinformatics, 117999, Moscow, Russia.
| | - Daria V Dibrova
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 117999, Moscow, Russia.
| | - Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 20894, Bethesda, MD, USA.
| | - Armen Y Mulkidjanian
- School of Physics, Osnabrück University, 49069, Osnabrück, Germany. .,School of Bioengineering and Bioinformatics, 117999, Moscow, Russia. .,A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 117999, Moscow, Russia.
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31
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Shalaeva DN, Dibrova DV, Galperin MY, Mulkidjanian AY. Modeling of interaction between cytochrome c and the WD domains of Apaf-1: bifurcated salt bridges underlying apoptosome assembly. Biol Direct 2015; 10:29. [PMID: 26014357 PMCID: PMC4445527 DOI: 10.1186/s13062-015-0059-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Accepted: 05/13/2015] [Indexed: 12/19/2022] Open
Abstract
Background Binding of cytochrome c, released from the damaged mitochondria, to the apoptotic protease activating factor 1 (Apaf-1) is a key event in the apoptotic signaling cascade. The binding triggers a major domain rearrangement in Apaf-1, which leads to oligomerization of Apaf-1/cytochrome c complexes into an apoptosome. Despite the availability of crystal structures of cytochrome c and Apaf-1 and cryo-electron microscopy models of the entire apoptosome, the binding mode of cytochrome c to Apaf-1, as well as the nature of the amino acid residues of Apaf-1 involved remain obscure. Results We investigated the interaction between cytochrome c and Apaf-1 by combining several modeling approaches. We have applied protein-protein docking and energy minimization, evaluated the resulting models of the Apaf-1/cytochrome c complex, and carried out a further analysis by means of molecular dynamics simulations. We ended up with a single model structure where all the lysine residues of cytochrome c that are known as functionally-relevant were involved in forming salt bridges with acidic residues of Apaf-1. This model has revealed three distinctive bifurcated salt bridges, each involving a single lysine residue of cytochrome c and two neighboring acidic resides of Apaf-1. Salt bridge-forming amino acids of Apaf-1 showed a clear evolutionary pattern within Metazoa, with pairs of acidic residues of Apaf-1, involved in bifurcated salt bridges, reaching their highest numbers in the sequences of vertebrates, in which the cytochrome c-mediated mechanism of apoptosome formation seems to be typical. Conclusions The reported model of an Apaf-1/cytochrome c complex provides insights in the nature of protein-protein interactions which are hard to observe in crystallographic or electron microscopy studies. Bifurcated salt bridges can be expected to be stronger than simple salt bridges, and their formation might promote the conformational change of Apaf-1, leading to the formation of an apoptosome. Combination of structural and sequence analyses provides hints on the evolution of the cytochrome c-mediated apoptosis. Reviewers This article was reviewed by Andrei L. Osterman, Narayanaswamy Srinivasan, Igor N. Berezovsky, and Gerrit Vriend (nominated by Martijn Huynen). Electronic supplementary material The online version of this article (doi:10.1186/s13062-015-0059-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daria N Shalaeva
- School of Physics, Osnabrück University, 49069, Osnabrück, Germany. .,School of Bioengineering and Bioinformatics, 117999, Moscow, Russia.
| | - Daria V Dibrova
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 117999, Moscow, Russia.
| | - Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 20894, Bethesda, MD, USA.
| | - Armen Y Mulkidjanian
- School of Physics, Osnabrück University, 49069, Osnabrück, Germany. .,School of Bioengineering and Bioinformatics, 117999, Moscow, Russia. .,A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 117999, Moscow, Russia.
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32
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Affiliation(s)
- Shinya Yoshikawa
- Picobiology Institute, Graduate
School of Life Science, University of Hyogo, Kamigohri Akoh Hyogo, 678-1297, Japan
| | - Atsuhiro Shimada
- Picobiology Institute, Graduate
School of Life Science, University of Hyogo, Kamigohri Akoh Hyogo, 678-1297, Japan
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De March M, Demitri N, De Zorzi R, Casini A, Gabbiani C, Guerri A, Messori L, Geremia S. Nitrate as a probe of cytochrome c surface: Crystallographic identification of crucial “hot spots” for protein–protein recognition. J Inorg Biochem 2014; 135:58-67. [DOI: 10.1016/j.jinorgbio.2014.02.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Revised: 02/23/2014] [Accepted: 02/27/2014] [Indexed: 11/30/2022]
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Groocock LM, Nie M, Prudden J, Moiani D, Wang T, Cheltsov A, Rambo RP, Arvai AS, Hitomi C, Tainer JA, Luger K, Perry JJP, Lazzerini-Denchi E, Boddy MN. RNF4 interacts with both SUMO and nucleosomes to promote the DNA damage response. EMBO Rep 2014; 15:601-8. [PMID: 24714598 DOI: 10.1002/embr.201338369] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The post-translational modification of DNA repair and checkpoint proteins by ubiquitin and small ubiquitin-like modifier (SUMO) critically orchestrates the DNA damage response (DDR). The ubiquitin ligase RNF4 integrates signaling by SUMO and ubiquitin, through its selective recognition and ubiquitination of SUMO-modified proteins. Here, we define a key new determinant for target discrimination by RNF4, in addition to interaction with SUMO. We identify a nucleosome-targeting motif within the RNF4 RING domain that can bind DNA and thereby enables RNF4 to selectively ubiquitinate nucleosomal histones. Furthermore, RNF4 nucleosome-targeting is crucially required for the repair of TRF2-depleted dysfunctional telomeres by 53BP1-mediated non-homologous end joining.
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Affiliation(s)
- Lynda M Groocock
- Department of Cell and Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
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35
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Alvarez-Paggi D, Zitare U, Murgida DH. The role of protein dynamics and thermal fluctuations in regulating cytochrome c/cytochrome c oxidase electron transfer. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:1196-207. [PMID: 24502917 DOI: 10.1016/j.bbabio.2014.01.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 01/22/2014] [Accepted: 01/28/2014] [Indexed: 01/06/2023]
Abstract
In this overview we present recent combined electrochemical, spectroelectrochemical, spectroscopic and computational studies from our group on the electron transfer reactions of cytochrome c and of the primary electron acceptor of cytochrome c oxidase, the CuA site, in biomimetic complexes. Based on these results, we discuss how protein dynamics and thermal fluctuations may impact on protein ET reactions, comment on the possible physiological relevance of these results, and finally propose a regulatory mechanism that may operate in the Cyt/CcO electron transfer reaction in vivo. This article is part of a Special Issue entitled: 18th European Bioenergetic Conference.
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Affiliation(s)
- Damian Alvarez-Paggi
- INQUIMAE-CONICET, Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, pab. 2, piso 3, C1428EHA Buenos Aires, Argentina
| | - Ulises Zitare
- INQUIMAE-CONICET, Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, pab. 2, piso 3, C1428EHA Buenos Aires, Argentina
| | - Daniel H Murgida
- INQUIMAE-CONICET, Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, pab. 2, piso 3, C1428EHA Buenos Aires, Argentina.
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36
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Gu J, Yang S, Rajic AJ, Kurnikov IV, Prytkova TR, Pletneva EV. Control of cytochrome c redox reactivity through off-pathway modifications in the protein hydrogen-bonding network. Chem Commun (Camb) 2014; 50:5355-7. [DOI: 10.1039/c3cc47943a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Roberts VA, Pique ME, Ten Eyck LF, Li S. Predicting protein-DNA interactions by full search computational docking. Proteins 2013; 81:2106-18. [PMID: 23966176 PMCID: PMC4045845 DOI: 10.1002/prot.24395] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 07/31/2013] [Accepted: 08/09/2013] [Indexed: 11/06/2022]
Abstract
Protein-DNA interactions are essential for many biological processes. X-ray crystallography can provide high-resolution structures, but protein-DNA complexes are difficult to crystallize and typically contain only small DNA fragments. Thus, there is a need for computational methods that can provide useful predictions to give insights into mechanisms and guide the design of new experiments. We used the program DOT, which performs an exhaustive, rigid-body search between two macromolecules, to investigate four diverse protein-DNA interactions. Here, we compare our computational results with subsequent experimental data on related systems. In all cases, the experimental data strongly supported our structural hypotheses from the docking calculations: a mechanism for weak, nonsequence-specific DNA binding by a transcription factor, a large DNA-binding footprint on the surface of the DNA-repair enzyme uracil-DNA glycosylase (UNG), viral and host DNA-binding sites on the catalytic domain of HIV integrase, and a three-DNA-contact model of the linker histone bound to the nucleosome. In the case of UNG, the experimental design was based on the DNA-binding surface found by docking, rather than the much smaller surface observed in the crystallographic structure. These comparisons demonstrate that the DOT electrostatic energy gives a good representation of the distinctive electrostatic properties of DNA and DNA-binding proteins. The large, favourably ranked clusters resulting from the dockings identify active sites, map out large DNA-binding sites, and reveal multiple DNA contacts with a protein. Thus, computational docking can not only help to identify protein-DNA interactions in the absence of a crystal structure, but also expand structural understanding beyond known crystallographic structures.
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Affiliation(s)
- Victoria A. Roberts
- San Diego Supercomputer Center, University of California, San Diego,9500 Gilman Drive, MC 0505, La Jolla, CA 92093, USA
| | - Michael E. Pique
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Lynn F. Ten Eyck
- San Diego Supercomputer Center, University of California, San Diego,9500 Gilman Drive, MC 0505, La Jolla, CA 92093, USA
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Sheng Li
- School of Medicine, University of California, San Diego, 9500 Gilman Drive, MC 0602, La Jolla, CA 92093, USA
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38
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Buhrow L, Hiser C, Van Voorst JR, Ferguson-Miller S, Kuhn LA. Computational prediction and in vitro analysis of potential physiological ligands of the bile acid binding site in cytochrome c oxidase. Biochemistry 2013; 52:6995-7006. [PMID: 24073649 DOI: 10.1021/bi400674h] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
A conserved bile acid site has been crystallographically defined in the membrane domain of mammalian and Rhodobacter sphaeroides cytochrome c oxidase (RsCcO). Diverse amphipathic ligands were shown previously to bind to this site and affect the electron transfer equilibrium between heme a and a3 cofactors by blocking the K proton uptake path. Current studies identify physiologically relevant ligands for the bile acid site using a novel three-pronged computational approach: ROCS comparison of ligand shape and electrostatics, SimSite3D comparison of ligand binding site features, and SLIDE screening of potential ligands by docking. Identified candidate ligands include steroids, nicotinamides, flavins, nucleotides, retinoic acid, and thyroid hormones, which are predicted to make key protein contacts with the residues involved in bile acid binding. In vitro oxygen consumption and ligand competition assays on RsCcO wildtype and its Glu101Ala mutant support regulatory activity and specificity of some of these ligands. An ATP analog and GDP inhibit RsCcO under low substrate conditions, while fusidic acid, cholesteryl hemisuccinate, retinoic acid, and T3 thyroid hormone are more potent inhibitors under both high and low substrate conditions. The sigmoidal kinetics of RsCcO inhibition in the presence of certain nucleotides is reminiscent of previously reported ATP inhibition of mammalian CcO, suggesting regulation involving the conserved core subunits of both mammalian and bacterial oxidases. Ligand binding to the bile acid site is noncompetitive with respect to cytochrome c and appears to arrest CcO in a semioxidized state with some resemblance to the "resting" state of the enzyme.
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Affiliation(s)
- Leann Buhrow
- Departments of Biochemistry and Molecular Biology and ¶Computer Science & Engineering, Michigan State University , East Lansing, Michigan 48824, United States
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39
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Chaves RC, Pellequer JL. DockAFM: benchmarking protein structures by docking under AFM topographs. ACTA ACUST UNITED AC 2013; 29:3230-1. [PMID: 24078683 DOI: 10.1093/bioinformatics/btt561] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
UNLABELLED Proteins can adopt a variety of conformations. We present a simple server for scoring the agreement between 3D atomic structures and experimental envelopes obtained by atomic force microscopy. Three different structures of immunoglobulins (IgG) or blood coagulation factor V activated were tested and their agreement with several topographical surfaces was computed. This approach can be used to test structural variability within a family of proteins. AVAILABILITY AND IMPLEMENTATION DockAFM is available at http://biodev.cea.fr/dockafm.
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Affiliation(s)
- Rui C Chaves
- CEA, iBEB, Service de Biochimie et Toxicologie Nucléaire, F-30207 Bagnols sur Cèze, France
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40
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Roberts VA, Thompson EE, Pique ME, Perez MS, Ten Eyck LF. DOT2: Macromolecular docking with improved biophysical models. J Comput Chem 2013; 34:1743-58. [PMID: 23695987 PMCID: PMC4370774 DOI: 10.1002/jcc.23304] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Revised: 02/20/2013] [Accepted: 04/07/2013] [Indexed: 12/11/2022]
Abstract
Computational docking is a useful tool for predicting macromolecular complexes, which are often difficult to determine experimentally. Here, we present the DOT2 software suite, an updated version of the DOT intermolecular docking program. DOT2 provides straightforward, automated construction of improved biophysical models based on molecular coordinates, offering checkpoints that guide the user to include critical features. DOT has been updated to run more quickly, allow flexibility in grid size and spacing, and generate an infinitive complete list of favorable candidate configurations. Output can be filtered by experimental data and rescored by the sum of electrostatic and atomic desolvation energies. We show that this rescoring method improves the ranking of correct complexes for a wide range of macromolecular interactions and demonstrate that biologically relevant models are essential for biologically relevant results. The flexibility and versatility of DOT2 accommodate realistic models of complex biological systems, improving the likelihood of a successful docking outcome.
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Affiliation(s)
- Victoria A Roberts
- San Diego Supercomputer Center, University of California, San Diego, La Jolla, California 92093, USA.
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41
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Hall A, Larsen AK, Parhamifar L, Meyle KD, Wu LP, Moghimi SM. High resolution respirometry analysis of polyethylenimine-mediated mitochondrial energy crisis and cellular stress: Mitochondrial proton leak and inhibition of the electron transport system. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:1213-25. [PMID: 23850549 DOI: 10.1016/j.bbabio.2013.07.001] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 06/07/2013] [Accepted: 07/02/2013] [Indexed: 01/09/2023]
Abstract
Polyethylenimines (PEIs) are highly efficient non-viral transfectants, but can induce cell death through poorly understood necrotic and apoptotic processes as well as autophagy. Through high resolution respirometry studies in H1299 cells we demonstrate that the 25kDa branched polyethylenimine (25k-PEI-B), in a concentration and time-dependent manner, facilitates mitochondrial proton leak and inhibits the electron transport system. These events were associated with gradual reduction of the mitochondrial membrane potential and mitochondrial ATP synthesis. The intracellular ATP levels further declined as a consequence of PEI-mediated plasma membrane damage and subsequent ATP leakage to the extracellular medium. Studies with freshly isolated mouse liver mitochondria corroborated with bioenergetic findings and demonstrated parallel polycation concentration- and time-dependent changes in state 2 and state 4o oxygen flux as well as lowered ADP phosphorylation (state 3) and mitochondrial ATP synthesis. Polycation-mediated reduction of electron transport system activity was further demonstrated in 'broken mitochondria' (freeze-thawed mitochondrial preparations). Moreover, by using both high-resolution respirometry and spectrophotometry analysis of cytochrome c oxidase activity we were able to identify complex IV (cytochrome c oxidase) as a likely specific site of PEI mediated inhibition within the electron transport system. Unraveling the mechanisms of PEI-mediated mitochondrial energy crisis is central for combinatorial design of safer polymeric non-viral gene delivery systems.
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Affiliation(s)
- Arnaldur Hall
- Centre for Pharmaceutical Nanotechnology and Nanotoxicology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen Ø, Denmark
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42
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Alvarez-Paggi D, Meister W, Kuhlmann U, Weidinger I, Tenger K, Zimányi L, Rákhely G, Hildebrandt P, Murgida DH. Disentangling Electron Tunneling and Protein Dynamics of Cytochrome c through a Rationally Designed Surface Mutation. J Phys Chem B 2013; 117:6061-8. [DOI: 10.1021/jp400832m] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Damián Alvarez-Paggi
- INQUIMAE-CONICET and Departamento
de Química Inorgánica, Analítica y Química
Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria,
pab. 2, piso 3, C1428EHA-Buenos Aires, Argentina
| | - Wiebke Meister
- Institut für Chemie, Technische Universität Berlin, Strasse des 17.
Juni 135, Sekr. PC14, D-10623-Berlin, Germany
| | - Uwe Kuhlmann
- Institut für Chemie, Technische Universität Berlin, Strasse des 17.
Juni 135, Sekr. PC14, D-10623-Berlin, Germany
| | - Inez Weidinger
- Institut für Chemie, Technische Universität Berlin, Strasse des 17.
Juni 135, Sekr. PC14, D-10623-Berlin, Germany
| | - Katalin Tenger
- Biological Research Center, Institute of Biophysics, H-6726 Szeged, Temesvári
krt. 62, Hungary
| | - László Zimányi
- Biological Research Center, Institute of Biophysics, H-6726 Szeged, Temesvári
krt. 62, Hungary
| | - Gábor Rákhely
- Department
of Biotechnology, University of Szeged,
H-6726, Közép fasor
52, Hungary
| | - Peter Hildebrandt
- Institut für Chemie, Technische Universität Berlin, Strasse des 17.
Juni 135, Sekr. PC14, D-10623-Berlin, Germany
| | - Daniel H. Murgida
- INQUIMAE-CONICET and Departamento
de Química Inorgánica, Analítica y Química
Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria,
pab. 2, piso 3, C1428EHA-Buenos Aires, Argentina
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43
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Ashe D, Alleyne T, Sampson V. Substrate binding-dissociation and intermolecular electron transfer in cytochrome c oxidase are driven by energy-dependent conformational changes in the enzyme and substrate. Biotechnol Appl Biochem 2013; 59:213-22. [PMID: 23586831 DOI: 10.1002/bab.1015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Accepted: 02/23/2012] [Indexed: 12/21/2022]
Abstract
Reduction of O₂ by cytochrome c oxidase (COX) is critical to the cellular production of adenosine-5'-triphosphate; COX obtains the four electrons required for this process from ferrocytochrome c. The COX-cytochrome c enzyme-substrate complex is stabilized by electrostatic interactions via carboxylates on COX and lysines on cytochrome c. Conformational changes are believed to play a role in ferrocytochrome c oxidation and release and in rapid intramolecular transfer of electrons within COX, but the details are unclear. To gather specific information about the extent and relevance of conformational changes, we performed bioinformatics studies using the published structures of both proteins. For both proteins, we studied the surface accessibility and energy, as a function of the proteins' oxidation state. The residues of reduced cytochrome c showed greater surface accessibility and were at a higher energy than those of the oxidized cytochrome c. Also, most residues of the core subunits (I, II, and III) of COX showed low accessibility, ∼35%, and compared to the oxidized subunits, the reduced subunits had higher energies. We concluded that substrate binding and dissociation is modulated by specific redox-dependent conformational changes. We further conclude that high energy and structural relaxation of reduced cytochrome c and core COX subunits drive their rapid electron transfer.
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Affiliation(s)
- Damian Ashe
- Department of Preclinical Sciences, Biochemistry Unit, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Trinidad, West Indies
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44
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Alvarez-Paggi D, Castro MA, Tórtora V, Castro L, Radi R, Murgida DH. Electrostatically Driven Second-Sphere Ligand Switch between High and Low Reorganization Energy Forms of Native Cytochrome c. J Am Chem Soc 2013; 135:4389-97. [DOI: 10.1021/ja311786b] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Damián Alvarez-Paggi
- Departamento
de Química Inorgánica, Analítica y Química
Física and ‡INQUIMAE (CONICET-UBA), Facultad de Ciencias Exactas
y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, piso 1, C1428EHA-Buenos Aires, Argentina
- Departamento
de Bioquímica and ⊥Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - María A. Castro
- Departamento
de Química Inorgánica, Analítica y Química
Física and ‡INQUIMAE (CONICET-UBA), Facultad de Ciencias Exactas
y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, piso 1, C1428EHA-Buenos Aires, Argentina
- Departamento
de Bioquímica and ⊥Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Verónica Tórtora
- Departamento
de Química Inorgánica, Analítica y Química
Física and ‡INQUIMAE (CONICET-UBA), Facultad de Ciencias Exactas
y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, piso 1, C1428EHA-Buenos Aires, Argentina
- Departamento
de Bioquímica and ⊥Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Laura Castro
- Departamento
de Química Inorgánica, Analítica y Química
Física and ‡INQUIMAE (CONICET-UBA), Facultad de Ciencias Exactas
y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, piso 1, C1428EHA-Buenos Aires, Argentina
- Departamento
de Bioquímica and ⊥Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Rafael Radi
- Departamento
de Química Inorgánica, Analítica y Química
Física and ‡INQUIMAE (CONICET-UBA), Facultad de Ciencias Exactas
y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, piso 1, C1428EHA-Buenos Aires, Argentina
- Departamento
de Bioquímica and ⊥Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Daniel H. Murgida
- Departamento
de Química Inorgánica, Analítica y Química
Física and ‡INQUIMAE (CONICET-UBA), Facultad de Ciencias Exactas
y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, piso 1, C1428EHA-Buenos Aires, Argentina
- Departamento
de Bioquímica and ⊥Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
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45
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Buhrow L, Ferguson-Miller S, Kuhn LA. From static structure to living protein: computational analysis of cytochrome c oxidase main-chain flexibility. Biophys J 2012; 102:2158-66. [PMID: 22824280 DOI: 10.1016/j.bpj.2012.03.040] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2011] [Revised: 02/23/2012] [Accepted: 03/12/2012] [Indexed: 10/28/2022] Open
Abstract
Crystallographic structure and deuterium accessibility comparisons of CcO in different redox states have suggested conformational changes of mechanistic significance. To predict the intrinsic flexibility and low energy motions in CcO, this work has analyzed available high-resolution crystallographic structures with ProFlex and elNémo computational methods. The results identify flexible regions and potential conformational changes in CcO that correlate well with published structural and biochemical data and provide mechanistic insights. CcO is predicted to undergo rotational motions on the interior and exterior of the membrane, driven by transmembrane helical tilting and bending, coupled with rocking of the β-sheet domain. Consequently, the proton K-pathway becomes sufficiently flexible for internal water molecules to alternately occupy upper and lower parts of the pathway, associated with conserved Thr-359 and Lys-362 residues. The D-pathway helices are found to be relatively rigid, with a highly flexible entrance region involving the subunit I C-terminus, potentially regulating the uptake of protons. Constriction and dilation of hydrophobic channels in RsCcO suggest regulation of the oxygen supply to the binuclear center. This analysis points to coupled conformational changes in CcO and their potential to influence both proton and oxygen access.
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Affiliation(s)
- Leann Buhrow
- Cell and Molecular Biology Program, Michigan State University, East Lansing, MI, USA
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46
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Volkov AN, van Nuland NAJ. Electron transfer interactome of cytochrome C. PLoS Comput Biol 2012; 8:e1002807. [PMID: 23236271 PMCID: PMC3516563 DOI: 10.1371/journal.pcbi.1002807] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Accepted: 10/12/2012] [Indexed: 01/31/2023] Open
Abstract
Lying at the heart of many vital cellular processes such as photosynthesis and respiration, biological electron transfer (ET) is mediated by transient interactions among proteins that recognize multiple binding partners. Accurate description of the ET complexes – necessary for a comprehensive understanding of the cellular signaling and metabolism – is compounded by their short lifetimes and pronounced binding promiscuity. Here, we used a computational approach relying solely on the steric properties of the individual proteins to predict the ET properties of protein complexes constituting the functional interactome of the eukaryotic cytochrome c (Cc). Cc is a small, soluble, highly-conserved electron carrier protein that coordinates the electron flow among different redox partners. In eukaryotes, Cc is a key component of the mitochondrial respiratory chain, where it shuttles electrons between its reductase and oxidase, and an essential electron donor or acceptor in a number of other redox systems. Starting from the structures of individual proteins, we performed extensive conformational sampling of the ET-competent binding geometries, which allowed mapping out functional epitopes in the Cc complexes, estimating the upper limit of the ET rate in a given system, assessing ET properties of different binding stoichiometries, and gauging the effect of domain mobility on the intermolecular ET. The resulting picture of the Cc interactome 1) reveals that most ET-competent binding geometries are located in electrostatically favorable regions, 2) indicates that the ET can take place from more than one protein-protein orientation, and 3) suggests that protein dynamics within redox complexes, and not the electron tunneling event itself, is the rate-limiting step in the intermolecular ET. Further, we show that the functional epitope size correlates with the extent of dynamics in the Cc complexes and thus can be used as a diagnostic tool for protein mobility. A number of vital cellular processes such as respiration, photosynthesis, and multifarious metabolic conversions rely on a long-range electron transfer (ET) among protein molecules. Full understanding of the biological ET requires accurate description of the redox protein complexes, which is hampered by their pronounced mobility and short lifetimes. Here we used a simple computational approach to predict the ET properties of the physiological protein complexes of cytochrome c (Cc) – a small electron carrier that coordinates the electron flow among different redox partners. By performing extensive conformational sampling of the possible binding geometries, we mapped out functional epitopes in the Cc complexes and assessed their ET properties. Our study suggests that protein dynamics within redox complexes is the rate-limiting step in the intermolecular ET and indicates that the functional epitope size correlates with the extent of dynamics in the Cc complexes. We believe that the latter finding can be used as a diagnostic tool for protein mobility and expect that this work will engender future studies of the intermolecular ET in biological networks.
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Affiliation(s)
- Alexander N Volkov
- Jean Jeener NMR Centre, Structural Biology Brussels, Vrije Universiteit Brussel, Belgium.
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47
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Limbo O, Moiani D, Kertokalio A, Wyman C, Tainer JA, Russell P. Mre11 ATLD17/18 mutation retains Tel1/ATM activity but blocks DNA double-strand break repair. Nucleic Acids Res 2012; 40:11435-49. [PMID: 23080121 PMCID: PMC3526295 DOI: 10.1093/nar/gks954] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The Mre11 complex (Mre11-Rad50-Nbs1 or MRN) binds double-strand breaks where it interacts with CtIP/Ctp1/Sae2 and ATM/Tel1 to preserve genome stability through its functions in homology-directed repair, checkpoint signaling and telomere maintenance. Here, we combine biochemical, structural and in vivo functional studies to uncover key properties of Mre11-W243R, a mutation identified in two pediatric cancer patients with enhanced ataxia telangiectasia-like disorder. Purified human Mre11-W243R retains nuclease and DNA binding activities in vitro. X-ray crystallography of Pyrococcus furiosus Mre11 indicates that an analogous mutation leaves the overall Mre11 three-dimensional structure and nuclease sites intact but disorders surface loops expected to regulate DNA and Rad50 interactions. The equivalent W248R allele in fission yeast allows Mre11 to form an MRN complex that efficiently binds double-strand breaks, activates Tel1/ATM and maintains telomeres; yet, it causes hypersensitivity to ionizing radiation and collapsed replication forks, increased Rad52 foci, defective Chk1 signaling and meiotic failure. W248R differs from other ataxia telangiectasia-like disorder analog alleles by the reduced stability of its interaction with Rad50 in cell lysates. Collective results suggest a separation-of-function mutation that disturbs interactions amongst the MRN subunits and Ctp1 required for DNA end processing in vivo but maintains interactions sufficient for Tel1/ATM checkpoint and telomere maintenance functions.
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Affiliation(s)
- Oliver Limbo
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Rd., La Jolla, CA 92037, USA
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48
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Lyons JA, Aragão D, Slattery O, Pisliakov AV, Soulimane T, Caffrey M. Structural insights into electron transfer in caa3-type cytochrome oxidase. Nature 2012; 487:514-8. [PMID: 22763450 PMCID: PMC3428721 DOI: 10.1038/nature11182] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Accepted: 05/04/2012] [Indexed: 11/30/2022]
Abstract
Cytochrome c oxidase is a member of the heme copper oxidase superfamily (HCO)1. HCOs function as the terminal enzymes in the respiratory chain of mitochondria and aerobic prokaryotes, coupling molecular oxygen reduction to transmembrane proton pumping. Integral to the enzyme’s function is the transfer of electrons from cytochrome c to the oxidase via a transient association of the two proteins. Electron entry and exit are proposed to occur from the same site on cytochrome c2–4. Here we report the crystal structure of the caa3-type cytochrome oxidase from Thermus thermophilus, which has a covalently tethered cytochrome c domain. Crystals were grown in a bicontinuous mesophase using a synthetic short-chain monoacylglycerol as the hosting lipid. From the electron density map, at 2.36 Å resolution, a novel integral membrane subunit and a native glycoglycerophospholipid embedded in the complex were identified. Contrary to previous electron transfer mechanisms observed for soluble cytochrome c, the structure reveals the architecture of the electron transfer complex for the fused cupredoxin/cytochrome c domain which implicates different sites on cytochrome c for electron entry and exit. Support for an alternative to the classical proton gate characteristic of this HCO class is presented.
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Affiliation(s)
- Joseph A Lyons
- Department of Chemical and Environmental Sciences, University of Limerick, Limerick, Ireland
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49
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Lin MT, Gennis RB. Product-controlled steady-state kinetics between cytochrome aa(3) from Rhodobacter sphaeroides and equine ferrocytochrome c analyzed by a novel spectrophotometric approach. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:1894-900. [PMID: 22516686 DOI: 10.1016/j.bbabio.2012.04.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Revised: 03/30/2012] [Accepted: 04/02/2012] [Indexed: 11/29/2022]
Abstract
Cytochrome c oxidase (CcO) catalyzes the reduction of molecular oxygen to water using ferrocytochrome c (cyt c(2+)) as the electron donor. In this study, the oxidation of horse cyt c(2+) by CcO from Rhodobacter sphaeroides, was monitored using stopped-flow spectrophotometry. A novel analytic procedure was applied in which the spectra were deconvoluted into the reduced and oxidized forms of cyt c by a least-squares fitting method, yielding the reaction rates at various concentrations of cyt c(2+) and cyt c(3+). This allowed an analysis of the effects of cyt c(3+) on the steady-state kinetics between CcO and cyt c(2+). The results show that cyt c(3+) exhibits product inhibition by two mechanisms: competition with cyt c(2+) at the catalytic site and, in addition, an interaction at a second site which further modulates the reaction of cyt c(2+) at the catalytic site. These results are generally consistent with previous reports, indicating the reliability of the new procedure. We also find that a 6×His-tag at the C-terminus of the subunit II of CcO affects the binding of cyt c at both sites. The approach presented here should be generally useful in spectrophotometric studies of complex enzyme kinetics. This article is part of a Special Issue entitled: 17th European Bioenergetics Conference (EBEC 2012).
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Affiliation(s)
- Myat T Lin
- Center for Biophysics and Computational Biology, University of Illinois, Urbana, IL 61801, USA
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50
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Hüttemann M, Helling S, Sanderson TH, Sinkler C, Samavati L, Mahapatra G, Varughese A, Lu G, Liu J, Ramzan R, Vogt S, Grossman LI, Doan JW, Marcus K, Lee I. Regulation of mitochondrial respiration and apoptosis through cell signaling: cytochrome c oxidase and cytochrome c in ischemia/reperfusion injury and inflammation. BIOCHIMICA ET BIOPHYSICA ACTA 2012; 1817:598-609. [PMID: 21771582 PMCID: PMC3229836 DOI: 10.1016/j.bbabio.2011.07.001] [Citation(s) in RCA: 194] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Revised: 06/30/2011] [Accepted: 07/01/2011] [Indexed: 01/09/2023]
Abstract
Cytochrome c (Cytc) and cytochrome c oxidase (COX) catalyze the terminal reaction of the mitochondrial electron transport chain (ETC), the reduction of oxygen to water. This irreversible step is highly regulated, as indicated by the presence of tissue-specific and developmentally expressed isoforms, allosteric regulation, and reversible phosphorylations, which are found in both Cytc and COX. The crucial role of the ETC in health and disease is obvious since it, together with ATP synthase, provides the vast majority of cellular energy, which drives all cellular processes. However, under conditions of stress, the ETC generates reactive oxygen species (ROS), which cause cell damage and trigger death processes. We here discuss current knowledge of the regulation of Cytc and COX with a focus on cell signaling pathways, including cAMP/protein kinase A and tyrosine kinase signaling. Based on the crystal structures we highlight all identified phosphorylation sites on Cytc and COX, and we present a new phosphorylation site, Ser126 on COX subunit II. We conclude with a model that links cell signaling with the phosphorylation state of Cytc and COX. This in turn regulates their enzymatic activities, the mitochondrial membrane potential, and the production of ATP and ROS. Our model is discussed through two distinct human pathologies, acute inflammation as seen in sepsis, where phosphorylation leads to strong COX inhibition followed by energy depletion, and ischemia/reperfusion injury, where hyperactive ETC complexes generate pathologically high mitochondrial membrane potentials, leading to excessive ROS production. Although operating at opposite poles of the ETC activity spectrum, both conditions can lead to cell death through energy deprivation or ROS-triggered apoptosis.
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Affiliation(s)
- Maik Hüttemann
- Wayne State University School of Medicine, Detroit, MI 48201, USA.
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