1
|
Rousseau DL, Ishigami I, Yeh SR. Structural and functional mechanisms of cytochrome c oxidase. J Inorg Biochem 2024; 262:112730. [PMID: 39276716 DOI: 10.1016/j.jinorgbio.2024.112730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2024] [Revised: 08/20/2024] [Accepted: 09/06/2024] [Indexed: 09/17/2024]
Abstract
Cytochrome c oxidase (CcO) is the terminal enzyme in the electron transfer chain in mitochondria. It catalyzes the four-electron reduction of O2 to H2O and harnesses the redox energy to drive unidirectional proton translocation against a proton electrochemical gradient. A great deal of research has been conducted to comprehend the molecular properties of CcO. However, the mechanism by which the oxygen reduction reaction is coupled to proton translocation remains poorly understood. Here, we review the chemical properties of a variety of key oxygen intermediates of bovine CcO (bCcO) revealed by time-resolved resonance Raman spectroscopy and the structural features of the enzyme uncovered by serial femtosecond crystallography, an innovative technique that allows structural determination at room temperature without radiation damage. The implications of these data on the proton translocation mechanism are discussed.
Collapse
Affiliation(s)
- Denis L Rousseau
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| | - Izumi Ishigami
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Syun-Ru Yeh
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| |
Collapse
|
2
|
Kariev AM, Green ME. Water, Protons, and the Gating of Voltage-Gated Potassium Channels. MEMBRANES 2024; 14:37. [PMID: 38392664 PMCID: PMC10890431 DOI: 10.3390/membranes14020037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/17/2024] [Accepted: 01/23/2024] [Indexed: 02/24/2024]
Abstract
Ion channels are ubiquitous throughout all forms of life. Potassium channels are even found in viruses. Every cell must communicate with its surroundings, so all cells have them, and excitable cells, in particular, especially nerve cells, depend on the behavior of these channels. Every channel must be open at the appropriate time, and only then, so that each channel opens in response to the stimulus that tells that channel to open. One set of channels, including those in nerve cells, responds to voltage. There is a standard model for the gating of these channels that has a section of the protein moving in response to the voltage. However, there is evidence that protons are moving, rather than protein. Water is critical as part of the gating process, although it is hard to see how this works in the standard model. Here, we review the extensive evidence of the importance of the role of water and protons in gating these channels. Our principal example, but by no means the only example, will be the Kv1.2 channel. Evidence comes from the effects of D2O, from mutations in the voltage sensing domain, as well as in the linker between that domain and the gate, and at the gate itself. There is additional evidence from computations, especially quantum calculations. Structural evidence comes from X-ray studies. The hydration of ions is critical in the transfer of ions in constricted spaces, such as the gate region and the pore of a channel; we will see how the structure of the hydrated ion fits with the structure of the channel. In addition, there is macroscopic evidence from osmotic experiments and streaming current measurements. The combined evidence is discussed in the context of a model that emphasizes the role of protons and water in gating these channels.
Collapse
Affiliation(s)
- Alisher M Kariev
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY 10031, USA
| | - Michael E Green
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY 10031, USA
| |
Collapse
|
3
|
Ishigami I, Sierra RG, Su Z, Peck A, Wang C, Poitevin F, Lisova S, Hayes B, Moss FR, Boutet S, Sublett RE, Yoon CH, Yeh SR, Rousseau DL. Structural insights into functional properties of the oxidized form of cytochrome c oxidase. Nat Commun 2023; 14:5752. [PMID: 37717031 PMCID: PMC10505203 DOI: 10.1038/s41467-023-41533-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 09/07/2023] [Indexed: 09/18/2023] Open
Abstract
Cytochrome c oxidase (CcO) is an essential enzyme in mitochondrial and bacterial respiration. It catalyzes the four-electron reduction of molecular oxygen to water and harnesses the chemical energy to translocate four protons across biological membranes. The turnover of the CcO reaction involves an oxidative phase, in which the reduced enzyme (R) is oxidized to the metastable OH state, and a reductive phase, in which OH is reduced back to the R state. During each phase, two protons are translocated across the membrane. However, if OH is allowed to relax to the resting oxidized state (O), a redox equivalent to OH, its subsequent reduction to R is incapable of driving proton translocation. Here, with resonance Raman spectroscopy and serial femtosecond X-ray crystallography (SFX), we show that the heme a3 iron and CuB in the active site of the O state, like those in the OH state, are coordinated by a hydroxide ion and a water molecule, respectively. However, Y244, critical for the oxygen reduction chemistry, is in the neutral protonated form, which distinguishes O from OH, where Y244 is in the deprotonated tyrosinate form. These structural characteristics of O provide insights into the proton translocation mechanism of CcO.
Collapse
Affiliation(s)
- Izumi Ishigami
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Raymond G Sierra
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Zhen Su
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
- Department of Applied Physics, Stanford University, Stanford, CA, 94305, USA
| | - Ariana Peck
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Cong Wang
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Frederic Poitevin
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Stella Lisova
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Brandon Hayes
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Frank R Moss
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
- Altos Labs, Redwood City, CA, 94065, USA
| | - Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Robert E Sublett
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Chun Hong Yoon
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Syun-Ru Yeh
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
| | - Denis L Rousseau
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
| |
Collapse
|
4
|
Luo W, Wu S, Jiang Y, Xu P, Zou J, Qian J, Zhou X, Ge Y, Nie H, Yang Z. Efficient Electrocatalytic Nitrate Reduction to Ammonia Based on DNA-Templated Copper Nanoclusters. ACS APPLIED MATERIALS & INTERFACES 2023; 15:18928-18939. [PMID: 37014152 DOI: 10.1021/acsami.3c00511] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
In alkaline solutions, the electrocatalytic conversion of nitrates to ammonia (NH3) (NO3RR) is hindered by the sluggish hydrogenation step due to the lack of protons on the electrode surface, making it a grand challenge to synthesize NH3 at a high rate and selectivity. Herein, single-stranded deoxyribonucleic acid (ssDNA)-templated copper nanoclusters (CuNCs) were synthesized for the electrocatalytic production of NH3. Because ssDNA was involved in the optimization of the interfacial water distribution and H-bond network connectivity, the water-electrolysis-induced proton generation was enhanced on the electrode surface, which facilitated the NO3RR kinetics. The activation energy (Ea) and in situ spectroscopy studies adequately demonstrated that the NO3RR was exothermic until NH3 desorption, indicating that, in alkaline media, the NO3RR catalyzed by ssDNA-templated CuNCs followed the same reaction path as the NO3RR in acidic media. Electrocatalytic tests further verified the efficiency of ssDNA-templated CuNCs, which achieved a high NH3 yield rate of 2.62 mg h-1 cm-2 and a Faraday efficiency of 96.8% at -0.6 V vs reversible hydrogen electrode. The results of this study lay the foundation for engineering catalyst surface ligands for the electrocatalytic NO3RR.
Collapse
Affiliation(s)
- Wenjie Luo
- Key Laboratory of Carbon Materials of Zhejiang Province, Wenzhou University, Wenzhou 325035, China
| | - Shilu Wu
- Key Laboratory of Carbon Materials of Zhejiang Province, Wenzhou University, Wenzhou 325035, China
| | - Yingyang Jiang
- Key Laboratory of Carbon Materials of Zhejiang Province, Wenzhou University, Wenzhou 325035, China
| | - Peng Xu
- Key Laboratory of Carbon Materials of Zhejiang Province, Wenzhou University, Wenzhou 325035, China
| | - Jinxuan Zou
- Key Laboratory of Carbon Materials of Zhejiang Province, Wenzhou University, Wenzhou 325035, China
| | - Jinjie Qian
- Key Laboratory of Carbon Materials of Zhejiang Province, Wenzhou University, Wenzhou 325035, China
| | - Xuemei Zhou
- Key Laboratory of Carbon Materials of Zhejiang Province, Wenzhou University, Wenzhou 325035, China
| | - Yongjie Ge
- Key Laboratory of Carbon Materials of Zhejiang Province, Wenzhou University, Wenzhou 325035, China
| | - Huagui Nie
- Key Laboratory of Carbon Materials of Zhejiang Province, Wenzhou University, Wenzhou 325035, China
| | - Zhi Yang
- Key Laboratory of Carbon Materials of Zhejiang Province, Wenzhou University, Wenzhou 325035, China
| |
Collapse
|
5
|
Ishigami I, Sierra RG, Su Z, Peck A, Wang C, Poitevin F, Lisova S, Hayes B, Moss FR, Boutet S, Sublett RE, Yoon CH, Yeh SR, Rousseau DL. Structural basis for functional properties of cytochrome c oxidase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.20.530986. [PMID: 36993562 PMCID: PMC10055264 DOI: 10.1101/2023.03.20.530986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Cytochrome c oxidase (CcO) is an essential enzyme in mitochondrial and bacterial respiration. It catalyzes the four-electron reduction of molecular oxygen to water and harnesses the chemical energy to translocate four protons across biological membranes, thereby establishing the proton gradient required for ATP synthesis1. The full turnover of the CcO reaction involves an oxidative phase, in which the reduced enzyme (R) is oxidized by molecular oxygen to the metastable oxidized OH state, and a reductive phase, in which OH is reduced back to the R state. During each of the two phases, two protons are translocated across the membranes2. However, if OH is allowed to relax to the resting oxidized state (O), a redox equivalent to OH, its subsequent reduction to R is incapable of driving proton translocation2,3. How the O state structurally differs from OH remains an enigma in modern bioenergetics. Here, with resonance Raman spectroscopy and serial femtosecond X-ray crystallography (SFX)4, we show that the heme a3 iron and CuB in the active site of the O state, like those in the OH state5,6, are coordinated by a hydroxide ion and a water molecule, respectively. However, Y244, a residue covalently linked to one of the three CuB ligands and critical for the oxygen reduction chemistry, is in the neutral protonated form, which distinguishes O from OH, where Y244 is in the deprotonated tyrosinate form. These structural characteristics of O provide new insights into the proton translocation mechanism of CcO.
Collapse
Affiliation(s)
- Izumi Ishigami
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461 USA
| | - Raymond G. Sierra
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - Zhen Su
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
- Department of Applied Physics, Stanford University, Stanford, CA 94305 USA
| | - Ariana Peck
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - Cong Wang
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - Frederic Poitevin
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - Stella Lisova
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - Brandon Hayes
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - Frank R. Moss
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - Robert E. Sublett
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - Chun Hong Yoon
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - Syun-Ru Yeh
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461 USA
| | - Denis L. Rousseau
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461 USA
| |
Collapse
|
6
|
Enzyme-like water preorganization in a synthetic molecular cleft for homogeneous water oxidation catalysis. Nat Catal 2022. [DOI: 10.1038/s41929-022-00843-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
7
|
Saura P, Riepl D, Frey DM, Wikström M, Kaila VRI. Electric fields control water-gated proton transfer in cytochrome c oxidase. Proc Natl Acad Sci U S A 2022; 119:e2207761119. [PMID: 36095184 PMCID: PMC9499568 DOI: 10.1073/pnas.2207761119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/18/2022] [Indexed: 11/18/2022] Open
Abstract
Aerobic life is powered by membrane-bound enzymes that catalyze the transfer of electrons to oxygen and protons across a biological membrane. Cytochrome c oxidase (CcO) functions as a terminal electron acceptor in mitochondrial and bacterial respiratory chains, driving cellular respiration and transducing the free energy from O2 reduction into proton pumping. Here we show that CcO creates orientated electric fields around a nonpolar cavity next to the active site, establishing a molecular switch that directs the protons along distinct pathways. By combining large-scale quantum chemical density functional theory (DFT) calculations with hybrid quantum mechanics/molecular mechanics (QM/MM) simulations and atomistic molecular dynamics (MD) explorations, we find that reduction of the electron donor, heme a, leads to dissociation of an arginine (Arg438)-heme a3 D-propionate ion-pair. This ion-pair dissociation creates a strong electric field of up to 1 V Å-1 along a water-mediated proton array leading to a transient proton loading site (PLS) near the active site. Protonation of the PLS triggers the reduction of the active site, which in turn aligns the electric field vectors along a second, "chemical," proton pathway. We find a linear energy relationship of the proton transfer barrier with the electric field strength that explains the effectivity of the gating process. Our mechanism shows distinct similarities to principles also found in other energy-converting enzymes, suggesting that orientated electric fields generally control enzyme catalysis.
Collapse
Affiliation(s)
- Patricia Saura
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm 10691, Sweden
| | - Daniel Riepl
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm 10691, Sweden
| | - Daniel M. Frey
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm 10691, Sweden
| | - Mårten Wikström
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | - Ville R. I. Kaila
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm 10691, Sweden
| |
Collapse
|
8
|
Allgöwer F, Gamiz-Hernandez AP, Rutherford AW, Kaila VRI. Molecular Principles of Redox-Coupled Protonation Dynamics in Photosystem II. J Am Chem Soc 2022; 144:7171-7180. [PMID: 35421304 PMCID: PMC9052759 DOI: 10.1021/jacs.1c13041] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Photosystem II (PSII) catalyzes light-driven water oxidization, releasing O2 into the atmosphere and transferring the electrons for the synthesis of biomass. However, despite decades of structural and functional studies, the water oxidation mechanism of PSII has remained puzzling and a major challenge for modern chemical research. Here, we show that PSII catalyzes redox-triggered proton transfer between its oxygen-evolving Mn4O5Ca cluster and a nearby cluster of conserved buried ion-pairs, which are connected to the bulk solvent via a proton pathway. By using multi-scale quantum and classical simulations, we find that oxidation of a redox-active Tyrz (Tyr161) lowers the reaction barrier for the water-mediated proton transfer from a Ca2+-bound water molecule (W3) to Asp61 via conformational changes in a nearby ion-pair (Asp61/Lys317). Deprotonation of this W3 substrate water triggers its migration toward Mn1 to a position identified in recent X-ray free-electron laser (XFEL) experiments [Ibrahim et al. Proc. Natl. Acad. Sci. USA 2020, 117, 12,624-12,635]. Further oxidation of the Mn4O5Ca cluster lowers the proton transfer barrier through the water ligand sphere of the Mn4O5Ca cluster to Asp61 via a similar ion-pair dissociation process, while the resulting Mn-bound oxo/oxyl species leads to O2 formation by a radical coupling mechanism. The proposed redox-coupled protonation mechanism shows a striking resemblance to functional motifs in other enzymes involved in biological energy conversion, with an interplay between hydration changes, ion-pair dynamics, and electric fields that modulate the catalytic barriers.
Collapse
Affiliation(s)
- Friederike Allgöwer
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden
| | - Ana P Gamiz-Hernandez
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden
| | - A William Rutherford
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Ville R I Kaila
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden
| |
Collapse
|
9
|
Yu L, Lin Z, Cheng X, Chu J, Li X, Chen C, Zhu T, Li W, Lin W, Tang W. Thorium inhibits human respiratory chain complex IV (cytochrome c oxidase). JOURNAL OF HAZARDOUS MATERIALS 2022; 424:127546. [PMID: 34879532 DOI: 10.1016/j.jhazmat.2021.127546] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 10/15/2021] [Accepted: 10/15/2021] [Indexed: 06/13/2023]
Abstract
Thorium is a radioactive heavy metal and an emerging environmental pollutant. Ecological and human health risks from thorium exposure are growing with the excavation of rare earth metals and implementation of thorium-based nuclear reactors. Thorium poisoning is associated with carcinogenesis, liver impairments, and congenital anomalies. To date, the biomolecular targets that underlie thorium-induced toxicity remain unknown. Here, we used in vitro enzymatic activity assays to comprehensively evaluate the effects of thorium on the mitochondrial respiration process. Thorium was found to inhibit respiratory chain complex IV (cytochrome c oxidase) at sub-micromolar concentrations (IC50 ~ 0.4 μM, 90 μg/L). This is lower than the thorium level limit (246 μg/L) in drinking water specified by the World Health Organization. The inhibitory effects were further verified in mitochondria from human bone and liver cells (thorium mainly deposits in these organs). The inhibition of cytochrome c oxidase can readily rationalize well-documented cellular toxicities of thorium, such as alteration of mitochondrial membrane potential and production of reactive oxygen species. Therefore, cytochrome c oxidase is potentially a key molecular target underlying thorium-induced toxicological effect.
Collapse
Affiliation(s)
- Libing Yu
- Institute of Materials, China Academy of Engineering Physics, Mianyang 621907, China.
| | - Zhaozhu Lin
- Department of Pathogen Biology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Xuedan Cheng
- Institute of Materials, China Academy of Engineering Physics, Mianyang 621907, China; School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621010, China
| | - Jian Chu
- Institute of Materials, China Academy of Engineering Physics, Mianyang 621907, China
| | - Xijian Li
- Institute of Materials, China Academy of Engineering Physics, Mianyang 621907, China
| | - Chun Chen
- Institute of Materials, China Academy of Engineering Physics, Mianyang 621907, China
| | - Tinghua Zhu
- Guizhou Shengyada Biotech Co., Ltd., Guiyang 550000, China
| | - Wenjing Li
- Institute of Materials, China Academy of Engineering Physics, Mianyang 621907, China; School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621010, China
| | - Wei Lin
- Department of Pathogen Biology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China.
| | - Wei Tang
- Institute of Materials, China Academy of Engineering Physics, Mianyang 621907, China.
| |
Collapse
|
10
|
Li X, Lv B, Zhang X, Jin X, Guo K, Zhou D, Bian H, Zhang W, Apfel U, Cao R. Introducing Water‐Network‐Assisted Proton Transfer for Boosted Electrocatalytic Hydrogen Evolution with Cobalt Corrole. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202114310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Xialiang Li
- Key Laboratory of Applied Surface and Colloid Chemistry Ministry of Education School of Chemistry and Chemical Engineering Shaanxi Normal University Xi'an 710119 China
| | - Bin Lv
- Key Laboratory of Applied Surface and Colloid Chemistry Ministry of Education School of Chemistry and Chemical Engineering Shaanxi Normal University Xi'an 710119 China
| | - Xue‐Peng Zhang
- Key Laboratory of Applied Surface and Colloid Chemistry Ministry of Education School of Chemistry and Chemical Engineering Shaanxi Normal University Xi'an 710119 China
| | - Xiaotong Jin
- Key Laboratory of Applied Surface and Colloid Chemistry Ministry of Education School of Chemistry and Chemical Engineering Shaanxi Normal University Xi'an 710119 China
| | - Kai Guo
- Key Laboratory of Applied Surface and Colloid Chemistry Ministry of Education School of Chemistry and Chemical Engineering Shaanxi Normal University Xi'an 710119 China
| | - Dexia Zhou
- Key Laboratory of Applied Surface and Colloid Chemistry Ministry of Education School of Chemistry and Chemical Engineering Shaanxi Normal University Xi'an 710119 China
| | - Hongtao Bian
- Key Laboratory of Applied Surface and Colloid Chemistry Ministry of Education School of Chemistry and Chemical Engineering Shaanxi Normal University Xi'an 710119 China
| | - Wei Zhang
- Key Laboratory of Applied Surface and Colloid Chemistry Ministry of Education School of Chemistry and Chemical Engineering Shaanxi Normal University Xi'an 710119 China
| | - Ulf‐Peter Apfel
- Ruhr-Universität Bochum Fakultät für Chemie und Biochemie Anorganische Chemie I Universitätsstrasse 150 44801 Bochum Germany
- Fraunhofer UMSICHT Osterfelder Strasse 3 46047 Oberhausen Germany
| | - Rui Cao
- Key Laboratory of Applied Surface and Colloid Chemistry Ministry of Education School of Chemistry and Chemical Engineering Shaanxi Normal University Xi'an 710119 China
| |
Collapse
|
11
|
Li X, Lv B, Zhang XP, Jin X, Guo K, Zhou D, Bian H, Zhang W, Apfel UP, Cao R. Introducing Water-Network-Assisted Proton Transfer for Boosted Electrocatalytic Hydrogen Evolution with Cobalt Corrole. Angew Chem Int Ed Engl 2021; 61:e202114310. [PMID: 34913230 DOI: 10.1002/anie.202114310] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Indexed: 11/10/2022]
Abstract
Proton transfer is vital for many biological and chemical reactions. Hydrogen-bonded water-containing networks are often found in enzymes to assist proton transfer, but similar strategy has been rarely presented by synthetic catalysts. We herein report the Co corrole 1 with an appended crown ether unit and its boosted activity for the hydrogen evolution reaction (HER). Crystallographic and 1H NMR studies proved that the crown ether of 1 can grab water via hydrogen bonds. By using protic acids as proton sources, the HER activity of 1 was largely boosted with added water, while the activity of crown-ether-free analogues showed very small enhancement. Inhibition studies by adding (1) external 18-crown-6-ether to extract water molecules and (2) potassium ion or N-benzyl-n-butylamine to block the crown ether of 1 further confirmed its critical role in assisting proton transfer via grabbed water molecules. This work presents a synthetic example to boost HER through water-containing networks.
Collapse
Affiliation(s)
- Xialiang Li
- Shaanxi Normal University, School of Chemistry and Chemical Engineering, CHINA
| | - Bin Lv
- Shaanxi Normal University, School of Chemistry and Chemical Engineering, CHINA
| | - Xue-Peng Zhang
- Shaanxi Normal University, School of Chemistry and Chemical Engineering, CHINA
| | - Xiaotong Jin
- Shaanxi Normal University, School of Chemistry and Chemical Engineering, CHINA
| | - Kai Guo
- shaanxi normal university, School of Chemistry and Chemical Engineering, CHINA
| | - Dexia Zhou
- Shaanxi Normal University, School of Chemistry and Chemical Engineering, CHINA
| | - Hongtao Bian
- Shaanxi Normal University, School of Chemistry and Chemical Engineering, CHINA
| | - Wei Zhang
- Shaanxi Normal University, School of Chemistry and Chemical Engineering, CHINA
| | - Ulf-Peter Apfel
- Ruhr-Universität Bochum: Ruhr-Universitat Bochum, Fakultät fur Chemie und Biochemie, GERMANY
| | - Rui Cao
- Shaanxi Normal University, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Chang'an Campus, Number 620 West Chang'an Avenue, Chang'an District, 710119, Xi'an, CHINA
| |
Collapse
|
12
|
Dragelj J, Mroginski MA, Knapp EW. Beating Heart of Cytochrome c Oxidase: The Shared Proton of Heme a3 Propionates. J Phys Chem B 2021; 125:9668-9677. [PMID: 34427096 DOI: 10.1021/acs.jpcb.1c03619] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Cytochrome c oxidase (CcO) pumps protons from the N-side to the P-side and consumes electrons from the P-side of the mitochondrial membrane driven by energy gained from reduction of dioxygen to water. ATP synthesis uses the resulting proton gradient and electrostatic potential difference. Since the distance a proton travels through CcO is too large for a one-step transfer process, proton-loading sites (PLS) that can carry protons transiently are necessary. One specific pump-active PLS couples to the redox reaction, thus energizing the proton to move across the membrane against electric potential and proton gradient. The PLS should also prevent proton backflow. Therefore, the propionates of the two redox-active hemes in CcO were suggested as PLS candidates although, according to CcO crystal structures, none of the four propionates can be protonated on account of strong H-bonds. Here, we show that modeling the local structure around heme a3 propionates enhances significantly their capability of carrying a proton jointly. This was not possible for the propionates of heme a. The modeled structures are stable in molecular dynamics simulations (MDS) and are energetically similar to the crystal structure. Precise electrostatic energy computations of MDS data are used to estimate the pKA values of all titratable residues in CcO. For the modeled structures, the heme a3 propionates have pKA values high enough to host a proton transiently but not too high to fix the proton permanently. The change in pKA throughout the redox reaction is sufficient to push the proton to the P-side of the membrane and to provide the protons with the necessary amount of energy for ATP synthesis.
Collapse
Affiliation(s)
- Jovan Dragelj
- Freie Universität Berlin, Institute for Chemistry and Biochemistry, Fabeckstrasse 36a, 14195 Berlin, Germany.,Department of Chemistry, Technische Universität Berlin, Strasse des 17. Juni 135, 10623 Berlin, Germany
| | - Maria Andrea Mroginski
- Department of Chemistry, Technische Universität Berlin, Strasse des 17. Juni 135, 10623 Berlin, Germany
| | - Ernst Walter Knapp
- Freie Universität Berlin, Institute for Chemistry and Biochemistry, Fabeckstrasse 36a, 14195 Berlin, Germany
| |
Collapse
|
13
|
Kaur D, Khaniya U, Zhang Y, Gunner MR. Protein Motifs for Proton Transfers That Build the Transmembrane Proton Gradient. Front Chem 2021; 9:660954. [PMID: 34211960 PMCID: PMC8239185 DOI: 10.3389/fchem.2021.660954] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 05/31/2021] [Indexed: 11/13/2022] Open
Abstract
Biological membranes are barriers to polar molecules, so membrane embedded proteins control the transfers between cellular compartments. Protein controlled transport moves substrates and activates cellular signaling cascades. In addition, the electrochemical gradient across mitochondrial, bacterial and chloroplast membranes, is a key source of stored cellular energy. This is generated by electron, proton and ion transfers through proteins. The gradient is used to fuel ATP synthesis and to drive active transport. Here the mechanisms by which protons move into the buried active sites of Photosystem II (PSII), bacterial RCs (bRCs) and through the proton pumps, Bacteriorhodopsin (bR), Complex I and Cytochrome c oxidase (CcO), are reviewed. These proteins all use water filled proton transfer paths. The proton pumps, that move protons uphill from low to high concentration compartments, also utilize Proton Loading Sites (PLS), that transiently load and unload protons and gates, which block backflow of protons. PLS and gates should be synchronized so PLS proton affinity is high when the gate opens to the side with few protons and low when the path is open to the high concentration side. Proton transfer paths in the proteins we describe have different design features. Linear paths are seen with a unique entry and exit and a relatively straight path between them. Alternatively, paths can be complex with a tangle of possible routes. Likewise, PLS can be a single residue that changes protonation state or a cluster of residues with multiple charge and tautomer states.
Collapse
Affiliation(s)
- Divya Kaur
- Department of Chemistry, The Graduate Center, City University of New York, New York, NY, United States.,Department of Physics, City College of New York, New York, NY, United States
| | - Umesh Khaniya
- Department of Physics, City College of New York, New York, NY, United States.,Department of Physics, The Graduate Center, City University of New York, New York, NY, United States
| | - Yingying Zhang
- Department of Physics, City College of New York, New York, NY, United States.,Department of Physics, The Graduate Center, City University of New York, New York, NY, United States
| | - M R Gunner
- Department of Chemistry, The Graduate Center, City University of New York, New York, NY, United States.,Department of Physics, City College of New York, New York, NY, United States.,Department of Physics, The Graduate Center, City University of New York, New York, NY, United States
| |
Collapse
|
14
|
Probing the Proton-Loading Site of Cytochrome C Oxidase Using Time-Resolved Fourier Transform Infrared Spectroscopy. Molecules 2020; 25:molecules25153393. [PMID: 32727022 PMCID: PMC7435947 DOI: 10.3390/molecules25153393] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 07/21/2020] [Accepted: 07/23/2020] [Indexed: 01/08/2023] Open
Abstract
Crystal structure analyses at atomic resolution and FTIR spectroscopic studies of cytochrome c oxidase have yet not revealed protonation or deprotonation of key sites of proton transfer in a time-resolved mode. Here, a sensitive technique to detect protolytic transitions is employed. In this work, probing a proton-loading site of cytochrome c oxidase from Paracoccus denitrificans with time-resolved Fourier transform infrared spectroscopy is presented for the first time. For this purpose, variants with single-site mutations of N131V, D124N, and E278Q, the key residues in the D-channel, were studied. The reaction of mutated CcO enzymes with oxygen was monitored and analyzed. Seven infrared bands in the “fast” kinetic spectra were found based on the following three requirements: (1) they are present in the “fast” phases of N131V and D124N mutants, (2) they have reciprocal counterparts in the “slow” kinetic spectra in these mutants, and (3) they are absent in “fast” kinetic spectra of the E278Q mutant. Moreover, the double-difference spectra between the first two mutants and E278Q revealed more IR bands that may belong to the proton-loading site protolytic transitions. From these results, it is assumed that several polar residues and/or water molecule cluster(s) share a proton as a proton-loading site. This site can be propionate itself (holding only a fraction of H+), His403, and/or water cluster(s).
Collapse
|
15
|
Cai X, Son CY, Mao J, Kaur D, Zhang Y, Khaniya U, Cui Q, Gunner MR. Identifying the proton loading site cluster in the ba 3 cytochrome c oxidase that loads and traps protons. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1861:148239. [PMID: 32531221 DOI: 10.1016/j.bbabio.2020.148239] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 05/05/2020] [Accepted: 06/04/2020] [Indexed: 12/29/2022]
Abstract
Cytochrome c Oxidase (CcO) is the terminal electron acceptor in aerobic respiratory chain, reducing O2 to water. The released free energy is stored by pumping protons through the protein, maintaining the transmembrane electrochemical gradient. Protons are held transiently in a proton loading site (PLS) that binds and releases protons driven by the electron transfer reaction cycle. Multi-Conformation Continuum Electrostatics (MCCE) was applied to crystal structures and Molecular Dynamics snapshots of the B-type Thermus thermophilus CcO. Six residues are identified as the PLS, binding and releasing protons as the charges on heme b and the binuclear center are changed: the heme a3 propionic acids, Asp287, Asp372, His376 and Glu126B. The unloaded state has one proton and the loaded state two protons on these six residues. Different input structures, modifying the PLS conformation, show different proton distributions and result in different proton pumping behaviors. One loaded and one unloaded protonation states have the loaded/unloaded states close in energy so the PLS binds and releases a proton through the reaction cycle. The alternative proton distributions have state energies too far apart to be shifted by the electron transfers so are locked in loaded or unloaded states. Here the protein can use active states to load and unload protons, but has nearby trapped states, which stabilize PLS protonation state, providing new ideas about the CcO proton pumping mechanism. The distance between the PLS residues Asp287 and His376 correlates with the energy difference between loaded and unloaded states.
Collapse
Affiliation(s)
- Xiuhong Cai
- Department of Physics, City College of New York, 160 Convent Avenue, New York, NY 10031, USA; Department of Physics, Graduate Center, City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
| | - Chang Yun Son
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Department of Chemistry and Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, South Korea
| | - Junjun Mao
- Department of Physics, City College of New York, 160 Convent Avenue, New York, NY 10031, USA
| | - Divya Kaur
- Department of Physics, City College of New York, 160 Convent Avenue, New York, NY 10031, USA; Department of Chemistry, Graduate Center, City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
| | - Yingying Zhang
- Department of Physics, City College of New York, 160 Convent Avenue, New York, NY 10031, USA; Department of Physics, Graduate Center, City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
| | - Umesh Khaniya
- Department of Physics, City College of New York, 160 Convent Avenue, New York, NY 10031, USA; Department of Physics, Graduate Center, City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
| | - Qiang Cui
- Department of Chemistry & Department of Biomedical Engineering & Department of Physics, Boston University, 590 Commonwealth Avenue, Boston, MA 02215, USA
| | - M R Gunner
- Department of Physics, City College of New York, 160 Convent Avenue, New York, NY 10031, USA; Department of Physics, Graduate Center, City University of New York, 365 Fifth Avenue, New York, NY 10016, USA; Department of Chemistry, Graduate Center, City University of New York, 365 Fifth Avenue, New York, NY 10016, USA.
| |
Collapse
|
16
|
A common coupling mechanism for A-type heme-copper oxidases from bacteria to mitochondria. Proc Natl Acad Sci U S A 2020; 117:9349-9355. [PMID: 32291342 PMCID: PMC7196763 DOI: 10.1073/pnas.2001572117] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We present a comprehensive investigation of mitochondrial DNA-encoded variants of cytochrome c oxidase (CcO) that harbor mutations within their core catalytic subunit I, designed to interrogate the presently disputed functions of the three putative proton channels. We assess overall respiratory competence, specific CcO catalytic activity, and, most importantly, proton/electron (H+/e−) stoichiometry from adenosine diphosphate to oxygen ratio measurements on preparations of intact mitochondria. We unequivocally show that yeast mitochondrial CcO uses the D-channel to translocate protons across its hydrophilic core, providing direct evidence in support of a common proton pumping mechanism across all members of the A-type heme-copper oxidase superfamily, independent of their bacterial or mitochondrial origin. Mitochondria metabolize almost all the oxygen that we consume, reducing it to water by cytochrome c oxidase (CcO). CcO maximizes energy capture into the protonmotive force by pumping protons across the mitochondrial inner membrane. Forty years after the H+/e− stoichiometry was established, a consensus has yet to be reached on the route taken by pumped protons to traverse CcO’s hydrophobic core and on whether bacterial and mitochondrial CcOs operate via the same coupling mechanism. To resolve this, we exploited the unique amenability to mitochondrial DNA mutagenesis of the yeast Saccharomyces cerevisiae to introduce single point mutations in the hydrophilic pathways of CcO to test function. From adenosine diphosphate to oxygen ratio measurements on preparations of intact mitochondria, we definitely established that the D-channel, and not the H-channel, is the proton pump of the yeast mitochondrial enzyme, supporting an identical coupling mechanism in all forms of the enzyme.
Collapse
|
17
|
Palese LL. Oxygen-oxygen distances in protein-bound crystallographic water suggest the presence of protonated clusters. Biochim Biophys Acta Gen Subj 2020; 1864:129480. [DOI: 10.1016/j.bbagen.2019.129480] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 10/27/2019] [Accepted: 10/28/2019] [Indexed: 12/11/2022]
|
18
|
Wolf A, Wonneberg J, Balke J, Alexiev U. Electronation-dependent structural change at the proton exit side of cytochrome c oxidase as revealed by site-directed fluorescence labeling. FEBS J 2019; 287:1232-1246. [PMID: 31597007 DOI: 10.1111/febs.15084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 08/17/2019] [Accepted: 10/04/2019] [Indexed: 02/05/2023]
Abstract
Cytochrome c oxidase (CcO), the terminal enzyme of the respiratory chain of mitochondria and many aerobic prokaryotes that function as a redox-coupled proton pump, catalyzes the reduction of molecular oxygen to water. As part of the respiratory chain, CcO contributes to the proton motive force driving ATP synthesis. While many aspects of the enzyme's catalytic mechanisms have been established, a clear picture of the proton exit pathway(s) remains elusive. Here, we aim to gain insight into the molecular mechanisms of CcO through the development of a new homologous mutagenesis/expression system in Paracoccus denitrificans, which allows mutagenesis of CcO subunits 1, 2, and 3. Our system provides true single thiol-reactive CcO variants in a three-subunit base variant with unique labeling sites for the covalent attachment of reporter groups sensitive to nanoenvironmental factors like protonation, polarity, and hydration. To this end, we exchanged six residues on both membrane sides of CcO for cysteines. We show redox-dependent wetting changes at the proton uptake channel and increased polarity at the proton exit side of CcO upon electronation. We suggest an electronation-dependent conformational change to play a role in proton exit from CcO.
Collapse
Affiliation(s)
- Alexander Wolf
- Institute of Experimental Physics, Freie Universität Berlin, Germany
| | - Juliane Wonneberg
- Institute of Experimental Physics, Freie Universität Berlin, Germany
| | - Jens Balke
- Institute of Experimental Physics, Freie Universität Berlin, Germany
| | - Ulrike Alexiev
- Institute of Experimental Physics, Freie Universität Berlin, Germany
| |
Collapse
|
19
|
Capitanio G, Palese LL, Papa F, Papa S. Allosteric Cooperativity in Proton Energy Conversion in A1-Type Cytochrome c Oxidase. J Mol Biol 2019; 432:534-551. [PMID: 31626808 DOI: 10.1016/j.jmb.2019.09.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 09/06/2019] [Accepted: 09/24/2019] [Indexed: 12/30/2022]
Abstract
Cytochrome c oxidase (CcO), the CuA, heme a, heme a3, CuB enzyme of respiratory chain, converts the free energy released by aerobic cytochrome c oxidation into a membrane electrochemical proton gradient (ΔμH+). ΔμH+ derives from the membrane anisotropic arrangement of dioxygen reduction to two water molecules and transmembrane proton pumping from a negative (N) space to a positive (P) space separated by the membrane. Spectroscopic, potentiometric, and X-ray crystallographic analyses characterize allosteric cooperativity of dioxygen binding and reduction with protonmotive conformational states of CcO. These studies show that allosteric cooperativity stabilizes the favorable conformational state for conversion of redox energy into a transmembrane ΔμH+.
Collapse
Affiliation(s)
- Giuseppe Capitanio
- Department of Basic Medical Sciences, Neurosciences and Sense Organs, University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Luigi Leonardo Palese
- Department of Basic Medical Sciences, Neurosciences and Sense Organs, University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Francesco Papa
- Department of Basic Medical Sciences, Neurosciences and Sense Organs, University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Sergio Papa
- Department of Basic Medical Sciences, Neurosciences and Sense Organs, University of Bari "Aldo Moro", 70124 Bari, Italy; Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, 80121 Napoli, Italy.
| |
Collapse
|
20
|
Saura P, Frey DM, Gamiz-Hernandez AP, Kaila VRI. Electric field modulated redox-driven protonation and hydration energetics in energy converting enzymes. Chem Commun (Camb) 2019; 55:6078-6081. [PMID: 31066378 PMCID: PMC6932871 DOI: 10.1039/c9cc01135h] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Biological energy conversion is catalysed by proton-coupled electron transfer (PCET) reactions that form the chemical basis of respiratory and photosynthetic enzymes. Despite recent advances in structural, biophysical, and computational experiments, the mechanistic principles of these reactions still remain elusive. Based on common functional features observed in redox enzymes, we study here generic mechanistic models for water-mediated long-range PCET reactions. We show how a redox reaction within a buried protein environment creates an electric field that induces hydration changes between the proton acceptor and donor groups, and in turn, lowers the reaction barrier and increases the thermodynamic driving forces for the water-mediated PCET process. We predict linear free energy relationships, and discuss the proposed mechanism in context of PCET in cytochrome c oxidase.
Collapse
Affiliation(s)
- Patricia Saura
- Center for Integrated Protein Science Munich (CIPSM), Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85748, Garching, Germany.
| | | | | | | |
Collapse
|
21
|
Adam SM, Wijeratne GB, Rogler PJ, Diaz DE, Quist DA, Liu JJ, Karlin KD. Synthetic Fe/Cu Complexes: Toward Understanding Heme-Copper Oxidase Structure and Function. Chem Rev 2018; 118:10840-11022. [PMID: 30372042 PMCID: PMC6360144 DOI: 10.1021/acs.chemrev.8b00074] [Citation(s) in RCA: 145] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Heme-copper oxidases (HCOs) are terminal enzymes on the mitochondrial or bacterial respiratory electron transport chain, which utilize a unique heterobinuclear active site to catalyze the 4H+/4e- reduction of dioxygen to water. This process involves a proton-coupled electron transfer (PCET) from a tyrosine (phenolic) residue and additional redox events coupled to transmembrane proton pumping and ATP synthesis. Given that HCOs are large, complex, membrane-bound enzymes, bioinspired synthetic model chemistry is a promising approach to better understand heme-Cu-mediated dioxygen reduction, including the details of proton and electron movements. This review encompasses important aspects of heme-O2 and copper-O2 (bio)chemistries as they relate to the design and interpretation of small molecule model systems and provides perspectives from fundamental coordination chemistry, which can be applied to the understanding of HCO activity. We focus on recent advancements from studies of heme-Cu models, evaluating experimental and computational results, which highlight important fundamental structure-function relationships. Finally, we provide an outlook for future potential contributions from synthetic inorganic chemistry and discuss their implications with relevance to biological O2-reduction.
Collapse
Affiliation(s)
- Suzanne M. Adam
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Gayan B. Wijeratne
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Patrick J. Rogler
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Daniel E. Diaz
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - David A. Quist
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Jeffrey J. Liu
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Kenneth D. Karlin
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| |
Collapse
|
22
|
Malkamäki A, Sharma V. Atomistic insights into cardiolipin binding sites of cytochrome c oxidase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1860:224-232. [PMID: 30414931 DOI: 10.1016/j.bbabio.2018.11.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 09/21/2018] [Accepted: 11/07/2018] [Indexed: 11/19/2022]
Abstract
Mitochondrial cytochrome c oxidase couples the reduction of oxygen to proton pumping. Despite an overall good understanding of its molecular mechanism, the role of cardiolipin in protein function is not understood. Here, we have studied the cardiolipin-protein interactions in a dynamic context by means of atomistic molecular dynamics simulations performed on the entire structure of monomeric and dimeric forms of the enzyme. Several microseconds of simulation data reveal that the crystallographic cardiolipin molecules that glue two monomers together bind weakly in hybrid and single-component lipid bilayers and dissociate rapidly. Atomistic simulations performed in the absence of tightly bound cardiolipin molecules strongly perturb the structural integrity of subunits III and VIIa, thereby highlighting an indispensable nature of lipid-protein interactions in enzyme function such as proton uptake and oxygen channeling. Our results demonstrate the strength of molecular simulations in providing direct atomic description of lipid-protein processes that are difficult to achieve experimentally.
Collapse
Affiliation(s)
- Aapo Malkamäki
- Department of Physics, P. O. Box 64, University of Helsinki, Helsinki 00014, Finland
| | - Vivek Sharma
- Department of Physics, P. O. Box 64, University of Helsinki, Helsinki 00014, Finland; Institute of Biotechnology, P. O. Box 56, University of Helsinki, Helsinki 00014, Finland.
| |
Collapse
|
23
|
Cai X, Haider K, Lu J, Radic S, Son CY, Cui Q, Gunner M. Network analysis of a proposed exit pathway for protons to the P-side of cytochrome c oxidase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:997-1005. [DOI: 10.1016/j.bbabio.2018.05.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 05/11/2018] [Accepted: 05/16/2018] [Indexed: 11/25/2022]
|
24
|
Farahvash A, Stuchebrukhov A. Investigating the Many Roles of Internal Water in Cytochrome c Oxidase. J Phys Chem B 2018; 122:7625-7635. [PMID: 30011995 DOI: 10.1021/acs.jpcb.7b11920] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cytochrome c oxidase (C cO) is the terminal enzyme in the respiratory electron transport chain. As part of its catalytic cycle, C cO transfers protons to its Fe-Cu binuclear center (BNC) to reduce oxygen, and in addition, it pumps protons across the mitochondrial inner, or bacterial, membrane where it is located. It is believed that this proton transport is facilitated by a network of water chains inside the enzyme. Here we present an analysis of the hydration of C cO, including the BNC region, using a semi-empirical hydration program, Dowser++, recently developed in our group. Using high-resolution X-ray data, we show that Dowser++ predictions match very accurately the water molecules seen in the D- and K-channels of C cO, as well as in the vicinity of its BNC. Moreover, Dowser++ predicts many more internal water molecules than is typically seen in the experiment. However, no significant hydration of the catalytic cavity in C cO described recently in the literature is observed. As Dowser++ itself does not account for structural changes of the protein, this result supports the earlier assessment that the proposed wetting transition in the catalytic cavity can only either be due to structural rearrangements of BNC, possibly induced by the charges during the catalytic cycle, or occur transiently, in concert with the proton transfer. Molecular dynamics simulations were performed to investigate the global dynamic nature of Dowser++ waters in C cO, and the results suggest a consistent explanation as to why some predicted water molecules would be missing in the experimental structures. Furthermore, in light of the significant protein hydration predicted by Dowser++, the dielectric constant of the hydrated cavities in C cO was also investigated using the Fröhlich-Kirkwood model; the results indicate that in the cavities where water is packed sufficiently densely the dielectric constant can approach values comparable even to that of bulk water.
Collapse
Affiliation(s)
- Ardavan Farahvash
- Department of Chemistry , University of California-Davis , One Shields Avenue , Davis , California 95616 , United States
| | - Alexei Stuchebrukhov
- Department of Chemistry , University of California-Davis , One Shields Avenue , Davis , California 95616 , United States
| |
Collapse
|
25
|
Supekar S, Kaila VRI. Dewetting transitions coupled to K-channel activation in cytochrome c oxidase. Chem Sci 2018; 9:6703-6710. [PMID: 30310604 PMCID: PMC6115622 DOI: 10.1039/c8sc01587b] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Accepted: 07/08/2018] [Indexed: 12/20/2022] Open
Abstract
Cytochrome c oxidase (CcO) drives aerobic respiratory chains in all organisms by transducing the free energy from oxygen reduction into an electrochemical proton gradient across a biological membrane.
Cytochrome c oxidase (CcO) drives aerobic respiratory chains in all organisms by transducing the free energy from oxygen reduction into an electrochemical proton gradient across a biological membrane. CcO employs the so-called D- and K-channels for proton uptake, but the molecular mechanism for activation of the K-channel has remained elusive for decades. We show here by combining large-scale atomistic molecular simulations with graph-theoretical water network analysis, and hybrid quantum/classical (QM/MM) free energy calculations, that the K-channel is activated by formation of a reactive oxidized intermediate in the binuclear heme a3/CuB active site. This state induces electrostatic, hydration, and conformational changes that lower the barrier for proton transfer along the K-channel by dewetting pathways that connect the D-channel with the active site. Our combined results reconcile previous experimental findings and indicate that water dynamics plays a decisive role in the proton pumping machinery in CcO.
Collapse
Affiliation(s)
- Shreyas Supekar
- Department Chemie , Technische Universität München , Lichtenbergstraße 4 , D-85748 Garching , Germany .
| | - Ville R I Kaila
- Department Chemie , Technische Universität München , Lichtenbergstraße 4 , D-85748 Garching , Germany .
| |
Collapse
|
26
|
Catalytic mechanism and molecular engineering of quinolone biosynthesis in dioxygenase AsqJ. Nat Commun 2018; 9:1168. [PMID: 29563492 PMCID: PMC5862883 DOI: 10.1038/s41467-018-03442-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Accepted: 02/13/2018] [Indexed: 12/02/2022] Open
Abstract
The recently discovered FeII/α-ketoglutarate-dependent dioxygenase AsqJ from Aspergillus nidulans stereoselectively catalyzes a multistep synthesis of quinolone alkaloids, natural products with significant biomedical applications. To probe molecular mechanisms of this elusive catalytic process, we combine here multi-scale quantum and classical molecular simulations with X-ray crystallography, and in vitro biochemical activity studies. We discover that methylation of the substrate is essential for the activity of AsqJ, establishing molecular strain that fine-tunes π-stacking interactions within the active site. To rationally engineer AsqJ for modified substrates, we amplify dispersive interactions within the active site. We demonstrate that the engineered enzyme has a drastically enhanced catalytic activity for non-methylated surrogates, confirming our computational data and resolved high-resolution X-ray structures at 1.55 Å resolution. Our combined findings provide crucial mechanistic understanding of the function of AsqJ and showcase how combination of computational and experimental data enables to rationally engineer enzymes. The catalytic activity of dioxygenase AsqJ is strictly relying on the methylation of quinolone substrates. Here, the authors apply molecular simulations, X-ray crystallography and in vitro biochemical studies to the engineering of dioxygenase AsqJ with improved catalytic activity for modified non-methylated surrogates.
Collapse
|
27
|
Wikström M, Krab K, Sharma V. Oxygen Activation and Energy Conservation by Cytochrome c Oxidase. Chem Rev 2018; 118:2469-2490. [PMID: 29350917 PMCID: PMC6203177 DOI: 10.1021/acs.chemrev.7b00664] [Citation(s) in RCA: 245] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
![]()
This review focuses on the type
A cytochrome c oxidases (CcO), which
are found in all mitochondria
and also in several aerobic bacteria. CcO catalyzes
the respiratory reduction of dioxygen (O2) to water by
an intriguing mechanism, the details of which are fairly well understood
today as a result of research for over four decades. Perhaps even
more intriguingly, the membrane-bound CcO couples
the O2 reduction chemistry to translocation of protons
across the membrane, thus contributing to generation of the electrochemical
proton gradient that is used to drive the synthesis of ATP as catalyzed
by the rotary ATP synthase in the same membrane. After reviewing the
structure of the core subunits of CcO, the active
site, and the transfer paths of electrons, protons, oxygen, and water,
we describe the states of the catalytic cycle and point out the few
remaining uncertainties. Finally, we discuss the mechanism of proton
translocation and the controversies in that area that still prevail.
Collapse
Affiliation(s)
- Mårten Wikström
- Institute of Biotechnology , University of Helsinki , P.O. Box 56 , Helsinki FI-00014 , Finland
| | - Klaas Krab
- Department of Molecular Cell Physiology , Vrije Universiteit , P.O. Box 7161 , Amsterdam 1007 MC , The Netherlands
| | - Vivek Sharma
- Institute of Biotechnology , University of Helsinki , P.O. Box 56 , Helsinki FI-00014 , Finland.,Department of Physics , University of Helsinki , P.O. Box 64 , Helsinki FI-00014 , Finland
| |
Collapse
|
28
|
Han Du WG, Götz AW, Noodleman L. A Water Dimer Shift Activates a Proton Pumping Pathway in the P R → F Transition of ba 3 Cytochrome c Oxidase. Inorg Chem 2018; 57:1048-1059. [PMID: 29308889 DOI: 10.1021/acs.inorgchem.7b02461] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Broken-symmetry density functional calculations have been performed on the [Fea34+,CuB2+] state of the dinuclear center (DNC) for the PR → F part of the catalytic cycle of ba3 cytochrome c oxidase (CcO) from Thermus thermophilus (Tt), using the OLYP-D3-BJ functional. The calculations show that the movement of the H2O molecules in the DNC affects the pKa values of the residue side chains of Tyr237 and His376+, which are crucial for proton transfer/pumping in ba3 CcO from Tt. The calculated lowest energy structure of the DNC in the [Fea34+,CuB2+] state (state F) is of the form Fea34+═O2-···CuB2+, in which the H2O ligand that resulted from protonation of the OH- ligand in the PR state is dissociated from the CuB2+ site. The calculated Fea34+═O2- distance in F (1.68 Å) is 0.03 Å longer than that in PR (1.65 Å), which can explain the different Fea34+═O2- stretching modes in P (804 cm-1) and F (785 cm-1) identified by resonance Raman experiments. In this F state, the CuB2+···O2- (ferryl-oxygen) distance is only around 2.4 Å. Hence, the subsequent OH state [Fea33+-OH--CuB2+] with a μ-hydroxo bridge can be easily formed, as shown by our calculations.
Collapse
Affiliation(s)
- Wen-Ge Han Du
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Andreas W Götz
- San Diego Supercomputer Center, University of California San Diego , 9500 Gilman Drive MC0505, La Jolla, California 92093, United States
| | - Louis Noodleman
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| |
Collapse
|
29
|
Mohrmann H, Dragelj J, Baserga F, Knapp EW, Stripp ST, Heberle J. The reductive phase of Rhodobacter sphaeroides cytochrome c oxidase disentangled by CO ligation. Phys Chem Chem Phys 2017. [PMID: 29067359 DOI: 10.1039/c7cp06480b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cytochrome c oxidase (CcO) is a membrane protein of the respiratory chain that catalytically reduces molecular oxygen (O2) to water while translocating protons across the membrane. The enzyme hosts two copper and two heme iron moieties (heme a/heme a3). The atomic details of the sequential steps that go along with this redox-driven proton translocation are a matter of debate. Particularly for the reductive phase of CcO that precedes oxygen binding experimental data are scarce. Here, we use CcO under anaerobic conditions where carbon monoxide (CO) is bound to heme a3 which in tandem with CuB forms the binuclear center (BNC). Fourier-transform infrared (FTIR) absorption spectroscopy is combined with electro-chemistry to probe different redox and protonation states populated by variation of the external electrostatic potential. With this approach, the redox behavior of heme a and the BNC could be separated and the corresponding redox potentials were determined. We also infer the protonation of one of the propionate side chains of heme a3 to correlate with the oxidation of heme a. Experimental changes in the local electric field surrounding CO bound to heme a3 are determined by their vibrational Stark effect and agree well with electrostatic computations. The comparison of experimental and computational results indicates that changes of the heme a3/CuB redox state are coupled to proton transfer towards heme a3. The latter supports the role of the heme a3 propionate D as proton loading site.
Collapse
Affiliation(s)
- Hendrik Mohrmann
- Experimental Molecular Biophysics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany.
| | - Jovan Dragelj
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Fabeckstraße 36A, 14195 Berlin, Germany
| | - Federico Baserga
- Experimental Molecular Biophysics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany.
| | - Ernst-Walter Knapp
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Fabeckstraße 36A, 14195 Berlin, Germany
| | - Sven T Stripp
- Experimental Molecular Biophysics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany.
| | - Joachim Heberle
- Experimental Molecular Biophysics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany.
| |
Collapse
|
30
|
A pathway for protective quenching in antenna proteins of Photosystem II. Sci Rep 2017; 7:2523. [PMID: 28566748 PMCID: PMC5451436 DOI: 10.1038/s41598-017-02892-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 04/19/2017] [Indexed: 11/08/2022] Open
Abstract
Photosynthesis is common in nature, converting sunlight energy into proton motive force and reducing power. The increased spectral range absorption of light exerted by pigments (i.e. chlorophylls, Chls) within Light Harvesting Complexes (LHCs) proves an important advantage under low light conditions. However, in the exposure to excess light, oxidative damages and ultimately cell death can occur. A down-regulatory mechanism, thus, has been evolved (non-photochemical quenching, NPQ). The mechanistic details of its major component (qE) are missing at the atomic scale. The research herein, initiates on solid evidence from the current NPQ state of the art, and reveals a detailed atomistic view by large scale Molecular Dynamics, Metadynamics and ab initio Simulations. The results demonstrate a complete picture of an elaborate common molecular design. All probed antenna proteins (major LHCII from spinach-pea, CP29 from spinach) show striking plasticity in helix-D, under NPQ conditions. This induces changes in Qy bands in excitation and absorption spectra of the near-by pigment pair (Chl613-614) that could emerge as a new quenching site. Zeaxanthin enhances this plasticity (and possibly the quenching) even at milder NPQ conditions.
Collapse
|
31
|
Ioannou A, Lambrou A, Daskalakis V, Pinakoulaki E. Coupling of helix E-F motion with the O-nitrito and 2-nitrovinyl coordination in myoglobin. Biophys Chem 2017; 221:10-16. [DOI: 10.1016/j.bpc.2016.11.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 11/15/2016] [Accepted: 11/23/2016] [Indexed: 10/20/2022]
|